量化柔性生物分子构象动力学的能量地貌
|
摘要
生物分子的动力学过程在细胞中是普遍存在的，同时也是最基本的生命活动。生物分子的动力学过程一般都是柔性的，通常伴随有大的构象变化。人们已经认识到柔性或者构象转变在许多生物过程，包括蛋白质折叠，蛋白质结合和蛋白质变构等，中扮演着举足轻重的作用。生物分子通过与其他分子结合来发挥其生物功能，而结合过程中的构象动力学对生物分子的功能实现也是至关重要的。但是，对柔性生物分子动力学全面的物理解释一直以来都是分子生物学中一个巨大的挑战。在本文中，我们通过量化能量地貌拓扑结构的方法将理论和实验联系在了一起，解决了这个难题。
1.我们通过探索态密度的方法量化了蛋白质折叠的能量地貌。我们计算了三个能量地貌拓扑结构的量度：能量间隙，能量粗糙度和熵。这三项分别表示了折叠漏斗的倾斜度，漏斗表面的粗糙度和漏斗的体积大小。通过这三项，我们计算了一个无量纲的比值，它描述了能量地貌的拓扑结构。我们发现能量地貌的拓扑结构可以预测出折叠的热力学稳定性相对于陷阱的比值和动力学速率。能量地貌的拓扑形状越像漏斗，那么折叠的热力学稳定性越高，折叠的动力学速率也越快。我们研究了对于不同体积大小的蛋白质和具有相同体积大小但是不同拓扑结构的蛋白质的拓扑阻挫和能量阻挫对蛋白质折叠的影响。我们发现这种能量地貌拓扑结构同折叠热力学和动力学单调相关的现象在上述所有情况中都存在。也就是说，我们证明了蛋白质折叠的能量地貌是决定蛋白质折叠热力学和动力学的关键因素。我们的工作连接了理论和实验。
2.利用态密度，我们量化了15个同源二聚体的柔性生物分子识别过程中有效结合和折叠，以及全局的结合-折叠能量地貌的拓扑结构。通过有效的结合和折叠的能量地貌的拓扑结构之间的关系，我们成功地将这15个同源二聚体划分为协同的结合-折叠耦合的两态识别机制和非协同的折叠先于结合的三态识别机制。这个结果与之前的理论和实验保持一致。我们发现非天然相互作用通过调节能量地貌的拓扑结构来调节识别机制。通过量化全局的结合-折叠的能量地貌的拓扑结构，我们发现结合-折叠的全局热力学稳定性与陷阱的比值和能量地貌拓扑结构量，以及全局动力学速率和能量地貌拓扑结构量强烈相关。因此，我们证明了能量地貌拓扑结构决定着柔性识别的热力学和动力学。我们同样发现了识别的动力学与温度之间是“U”型的关系，同时会有一个动力学交叉温度来区分e指数和非e指数的动力学行为。这些结果都与能量地貌的拓扑结构有关。我们的方法可以定量地将理论预测同实验测量联系在一起。
3.通过发展一种基于结构的粗粒化的包含用德拜-休克尔模型描述的静电相互作用的模型，我们研究了组蛋白伴侣Chz1与其目标组蛋白H2A.Z-H2B结合的过程。未结合的Chz1是典型的天然无规蛋白质。我们发现Chz1折叠的构象转变只发生在主过渡态之后，并且越过主过渡态之后耦合的结合和折叠行为会通过两条平行的路径进行。我们发现链间的静电相互作用起着“引导力”的作用来加速结合的过程。有趣的是，增加静电相互作用的强度，会导致形成最终复合体的速率变慢。这是因为强的链内静电相互作用使得Chz1坍缩形成一系列紧密的非天然结构。结合会由于这些能量地貌表面上的陷阱而变慢。我们提供了一种静电相互作用控制的柔性分子识别机制。我们的发现导致了一种“局部坍缩或陷阱”和“飞掷”协同在一起的动力学结合机制，我们的结果提供了一种新的理解天然无规蛋白质结合中静电相互作用的方式。
Biomolecular dynamics is prevalent and fundamental in cellar activity.Biomolecular dynamics is often flexible and associated with large conformationalchanges. It has been recognized that the flexibility or conformational transition playsa major role in many biomolecular process, including protein folding, protein bindingand protein allostery. Biomolecules realize their function by binding to the partners.The conformational dynamics in binding is also critical for the biomolecular function.However, the physical and global understanding for the flexible biomoleculardynamics is still challenging. In this thesis, we meet this challenge by quantifying theenergy landscape topography and establishing the connections between theoreticalpredications and experiment measurements.
1. We quantify the protein folding energy landscapes by exploring the density ofstates. We calculate three energy landscape topography quantities: energy gap, energyroughness and entropy, corresponding to the slope, bumpiness and size of the foldingfunnels, respectively. We show that the dimensionless ratio between gap, roughnessand entropy can accurately describe the energy landscape topography. We find that theenergy landscape topography can predict the folding thermodynamic stability againsttrapping and the kinetic rates. More funneled energy landscapes lead to more stablethermodynamics and faster kinetics. We investigate the role of topological andenergetic roughness for protein of different sizes and for protein of same size, but withdifferent structural topologies. We find that the monotonic correlations between theenergy landscape topography and folding thermodynamics as well as kinetics arepresent in all the cases. In short, we demonstrate that the folding energy landscape isthe underlying factor to determine the folding thermodynamics and kinetics. Thiswork bridges the gap between theories and experiments.
2. Using density of states, we quantify the effective binding and folding, as wellas the whole global binding-folding energy landscape topography in flexiblebiomolecular recognition for15homodimers. Based on the interplay betweentopography of the effective binding and folding energy landscape topography, the15homodimers can be successfully classified into two-state cooperative “coupledbinding-folding” and three-state non-cooperative “folding prior to binding” scenario.The results are consistent with the previous theoretical and experimentalinvestigations. We find that the non-native interactions modulate the associationmechanism through the underlying binding and folding energy landscapes. Byquantifying the whole global binding-folding energy landscapes, we find the strongcorrelation between the landscape topography measure and the thermodynamicstability versus trapping, as well as the kinetic rates. Therefore, we demonstrate thatenergy landscape determines the thermodynamics and kinetics of the flexiblebiomolecular recognition. We also find “U-shape” temperature-dependent kineticbehavior and a dynamical cross-over temperature of dividing exponential andnonexponential kinetics for two-state homodimers. The findings are controlled by thetopography of the underlying energy landscapes. Our results provide the quantitativebridge between the landscape topography and experimental measurements.
3. By developing a structure-based coarse-grained model, in whichDebye-Hückel model is implemented for describing the electrostatic interactions, weinvestigate the histone chaperone Chz1binding to its target histone variantH2A.Z-H2B. Free Chz1is a typical Intrinsically Disordered Protein (IDP). We findthat the folding conformational changes in Chz1only happens after the majortransition states and then Chz1undergoes coupled binding-folding through twoparallel pathways. We find that the inter-chain electrostatic interactions serve as“steering forces” to facilitate the association. Interestingly, we find increasing thestrength of electrostatic interactions leads to decreasing rate of formation of the finalcomplex. It is due to that the strong intra-chain electrostatic interactions collapse theChz1into non-native compact structures. Binding is slowed by the escape of the trapson the energy landscapes. Our studies provide an ionic-strength-controlled flexible binding-folding mechanism. The findings lead to a cooperative binding mechanism of“local collapse or trapping” and “fly-casting” together and a new understanding of theroles of electrostatic interactions in IDPs’ binding.
1.我们通过探索态密度的方法量化了蛋白质折叠的能量地貌。我们计算了三个能量地貌拓扑结构的量度：能量间隙，能量粗糙度和熵。这三项分别表示了折叠漏斗的倾斜度，漏斗表面的粗糙度和漏斗的体积大小。通过这三项，我们计算了一个无量纲的比值，它描述了能量地貌的拓扑结构。我们发现能量地貌的拓扑结构可以预测出折叠的热力学稳定性相对于陷阱的比值和动力学速率。能量地貌的拓扑形状越像漏斗，那么折叠的热力学稳定性越高，折叠的动力学速率也越快。我们研究了对于不同体积大小的蛋白质和具有相同体积大小但是不同拓扑结构的蛋白质的拓扑阻挫和能量阻挫对蛋白质折叠的影响。我们发现这种能量地貌拓扑结构同折叠热力学和动力学单调相关的现象在上述所有情况中都存在。也就是说，我们证明了蛋白质折叠的能量地貌是决定蛋白质折叠热力学和动力学的关键因素。我们的工作连接了理论和实验。
2.利用态密度，我们量化了15个同源二聚体的柔性生物分子识别过程中有效结合和折叠，以及全局的结合-折叠能量地貌的拓扑结构。通过有效的结合和折叠的能量地貌的拓扑结构之间的关系，我们成功地将这15个同源二聚体划分为协同的结合-折叠耦合的两态识别机制和非协同的折叠先于结合的三态识别机制。这个结果与之前的理论和实验保持一致。我们发现非天然相互作用通过调节能量地貌的拓扑结构来调节识别机制。通过量化全局的结合-折叠的能量地貌的拓扑结构，我们发现结合-折叠的全局热力学稳定性与陷阱的比值和能量地貌拓扑结构量，以及全局动力学速率和能量地貌拓扑结构量强烈相关。因此，我们证明了能量地貌拓扑结构决定着柔性识别的热力学和动力学。我们同样发现了识别的动力学与温度之间是“U”型的关系，同时会有一个动力学交叉温度来区分e指数和非e指数的动力学行为。这些结果都与能量地貌的拓扑结构有关。我们的方法可以定量地将理论预测同实验测量联系在一起。
3.通过发展一种基于结构的粗粒化的包含用德拜-休克尔模型描述的静电相互作用的模型，我们研究了组蛋白伴侣Chz1与其目标组蛋白H2A.Z-H2B结合的过程。未结合的Chz1是典型的天然无规蛋白质。我们发现Chz1折叠的构象转变只发生在主过渡态之后，并且越过主过渡态之后耦合的结合和折叠行为会通过两条平行的路径进行。我们发现链间的静电相互作用起着“引导力”的作用来加速结合的过程。有趣的是，增加静电相互作用的强度，会导致形成最终复合体的速率变慢。这是因为强的链内静电相互作用使得Chz1坍缩形成一系列紧密的非天然结构。结合会由于这些能量地貌表面上的陷阱而变慢。我们提供了一种静电相互作用控制的柔性分子识别机制。我们的发现导致了一种“局部坍缩或陷阱”和“飞掷”协同在一起的动力学结合机制，我们的结果提供了一种新的理解天然无规蛋白质结合中静电相互作用的方式。
Biomolecular dynamics is prevalent and fundamental in cellar activity.Biomolecular dynamics is often flexible and associated with large conformationalchanges. It has been recognized that the flexibility or conformational transition playsa major role in many biomolecular process, including protein folding, protein bindingand protein allostery. Biomolecules realize their function by binding to the partners.The conformational dynamics in binding is also critical for the biomolecular function.However, the physical and global understanding for the flexible biomoleculardynamics is still challenging. In this thesis, we meet this challenge by quantifying theenergy landscape topography and establishing the connections between theoreticalpredications and experiment measurements.
1. We quantify the protein folding energy landscapes by exploring the density ofstates. We calculate three energy landscape topography quantities: energy gap, energyroughness and entropy, corresponding to the slope, bumpiness and size of the foldingfunnels, respectively. We show that the dimensionless ratio between gap, roughnessand entropy can accurately describe the energy landscape topography. We find that theenergy landscape topography can predict the folding thermodynamic stability againsttrapping and the kinetic rates. More funneled energy landscapes lead to more stablethermodynamics and faster kinetics. We investigate the role of topological andenergetic roughness for protein of different sizes and for protein of same size, but withdifferent structural topologies. We find that the monotonic correlations between theenergy landscape topography and folding thermodynamics as well as kinetics arepresent in all the cases. In short, we demonstrate that the folding energy landscape isthe underlying factor to determine the folding thermodynamics and kinetics. Thiswork bridges the gap between theories and experiments.
2. Using density of states, we quantify the effective binding and folding, as wellas the whole global binding-folding energy landscape topography in flexiblebiomolecular recognition for15homodimers. Based on the interplay betweentopography of the effective binding and folding energy landscape topography, the15homodimers can be successfully classified into two-state cooperative “coupledbinding-folding” and three-state non-cooperative “folding prior to binding” scenario.The results are consistent with the previous theoretical and experimentalinvestigations. We find that the non-native interactions modulate the associationmechanism through the underlying binding and folding energy landscapes. Byquantifying the whole global binding-folding energy landscapes, we find the strongcorrelation between the landscape topography measure and the thermodynamicstability versus trapping, as well as the kinetic rates. Therefore, we demonstrate thatenergy landscape determines the thermodynamics and kinetics of the flexiblebiomolecular recognition. We also find “U-shape” temperature-dependent kineticbehavior and a dynamical cross-over temperature of dividing exponential andnonexponential kinetics for two-state homodimers. The findings are controlled by thetopography of the underlying energy landscapes. Our results provide the quantitativebridge between the landscape topography and experimental measurements.
3. By developing a structure-based coarse-grained model, in whichDebye-Hückel model is implemented for describing the electrostatic interactions, weinvestigate the histone chaperone Chz1binding to its target histone variantH2A.Z-H2B. Free Chz1is a typical Intrinsically Disordered Protein (IDP). We findthat the folding conformational changes in Chz1only happens after the majortransition states and then Chz1undergoes coupled binding-folding through twoparallel pathways. We find that the inter-chain electrostatic interactions serve as“steering forces” to facilitate the association. Interestingly, we find increasing thestrength of electrostatic interactions leads to decreasing rate of formation of the finalcomplex. It is due to that the strong intra-chain electrostatic interactions collapse theChz1into non-native compact structures. Binding is slowed by the escape of the trapson the energy landscapes. Our studies provide an ionic-strength-controlled flexible binding-folding mechanism. The findings lead to a cooperative binding mechanism of“local collapse or trapping” and “fly-casting” together and a new understanding of theroles of electrostatic interactions in IDPs’ binding.
引文
[1] So much more to know[J]. Science,2005,309(5731):78-102.
[2] Anfinsen C B. Principles that Govern the Folding of Protein Chains[J]. Science,1973,181(4096):223-230.
[3] Anfinsen C, Scheraga H. Experimental and theoretical aspects of proteinfolding[J]. Advances in Protein Chemistry,1975,29:205-300.
[4] Levinthal C. Proceedings in Mossbauer Spectroscopy in Biological Systems[J].Proceedings of a meeting held at Allerton house, Monticello, Illinois,1969:22-24.
[5] Levinthal.C. Are There Pathways for Protein Folding[J]. Journal De ChimiePhysique Et De Physico-Chimie Biologique,1968,65(1):44-45.
[6] Dill K A, Maccallum J L. The Protein-Folding Problem,50Years On[J].Science,2012,338(6110):1042-1046.
[7] Wolynes P G, Lutheyschulten Z, Onuchic J N. Fast folding experiments and thetopography of protein folding energy landscapes[J]. Chemistry&Biology,1996,3(6):425-432.
[8] Wolynes P G, Onuchic J N, Thirumalai D. Navigating the Folding Routes[J].Science,1995,267(5204):1619-1620.
[9] Onuchic J N, Nymeyer H, Garcia A E, et al. The energy landscape theory ofprotein folding: Insights into folding mechanisms and scenarios[J]. Advances inProtein Chemistry, Vol53,2000,53:87-152.
[10] Onuchic J N, Wolynes P G. Theory of protein folding[J]. Current Opinion inStructural Biology,2004,14(1):70-75.
[11] Onuchic J N, Wolynes P G, Lutheyschulten Z, et al. Toward an Outline of theTopography of a Realistic Protein-Folding Funnel[J]. Proceedings of theNational Academy of Sciences of the United States of America,1995,92(8):3626-3630.
[12] Bryngelson J D, Onuchic J N, Socci N D, et al. Funnels, Pathways, and theEnergy Landscape of Protein-Folding-a Synthesis[J]. Proteins-StructureFunction and Genetics,1995,21(3):167-195.
[13] Dobson C M. Protein folding and misfolding[J]. Nature,2003,426(6968):884-890.
[14] Derrida B. Random-Energy Model-an Exactly Solvable Model ofDisordered-Systems[J]. Physical Review B,1981,24(5):2613-2626.
[15] Bryngelson J D, Wolynes P G. Spin-Glasses and the Statistical-Mechanics ofProtein Folding[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1987,84(21):7524-7528.
[16] Bryngelson J D, Wolynes P G. Intermediates and Barrier Crossing in a RandomEnergy-Model (with Applications to Protein Folding)[J]. Journal of PhysicalChemistry,1989,93(19):6902-6915.
[17] Plotkin S S, Onuchic J N. Understanding protein folding with energy landscapetheory-Part II: Quantitative aspects[J]. Quarterly Reviews of Biophysics,2002,35(3):205-286.
[18] Plotkin S S, Onuchic J N. Understanding protein folding with energy landscapetheory-Part I: Basic concepts[J]. Quarterly Reviews of Biophysics,2002,35(2):111-167.
[19] Wang J, Lee C, Stell G. The cooperative nature of hydrophobic forces andprotein folding kinetics[J]. Chemical Physics,2005,316(1-3):53-60.
[20] Wang J, Oliveira R J, Chu X, et al. Topography of funneled landscapesdetermines the thermodynamics and kinetics of protein folding[J]. Proceedingsof the National Academy of Sciences of the United States of America,2012,109(39):15763-8.
[21] Wang J, Onuchic J, Wolynes P. Statistics of kinetic pathways on biased roughenergy landscapes with applications to protein folding[J]. Physical ReviewLetters,1996,76(25):4861-4864.
[22] Wang J, Verkhivker G M. Energy landscape theory, funnels, specificity, andoptimal criterion of biomolecular binding[J]. Physical Review Letters,2003,90(18).
[23] Wang J, Xu L, Wang E. Optimal specificity and function for flexiblebiomolecular recognition[J]. Biophysical Journal,2007,92(12): L109-L111.
[24] Leopold P E, Montal M, Onuchic J N. Protein Folding Funnels-a KineticApproach to the Sequence Structure Relationship[J]. Proceedings of theNational Academy of Sciences of the United States of America,1992,89(18):8721-8725.
[25] Go N. Theoretical studies of protein folding[J]. Annual Review of Biophysicsand Bioengineering,1983,12(1):183-210.
[26] Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme[J]. Berichteder deutschen chemischen Gesellschaft,1894,27(3):2985-2993.
[27] Koshland D E. APPLICATION OF A THEORY OF ENZYME SPECIFICITYTO PROTEIN SYNTHESIS[J]. Proceedings of the National Academy ofSciences of the United States of America,1958,44(2):98-104.
[28] Boehr D D, Nussinov R, Wright P E. The role of dynamic conformationalensembles in biomolecular recognition[J]. Nature Chemical Biology,2009,5(11):789-796.
[29] Boehr D D, Wright P E. How do proteins interact?[J]. Science,2008,320(5882):1429-1430.
[30] Ma B Y, Kumar S, Tsai C J, et al. Folding funnels and binding mechanisms[J].Protein Engineering,1999,12(9):713-720.
[31] Tsai C J, Kumar S, Ma B Y, et al. Folding funnels, binding funnels, and proteinfunction[J]. Protein Science,1999,8(6):1181-1190.
[32] Tsai C J, Ma B Y, Nussinov R. Folding and binding cascades: Shifts in energylandscapes[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,1999,96(18):9970-9972.
[33] Kumar S, Ma B Y, Tsai C J, et al. Folding and binding cascades: Dynamiclandscapes and population shifts[J]. Protein Science,2000,9(1):10-19.
[34] Tsai C J, Ma B Y, Sham Y Y, et al. Structured disorder and conformationalselection[J]. Proteins-Structure Function and Genetics,2001,44(4):418-427.
[35] Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection andindependent dynamic segments: an extended view of binding events[J]. Trendsin Biochemical Sciences,2010,35(10):539-546.
[36] Dunker A K, Brown C J, Lawson J D, et al. Intrinsic disorder and proteinfunction[J]. Biochemistry,2002,41(21):6573-6582.
[37] Uversky V N. Natively unfolded proteins: A point where biology waits forphysics[J]. Protein Science,2002,11(4):739-756.
[38] Uversky V N, Oldfield C J, Dunker A K. Showing your ID: intrinsic disorder asan ID for recognition, regulation and cell signaling[J]. Journal Of MolecularRecognition,2005,18(5):343-384.
[39] Tompa P. Intrinsically unstructured proteins[J]. Trends in Biochemical Sciences,2002,27(10):527-533.
[40] Tompa P. The interplay between structure and function in intrinsicallyunstructured proteins[J]. FEBS Letters,2005,579(15):3346-3354.
[41] Tompa P. Unstructural biology coming of age[J]. Current Opinion in StructuralBiology,2011,21(3):419-425.
[42] Dyson H J. Expanding the proteome: disordered and alternatively foldedproteins[J]. Quarterly Reviews of Biophysics,2011,44(4):467-518.
[43] Dyson H J, Wright P E. Coupling of folding and binding for unstructuredproteins[J]. Current Opinion in Structural Biology,2002,12(1):54-60.
[44] Dyson H J, Wright P E. Intrinsically unstructured proteins and their functions[J].Nature Reviews Molecular Cell Biology,2005,6(3):197-208.
[45] Dyson H J, Wright P E. According to current textbooks, a well-definedthree-dimensional structure is a prerequisite for the function of a protein. Is thiscorrect?[J]. IUBMB Life,2006,58(2):107-109.
[46] Wright P E, Dyson H J. Intrinsically unstructured proteins: Re-assessing theprotein structure-function paradigm[J]. Journal of Molecular Biology,1999,293(2):321-331.
[47] Wright P E, Dyson H J. Linking folding and binding[J]. Current Opinion InStructural Biology,2009,19(1):31-38.
[48] Wang J, Zheng X, Yang Y, et al. Quantifying intrinsic specificity: A potentialcomplement to affinity in drug screening[J]. Physical Review Letters,2007,99(19).
[49] Yan Z Q, Zheng X L, Wang E K, et al. Thermodynamic and kinetic specificitiesof ligand binding[J]. Chemical Science,2013,4(6):2387-2395.
[50] Shirts M, Pande V S. Screen Savers of the World Unite![J]. Science,2000,290(5498):1903-1904.
[51] Shaw D E, Maragakis P, Lindorff-Larsen K, et al. Atomic-level characterizationof the structural dynamics of proteins[J]. Science,2010,330(6002):341-346.
[52] Lindorff-Larsen K, Piana S, Dror R O, et al. How fast-folding proteins fold[J].Science,2011,334(6055):517-520.
[53] Mccammon J A, Gelin B R, Karplus M. Dynamics of folded proteins[J]. Nature,1977,267:16.
[54] Abkevich V I, Gutin A M, Shakhnovich E I. Free-Energy Landscape forProtein-Folding Kinetics-Intermediates, Traps, and Multiple Pathways inTheory and Lattice Model Simulations[J]. Journal of Chemical Physics,1994,101(7):6052-6062.
[55] Brooks C L, Onuchic J N, Wales D J. Statistical thermodynamics-Taking awalk on a landscape[J]. Science,2001,293(5530):612-613.
[56] Chan H S, Dill K A. Transition-States and Folding Dynamics of Proteins andHeteropolymers[J]. Journal of Chemical Physics,1994,100(12):9238-9257.
[57] Clementi C, Nymeyer H, Onuchic J N. Topological and energetic factors: Whatdetermines the structural details of the transition state ensemble and "en-route"intermediates for protein folding? An investigation for small globularproteins[J]. Journal of Molecular Biology,2000,298(5):937-953.
[58] Eaton W A, Schuler B, Lipman E A. Probing the free-energy surface for proteinfolding with single-molecule fluorescence spectroscopy[J]. Nature,2002,419(6908):743-747.
[59] Gruebele M, Sabelko J, Ervin J. Observation of strange kinetics in proteinfolding[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,1999,96(11):6031-6036.
[60] Itzhaki L S, Otzen D E, Fersht A R. The Structure of the Transition-State forFolding of Chymotrypsin Inhibitor-2Analyzed by Protein Engineering Methods-Evidence for a Nucleation-Condensation Mechanism for Protein-Folding[J].Journal of Molecular Biology,1995,254(2):260-288.
[61] Klimov D K, Thirumalai D. Linking rates of folding in lattice models ofproteins with underlying thermodynamic characteristics[J]. Journal of ChemicalPhysics,1998,109(10):4119-4125.
[62] Nymeyer H, Garcia A E, Onuchic J N. Folding funnels and frustration inoff-lattice minimalist protein landscapes[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,1998,95(11):5921-5928.
[63] Stell G, Lee C L, Wang J. First-passage time distribution and non-Markoviandiffusion dynamics of protein folding[J]. Journal of Chemical Physics,2003,118(2):959-968.
[64] Zhou Y Q, Zhang C, Stell G, et al. Temperature dependence of the distributionof the first passage time: Results from discontinuous molecular dynamicssimulations of an all-atom model of the second beta-hairpin fragment of proteinG[J]. Journal of the American Chemical Society,2003,125(20):6300-6305.
[65] Wolynes P G. Biomolecular Folding in Vacuo()[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,1995,92(7):2426-2427.
[66] Plotkin S S, Wang J, Wolynes P G. Statistical mechanics of a correlated energylandscape model for protein folding funnels[J]. Journal of Chemical Physics,1997,106(7):2932-2948.
[67] Shakhnovich E I. Proteins with Selected Sequences Fold into Unique NativeConformation[J]. Physical Review Letters,1994,72(24):3907-3910.
[68] Goldstein R A, Lutheyschulten Z A, Wolynes P G. Optimal Protein-FoldingCodes from Spin-Glass Theory[J]. Proceedings of the National Academy ofSciences of the United States of America,1992,89(11):4918-4922.
[69] Sobolev V, Sorokine A, Prilusky J, et al. Automated analysis of interatomiccontacts in proteins[J]. Bioinformatics,1999,15(4):327-332.
[70] Hess B, Kutzner C, Van Der Spoel D, et al. GROMACS4: Algorithms forhighly efficient, load-balanced, and scalable molecular simulation[J]. Journal ofChemical Theory and Computation,2008,4(3):435-447.
[71] Noel J K, Whitford P C, Sanbonmatsu K Y, et al. SMOG@ctbp: simplifieddeployment of structure-based models in GROMACS[J]. Nucleic AcidsResearch,2010,38: W657-W661.
[72] Kumar S, Bouzida D, Swendsen R H, et al. The Weighted Histogram AnalysisMethod for Free-Energy Calculations on Biomolecules.1. The Method[J].Journal of Computational Chemistry,1992,13(8):1011-1021.
[73] Andrec M, Felts A K, Gallicchio E, et al. Protein folding pathways from replicaexchange simulations and a kinetic network model[J]. Proceedings of theNational Academy of Sciences of the United States of America,2005,102(19):6801-6806.
[74] Buchete N V, Hummer G. Peptide folding kinetics from replica exchangemolecular dynamics[J]. Physical Review E,2008,77(3).
[75] Muff S, Caflisch A. ETNA: Equilibrium Transitions Network and ArrheniusEquation for Extracting Folding Kinetics from REMD Simulations[J]. Journalof Physical Chemistry B,2009,113(10):3218-3226.
[76] Van Der Spoel D, Seibert M M. Protein folding kinetics and thermodynamicsfrom atomistic simulations[J]. Physical Review Letters,2006,96(23).
[77] Yang S C, Onuchic J N, Garcia A E, et al. Folding time predictions fromall-atom replica exchange simulations[J]. Journal of Molecular Biology,2007,372(3):756-763.
[78] Shakhnovich E I, Gutin A M. Engineering of Stable and Fast-Folding Sequencesof Model Proteins[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1993,90(15):7195-7199.
[79] Sali A, Shakhnovich E, Karplus M. Kinetics of Protein-Folding-a LatticeModel Study of the Requirements for Folding to the Native-State[J]. Journal ofMolecular Biology,1994,235(5):1614-1636.
[80] Sali A, Shakhnovich E, Karplus M. How Does a Protein Fold[J]. Nature,1994,369(6477):248-251.
[81] Shakhnovich E I, Gutin A M. Implications of Thermodynamics of ProteinFolding for Evolution of Primary Sequences[J]. Nature,1990,346(6286):773-775.
[82] Klimov D K, Thirumalai D. Factors governing the foldability of proteins[J].Proteins-Structure Function and Genetics,1996,26(4):411-441.
[83] Klimov D K, Thirumalai D. Criterion that determines the foldability ofproteins[J]. Physical Review Letters,1996,76(21):4070-4073.
[84] Dinner A R, Abkevich V, Shakhnovich E, et al. Factors that affect the foldingability of proteins[J]. Proteins-Structure Function and Genetics,1999,35(1):34-40.
[85] Karplus M, Dinner A R, Verosub E. Use of a quantitative structure-propertyrelationship to design larger model proteins that fold rapidly[J]. ProteinEngineering,1999,12(11):909-917.
[86] Melin R, Li H, Wingreen N S, et al. Designability, thermodynamic stability, anddynamics in protein folding: A lattice model study[J]. Journal of ChemicalPhysics,1999,110(2):1252-1262.
[87] Onuchic J N, Lutheyschulten Z, Wolynes P G. Theory of protein folding: Theenergy landscape perspective[J]. Annual Review of Physical Chemistry,1997,48:545-600.
[88] Das P, Clementi C, Matysiak S. Balancing energy and entropy: A minimalistmodel for the characterization of protein folding landscapes[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2005,102(29):10141-10146.
[89] Clementi C, Plotkin S S. The effects of nonnative interactions on protein foldingrates: Theory and simulation[J]. Protein Science,2004,13(7):1750-1766.
[90] Thirumalai D, Klimov D K. Deciphering the timescales and mechanisms ofprotein folding using minimal off-lattice models[J]. Current Opinion inStructural Biology,1999,9(2):197-207.
[91] Thirumalai D, Klimov D K, Woodson S A. Kinetic partitioning mechanism as aunifying theme in the folding of biomolecules[J]. Theoretical ChemistryAccounts,1997,96(1):14-22.
[92] Camacho C J, Thirumalai D. Kinetics and Thermodynamics of Folding inModel Proteins[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1993,90(13):6369-6372.
[93] Thirumalai D. From Minimal Models to Real Proteins-Time Scales forProtein-Folding Kinetics[J]. Journal De Physique I,1995,5(11):1457-1467.
[94] Honeycutt J D, Thirumalai D. The Nature of Folded States ofGlobular-Proteins[J]. Biopolymers,1992,32(6):695-709.
[95] Angelani L, Ruocco G. Saddles of the energy landscape and folding of modelproteins[J]. Europhysics Letters,2009,87(1).
[96] Chan H S, Dill K A. Solvation-Effects of Molecular-Size and Shape[J]. Journalof Chemical Physics,1994,101(8):7007-7026.
[97] Chan H S, Kaya H. Towards a consistent modeling of protein thermodynamicand kinetic cooperativity: How applicable is the transition state picture tofolding and unfolding?[J]. Journal of Molecular Biology,2002,315(4):899-909.
[98] Cieplak M, Hoang T X. Scaling of folding properties in Go models ofproteins[J]. Journal of Biological Physics,2000,26(4):273-294.
[99] Cieplak M, Hoang T X, Li M S. Scaling of folding properties in simple modelsof proteins[J]. Physical Review Letters,1999,83(8):1684-1687.
[100] Eaton W A, Lipman E A, Schuler B, et al. Single-molecule measurement ofprotein folding kinetics[J]. Science,2003,301(5637):1233-1235.
[101] Frauenfelder H, Parak F, Young R D. Conformational Substates in Proteins[J].Annual Review of Biophysics and Biophysical Chemistry,1988,17:451-479.
[102] Frauenfelder H, Sligar S G, Wolynes P G. The Energy Landscapes and Motionsof Proteins[J]. Science,1991,254(5038):1598-1603.
[103] Gruebele M, Nguyen H, Jager M, et al. Tuning the free-energy landscape of aWW domain by temperature, mutation, and truncation[J]. Proceedings of theNational Academy of Sciences of the United States of America,2003,100(7):3948-3953.
[104] Gutin A M, Abkevich V I, Shakhnovich E I. Chain length scaling of proteinfolding time[J]. Physical Review Letters,1996,77(27):5433-5436.
[105] Hardin C, Eastwood M P, Prentiss M C, et al. Associative memoryHamiltonians for structure prediction without homology: alpha/beta proteins[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2003,100(4):1679-1684.
[106] Kaya H, Chan H S. Energetic components of cooperative protein folding[J].Physical Review Letters,2000,85(22):4823-4826.
[107] Leite V B P, Onuchic J N, Stell G, et al. Probing the kinetics of single moleculeprotein folding[J]. Biophysical Journal,2004,87(6):3633-3641.
[108] Seno F, Micheletti C, Maritan A, et al. Variational approach to protein designand extraction of interaction potentials[J]. Physical Review Letters,1998,81(10):2172-2175.
[109] Socci N D, Onuchic J N. Kinetic and Thermodynamic Analysis of ProteinlikeHeteropolymers-Monte-Carlo Histogram Technique[J]. Journal of ChemicalPhysics,1995,103(11):4732-4744.
[110] Stell G, Lee C L, Lin C T, et al. Diffusion dynamics, moments, and distributionof first-passage time on the protein-folding energy landscape, with applicationsto single molecules[J]. Physical Review E,2003,67(4).
[111] Wang J. The complex kinetics of protein folding in wide temperature ranges[J].Biophysical Journal,2004,87(4):2164-2171.
[112] Xie X S, Yang H. Probing single-molecule dynamics photon by photon[J].Journal of Chemical Physics,2002,117(24):10965-10979.
[113] Garcia A E, Onuchic J N. Folding a protein in a computer: An atomicdescription of the folding/unfolding of protein A[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2003,100(24):13898-13903.
[114] Okamoto Y, Sugita Y. Replica-exchange molecular dynamics method for proteinfolding[J]. Chemical Physics Letters,1999,314(1-2):141-151.
[115] Rauscher S, Neale C, Pomes R. Simulated Tempering Distributed ReplicaSampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methodsfor Conformational Sampling[J]. Journal of Chemical Theory and Computation,2009,5(10):2640-2662.
[116] Rodinger T, Howell P L, Pomes R. Distributed replica sampling[J]. Journal ofChemical Theory and Computation,2006,2(3):725-731.
[117] Rodinger T, Pomes R. Enhancing the accuracy, the efficiency and the scope offree energy simulations[J]. Current Opinion in Structural Biology,2005,15(2):164-170.
[118] Zhang C, Ma J P. Comparison of sampling efficiency between simulatedtempering and replica exchange[J]. Journal of Chemical Physics,2008,129(13).
[119] Zhang C, Ma J P. Enhanced sampling in generalized ensemble with large gap ofsampling parameter: Case study in temperature space random walk[J]. Journalof Chemical Physics,2009,130(19).
[120] Zhang C, Ma J P. Enhanced sampling and applications in protein folding inexplicit solvent[J]. Journal of Chemical Physics,2010,132(24).
[121] Cho S S, Levy Y, Wolynes P G. P versus Q: Structural reaction coordinatescapture protein folding on smooth landscapes[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2006,103(3):586-591.
[122] Plotkin S S, Wang J, Wolynes P G. Statistical mechanics of correlated energylandscape models for random heteropolymers and proteins[J]. Physica D,1997,107(2-4):322-325.
[123] Eastwood M P, Hardin C, Luthey-Schulten Z, et al. Evaluating proteinstructure-prediction schemes using energy landscape theory[J]. Ibm Journal OfResearch And Development,2001,45(3.4):475-497.
[124] Fujitsuka Y, Takada S, Luthey-Schulten Z A, et al. Optimizing physical energyfunctions for protein folding[J]. Proteins-Structure Function and Genetics,2004,54(1):88-103.
[125] Hardin C, Eastwood M P, Prentiss M, et al. Folding funnels: The key to robustprotein structure prediction[J]. Journal of Computational Chemistry,2002,23(1):138-146.
[126] Iben I E T, Braunstein D, Doster W, et al. GLASSY BEHAVIOR OF APROTEIN[J]. Physical Review Letters,1989,62(16):1916-1919.
[127] Wolynes P G. Folding funnels and energy landscapes of larger proteins withinthe capillarity approximation[J]. Proceedings of the National Academy ofSciences of the United States of America,1997,94(12):6170-6175.
[128] Finkelstein A V, Badretdinov A Y. Rate of protein folding near the point ofthermodynamic equilibrium between the coil and the most stable chain fold[J].Folding&Design,1997,2(2):115-121.
[129] Finkelstein A V, Ivankov D N, Garbuzynskiy S O, et al. Contact order revisited:Influence of protein size on the folding rate[J]. Protein Science,2003,12(9):2057-2062.
[130] Galzitskaya O V, Garbuzynskiy S O, Ivankov D N, et al. Chain length is themain determinant of the folding rate for proteins with three-state foldingkinetics[J]. Proteins-Structure Function and Genetics,2003,51(2):162-166.
[131] Kouza M, Li M S, O'brien E P, et al. Effect of finite size on cooperativity andrates of protein folding[J]. Journal of Physical Chemistry A,2006,110:671-676.
[132] Li M S, Klimov D K, Thirumalai D. Dependence of folding rates on proteinlength[J]. Journal of Physical Chemistry B,2002,106(33):8302-8305.
[133] Li M S, Klimov D K, Thirumalai D. Thermal denaturation and folding rates ofsingle domain proteins: size matters[J]. Polymer,2004,45(2):573-579.
[134] Munoz V, Naganathan A N, Sanchez-Ruiz J M. Direct measurement of barrierheights in protein folding[J]. Journal of the American Chemical Society,2005,127(51):17970-17971.
[135] Naganathan A N, Munoz V. Scaling of folding times with protein size[J].Journal of the American Chemical Society,2005,127(2):480-481.
[136] Takada S, Koga N. Roles of native topology and chain-length scaling in proteinfolding: A simulation study with a Go-like model[J]. Journal of MolecularBiology,2001,313(1):171-180.
[137] Saven J G, Wang J, Wolynes P G. Protein-Folding Kinetics-Relaxation in aGlobally Connected Random Energy-Model[J]. Abstracts of Papers of theAmerican Chemical Society,1994,208:250-PHYS.
[138] Socci N D, Onuchic J N, Wolynes P G. Diffusive dynamics of the reactioncoordinate for protein folding funnels[J]. Journal of Chemical Physics,1996,104(15):5860-5868.
[139] Plotkin S S. Speeding protein folding beyond the Go model: How a littlefrustration sometimes helps[J]. Proteins-Structure Function and Bioinformatics,2001,45(4):337-345.
[140] Baker D, Plaxco K W, Simons K T. Contact order, transition state placementand the refolding rates of single domain proteins[J]. Journal of MolecularBiology,1998,277(4):985-994.
[141] Dinner A R, Karplus M. The roles of stability and contact order in determiningprotein folding rates[J]. Nature Structural Biology,2001,8(1):21-22.
[142] Raleigh D P, Kuhlman B, Luisi D L, et al. Global analysis of the effects oftemperature and denaturant on the folding and unfolding kinetics of theN-terminal domain of the protein L9[J]. Journal of Molecular Biology,1998,284(5):1661-1670.
[143] Chen J. Towards the physical basis of how intrinsic disorder mediates proteinfunction[J]. Archives of Biochemistry and Biophysics,2012,524(2):123-131.
[144] Tompa P, Szasz C, Buday L. Structural disorder throws new light onmoonlighting[J]. Trends in Biochemical Sciences,2005,30(9):484-489.
[145] Papoian G A. Proteins with weakly funneled energy landscapes challenge theclassical structure-function paradigm[J]. Proceedings of the National Academyof Sciences of the United States of America,2008,105(38):14237-14238.
[146] Meszaros B, Simon I, Dosztanyi Z. The expanding view of protein-proteininteractions: complexes involving intrinsically disordered proteins[J]. PhysicalBiology,2011,8(3).
[147] Whitford P C. Disorder guides protein function[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2013,110(18):7114-7115.
[148] Mosca R, Pache R A, Aloy P. The Role of Structural Disorder in the Rewiring ofProtein Interactions through Evolution[J]. Molecular&Cellular Proteomics,2012,11(7).
[149] Zhou H X. Intrinsic disorder: signaling via highly specific but short-livedassociation[J]. Trends in Biochemical Sciences,2012,37(2):43-48.
[150] Sugase K, Dyson H J, Wright P E. Mechanism of coupled folding and bindingof an intrinsically disordered protein[J]. Nature,2007,447(7147):1021-U11.
[151] Dunker A K, Radivojac P, Iakoucheva L M, et al. Intrinsic disorder andfunctional proteomics[J]. Biophysical Journal,2007,92(5):1439-1456.
[152] Ward J J, Sodhi J S, Mcguffin L J, et al. Prediction and functional analysis ofnative disorder in proteins from the three kingdoms of life[J]. Journal ofMolecular Biology,2004,337(3):635-645.
[153] Xie H B, Vucetic S, Iakoucheva L M, et al. Functional anthology of intrinsicdisorder.1. Biological processes and functions of proteins with long disorderedregions[J]. Journal of Proteome Research,2007,6(5):1882-1898.
[154] Fuxreiter M, Tompa P, Simon I, et al. Malleable machines take shape ineukaryotic transcriptional regulation[J]. Nature Chemical Biology,2008,4(12):728-737.
[155] Dunker A K, Silman I, Uversky V N, et al. Function and structure of inherentlydisordered proteins[J]. Current Opinion in Structural Biology,2008,18(6):756-764.
[156] Dunker A K, Uversky V N. Signal transduction via unstructured proteinconduits[J]. Nature Chemical Biology,2008,4(4):229-230.
[157] Dunker A K, Oldfield C J, Meng J W, et al. The unfoldomics decade: an updateon intrinsically disordered proteins[J]. BMC Genomics,2008,9.
[158] Gsponer J, Futschik M E, Teichmann S A, et al. Tight Regulation ofUnstructured Proteins: From Transcript Synthesis to Protein Degradation[J].Science,2008,322(5906):1365-1368.
[159] Smock R G, Gierasch L M. Sending Signals Dynamically[J]. Science,2009,324(5924):198-203.
[160] Babu M M, Van Der Lee R, De Groot N S, et al. Intrinsically disorderedproteins: regulation and disease[J]. Current Opinion in Structural Biology,2011,21(3):432-440.
[161] Tantos A, Han K H, Tompa P. Intrinsic disorder in cell signaling and genetranscription[J]. Molecular And Cellular Endocrinology,2012,348(2):457-465.
[162] Dill K A, Chan H S. From Levinthal to pathways to funnels[J]. NatureStructural Biology,1997,4(1):10-19.
[163] Oliveberg M, Wolynes P G. The experimental survey of protein-folding energylandscapes[J]. Quarterly Reviews of Biophysics,2005,38(3):245-288.
[164] Wolynes P G. Recent successes of the energy landscape theory of proteinfolding and function[J]. Quarterly Reviews of Biophysics,2005,38(4):405-410.
[165] Papoian G A, Wolynes P G. The physics and Bioinformatics of binding andfolding-An energy landscape perspective[J]. Biopolymers,2003,68(3):333-349.
[166] Austin R H, Beeson K W, Eisenstein L, et al. DYNAMICS OFLIGAND-BINDING TO MYOGLOBIN[J]. Biochemistry,1975,14(24):5355-5373.
[167] Rumfeldt J a O, Galvagnion C, Vassall K A, et al. Conformational stability andfolding mechanisms of dimeric proteins[J]. Progress in Biophysics&MolecularBiology,2008,98(1):61-84.
[168] Wang J. Diffusion and single molecule dynamics on biomolecular interfacebinding energy landscape[J]. Chemical Physics Letters,2006,418(4-6):544-548.
[169] Reat V, Patzelt H, Ferrand M, et al. Dynamics of different functional parts ofbacteriorhodopsin: H-H-2labeling and neutron scattering[J]. Proceedings of theNational Academy of Sciences of the United States of America,1998,95(9):4970-4975.
[170] Reddy G B, Bharadwaj S, Surolia A. Thermal stability and mode ofoligomerization of the tetrameric peanut agglutinin: A differential scanningcalorimetry study[J]. Biochemistry,1999,38(14):4464-4470.
[171] Levy Y. Protein topology determines binding mechanism[J]. Proceedings of theNational Academy of Sciences,2004,101(2):511-516.
[172] Levy Y, Cho S S, Onuchic J N, et al. A Survey of Flexible Protein BindingMechanisms and their Transition States Using Native Topology Based EnergyLandscapes[J]. Journal of Molecular Biology,2005,346(4):1121-1145.
[173] Levy Y, Onuchic J N. Mechanisms of protein assembly: Lessons fromminimalist models[J]. Accounts of Chemical Research,2006,39(2):135-142.
[174] Wang W, Xu W X, Levy Y, et al. Confinement effects on the kinetics andthermodynamics of protein dimerization[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2009,106(14):5517-5522.
[175] Kaplan E L, Meier P. Nonparametric-Estimation from IncompleteObservations[J]. Journal of the American Statistical Association,1958,53(282):457-481.
[176] Efron B. The two sample problem with censored data[C]. Proceedings of theFifth Berkeley Symposium on Mathematical Statistics and Probability, Berkeley,1967,4:831-853.
[177] Barker C. The Mean, Median, and Confidence Intervals of the Kaplan-MeierSurvival Estimate-Computations and Applications[J]. American Statistician,2009,63(1):78-80.
[178] Zhong M, Hess K R. Mean survival time from right censored data[J]. COBRAPreprint Series,2009: Working Paper66.
[179] Socci N D, Onuchic J N. Folding Kinetics of Proteinlike Heteropolymers[J].Journal of Chemical Physics,1994,101(2):1519-1528.
[180] Xu D, Tsai C J, Nussinov R. Mechanism and evolution of proteindimerization[J]. Protein Science,1998,7(3):533-544.
[181] Neet K E, Timm D E. Conformational stability of dimeric proteins: quantitativestudies by equilibrium denaturation [J]. Protein Science,1994,3(12):2167-2174.
[182] Gunasekaran K, Tsai C J, Nussinov R. Analysis of ordered and disorderedprotein complexes reveals structural features discriminating between stable andunstable monomers[J]. Journal of Molecular Biology,2004,341(5):1327-1341.
[183] Janin J. Quantifying biological specificity: The statistical mechanics ofmolecular recognition[J]. Proteins-Structure Function and Genetics,1996,25(4):438-445.
[184] Kohn J E, Gillespie B, Plaxco K W. Non-Sequence-Specific Interactions CanAccount for the Compaction of Proteins Unfolded under "Native" Conditions[J].Journal of Molecular Biology,2009,394(2):343-350.
[185] Weinkam P, Pletneva E V, Gray H B, et al. Electrostatic effects on funneledlandscapes and structural diversity in denatured protein ensembles[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(6):1796-1801.
[186] Mao A H, Crick S L, Vitalis A, et al. Net charge per residue modulatesconformational ensembles of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(18):8183-8188.
[187] Muller-Spath S, Soranno A, Hirschfeld V, et al. Charge interactions candominate the dimensions of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(33):14609-14614.
[188] Haran G. How, when and why proteins collapse: the relation to folding[J].Current Opinion in Structural Biology,2012,22(1):14-20.
[189] Chu X, Wang Y, Gan L, et al. Importance of Electrostatic Interactions in theAssociation of Intrinsically Disordered Histone Chaperone Chz1and HistoneH2A.Z-H2B[J]. Plos Computational Biology,2012,8(7): e1002608
[190] Zheng W H, Schafer N P, Davtyan A, et al. Predictive energy landscapes forprotein-protein association[J]. Proceedings of the National Academy ofSciences of the United States of America,2012,109(47):19244-19249.
[191] Trizac E, Levy Y, Wolynes P G. Capillarity theory for the fly-castingmechanism[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2010,107(7):2746-2750.
[192] Wang J. Statistics, pathways and dynamics of single molecule protein folding[J].Journal of Chemical Physics,2003,118(2):952-958.
[193] Kirkpatrick T R, Wolynes P G. Connections between Some Kinetic andEquilibrium Theories of the Glass-Transition[J]. Physical Review A,1987,35(7):3072-3080.
[194] Kirkpatrick T R, Wolynes P G. Stable and Metastable States in Mean-Field Pottsand Structural Glasses[J]. Physical Review B,1987,36(16):8552-8564.
[195] Shoemaker B A, Portman J J, Wolynes P G. Speeding molecular recognition byusing the folding funnel: The fly-casting mechanism[J]. Proceedings of theNational Academy of Sciences of the United States of America,2000,97(16):8868-8873.
[196] Wang Y, Chu X K, Suo Z C, et al. Multidomain Protein Solves the FoldingProblem by Multifunnel Combined Landscape: Theoretical Investigation of aY-Family DNA Polymerase[J]. Journal of the American Chemical Society,2012,134(33):13755-13764.
[197] Kornberg R D. Chromatin Structure-Repeating Unit of Histones and DNA[J].Science,1974,184(4139):868-871.
[198] Kornberg R D, Lorch Y L. Twenty-five years of the nucleosome, fundamentalparticle of the eukaryote chromosome[J]. Cell,1999,98(3):285-294.
[199] Luger K, Mader A W, Richmond R K, et al. Crystal structure of the nucleosomecore particle at2.8angstrom resolution[J]. Nature,1997,389(6648):251-260.
[200] Muthurajan U M, Bao Y H, Forsberg L J, et al. Crystal structures of histone Sinmutant nucleosomes reveal altered protein-DNA interactions[J]. Embo Journal,2004,23(2):260-271.
[201] Almouzni G, De Koning L, Corpet A, et al. Histone chaperones: an escortnetwork regulating histone traffic[J]. Nature Structural&Molecular Biology,2007,14(11):997-U1.
[202] Horikoshi M, Eitoku M, Sato L, et al. Histone chaperones:30years fromisolation to elucidation of the mechanisms of nucleosome assembly anddisassembly[J]. Cellular and Molecular Life Sciences,2008,65(3):414-444.
[203] Laskey R A, Honda B M, Mills A D, et al. Nucleosomes Are Assembled by anAcidic Protein Which Binds Histones and Transfers Them to DNA[J]. Nature,1978,275(5679):416-420.
[204] Das C, Tyler J K, Churchill M E A. The histone shuffle: histone chaperones inan energetic dance[J]. Trends in Biochemical Sciences,2010,35(9):476-489.
[205] Hondele M, Ladurner A G. The chaperone-histone partnership: for the greatergood of histone traffic and chromatin plasticity[J]. Current Opinion in StructuralBiology,2011,21(6):698-708.
[206] Park Y J, Luger K. Histone chaperones in nucleosome eviction and histoneexchange[J]. Current Opinion in Structural Biology,2008,18(3):282-289.
[207] Zhou Z, Feng H Q, Zhou B R, et al. Structural basis for recognition ofcentromere histone variant CenH3by the chaperone Scm3[J]. Nature,2011,472(7342):234-237.
[208] Korolev N, Vorontsova O V, Nordenskiold L. Physicochemical analysis ofelectrostatic foundation for DNA-protein interactions in chromatintransformations[J]. Progress in Biophysics&Molecular Biology,2007,95(1-3):23-49.
[209] Luk E, Vu N D, Patteson K, et al. Chz1, a nuclear chaperone for histoneH2AZ[J]. Molecular Cell,2007,25(3):357-368.
[210] Zhou Z, Feng H Q, Hansen D F, et al. NMR structure of chaperone Chz1complexed with histones H2A.Z-H2B[J]. Nature Structural&MolecularBiology,2008,15(8):868-869.
[211] Hansen D F, Zhou Z, Fen H Q, et al. Binding Kinetics of Histone ChaperoneChz1and Variant Histone H2A.Z-H2B by Relaxation Dispersion NMRSpectroscopy[J]. Journal of Molecular Biology,2009,387(1):1-9.
[212] Miyazawa S, Jernigan R L. Residue-residue potentials with a favorable contactpair term and an unfavorable high packing density term, for simulation andthreading[J]. Journal of Molecular Biology,1996,256(3):623-644.
[213] Oliveira L C, Schug A, Onuchic J N. Geometrical features of the protein foldingmechanism are a robust property of the energy landscape: A detailedinvestigation of several reduced models[J]. Journal of Physical Chemistry B,2008,112(19):6131-6136.
[214] Azia A, Levy Y. Nonnative Electrostatic Interactions Can Modulate ProteinFolding: Molecular Dynamics with a Grain of Salt[J]. Journal of MolecularBiology,2009,393(2):527-542.
[215] Whitford P C, Noel J K, Gosavi S, et al. An all-atom structure-based potentialfor proteins: Bridging minimal models with all-atom empirical force fields[J].Proteins-Structure Function and Bioinformatics,2009,75(2):430-441.
[216] Cho S S, Levy Y, Wolynes P G. Quantitative criteria for native energeticheterogeneity influences in the prediction of protein folding kinetics[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(2):434-439.
[217] Levy Y, Onuchic J N, Wolynes P G. Fly-casting in protein-DNA binding:Frustration between protein folding and electrostatics facilitates targetrecognition[J]. Journal of the American Chemical Society,2007,129(4):738-739.
[218] Huang Y, Liu Z. Kinetic Advantage of Intrinsically Disordered Proteins inCoupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting"Mechanism[J]. Journal of Molecular Biology,2009,393(5):1143-1159.
[219] Bonomi M, Branduardi D, Bussi G, et al. PLUMED: A portable plugin forfree-energy calculations with molecular dynamics[J]. Computer PhysicsCommunications,2009,180(10):1961-1972.
[220] Yang S C, Onuchic J, Levine H. Protein self-assembly via domain swapping:The effect of intermolecular interactions and protein concentration[J].Biophysical Journal,2005,88(1):198a-198a.
[221] Fersht A R, Sato S. Phi-Value analysis and the nature of protein-foldingtransition states[J]. Proceedings of the National Academy of Sciences of theUnited States of America,2004,101(21):7976-7981.
[222] Zhou H X. How do biomolecular systems speed up and regulate rates?[J].Physical Biology,2005,2(3): R1-R25.
[223] Schreiber G. Kinetic studies of protein-protein interactions[J]. Current Opinionin Structural Biology,2002,12(1):41-47.
[224] Plaxco K W, Kohn J E, Millett I S, et al. Random-coil behavior and thedimensions of chemically unfolded proteins[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2004,101(34):12491-12496.
[225] Turjanski A G, Gutkind J S, Best R B, et al. Binding-induced folding of anatively unstructured transcription factor[J]. PLoS Computational Biology,2008,4(4): e1000060.
[226] Chen J H. Intrinsically Disordered p53Extreme C-Terminus Binds toS100B(beta beta) through "Fly-Casting"[J]. Journal of the American ChemicalSociety,2009,131(6):2088-2089.
[227] Espinoza-Fonseca L M. Reconciling binding mechanisms of intrinsicallydisordered proteins[J]. Biochemical and Biophysical Research Communications,2009,382(3):479-482.
[228] Lu Q, Lu H P, Wang J. Exploring the mechanism of flexible biomolecularrecognition with single molecule dynamics[J]. Physical Review Letters,2007,98(12).
[229] Narayanan R, Ganesh O K, Edison A S, et al. Kinetics of folding and binding ofan intrinsically disordered protein: The inhibitor of yeast aspartic proteinaseYPrA[J]. Journal of the American Chemical Society,2008,130(34):11477-11485.
[230] Wang J, Lu Q, Lu H P. Single-molecule dynamics reveals cooperativebinding-folding in protein recognition[J]. PLoS Computational Biology,2006,2(7): e78.
[231] Wang J, Wang Y, Chu X K, et al. Multi-Scaled Explorations of Binding-InducedFolding of Intrinsically Disordered Protein Inhibitor IA3to its TargetEnzyme[J]. PLoS Computational Biology,2011,7(4): e1001118.
[232] Chan H S, Zhang Z Q, Wallin S, et al. Cooperativity, Local-Nonlocal Coupling,and Nonnative Interactions: Principles of Protein Folding from Coarse-GrainedModels[J]. Annual Review of Physical Chemistry, Vol62,2011,62:301-326.
[233] Zarrine-Afsar A, Wallin S, Neculai A M, et al. Theoretical and experimentaldemonstration of the importance of specific nonnative interactions in proteinfolding[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2008,105(29):9999-10004.
[234] Schreiber G, Fersht A R. Rapid, electrostatically assisted association ofproteins[J]. Nature Structural&Molecular Biology,1996,3(5):427-431.
[235] Chen H F. Molecular Dynamics Simulation of Phosphorylated KIDPost-Translational Modification[J]. PLoS ONE,2009,4(8): e6516.
[236] Ganguly D, Chen J H. Atomistic Details of the Disordered States of KID andpKID. Implications in Coupled Binding and Folding[J]. Journal of the AmericanChemical Society,2009,131(14):5214-5223.
[237] Kumar S, Nussinov R. Close-range electrostatic interactions in proteins[J].ChemBioChem,2002,3(7):604-617.
[238] Sussman J L, Dunker A K, Silman I, et al. Function and structure of inherentlydisordered proteins[J]. Current Opinion in Structural Biology,2008,18(6):756-764.
[239] Uversky V N, Gillespie J R, Fink A L. Why are "natively unfolded" proteinsunstructured under physiologic conditions?[J]. Proteins-Structure Function andGenetics,2000,41(3):415-427.
[240] Weathers E A, Paulaitis M E, Woolf T B, et al. Reduced amino acid alphabet issufficient to accurately recognize intrinsically disordered protein[J]. FEBS Lett,2004,576(3):348-352.
[241] Pappu R V, Mao A H, Crick S L, et al. Net charge per residue modulatesconformational ensembles of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(18):8183-8188.
[242] Haran G, England J L. To fold or expand-a charged question[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(33):14519-14520.
[243] Sheinerman F B, Norel R, Honig B. Electrostatic aspects of protein-proteininteractions[J]. Current Opinion in Structural Biology,2000,10(2):153-159.
[244] Das P, Matysiak S, Clementi C. Balancing energy and entropy: A minimalistmodel for the characterization of protein folding landscapes[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2005,102(29):10141-10146.
[2] Anfinsen C B. Principles that Govern the Folding of Protein Chains[J]. Science,1973,181(4096):223-230.
[3] Anfinsen C, Scheraga H. Experimental and theoretical aspects of proteinfolding[J]. Advances in Protein Chemistry,1975,29:205-300.
[4] Levinthal C. Proceedings in Mossbauer Spectroscopy in Biological Systems[J].Proceedings of a meeting held at Allerton house, Monticello, Illinois,1969:22-24.
[5] Levinthal.C. Are There Pathways for Protein Folding[J]. Journal De ChimiePhysique Et De Physico-Chimie Biologique,1968,65(1):44-45.
[6] Dill K A, Maccallum J L. The Protein-Folding Problem,50Years On[J].Science,2012,338(6110):1042-1046.
[7] Wolynes P G, Lutheyschulten Z, Onuchic J N. Fast folding experiments and thetopography of protein folding energy landscapes[J]. Chemistry&Biology,1996,3(6):425-432.
[8] Wolynes P G, Onuchic J N, Thirumalai D. Navigating the Folding Routes[J].Science,1995,267(5204):1619-1620.
[9] Onuchic J N, Nymeyer H, Garcia A E, et al. The energy landscape theory ofprotein folding: Insights into folding mechanisms and scenarios[J]. Advances inProtein Chemistry, Vol53,2000,53:87-152.
[10] Onuchic J N, Wolynes P G. Theory of protein folding[J]. Current Opinion inStructural Biology,2004,14(1):70-75.
[11] Onuchic J N, Wolynes P G, Lutheyschulten Z, et al. Toward an Outline of theTopography of a Realistic Protein-Folding Funnel[J]. Proceedings of theNational Academy of Sciences of the United States of America,1995,92(8):3626-3630.
[12] Bryngelson J D, Onuchic J N, Socci N D, et al. Funnels, Pathways, and theEnergy Landscape of Protein-Folding-a Synthesis[J]. Proteins-StructureFunction and Genetics,1995,21(3):167-195.
[13] Dobson C M. Protein folding and misfolding[J]. Nature,2003,426(6968):884-890.
[14] Derrida B. Random-Energy Model-an Exactly Solvable Model ofDisordered-Systems[J]. Physical Review B,1981,24(5):2613-2626.
[15] Bryngelson J D, Wolynes P G. Spin-Glasses and the Statistical-Mechanics ofProtein Folding[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1987,84(21):7524-7528.
[16] Bryngelson J D, Wolynes P G. Intermediates and Barrier Crossing in a RandomEnergy-Model (with Applications to Protein Folding)[J]. Journal of PhysicalChemistry,1989,93(19):6902-6915.
[17] Plotkin S S, Onuchic J N. Understanding protein folding with energy landscapetheory-Part II: Quantitative aspects[J]. Quarterly Reviews of Biophysics,2002,35(3):205-286.
[18] Plotkin S S, Onuchic J N. Understanding protein folding with energy landscapetheory-Part I: Basic concepts[J]. Quarterly Reviews of Biophysics,2002,35(2):111-167.
[19] Wang J, Lee C, Stell G. The cooperative nature of hydrophobic forces andprotein folding kinetics[J]. Chemical Physics,2005,316(1-3):53-60.
[20] Wang J, Oliveira R J, Chu X, et al. Topography of funneled landscapesdetermines the thermodynamics and kinetics of protein folding[J]. Proceedingsof the National Academy of Sciences of the United States of America,2012,109(39):15763-8.
[21] Wang J, Onuchic J, Wolynes P. Statistics of kinetic pathways on biased roughenergy landscapes with applications to protein folding[J]. Physical ReviewLetters,1996,76(25):4861-4864.
[22] Wang J, Verkhivker G M. Energy landscape theory, funnels, specificity, andoptimal criterion of biomolecular binding[J]. Physical Review Letters,2003,90(18).
[23] Wang J, Xu L, Wang E. Optimal specificity and function for flexiblebiomolecular recognition[J]. Biophysical Journal,2007,92(12): L109-L111.
[24] Leopold P E, Montal M, Onuchic J N. Protein Folding Funnels-a KineticApproach to the Sequence Structure Relationship[J]. Proceedings of theNational Academy of Sciences of the United States of America,1992,89(18):8721-8725.
[25] Go N. Theoretical studies of protein folding[J]. Annual Review of Biophysicsand Bioengineering,1983,12(1):183-210.
[26] Fischer E. Einfluss der Configuration auf die Wirkung der Enzyme[J]. Berichteder deutschen chemischen Gesellschaft,1894,27(3):2985-2993.
[27] Koshland D E. APPLICATION OF A THEORY OF ENZYME SPECIFICITYTO PROTEIN SYNTHESIS[J]. Proceedings of the National Academy ofSciences of the United States of America,1958,44(2):98-104.
[28] Boehr D D, Nussinov R, Wright P E. The role of dynamic conformationalensembles in biomolecular recognition[J]. Nature Chemical Biology,2009,5(11):789-796.
[29] Boehr D D, Wright P E. How do proteins interact?[J]. Science,2008,320(5882):1429-1430.
[30] Ma B Y, Kumar S, Tsai C J, et al. Folding funnels and binding mechanisms[J].Protein Engineering,1999,12(9):713-720.
[31] Tsai C J, Kumar S, Ma B Y, et al. Folding funnels, binding funnels, and proteinfunction[J]. Protein Science,1999,8(6):1181-1190.
[32] Tsai C J, Ma B Y, Nussinov R. Folding and binding cascades: Shifts in energylandscapes[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,1999,96(18):9970-9972.
[33] Kumar S, Ma B Y, Tsai C J, et al. Folding and binding cascades: Dynamiclandscapes and population shifts[J]. Protein Science,2000,9(1):10-19.
[34] Tsai C J, Ma B Y, Sham Y Y, et al. Structured disorder and conformationalselection[J]. Proteins-Structure Function and Genetics,2001,44(4):418-427.
[35] Csermely P, Palotai R, Nussinov R. Induced fit, conformational selection andindependent dynamic segments: an extended view of binding events[J]. Trendsin Biochemical Sciences,2010,35(10):539-546.
[36] Dunker A K, Brown C J, Lawson J D, et al. Intrinsic disorder and proteinfunction[J]. Biochemistry,2002,41(21):6573-6582.
[37] Uversky V N. Natively unfolded proteins: A point where biology waits forphysics[J]. Protein Science,2002,11(4):739-756.
[38] Uversky V N, Oldfield C J, Dunker A K. Showing your ID: intrinsic disorder asan ID for recognition, regulation and cell signaling[J]. Journal Of MolecularRecognition,2005,18(5):343-384.
[39] Tompa P. Intrinsically unstructured proteins[J]. Trends in Biochemical Sciences,2002,27(10):527-533.
[40] Tompa P. The interplay between structure and function in intrinsicallyunstructured proteins[J]. FEBS Letters,2005,579(15):3346-3354.
[41] Tompa P. Unstructural biology coming of age[J]. Current Opinion in StructuralBiology,2011,21(3):419-425.
[42] Dyson H J. Expanding the proteome: disordered and alternatively foldedproteins[J]. Quarterly Reviews of Biophysics,2011,44(4):467-518.
[43] Dyson H J, Wright P E. Coupling of folding and binding for unstructuredproteins[J]. Current Opinion in Structural Biology,2002,12(1):54-60.
[44] Dyson H J, Wright P E. Intrinsically unstructured proteins and their functions[J].Nature Reviews Molecular Cell Biology,2005,6(3):197-208.
[45] Dyson H J, Wright P E. According to current textbooks, a well-definedthree-dimensional structure is a prerequisite for the function of a protein. Is thiscorrect?[J]. IUBMB Life,2006,58(2):107-109.
[46] Wright P E, Dyson H J. Intrinsically unstructured proteins: Re-assessing theprotein structure-function paradigm[J]. Journal of Molecular Biology,1999,293(2):321-331.
[47] Wright P E, Dyson H J. Linking folding and binding[J]. Current Opinion InStructural Biology,2009,19(1):31-38.
[48] Wang J, Zheng X, Yang Y, et al. Quantifying intrinsic specificity: A potentialcomplement to affinity in drug screening[J]. Physical Review Letters,2007,99(19).
[49] Yan Z Q, Zheng X L, Wang E K, et al. Thermodynamic and kinetic specificitiesof ligand binding[J]. Chemical Science,2013,4(6):2387-2395.
[50] Shirts M, Pande V S. Screen Savers of the World Unite![J]. Science,2000,290(5498):1903-1904.
[51] Shaw D E, Maragakis P, Lindorff-Larsen K, et al. Atomic-level characterizationof the structural dynamics of proteins[J]. Science,2010,330(6002):341-346.
[52] Lindorff-Larsen K, Piana S, Dror R O, et al. How fast-folding proteins fold[J].Science,2011,334(6055):517-520.
[53] Mccammon J A, Gelin B R, Karplus M. Dynamics of folded proteins[J]. Nature,1977,267:16.
[54] Abkevich V I, Gutin A M, Shakhnovich E I. Free-Energy Landscape forProtein-Folding Kinetics-Intermediates, Traps, and Multiple Pathways inTheory and Lattice Model Simulations[J]. Journal of Chemical Physics,1994,101(7):6052-6062.
[55] Brooks C L, Onuchic J N, Wales D J. Statistical thermodynamics-Taking awalk on a landscape[J]. Science,2001,293(5530):612-613.
[56] Chan H S, Dill K A. Transition-States and Folding Dynamics of Proteins andHeteropolymers[J]. Journal of Chemical Physics,1994,100(12):9238-9257.
[57] Clementi C, Nymeyer H, Onuchic J N. Topological and energetic factors: Whatdetermines the structural details of the transition state ensemble and "en-route"intermediates for protein folding? An investigation for small globularproteins[J]. Journal of Molecular Biology,2000,298(5):937-953.
[58] Eaton W A, Schuler B, Lipman E A. Probing the free-energy surface for proteinfolding with single-molecule fluorescence spectroscopy[J]. Nature,2002,419(6908):743-747.
[59] Gruebele M, Sabelko J, Ervin J. Observation of strange kinetics in proteinfolding[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,1999,96(11):6031-6036.
[60] Itzhaki L S, Otzen D E, Fersht A R. The Structure of the Transition-State forFolding of Chymotrypsin Inhibitor-2Analyzed by Protein Engineering Methods-Evidence for a Nucleation-Condensation Mechanism for Protein-Folding[J].Journal of Molecular Biology,1995,254(2):260-288.
[61] Klimov D K, Thirumalai D. Linking rates of folding in lattice models ofproteins with underlying thermodynamic characteristics[J]. Journal of ChemicalPhysics,1998,109(10):4119-4125.
[62] Nymeyer H, Garcia A E, Onuchic J N. Folding funnels and frustration inoff-lattice minimalist protein landscapes[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,1998,95(11):5921-5928.
[63] Stell G, Lee C L, Wang J. First-passage time distribution and non-Markoviandiffusion dynamics of protein folding[J]. Journal of Chemical Physics,2003,118(2):959-968.
[64] Zhou Y Q, Zhang C, Stell G, et al. Temperature dependence of the distributionof the first passage time: Results from discontinuous molecular dynamicssimulations of an all-atom model of the second beta-hairpin fragment of proteinG[J]. Journal of the American Chemical Society,2003,125(20):6300-6305.
[65] Wolynes P G. Biomolecular Folding in Vacuo()[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,1995,92(7):2426-2427.
[66] Plotkin S S, Wang J, Wolynes P G. Statistical mechanics of a correlated energylandscape model for protein folding funnels[J]. Journal of Chemical Physics,1997,106(7):2932-2948.
[67] Shakhnovich E I. Proteins with Selected Sequences Fold into Unique NativeConformation[J]. Physical Review Letters,1994,72(24):3907-3910.
[68] Goldstein R A, Lutheyschulten Z A, Wolynes P G. Optimal Protein-FoldingCodes from Spin-Glass Theory[J]. Proceedings of the National Academy ofSciences of the United States of America,1992,89(11):4918-4922.
[69] Sobolev V, Sorokine A, Prilusky J, et al. Automated analysis of interatomiccontacts in proteins[J]. Bioinformatics,1999,15(4):327-332.
[70] Hess B, Kutzner C, Van Der Spoel D, et al. GROMACS4: Algorithms forhighly efficient, load-balanced, and scalable molecular simulation[J]. Journal ofChemical Theory and Computation,2008,4(3):435-447.
[71] Noel J K, Whitford P C, Sanbonmatsu K Y, et al. SMOG@ctbp: simplifieddeployment of structure-based models in GROMACS[J]. Nucleic AcidsResearch,2010,38: W657-W661.
[72] Kumar S, Bouzida D, Swendsen R H, et al. The Weighted Histogram AnalysisMethod for Free-Energy Calculations on Biomolecules.1. The Method[J].Journal of Computational Chemistry,1992,13(8):1011-1021.
[73] Andrec M, Felts A K, Gallicchio E, et al. Protein folding pathways from replicaexchange simulations and a kinetic network model[J]. Proceedings of theNational Academy of Sciences of the United States of America,2005,102(19):6801-6806.
[74] Buchete N V, Hummer G. Peptide folding kinetics from replica exchangemolecular dynamics[J]. Physical Review E,2008,77(3).
[75] Muff S, Caflisch A. ETNA: Equilibrium Transitions Network and ArrheniusEquation for Extracting Folding Kinetics from REMD Simulations[J]. Journalof Physical Chemistry B,2009,113(10):3218-3226.
[76] Van Der Spoel D, Seibert M M. Protein folding kinetics and thermodynamicsfrom atomistic simulations[J]. Physical Review Letters,2006,96(23).
[77] Yang S C, Onuchic J N, Garcia A E, et al. Folding time predictions fromall-atom replica exchange simulations[J]. Journal of Molecular Biology,2007,372(3):756-763.
[78] Shakhnovich E I, Gutin A M. Engineering of Stable and Fast-Folding Sequencesof Model Proteins[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1993,90(15):7195-7199.
[79] Sali A, Shakhnovich E, Karplus M. Kinetics of Protein-Folding-a LatticeModel Study of the Requirements for Folding to the Native-State[J]. Journal ofMolecular Biology,1994,235(5):1614-1636.
[80] Sali A, Shakhnovich E, Karplus M. How Does a Protein Fold[J]. Nature,1994,369(6477):248-251.
[81] Shakhnovich E I, Gutin A M. Implications of Thermodynamics of ProteinFolding for Evolution of Primary Sequences[J]. Nature,1990,346(6286):773-775.
[82] Klimov D K, Thirumalai D. Factors governing the foldability of proteins[J].Proteins-Structure Function and Genetics,1996,26(4):411-441.
[83] Klimov D K, Thirumalai D. Criterion that determines the foldability ofproteins[J]. Physical Review Letters,1996,76(21):4070-4073.
[84] Dinner A R, Abkevich V, Shakhnovich E, et al. Factors that affect the foldingability of proteins[J]. Proteins-Structure Function and Genetics,1999,35(1):34-40.
[85] Karplus M, Dinner A R, Verosub E. Use of a quantitative structure-propertyrelationship to design larger model proteins that fold rapidly[J]. ProteinEngineering,1999,12(11):909-917.
[86] Melin R, Li H, Wingreen N S, et al. Designability, thermodynamic stability, anddynamics in protein folding: A lattice model study[J]. Journal of ChemicalPhysics,1999,110(2):1252-1262.
[87] Onuchic J N, Lutheyschulten Z, Wolynes P G. Theory of protein folding: Theenergy landscape perspective[J]. Annual Review of Physical Chemistry,1997,48:545-600.
[88] Das P, Clementi C, Matysiak S. Balancing energy and entropy: A minimalistmodel for the characterization of protein folding landscapes[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2005,102(29):10141-10146.
[89] Clementi C, Plotkin S S. The effects of nonnative interactions on protein foldingrates: Theory and simulation[J]. Protein Science,2004,13(7):1750-1766.
[90] Thirumalai D, Klimov D K. Deciphering the timescales and mechanisms ofprotein folding using minimal off-lattice models[J]. Current Opinion inStructural Biology,1999,9(2):197-207.
[91] Thirumalai D, Klimov D K, Woodson S A. Kinetic partitioning mechanism as aunifying theme in the folding of biomolecules[J]. Theoretical ChemistryAccounts,1997,96(1):14-22.
[92] Camacho C J, Thirumalai D. Kinetics and Thermodynamics of Folding inModel Proteins[J]. Proceedings of the National Academy of Sciences of theUnited States of America,1993,90(13):6369-6372.
[93] Thirumalai D. From Minimal Models to Real Proteins-Time Scales forProtein-Folding Kinetics[J]. Journal De Physique I,1995,5(11):1457-1467.
[94] Honeycutt J D, Thirumalai D. The Nature of Folded States ofGlobular-Proteins[J]. Biopolymers,1992,32(6):695-709.
[95] Angelani L, Ruocco G. Saddles of the energy landscape and folding of modelproteins[J]. Europhysics Letters,2009,87(1).
[96] Chan H S, Dill K A. Solvation-Effects of Molecular-Size and Shape[J]. Journalof Chemical Physics,1994,101(8):7007-7026.
[97] Chan H S, Kaya H. Towards a consistent modeling of protein thermodynamicand kinetic cooperativity: How applicable is the transition state picture tofolding and unfolding?[J]. Journal of Molecular Biology,2002,315(4):899-909.
[98] Cieplak M, Hoang T X. Scaling of folding properties in Go models ofproteins[J]. Journal of Biological Physics,2000,26(4):273-294.
[99] Cieplak M, Hoang T X, Li M S. Scaling of folding properties in simple modelsof proteins[J]. Physical Review Letters,1999,83(8):1684-1687.
[100] Eaton W A, Lipman E A, Schuler B, et al. Single-molecule measurement ofprotein folding kinetics[J]. Science,2003,301(5637):1233-1235.
[101] Frauenfelder H, Parak F, Young R D. Conformational Substates in Proteins[J].Annual Review of Biophysics and Biophysical Chemistry,1988,17:451-479.
[102] Frauenfelder H, Sligar S G, Wolynes P G. The Energy Landscapes and Motionsof Proteins[J]. Science,1991,254(5038):1598-1603.
[103] Gruebele M, Nguyen H, Jager M, et al. Tuning the free-energy landscape of aWW domain by temperature, mutation, and truncation[J]. Proceedings of theNational Academy of Sciences of the United States of America,2003,100(7):3948-3953.
[104] Gutin A M, Abkevich V I, Shakhnovich E I. Chain length scaling of proteinfolding time[J]. Physical Review Letters,1996,77(27):5433-5436.
[105] Hardin C, Eastwood M P, Prentiss M C, et al. Associative memoryHamiltonians for structure prediction without homology: alpha/beta proteins[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2003,100(4):1679-1684.
[106] Kaya H, Chan H S. Energetic components of cooperative protein folding[J].Physical Review Letters,2000,85(22):4823-4826.
[107] Leite V B P, Onuchic J N, Stell G, et al. Probing the kinetics of single moleculeprotein folding[J]. Biophysical Journal,2004,87(6):3633-3641.
[108] Seno F, Micheletti C, Maritan A, et al. Variational approach to protein designand extraction of interaction potentials[J]. Physical Review Letters,1998,81(10):2172-2175.
[109] Socci N D, Onuchic J N. Kinetic and Thermodynamic Analysis of ProteinlikeHeteropolymers-Monte-Carlo Histogram Technique[J]. Journal of ChemicalPhysics,1995,103(11):4732-4744.
[110] Stell G, Lee C L, Lin C T, et al. Diffusion dynamics, moments, and distributionof first-passage time on the protein-folding energy landscape, with applicationsto single molecules[J]. Physical Review E,2003,67(4).
[111] Wang J. The complex kinetics of protein folding in wide temperature ranges[J].Biophysical Journal,2004,87(4):2164-2171.
[112] Xie X S, Yang H. Probing single-molecule dynamics photon by photon[J].Journal of Chemical Physics,2002,117(24):10965-10979.
[113] Garcia A E, Onuchic J N. Folding a protein in a computer: An atomicdescription of the folding/unfolding of protein A[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2003,100(24):13898-13903.
[114] Okamoto Y, Sugita Y. Replica-exchange molecular dynamics method for proteinfolding[J]. Chemical Physics Letters,1999,314(1-2):141-151.
[115] Rauscher S, Neale C, Pomes R. Simulated Tempering Distributed ReplicaSampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methodsfor Conformational Sampling[J]. Journal of Chemical Theory and Computation,2009,5(10):2640-2662.
[116] Rodinger T, Howell P L, Pomes R. Distributed replica sampling[J]. Journal ofChemical Theory and Computation,2006,2(3):725-731.
[117] Rodinger T, Pomes R. Enhancing the accuracy, the efficiency and the scope offree energy simulations[J]. Current Opinion in Structural Biology,2005,15(2):164-170.
[118] Zhang C, Ma J P. Comparison of sampling efficiency between simulatedtempering and replica exchange[J]. Journal of Chemical Physics,2008,129(13).
[119] Zhang C, Ma J P. Enhanced sampling in generalized ensemble with large gap ofsampling parameter: Case study in temperature space random walk[J]. Journalof Chemical Physics,2009,130(19).
[120] Zhang C, Ma J P. Enhanced sampling and applications in protein folding inexplicit solvent[J]. Journal of Chemical Physics,2010,132(24).
[121] Cho S S, Levy Y, Wolynes P G. P versus Q: Structural reaction coordinatescapture protein folding on smooth landscapes[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2006,103(3):586-591.
[122] Plotkin S S, Wang J, Wolynes P G. Statistical mechanics of correlated energylandscape models for random heteropolymers and proteins[J]. Physica D,1997,107(2-4):322-325.
[123] Eastwood M P, Hardin C, Luthey-Schulten Z, et al. Evaluating proteinstructure-prediction schemes using energy landscape theory[J]. Ibm Journal OfResearch And Development,2001,45(3.4):475-497.
[124] Fujitsuka Y, Takada S, Luthey-Schulten Z A, et al. Optimizing physical energyfunctions for protein folding[J]. Proteins-Structure Function and Genetics,2004,54(1):88-103.
[125] Hardin C, Eastwood M P, Prentiss M, et al. Folding funnels: The key to robustprotein structure prediction[J]. Journal of Computational Chemistry,2002,23(1):138-146.
[126] Iben I E T, Braunstein D, Doster W, et al. GLASSY BEHAVIOR OF APROTEIN[J]. Physical Review Letters,1989,62(16):1916-1919.
[127] Wolynes P G. Folding funnels and energy landscapes of larger proteins withinthe capillarity approximation[J]. Proceedings of the National Academy ofSciences of the United States of America,1997,94(12):6170-6175.
[128] Finkelstein A V, Badretdinov A Y. Rate of protein folding near the point ofthermodynamic equilibrium between the coil and the most stable chain fold[J].Folding&Design,1997,2(2):115-121.
[129] Finkelstein A V, Ivankov D N, Garbuzynskiy S O, et al. Contact order revisited:Influence of protein size on the folding rate[J]. Protein Science,2003,12(9):2057-2062.
[130] Galzitskaya O V, Garbuzynskiy S O, Ivankov D N, et al. Chain length is themain determinant of the folding rate for proteins with three-state foldingkinetics[J]. Proteins-Structure Function and Genetics,2003,51(2):162-166.
[131] Kouza M, Li M S, O'brien E P, et al. Effect of finite size on cooperativity andrates of protein folding[J]. Journal of Physical Chemistry A,2006,110:671-676.
[132] Li M S, Klimov D K, Thirumalai D. Dependence of folding rates on proteinlength[J]. Journal of Physical Chemistry B,2002,106(33):8302-8305.
[133] Li M S, Klimov D K, Thirumalai D. Thermal denaturation and folding rates ofsingle domain proteins: size matters[J]. Polymer,2004,45(2):573-579.
[134] Munoz V, Naganathan A N, Sanchez-Ruiz J M. Direct measurement of barrierheights in protein folding[J]. Journal of the American Chemical Society,2005,127(51):17970-17971.
[135] Naganathan A N, Munoz V. Scaling of folding times with protein size[J].Journal of the American Chemical Society,2005,127(2):480-481.
[136] Takada S, Koga N. Roles of native topology and chain-length scaling in proteinfolding: A simulation study with a Go-like model[J]. Journal of MolecularBiology,2001,313(1):171-180.
[137] Saven J G, Wang J, Wolynes P G. Protein-Folding Kinetics-Relaxation in aGlobally Connected Random Energy-Model[J]. Abstracts of Papers of theAmerican Chemical Society,1994,208:250-PHYS.
[138] Socci N D, Onuchic J N, Wolynes P G. Diffusive dynamics of the reactioncoordinate for protein folding funnels[J]. Journal of Chemical Physics,1996,104(15):5860-5868.
[139] Plotkin S S. Speeding protein folding beyond the Go model: How a littlefrustration sometimes helps[J]. Proteins-Structure Function and Bioinformatics,2001,45(4):337-345.
[140] Baker D, Plaxco K W, Simons K T. Contact order, transition state placementand the refolding rates of single domain proteins[J]. Journal of MolecularBiology,1998,277(4):985-994.
[141] Dinner A R, Karplus M. The roles of stability and contact order in determiningprotein folding rates[J]. Nature Structural Biology,2001,8(1):21-22.
[142] Raleigh D P, Kuhlman B, Luisi D L, et al. Global analysis of the effects oftemperature and denaturant on the folding and unfolding kinetics of theN-terminal domain of the protein L9[J]. Journal of Molecular Biology,1998,284(5):1661-1670.
[143] Chen J. Towards the physical basis of how intrinsic disorder mediates proteinfunction[J]. Archives of Biochemistry and Biophysics,2012,524(2):123-131.
[144] Tompa P, Szasz C, Buday L. Structural disorder throws new light onmoonlighting[J]. Trends in Biochemical Sciences,2005,30(9):484-489.
[145] Papoian G A. Proteins with weakly funneled energy landscapes challenge theclassical structure-function paradigm[J]. Proceedings of the National Academyof Sciences of the United States of America,2008,105(38):14237-14238.
[146] Meszaros B, Simon I, Dosztanyi Z. The expanding view of protein-proteininteractions: complexes involving intrinsically disordered proteins[J]. PhysicalBiology,2011,8(3).
[147] Whitford P C. Disorder guides protein function[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2013,110(18):7114-7115.
[148] Mosca R, Pache R A, Aloy P. The Role of Structural Disorder in the Rewiring ofProtein Interactions through Evolution[J]. Molecular&Cellular Proteomics,2012,11(7).
[149] Zhou H X. Intrinsic disorder: signaling via highly specific but short-livedassociation[J]. Trends in Biochemical Sciences,2012,37(2):43-48.
[150] Sugase K, Dyson H J, Wright P E. Mechanism of coupled folding and bindingof an intrinsically disordered protein[J]. Nature,2007,447(7147):1021-U11.
[151] Dunker A K, Radivojac P, Iakoucheva L M, et al. Intrinsic disorder andfunctional proteomics[J]. Biophysical Journal,2007,92(5):1439-1456.
[152] Ward J J, Sodhi J S, Mcguffin L J, et al. Prediction and functional analysis ofnative disorder in proteins from the three kingdoms of life[J]. Journal ofMolecular Biology,2004,337(3):635-645.
[153] Xie H B, Vucetic S, Iakoucheva L M, et al. Functional anthology of intrinsicdisorder.1. Biological processes and functions of proteins with long disorderedregions[J]. Journal of Proteome Research,2007,6(5):1882-1898.
[154] Fuxreiter M, Tompa P, Simon I, et al. Malleable machines take shape ineukaryotic transcriptional regulation[J]. Nature Chemical Biology,2008,4(12):728-737.
[155] Dunker A K, Silman I, Uversky V N, et al. Function and structure of inherentlydisordered proteins[J]. Current Opinion in Structural Biology,2008,18(6):756-764.
[156] Dunker A K, Uversky V N. Signal transduction via unstructured proteinconduits[J]. Nature Chemical Biology,2008,4(4):229-230.
[157] Dunker A K, Oldfield C J, Meng J W, et al. The unfoldomics decade: an updateon intrinsically disordered proteins[J]. BMC Genomics,2008,9.
[158] Gsponer J, Futschik M E, Teichmann S A, et al. Tight Regulation ofUnstructured Proteins: From Transcript Synthesis to Protein Degradation[J].Science,2008,322(5906):1365-1368.
[159] Smock R G, Gierasch L M. Sending Signals Dynamically[J]. Science,2009,324(5924):198-203.
[160] Babu M M, Van Der Lee R, De Groot N S, et al. Intrinsically disorderedproteins: regulation and disease[J]. Current Opinion in Structural Biology,2011,21(3):432-440.
[161] Tantos A, Han K H, Tompa P. Intrinsic disorder in cell signaling and genetranscription[J]. Molecular And Cellular Endocrinology,2012,348(2):457-465.
[162] Dill K A, Chan H S. From Levinthal to pathways to funnels[J]. NatureStructural Biology,1997,4(1):10-19.
[163] Oliveberg M, Wolynes P G. The experimental survey of protein-folding energylandscapes[J]. Quarterly Reviews of Biophysics,2005,38(3):245-288.
[164] Wolynes P G. Recent successes of the energy landscape theory of proteinfolding and function[J]. Quarterly Reviews of Biophysics,2005,38(4):405-410.
[165] Papoian G A, Wolynes P G. The physics and Bioinformatics of binding andfolding-An energy landscape perspective[J]. Biopolymers,2003,68(3):333-349.
[166] Austin R H, Beeson K W, Eisenstein L, et al. DYNAMICS OFLIGAND-BINDING TO MYOGLOBIN[J]. Biochemistry,1975,14(24):5355-5373.
[167] Rumfeldt J a O, Galvagnion C, Vassall K A, et al. Conformational stability andfolding mechanisms of dimeric proteins[J]. Progress in Biophysics&MolecularBiology,2008,98(1):61-84.
[168] Wang J. Diffusion and single molecule dynamics on biomolecular interfacebinding energy landscape[J]. Chemical Physics Letters,2006,418(4-6):544-548.
[169] Reat V, Patzelt H, Ferrand M, et al. Dynamics of different functional parts ofbacteriorhodopsin: H-H-2labeling and neutron scattering[J]. Proceedings of theNational Academy of Sciences of the United States of America,1998,95(9):4970-4975.
[170] Reddy G B, Bharadwaj S, Surolia A. Thermal stability and mode ofoligomerization of the tetrameric peanut agglutinin: A differential scanningcalorimetry study[J]. Biochemistry,1999,38(14):4464-4470.
[171] Levy Y. Protein topology determines binding mechanism[J]. Proceedings of theNational Academy of Sciences,2004,101(2):511-516.
[172] Levy Y, Cho S S, Onuchic J N, et al. A Survey of Flexible Protein BindingMechanisms and their Transition States Using Native Topology Based EnergyLandscapes[J]. Journal of Molecular Biology,2005,346(4):1121-1145.
[173] Levy Y, Onuchic J N. Mechanisms of protein assembly: Lessons fromminimalist models[J]. Accounts of Chemical Research,2006,39(2):135-142.
[174] Wang W, Xu W X, Levy Y, et al. Confinement effects on the kinetics andthermodynamics of protein dimerization[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2009,106(14):5517-5522.
[175] Kaplan E L, Meier P. Nonparametric-Estimation from IncompleteObservations[J]. Journal of the American Statistical Association,1958,53(282):457-481.
[176] Efron B. The two sample problem with censored data[C]. Proceedings of theFifth Berkeley Symposium on Mathematical Statistics and Probability, Berkeley,1967,4:831-853.
[177] Barker C. The Mean, Median, and Confidence Intervals of the Kaplan-MeierSurvival Estimate-Computations and Applications[J]. American Statistician,2009,63(1):78-80.
[178] Zhong M, Hess K R. Mean survival time from right censored data[J]. COBRAPreprint Series,2009: Working Paper66.
[179] Socci N D, Onuchic J N. Folding Kinetics of Proteinlike Heteropolymers[J].Journal of Chemical Physics,1994,101(2):1519-1528.
[180] Xu D, Tsai C J, Nussinov R. Mechanism and evolution of proteindimerization[J]. Protein Science,1998,7(3):533-544.
[181] Neet K E, Timm D E. Conformational stability of dimeric proteins: quantitativestudies by equilibrium denaturation [J]. Protein Science,1994,3(12):2167-2174.
[182] Gunasekaran K, Tsai C J, Nussinov R. Analysis of ordered and disorderedprotein complexes reveals structural features discriminating between stable andunstable monomers[J]. Journal of Molecular Biology,2004,341(5):1327-1341.
[183] Janin J. Quantifying biological specificity: The statistical mechanics ofmolecular recognition[J]. Proteins-Structure Function and Genetics,1996,25(4):438-445.
[184] Kohn J E, Gillespie B, Plaxco K W. Non-Sequence-Specific Interactions CanAccount for the Compaction of Proteins Unfolded under "Native" Conditions[J].Journal of Molecular Biology,2009,394(2):343-350.
[185] Weinkam P, Pletneva E V, Gray H B, et al. Electrostatic effects on funneledlandscapes and structural diversity in denatured protein ensembles[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(6):1796-1801.
[186] Mao A H, Crick S L, Vitalis A, et al. Net charge per residue modulatesconformational ensembles of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(18):8183-8188.
[187] Muller-Spath S, Soranno A, Hirschfeld V, et al. Charge interactions candominate the dimensions of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(33):14609-14614.
[188] Haran G. How, when and why proteins collapse: the relation to folding[J].Current Opinion in Structural Biology,2012,22(1):14-20.
[189] Chu X, Wang Y, Gan L, et al. Importance of Electrostatic Interactions in theAssociation of Intrinsically Disordered Histone Chaperone Chz1and HistoneH2A.Z-H2B[J]. Plos Computational Biology,2012,8(7): e1002608
[190] Zheng W H, Schafer N P, Davtyan A, et al. Predictive energy landscapes forprotein-protein association[J]. Proceedings of the National Academy ofSciences of the United States of America,2012,109(47):19244-19249.
[191] Trizac E, Levy Y, Wolynes P G. Capillarity theory for the fly-castingmechanism[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2010,107(7):2746-2750.
[192] Wang J. Statistics, pathways and dynamics of single molecule protein folding[J].Journal of Chemical Physics,2003,118(2):952-958.
[193] Kirkpatrick T R, Wolynes P G. Connections between Some Kinetic andEquilibrium Theories of the Glass-Transition[J]. Physical Review A,1987,35(7):3072-3080.
[194] Kirkpatrick T R, Wolynes P G. Stable and Metastable States in Mean-Field Pottsand Structural Glasses[J]. Physical Review B,1987,36(16):8552-8564.
[195] Shoemaker B A, Portman J J, Wolynes P G. Speeding molecular recognition byusing the folding funnel: The fly-casting mechanism[J]. Proceedings of theNational Academy of Sciences of the United States of America,2000,97(16):8868-8873.
[196] Wang Y, Chu X K, Suo Z C, et al. Multidomain Protein Solves the FoldingProblem by Multifunnel Combined Landscape: Theoretical Investigation of aY-Family DNA Polymerase[J]. Journal of the American Chemical Society,2012,134(33):13755-13764.
[197] Kornberg R D. Chromatin Structure-Repeating Unit of Histones and DNA[J].Science,1974,184(4139):868-871.
[198] Kornberg R D, Lorch Y L. Twenty-five years of the nucleosome, fundamentalparticle of the eukaryote chromosome[J]. Cell,1999,98(3):285-294.
[199] Luger K, Mader A W, Richmond R K, et al. Crystal structure of the nucleosomecore particle at2.8angstrom resolution[J]. Nature,1997,389(6648):251-260.
[200] Muthurajan U M, Bao Y H, Forsberg L J, et al. Crystal structures of histone Sinmutant nucleosomes reveal altered protein-DNA interactions[J]. Embo Journal,2004,23(2):260-271.
[201] Almouzni G, De Koning L, Corpet A, et al. Histone chaperones: an escortnetwork regulating histone traffic[J]. Nature Structural&Molecular Biology,2007,14(11):997-U1.
[202] Horikoshi M, Eitoku M, Sato L, et al. Histone chaperones:30years fromisolation to elucidation of the mechanisms of nucleosome assembly anddisassembly[J]. Cellular and Molecular Life Sciences,2008,65(3):414-444.
[203] Laskey R A, Honda B M, Mills A D, et al. Nucleosomes Are Assembled by anAcidic Protein Which Binds Histones and Transfers Them to DNA[J]. Nature,1978,275(5679):416-420.
[204] Das C, Tyler J K, Churchill M E A. The histone shuffle: histone chaperones inan energetic dance[J]. Trends in Biochemical Sciences,2010,35(9):476-489.
[205] Hondele M, Ladurner A G. The chaperone-histone partnership: for the greatergood of histone traffic and chromatin plasticity[J]. Current Opinion in StructuralBiology,2011,21(6):698-708.
[206] Park Y J, Luger K. Histone chaperones in nucleosome eviction and histoneexchange[J]. Current Opinion in Structural Biology,2008,18(3):282-289.
[207] Zhou Z, Feng H Q, Zhou B R, et al. Structural basis for recognition ofcentromere histone variant CenH3by the chaperone Scm3[J]. Nature,2011,472(7342):234-237.
[208] Korolev N, Vorontsova O V, Nordenskiold L. Physicochemical analysis ofelectrostatic foundation for DNA-protein interactions in chromatintransformations[J]. Progress in Biophysics&Molecular Biology,2007,95(1-3):23-49.
[209] Luk E, Vu N D, Patteson K, et al. Chz1, a nuclear chaperone for histoneH2AZ[J]. Molecular Cell,2007,25(3):357-368.
[210] Zhou Z, Feng H Q, Hansen D F, et al. NMR structure of chaperone Chz1complexed with histones H2A.Z-H2B[J]. Nature Structural&MolecularBiology,2008,15(8):868-869.
[211] Hansen D F, Zhou Z, Fen H Q, et al. Binding Kinetics of Histone ChaperoneChz1and Variant Histone H2A.Z-H2B by Relaxation Dispersion NMRSpectroscopy[J]. Journal of Molecular Biology,2009,387(1):1-9.
[212] Miyazawa S, Jernigan R L. Residue-residue potentials with a favorable contactpair term and an unfavorable high packing density term, for simulation andthreading[J]. Journal of Molecular Biology,1996,256(3):623-644.
[213] Oliveira L C, Schug A, Onuchic J N. Geometrical features of the protein foldingmechanism are a robust property of the energy landscape: A detailedinvestigation of several reduced models[J]. Journal of Physical Chemistry B,2008,112(19):6131-6136.
[214] Azia A, Levy Y. Nonnative Electrostatic Interactions Can Modulate ProteinFolding: Molecular Dynamics with a Grain of Salt[J]. Journal of MolecularBiology,2009,393(2):527-542.
[215] Whitford P C, Noel J K, Gosavi S, et al. An all-atom structure-based potentialfor proteins: Bridging minimal models with all-atom empirical force fields[J].Proteins-Structure Function and Bioinformatics,2009,75(2):430-441.
[216] Cho S S, Levy Y, Wolynes P G. Quantitative criteria for native energeticheterogeneity influences in the prediction of protein folding kinetics[J].Proceedings of the National Academy of Sciences of the United States ofAmerica,2009,106(2):434-439.
[217] Levy Y, Onuchic J N, Wolynes P G. Fly-casting in protein-DNA binding:Frustration between protein folding and electrostatics facilitates targetrecognition[J]. Journal of the American Chemical Society,2007,129(4):738-739.
[218] Huang Y, Liu Z. Kinetic Advantage of Intrinsically Disordered Proteins inCoupled Folding-Binding Process: A Critical Assessment of the "Fly-Casting"Mechanism[J]. Journal of Molecular Biology,2009,393(5):1143-1159.
[219] Bonomi M, Branduardi D, Bussi G, et al. PLUMED: A portable plugin forfree-energy calculations with molecular dynamics[J]. Computer PhysicsCommunications,2009,180(10):1961-1972.
[220] Yang S C, Onuchic J, Levine H. Protein self-assembly via domain swapping:The effect of intermolecular interactions and protein concentration[J].Biophysical Journal,2005,88(1):198a-198a.
[221] Fersht A R, Sato S. Phi-Value analysis and the nature of protein-foldingtransition states[J]. Proceedings of the National Academy of Sciences of theUnited States of America,2004,101(21):7976-7981.
[222] Zhou H X. How do biomolecular systems speed up and regulate rates?[J].Physical Biology,2005,2(3): R1-R25.
[223] Schreiber G. Kinetic studies of protein-protein interactions[J]. Current Opinionin Structural Biology,2002,12(1):41-47.
[224] Plaxco K W, Kohn J E, Millett I S, et al. Random-coil behavior and thedimensions of chemically unfolded proteins[J]. Proceedings of the NationalAcademy of Sciences of the United States of America,2004,101(34):12491-12496.
[225] Turjanski A G, Gutkind J S, Best R B, et al. Binding-induced folding of anatively unstructured transcription factor[J]. PLoS Computational Biology,2008,4(4): e1000060.
[226] Chen J H. Intrinsically Disordered p53Extreme C-Terminus Binds toS100B(beta beta) through "Fly-Casting"[J]. Journal of the American ChemicalSociety,2009,131(6):2088-2089.
[227] Espinoza-Fonseca L M. Reconciling binding mechanisms of intrinsicallydisordered proteins[J]. Biochemical and Biophysical Research Communications,2009,382(3):479-482.
[228] Lu Q, Lu H P, Wang J. Exploring the mechanism of flexible biomolecularrecognition with single molecule dynamics[J]. Physical Review Letters,2007,98(12).
[229] Narayanan R, Ganesh O K, Edison A S, et al. Kinetics of folding and binding ofan intrinsically disordered protein: The inhibitor of yeast aspartic proteinaseYPrA[J]. Journal of the American Chemical Society,2008,130(34):11477-11485.
[230] Wang J, Lu Q, Lu H P. Single-molecule dynamics reveals cooperativebinding-folding in protein recognition[J]. PLoS Computational Biology,2006,2(7): e78.
[231] Wang J, Wang Y, Chu X K, et al. Multi-Scaled Explorations of Binding-InducedFolding of Intrinsically Disordered Protein Inhibitor IA3to its TargetEnzyme[J]. PLoS Computational Biology,2011,7(4): e1001118.
[232] Chan H S, Zhang Z Q, Wallin S, et al. Cooperativity, Local-Nonlocal Coupling,and Nonnative Interactions: Principles of Protein Folding from Coarse-GrainedModels[J]. Annual Review of Physical Chemistry, Vol62,2011,62:301-326.
[233] Zarrine-Afsar A, Wallin S, Neculai A M, et al. Theoretical and experimentaldemonstration of the importance of specific nonnative interactions in proteinfolding[J]. Proceedings of the National Academy of Sciences of the UnitedStates of America,2008,105(29):9999-10004.
[234] Schreiber G, Fersht A R. Rapid, electrostatically assisted association ofproteins[J]. Nature Structural&Molecular Biology,1996,3(5):427-431.
[235] Chen H F. Molecular Dynamics Simulation of Phosphorylated KIDPost-Translational Modification[J]. PLoS ONE,2009,4(8): e6516.
[236] Ganguly D, Chen J H. Atomistic Details of the Disordered States of KID andpKID. Implications in Coupled Binding and Folding[J]. Journal of the AmericanChemical Society,2009,131(14):5214-5223.
[237] Kumar S, Nussinov R. Close-range electrostatic interactions in proteins[J].ChemBioChem,2002,3(7):604-617.
[238] Sussman J L, Dunker A K, Silman I, et al. Function and structure of inherentlydisordered proteins[J]. Current Opinion in Structural Biology,2008,18(6):756-764.
[239] Uversky V N, Gillespie J R, Fink A L. Why are "natively unfolded" proteinsunstructured under physiologic conditions?[J]. Proteins-Structure Function andGenetics,2000,41(3):415-427.
[240] Weathers E A, Paulaitis M E, Woolf T B, et al. Reduced amino acid alphabet issufficient to accurately recognize intrinsically disordered protein[J]. FEBS Lett,2004,576(3):348-352.
[241] Pappu R V, Mao A H, Crick S L, et al. Net charge per residue modulatesconformational ensembles of intrinsically disordered proteins[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(18):8183-8188.
[242] Haran G, England J L. To fold or expand-a charged question[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2010,107(33):14519-14520.
[243] Sheinerman F B, Norel R, Honig B. Electrostatic aspects of protein-proteininteractions[J]. Current Opinion in Structural Biology,2000,10(2):153-159.
[244] Das P, Matysiak S, Clementi C. Balancing energy and entropy: A minimalistmodel for the characterization of protein folding landscapes[J]. Proceedings ofthe National Academy of Sciences of the United States of America,2005,102(29):10141-10146.