一种基于特征点匹配的生物大分子装配方法
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摘要
研究高分辨率的大分子三维结构,对于分析研究其功能和生物代谢路径具有很重要作用.许多大分子结构可以由低温电镜得到,然而低温电镜三维重构得到的三维结构仍然需要进一步提高其分辨率,所以这些结构仍然需要具体信息.大分子的单独组成部分可以通过结晶、NMR、或者蛋白质结构比较等方法得到.如何将这些高分辨率的组成部分正确装配到大分子结构中是一个很复杂的问题.该问题的实质可以理解为图像处理.在生物大分子的装配过程中,大部分研究者都会用到特征点的方法.现有的研究方法几乎都是基于几何体内的特征点,本文提出一种新的基于蛋白质和低温电镜密度图的表面高斯曲率的方法结合优化模型,对该问题进行研究.数值实验表明,我们的方法是有效的.
The study of high-resolution three-dimensional macromolecule structure plays an important role in the analysis of the function and metabolic pathways. Many macromolecule structures can be obtained by cryo-EM density maps. But high-resolution three-dimensional structures are still difficult to achieve. On the other hand, The individual components of macromolecules can be obtained by crystallization, NMR, or protein structure comparison.How to properly fit these high-resolution components into macromolecules is a very complicated problem. This problem can be described as image processing problem. In the process of assembly of biological macromolecules, The feature points method is used by most researchers. The existing research methods are always based on the feature points within the geometry, In this paper, we propose a new method which uses the Gaussian curvature of the geometric surface and the optimizing model. Numerical experiments show that our method is effective.
The study of high-resolution three-dimensional macromolecule structure plays an important role in the analysis of the function and metabolic pathways. Many macromolecule structures can be obtained by cryo-EM density maps. But high-resolution three-dimensional structures are still difficult to achieve. On the other hand, The individual components of macromolecules can be obtained by crystallization, NMR, or protein structure comparison.How to properly fit these high-resolution components into macromolecules is a very complicated problem. This problem can be described as image processing problem. In the process of assembly of biological macromolecules, The feature points method is used by most researchers. The existing research methods are always based on the feature points within the geometry, In this paper, we propose a new method which uses the Gaussian curvature of the geometric surface and the optimizing model. Numerical experiments show that our method is effective.
引文
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[25]Lee J H,Ozorowski G,Ward A B.Cryo-EM structure of a native,fully glycosylated,cleaved HIV-1 envelope trimer.Science,2016,351(6277):1043-1048.
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[29]Zhang S H,Daveb V,Min X,et al.A fast mathematical programming programming procedure for simultaneous fitting of assembly components into cryoem density maps[J].Bioinformatics,2010,26,261-268.
[30]Zhang L,Chen S,Ruan J,et al.Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.Science,2015,350(6259):404-409.
[31]Lowe D G.Distinctive Image Features from Scale-Invariant Key points[J].International Journal of Computer Vision,2004,60(2),91-110.
[32]Ji Z,shi J.A robust algorithm for feature point matching[J].Computers and Graphics,2002,26,429-436.
[33]Goddard TD,Huang CC,and Ferrin TE.Visualizing density maps with ucsf chimera[J].J.Struct.Biol.,2007,157,281-287.
[34]Zhang W,Kaufmann B,Chipman P R,et al.Membrane curvature in flaviviruses[J].Journal of Structural Biology,2013,183,86-94.
[35]徐国良,计算几何中的几何偏微分方程方法[M],科学出版社,北京,2008.
[36]Zhang W,Barbel K,Paul R C,et al.Membrane curvature if flaviviruses.Journal of Structural Biology[J],2013,183,86-94.
[37]Lu J,Xu G,Zhang S,et al.An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data[J].Algorithms Mol Biol,2016,11(18),1-10.
[38]Goldstein H,Classical Mechanics[M],Addison-Wesley,1965.
[39]Evans DJ.On the representation of orientation space[J].Molec.Phys.,1977,34,317-325.
[2]Chiu W,Baker M L,Jiang W,et al.Electron cryomicroscopy of biological machines at subnanometer resolution[J].Structure,2005,13,363-372.
[3]Eswar N,Webb B,Marti-Renom,M A,et al.Comparative protein structure modeling with modeller[J].Curr.Protoc.Protein Sci,2007,Nov;Chapter 2:Unit 2.9.doi:10.1002/0471140864.ps0209s50.
[4]Zhang K,Zhang Y,Hu Z J,et al.Development and frontier of electron microscopy 3d reconstruction[J].Acta Biophysica Sinica,2010,26(7),533-559.
[5]Gabashvili I S,Agrawal R K,Spahn C M,et al.Solution structure of the e.coli 70s ribosome at 11.5×A resolution[J].Cell,2000,100(5),537-549.
[6]Fabian K,Mareike K,Markus G G,et al.Projection structure of the secondary citrate/sodium symporter cits at 6xA resolution by electron crystallography[J].Journal of Molecular Biology,2012,418,117-126.
[7]Henderson R.The potential and limitations of neutrons,electrons and x-rays for atomic resolution microscopy of unstained biological molecules[J].Q Rev Biophys,1995,28(2),171-193.
[8]Wang D N,Werner K.High-resolution electron crystallography of light-harvesting chlorophyll a/b-protein complex in three different media[J].Journal of Molecular Biology,1991,217(4),691-699.
[9]Stefan B,Willy W.Multi-resolution anchor-point registration of biomolecular assemblies and their components[J].Journal of Structural Biology,2007,157,271-280.
[10]Rossmann M G,Morais M C,Leiman P G,et al.Combining x-ray crystallography and electron microscopy[J].Structure,2005,13,355-362.
[11]Fabiola F,Chapman M S.Fitting of high-resolution structures into electron microscopy reconstruction images[J].Structure,2005,13,389-400.
[12]Sali A,Glaeser R,Earnest T,et al.From words to literature in structural proteomics[J].Nature,2003,422(6928),216-225.
[13]Frank J.Single-particle imaging of macromolecules by cryo-electron microscopy[J].Annu Rev Biophys Biomol Struct,2002,31,303-319.
[14]Wriggers W,Birmanns S.Using situs for flexible and rigid-body fitting of multiresolution singlemolecule data[J].J Struct Biol,2001,133(3),193-202.
[15]Topf M,Sali A.Combining electron microscopy and comparative protein structure modeling[J].Curr.Opin.Struct.Biol,2005,15,578-585.
[16]Alber F,Dokudovskaya S,Veenhoff L M,et al.Determining the architectures of macromolecular assemblies[J].Nature,2007,450(7170),683-694.
[17]Robert M G,Kenneth H D.High-resolution electron crystallography of protein molecules[J].Ultramicroscopy,1993,52,478-486.
[18]Dempster A P,Laird N M,Rubin DB.Sur la division des corps materiels en parties[J].Bull.Acad.Polon.Sci,1957,4(12),801-804.
[19]MacKay,David.Chapter 20.an example inference task:Clustering.In:Information Theory,Inference and Learning Algorithms
[20]Wriggers W,Milligan R A,McCammon J A.Situs:A package for docking crystal structures intolow-resolution maps from electron microscopy[J].J Struct Biol,1999,125(2),185-195.
[21]Pintilie G D,Zhang J,Goddard T D,et al.Quantitative analysis of cryo-em density map segmentation by watershed and scale-space filtering,and fitting of structures by alignment to regions[J].Journal of Structural Biology,2010,170,427-438.
[22]Hugo C,Robert B R.Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization[J].J.Mol.Biol.2004,338,783-793.
[23]Yan C,Hang J,Wan R.,et al.Structure of a yeast spliceosome at 3.6-angstrom resolution[J].Science,2015,349(6253):1182-1191.
[24]Hang J,Wan R,Yan C,et al.Structural basis of pre-mRNA splicing[J].Science,2015,349(6253):1191-1198.
[25]Lee J H,Ozorowski G,Ward A B.Cryo-EM structure of a native,fully glycosylated,cleaved HIV-1 envelope trimer.Science,2016,351(6277):1043-1048.
[26]Louder R K,He Y,L 6 pez-Blanco J R,et al.Structure of promoter-bound TFIID and model of human pre-initiation complex assembly.Nature,2016,531(7596):604-609.
[27]Kawabata T.Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model[J].Biophysical Journal,2008,95,4643-4658.
[28]Topf M,Lasker K,Webb B,et al.Protein structure fitting and refinement guided by cryo-em density[J].Structure,2008,16,295-307.
[29]Zhang S H,Daveb V,Min X,et al.A fast mathematical programming programming procedure for simultaneous fitting of assembly components into cryoem density maps[J].Bioinformatics,2010,26,261-268.
[30]Zhang L,Chen S,Ruan J,et al.Cryo-EM structure of the activated NAIP2-NLRC4 inflammasome reveals nucleated polymerization.Science,2015,350(6259):404-409.
[31]Lowe D G.Distinctive Image Features from Scale-Invariant Key points[J].International Journal of Computer Vision,2004,60(2),91-110.
[32]Ji Z,shi J.A robust algorithm for feature point matching[J].Computers and Graphics,2002,26,429-436.
[33]Goddard TD,Huang CC,and Ferrin TE.Visualizing density maps with ucsf chimera[J].J.Struct.Biol.,2007,157,281-287.
[34]Zhang W,Kaufmann B,Chipman P R,et al.Membrane curvature in flaviviruses[J].Journal of Structural Biology,2013,183,86-94.
[35]徐国良,计算几何中的几何偏微分方程方法[M],科学出版社,北京,2008.
[36]Zhang W,Barbel K,Paul R C,et al.Membrane curvature if flaviviruses.Journal of Structural Biology[J],2013,183,86-94.
[37]Lu J,Xu G,Zhang S,et al.An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data[J].Algorithms Mol Biol,2016,11(18),1-10.
[38]Goldstein H,Classical Mechanics[M],Addison-Wesley,1965.
[39]Evans DJ.On the representation of orientation space[J].Molec.Phys.,1977,34,317-325.