大分子拥挤对酶蛋白及DNA的影响
|
摘要
大分子拥挤是指在蛋白质、多肽、核酸和多聚糖共同形成的环境中,由于大分子的不可穿透性,使任何一个大分子的实际可及空间大幅缩小,所形成的生物大分子环境是一种由于空间排斥引起的纯物理性非特异性效应。酶在机体中发挥高效专一的催化作用,细胞内分子环境改变可能导致酶活性的改变,影响细胞及机体的稳态,同时大分子拥挤还可能影响DNA的合成。本文主要从大分子拥挤对酶(包括酶蛋白性质、酶活性、酶蛋白最适温度)和DNA的影响及其可能的作用机制等方面作一综述。
Macromolecular crowding is caused by the remarkable reduction of practically achievable space of any macromolecule due to the impermeability of macromolecules in the environment formed by proteins,polypeptides,nucleic acids and polysaccharides,which is a ubiquitous physiological phenomenon caused by spatial exclusion. Since enzyme plays an effective and specific catalytic role in organism,the change of molecular environment may cause the change of enzyme activity,thus affects the steady-state of cell and organism. Meanwhile,macromolecular crowding may influence the DNA synthesis. This paper reviews the influence of macromolecular crowding on enzyme(including the property,activity and optimal temperature of enzyme)and DNA as well as the possible mechanism.
Macromolecular crowding is caused by the remarkable reduction of practically achievable space of any macromolecule due to the impermeability of macromolecules in the environment formed by proteins,polypeptides,nucleic acids and polysaccharides,which is a ubiquitous physiological phenomenon caused by spatial exclusion. Since enzyme plays an effective and specific catalytic role in organism,the change of molecular environment may cause the change of enzyme activity,thus affects the steady-state of cell and organism. Meanwhile,macromolecular crowding may influence the DNA synthesis. This paper reviews the influence of macromolecular crowding on enzyme(including the property,activity and optimal temperature of enzyme)and DNA as well as the possible mechanism.
引文
[1]MINTON A P.Macromolecular crowding:effects on association equilibria and kinetics[J].Encyclopedia of Biophysics,2013(1725):1338-1342.
[2]GENG Y N,WU D Y,ZHANG Z Y,et al.Macromolecular crowding agents for the extracellular matrix:mechanisms and unfavorable factors to be comfirmed[J].Chin J Tissue Engi Res,2018,22(6),945-951.
[3]SCHUMMEL P H,GAO M,WINTER R.Modulation of the polymerization kinetics ofα/β-tubulin by osmolytes and macromolecular crowding[J].Chemphyschem,2016,18(2):173.
[4]WIEDEMANN N,PFANNER N.Mitochondrial machineries for protein import and assembly[J].Annu Rev Biochem,2017,86(1):685-714.
[5]VARGAS-CORTEZ T,MORONES-RAMIREZ J R,BALDE-RAS-RENTERIA I,et al.Production of recombinant proteins in Escherichia coli tagged with the fusion protein CusF3H[J].Protein Expr Purif,2017,132:44-49.
[6]DHARA A,SAMIOTAKISB A,EBBINGHAUSA S,et al.Structure,function,and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding[J].PNAS,2010,107(41):17586-17591.
[7]SABINE R,AKABAYOV,AKABAYOV B,et al.Molecular crowding enhanced ATPase activity of the RNAhelicase e IF4Acorrelates with compaction of its quaternary structure and association with e IF4G[J].J Am Chem Soc,2013,135(27):10040-10047.
[8]THUY P,HUONG B T T,HOANG,et al.Effects of macromolecular crowding on protein folding[J].J Physics Conference Series,2015,627(1):2027.
[9]SINGH P,CHOWDHURY P K.Unravelling the intricacy of the crowded environment through tryptophan quenching in lysozyme[J].J Physical Chem B,2017,121(18):4687-4699.
[10]NORRIS M G S,MALYS N.What is the true enzyme kinetics in the biological system An investigation of macromolecular crowding effect upon enzyme kinetics of glucose-6-phosphate dehydrogenase[J].Biochem Biophys Res Communi,2011,405(3):388-392.
[11]MUKHERJEE S K,GAUTAM S,BISWAS S,et al.Do macromolecular crowding agents exert only an excluded volume effect A protein solvation study[J].J Physical Chem B,2015,119(44):14145-14156.
[12]BAI J.Nuclear magnetic resonance study of alpha-synuclein ensemble structure in different environments[D].Graduate University of Chinese Academy of Sciences(Wuhan Institute of Physics and Mathematics),2016.(in Chinese)白佳.不同环境下α-突触核蛋白系综结构的核磁共振研究[D].湖北武汉:中国科学院研究生院武汉物理与数学研究所,2016.
[13]SOHAIL A,BHAT S A,SIDDIQUI A A,et al.Conformational transitions induced by in vitro,macromolecular crowding lead to the amyloidogenesis of buffalo heart cystatin[J].J Mol Recogn,2015,28(12):699-709.
[14]JIA J,PENG X,QI W,et al.Effects of macromolecular crowding on alkaline phosphatase unfolding,conformation and stability[J].Int J Biol Macromol,2017,101:373-382.
[15]PREWITZ M C,STIβEL A,FRIEDRICHS J,et al.Extracellular matrix deposition of bone marrow stroma enhanced by macromolecular crowding[J].Biomaterials,2015,73:60-69.
[16]DAYTON J,GOODELL,TATIAN A,et al.CaMKII Binding to GluN2B is differentially affected by macromolecular crowding reagents[J].PLOS ONE,2014,9(5):e96522-e96530.
[17]XU G,ZHAO J,CHENG K,et al.The effects of macromolecular crowding on calmodulin structure and function[J].Chemistry,2017,23(28):6736-6740.
[18]LUO X D,KONG F L,DANG H B,et al.Macromolecular crowding favors the fibrillization ofβ2-microglobulin by accelerating the nucleation step and inhibiting fibril disassembly[J].Biochim Biophys Acta,2016,1864(11):1609-1619.
[19]HUANG L,WANG C,ZHAO S,et al.PKC and CaMK-II inhibitions coordinately rescue ischemia-induced GABAergic neuron dysfunction[J].Oncotarget,2017,8(24):39309-39322.
[20]BENNY P,RAGHUNATH M.Making microenvironments:Alook into incorporating macromolecular crowding into in vitro experiments,to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications[J].J Tissue Eng,2017,8:2041731417730467.
[21]BARCOMB K,HELL J W,BENKE T A,et al.The CaMKII/GluN2B protein interaction maintains synaptic strength[J].JBiol Chem,2016,291(31):16082-16089.
[22]GOODELL D J,ZAEGEL V,COULTRAP S,et al.DAPK1mediates LTD by making CaMKII/GluN2B binding LTPspecific[J].Cell Rep,2017,19(11):2231-2243.
[23]SHAHID S,AHMAD F,HASSAN M I,et al.Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture:An insight into stability-activity trade-off[J].Arch Biochem&Biophys,2015,584(1):42-50.
[24]YADAV J K.Macromolecular crowding enhances catalytic efficiency and stability of a-Amylase[J].ISRN Biotechnol,2014,2013(4),737805-737812.
[25]SENSKE M,TORK L,BORN B,et al.Protein stabilization by macromolecular crowding through enthalpy rather than entropy[J].J Am Chem Soc,2014,136(25):9036-9041.
[26]GNUTT D,EBBINGHAUS S.The macromolecular crowding effect--from in vitro into the cell[J].Biol Chem,2016,397(1):37-44.
[27]WU Y,TENG N,LI S.Effects of macro-molecular crowding and osmolyte on human Tau fibrillation[J].Int J Biol Macromol,2016,90(1):27-36.
[28]YADAV J K,PRAKASH V.Thermal stability of alpha-amylase in aqueous cosolvent systems[J].J Biosci,2009,34(3):377-387.
[29]WULAN D R,UTOMO E P,MAHDI C.Molecular modeling of Ruellia tuberosa L compounds as a-amylase inhibitor:an in silico comparation between human and rat enzyme model[J].Bioinformation,2014,10(4):209-215.
[30]JEMAA H B,JEMIA A B,KHLIFI S,et al.Antioxidant activity and a-amylase inhibitory potential of rosa caninal[J].Afr JTradit Complement Altern Med,2017,14(2):1-8.
[31]RIVAS G,MINTON A P.Macromolecular crowding in vitro,in vivo,and in between[J].Trends Biochem Sci,2016,41(11):970-981.
[32]RICE A M,ROSEN M K.ATP controls the crowd[J].Science,2017,356(6339):701-702.
[33]ZHAO S M,ZHU Q,RONALD L.Somerville.The 70 Transcription factor TyrR has zinc-stimulated phosphatase activity that is inhibited by ATP and tyrosine[J].J Bacteriol,2000,182(4):1053-1061.
[34]LI S,XU L D,ZHAO S.The internet of things:a survey[J].Inform Syst Frontiers,2015,17(2):243-259.
[35]BROWN C M.Live-cell techniques-advances and challenges[J].Cell Adhesion&Migration,2014,8(5):429.
[36]HOU S,TROCHIMCZYK P,SUN L L,et al.How can macromolecular crowding inhibit biological reactions The enhanced formation of DNA nanoparticles[J].Sci Rep,2016,6(1):22033.
[37]TAZAWA S,KOBAYASHI K,OYOSHI T,et al.Supramolecular gel electrophoresis of large DNA fragments[J].Electrophoresis,2017,38(20):2662-2665.
[38]Hind KR,Miller KA,Young M,et al.Resolving cryptic species of Bossiella(Corallinales,Rhodophyta)using contemporary and historical DNA[J].Am J Bot.2015 Nov;102(11):1912-30.
[39]PAL P D,DONGRE P M,CHITRE A V.Implications of volume exclusion:a look at thermodynamic perspective of DNA-hemoglobin complexes and their reconstitutes under macromolecular crowding[J].J Fluoresc,2016,26(1):355-362.
[40]STIEHL O,WEIDNER-HERTRAMPF K,WEISS M.Macromolecular crowding impacts on the diffusion and conformation of DNA hairpins[J].Phys Rev E Stat Nonlin Soft Matter Phys,2015,91(1):012703-012706.
[41]NORRED S E,CAVENEY P M,CHAUHAN G,et al.Macromolecular crowding induces spatial correlations that control gene expression bursting patterns[J].Acs Synthetic Biology,2018,7(5):1251.
[42]GOLKARAM M,HELLANDER S,DRAWERT B,et al.Macromolecular crowding regulates the gene expression profile by limiting diffusion[J].PLoS Comput Biol,2016,12(11):e1005122-e1005137.
[43]THIERRY A R,EL MESSAOUDI S,GAHAN P B,et al.Origins,structures,and functions of circulating DNA in oncology[J].Cancer Metastasis Rev,2016,35(3):347-376.
[44]SHRUTI M,RIMPY C,SINGH L,et al.Macromolecular crowding:macromolecules friend or foe[J].Biochimica et Biophysica Acta,2015,1850:1822-1831.
[45]ZILKENAT S,GRIN I,WAGNER S.Stoichiometry determination of macromolecular membrane protein complexes[J].Biol Chem,2017,398(2):155-164.
[46]SIDDIQUI G A,NAEEM A.Aggregation of globular protein as a consequences of macromolecular crowding:A time and concentration dependent study[J].Int J Biol Macromol,2018,108:360-366.
[47]PERUSKO M,AL-HANISH A,CIRKOVIC VELICKOVIC T,et al.Macromolecular crowding conditions enhance glycation and oxidation of whey proteins in ultrasound-induced Maillard rea-ction[J].Food Chem,2015,177:248-257.
[48]BISWAS S,KKUNDU J,MUKHERJEE S K,et al.Mixed macromolecular crowding A protent and solvent perspectival[J].ACS Omega,2018,3(4):4316-4330.
[49]SHARMA G S,MITTAL S,SINGH L R.Effect of dextran70on the thermodynamic and structural properties of proteins[J].Int J Biol Macromol,2015,79(1):86-94.
[50]PELLEGRINI L,COSTA A.New insights into the mechanism of DNA duplication by the eukaryotic replisome[J].Trends Biochem Sci,2016,41(10):859-871.
[2]GENG Y N,WU D Y,ZHANG Z Y,et al.Macromolecular crowding agents for the extracellular matrix:mechanisms and unfavorable factors to be comfirmed[J].Chin J Tissue Engi Res,2018,22(6),945-951.
[3]SCHUMMEL P H,GAO M,WINTER R.Modulation of the polymerization kinetics ofα/β-tubulin by osmolytes and macromolecular crowding[J].Chemphyschem,2016,18(2):173.
[4]WIEDEMANN N,PFANNER N.Mitochondrial machineries for protein import and assembly[J].Annu Rev Biochem,2017,86(1):685-714.
[5]VARGAS-CORTEZ T,MORONES-RAMIREZ J R,BALDE-RAS-RENTERIA I,et al.Production of recombinant proteins in Escherichia coli tagged with the fusion protein CusF3H[J].Protein Expr Purif,2017,132:44-49.
[6]DHARA A,SAMIOTAKISB A,EBBINGHAUSA S,et al.Structure,function,and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding[J].PNAS,2010,107(41):17586-17591.
[7]SABINE R,AKABAYOV,AKABAYOV B,et al.Molecular crowding enhanced ATPase activity of the RNAhelicase e IF4Acorrelates with compaction of its quaternary structure and association with e IF4G[J].J Am Chem Soc,2013,135(27):10040-10047.
[8]THUY P,HUONG B T T,HOANG,et al.Effects of macromolecular crowding on protein folding[J].J Physics Conference Series,2015,627(1):2027.
[9]SINGH P,CHOWDHURY P K.Unravelling the intricacy of the crowded environment through tryptophan quenching in lysozyme[J].J Physical Chem B,2017,121(18):4687-4699.
[10]NORRIS M G S,MALYS N.What is the true enzyme kinetics in the biological system An investigation of macromolecular crowding effect upon enzyme kinetics of glucose-6-phosphate dehydrogenase[J].Biochem Biophys Res Communi,2011,405(3):388-392.
[11]MUKHERJEE S K,GAUTAM S,BISWAS S,et al.Do macromolecular crowding agents exert only an excluded volume effect A protein solvation study[J].J Physical Chem B,2015,119(44):14145-14156.
[12]BAI J.Nuclear magnetic resonance study of alpha-synuclein ensemble structure in different environments[D].Graduate University of Chinese Academy of Sciences(Wuhan Institute of Physics and Mathematics),2016.(in Chinese)白佳.不同环境下α-突触核蛋白系综结构的核磁共振研究[D].湖北武汉:中国科学院研究生院武汉物理与数学研究所,2016.
[13]SOHAIL A,BHAT S A,SIDDIQUI A A,et al.Conformational transitions induced by in vitro,macromolecular crowding lead to the amyloidogenesis of buffalo heart cystatin[J].J Mol Recogn,2015,28(12):699-709.
[14]JIA J,PENG X,QI W,et al.Effects of macromolecular crowding on alkaline phosphatase unfolding,conformation and stability[J].Int J Biol Macromol,2017,101:373-382.
[15]PREWITZ M C,STIβEL A,FRIEDRICHS J,et al.Extracellular matrix deposition of bone marrow stroma enhanced by macromolecular crowding[J].Biomaterials,2015,73:60-69.
[16]DAYTON J,GOODELL,TATIAN A,et al.CaMKII Binding to GluN2B is differentially affected by macromolecular crowding reagents[J].PLOS ONE,2014,9(5):e96522-e96530.
[17]XU G,ZHAO J,CHENG K,et al.The effects of macromolecular crowding on calmodulin structure and function[J].Chemistry,2017,23(28):6736-6740.
[18]LUO X D,KONG F L,DANG H B,et al.Macromolecular crowding favors the fibrillization ofβ2-microglobulin by accelerating the nucleation step and inhibiting fibril disassembly[J].Biochim Biophys Acta,2016,1864(11):1609-1619.
[19]HUANG L,WANG C,ZHAO S,et al.PKC and CaMK-II inhibitions coordinately rescue ischemia-induced GABAergic neuron dysfunction[J].Oncotarget,2017,8(24):39309-39322.
[20]BENNY P,RAGHUNATH M.Making microenvironments:Alook into incorporating macromolecular crowding into in vitro experiments,to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications[J].J Tissue Eng,2017,8:2041731417730467.
[21]BARCOMB K,HELL J W,BENKE T A,et al.The CaMKII/GluN2B protein interaction maintains synaptic strength[J].JBiol Chem,2016,291(31):16082-16089.
[22]GOODELL D J,ZAEGEL V,COULTRAP S,et al.DAPK1mediates LTD by making CaMKII/GluN2B binding LTPspecific[J].Cell Rep,2017,19(11):2231-2243.
[23]SHAHID S,AHMAD F,HASSAN M I,et al.Relationship between protein stability and functional activity in the presence of macromolecular crowding agents alone and in mixture:An insight into stability-activity trade-off[J].Arch Biochem&Biophys,2015,584(1):42-50.
[24]YADAV J K.Macromolecular crowding enhances catalytic efficiency and stability of a-Amylase[J].ISRN Biotechnol,2014,2013(4),737805-737812.
[25]SENSKE M,TORK L,BORN B,et al.Protein stabilization by macromolecular crowding through enthalpy rather than entropy[J].J Am Chem Soc,2014,136(25):9036-9041.
[26]GNUTT D,EBBINGHAUS S.The macromolecular crowding effect--from in vitro into the cell[J].Biol Chem,2016,397(1):37-44.
[27]WU Y,TENG N,LI S.Effects of macro-molecular crowding and osmolyte on human Tau fibrillation[J].Int J Biol Macromol,2016,90(1):27-36.
[28]YADAV J K,PRAKASH V.Thermal stability of alpha-amylase in aqueous cosolvent systems[J].J Biosci,2009,34(3):377-387.
[29]WULAN D R,UTOMO E P,MAHDI C.Molecular modeling of Ruellia tuberosa L compounds as a-amylase inhibitor:an in silico comparation between human and rat enzyme model[J].Bioinformation,2014,10(4):209-215.
[30]JEMAA H B,JEMIA A B,KHLIFI S,et al.Antioxidant activity and a-amylase inhibitory potential of rosa caninal[J].Afr JTradit Complement Altern Med,2017,14(2):1-8.
[31]RIVAS G,MINTON A P.Macromolecular crowding in vitro,in vivo,and in between[J].Trends Biochem Sci,2016,41(11):970-981.
[32]RICE A M,ROSEN M K.ATP controls the crowd[J].Science,2017,356(6339):701-702.
[33]ZHAO S M,ZHU Q,RONALD L.Somerville.The 70 Transcription factor TyrR has zinc-stimulated phosphatase activity that is inhibited by ATP and tyrosine[J].J Bacteriol,2000,182(4):1053-1061.
[34]LI S,XU L D,ZHAO S.The internet of things:a survey[J].Inform Syst Frontiers,2015,17(2):243-259.
[35]BROWN C M.Live-cell techniques-advances and challenges[J].Cell Adhesion&Migration,2014,8(5):429.
[36]HOU S,TROCHIMCZYK P,SUN L L,et al.How can macromolecular crowding inhibit biological reactions The enhanced formation of DNA nanoparticles[J].Sci Rep,2016,6(1):22033.
[37]TAZAWA S,KOBAYASHI K,OYOSHI T,et al.Supramolecular gel electrophoresis of large DNA fragments[J].Electrophoresis,2017,38(20):2662-2665.
[38]Hind KR,Miller KA,Young M,et al.Resolving cryptic species of Bossiella(Corallinales,Rhodophyta)using contemporary and historical DNA[J].Am J Bot.2015 Nov;102(11):1912-30.
[39]PAL P D,DONGRE P M,CHITRE A V.Implications of volume exclusion:a look at thermodynamic perspective of DNA-hemoglobin complexes and their reconstitutes under macromolecular crowding[J].J Fluoresc,2016,26(1):355-362.
[40]STIEHL O,WEIDNER-HERTRAMPF K,WEISS M.Macromolecular crowding impacts on the diffusion and conformation of DNA hairpins[J].Phys Rev E Stat Nonlin Soft Matter Phys,2015,91(1):012703-012706.
[41]NORRED S E,CAVENEY P M,CHAUHAN G,et al.Macromolecular crowding induces spatial correlations that control gene expression bursting patterns[J].Acs Synthetic Biology,2018,7(5):1251.
[42]GOLKARAM M,HELLANDER S,DRAWERT B,et al.Macromolecular crowding regulates the gene expression profile by limiting diffusion[J].PLoS Comput Biol,2016,12(11):e1005122-e1005137.
[43]THIERRY A R,EL MESSAOUDI S,GAHAN P B,et al.Origins,structures,and functions of circulating DNA in oncology[J].Cancer Metastasis Rev,2016,35(3):347-376.
[44]SHRUTI M,RIMPY C,SINGH L,et al.Macromolecular crowding:macromolecules friend or foe[J].Biochimica et Biophysica Acta,2015,1850:1822-1831.
[45]ZILKENAT S,GRIN I,WAGNER S.Stoichiometry determination of macromolecular membrane protein complexes[J].Biol Chem,2017,398(2):155-164.
[46]SIDDIQUI G A,NAEEM A.Aggregation of globular protein as a consequences of macromolecular crowding:A time and concentration dependent study[J].Int J Biol Macromol,2018,108:360-366.
[47]PERUSKO M,AL-HANISH A,CIRKOVIC VELICKOVIC T,et al.Macromolecular crowding conditions enhance glycation and oxidation of whey proteins in ultrasound-induced Maillard rea-ction[J].Food Chem,2015,177:248-257.
[48]BISWAS S,KKUNDU J,MUKHERJEE S K,et al.Mixed macromolecular crowding A protent and solvent perspectival[J].ACS Omega,2018,3(4):4316-4330.
[49]SHARMA G S,MITTAL S,SINGH L R.Effect of dextran70on the thermodynamic and structural properties of proteins[J].Int J Biol Macromol,2015,79(1):86-94.
[50]PELLEGRINI L,COSTA A.New insights into the mechanism of DNA duplication by the eukaryotic replisome[J].Trends Biochem Sci,2016,41(10):859-871.