北大生化chapter43课件

蛋白质的三维结构蛋白质三维结构是由其氨基酸序列决定的；蛋白质功能依赖其结构，或结构决定功能；一般来讲，蛋白质具有（接近）唯一确定的结构；非共价相互作用是稳定蛋白结构的最主要因素；(疏水作用；氢键；离子键；VDW范德华…)在众多蛋白质结构中，其折叠类型（fold）是有限的（2000个？）；研究蛋白结构的方法（X光晶体学及核磁共振）；一些结构与功能关系的例子……本章要点尽管蛋白质结构比较复杂，但仍然有许多规律。蛋白质结构研究得出的第一个基本规律是：亲水表面疏水内核水溶性球蛋白的折叠是将其疏水侧链置于分子的内部，产生一个“疏水内核”和一个“亲水表面”。蛋白质分子的超二级结构(花样,motif)

若干二级结构单元(secondarystructureelement)可以形成特殊的几何组合出现在蛋白质结构中。这些由二级结构依据特殊的几何关系组合起来的结构称为超二级结构(super-secondarystructure)或花样(motif)。

超二级结构（花样）的存在，既可能与某些特殊的生物功能相关联，也可能仅仅作为蛋白质结构的组装模块。

蛋白质结构中的若干个二级结构和/或结构花样（motif）通常会依据特定的几何位置排列形成较为致密的称为“结构域(domain)”的球形结构。

三级结构（tertiarystructure）作为常用的术语有两重含义：其一，单条多肽链折叠形成的由一个或者多个结构域组成的全部结构；其二，二级结构和/或结构花样排列形成的结构域。蛋白质分子的结构域与三级结构FromScience.2003Apr18;300(5618):445-52a/b

structuresSCOPstatisticsGraphicalrepresentationofproteinstructuresSomecrystalsfromSuLab,PekingUniversitySomestructuressolvedAK6(AD-004)NCC27HumanLMWPTP-BOXY-1Aβ-lactamaseBs803(YjbK)BsYflLBs47(HutI)Bs99(YjcG)LC1WRKY1-CSm35Sm32B.s.YwlESm23BsTim344KurtWüthrich1938Nobelpris2002UtvecklademetoderattstuderastrukturochdynamikavproteinerilösningmedNMREttprion—proteinetsomgergalnako-sjukanBeijingNMRCenterProteinFolding?a-helix–localinteractionb-sheet–longrangeinteractionHydrophoicresidues–proteincoreProteinFoldingAboutequilibriumofanyprocessorreaction.Whatdirectionwillprocessproceedtowardequilibrium?Howfarwillitgotowardcompletionbeforeitreachesequilibrium?Notabouthowitgetsthere.(e.g.howfastorwhatpathittakes)FirstLaw:Energyisconserved.SecondLaw:Disorderincreases.ThermodynamicsDG=DH–TDSDGischangeinGibbsFreeEnergy.Iftheendingstateislowerinfreeenergythanthestartingstate,reactionwillproceedspontaneously.DHischangeinEnthalpy.Enthalpyistheenergyfrombondsandattractiveinteractions.Negative

DHisfavorable.(e.g.formingmorebonds.)DSischangeinEntropy.Entropyisdisorder.PositiveDSisfavorable.(e.g.increasingtheamountofdisorder.)DirectionofBiochemicalProcessesStudiesoftheRNaseASmallproteinwith4disulfidebonds.Fact1:UreaUnfoldsProteinsFact2:b-mercaptoethanolbreaksdisulfidebondsStudiesoftheRNaseAStudiesoftheRNaseAInactiveRNasehadformed“wrong”disulfidebondswhileunfolded.Thewronglinkspreventedthepolypeptidechainfromattainingtheactiveconfigurationwhenureawasremoved.TheactiveribonucleasehadformedthecorrectdisulfidebondswhenbMEwasremoved.Thebackbonehadrefoldedcorrectly,priortoreoxidationIf“wrong”disulfidescouldbefixed,theactivityofinactiveRNasecouldberestored?StudiesoftheRNaseATraceofb-MEpresentwiththe"scrambled"RNasepermitteddisulfidebondstore-reduceandthenreoxidize,sonativeactivestructurecouldform.WhenrightcombinationsofS-Sbondsformed,theyremained,becausenativestructurewasthethermodynamicallymoststable(favored)state.StudiesoftheRNaseATheNobelPrizeinChemistry1972ChristianB.Anfinsen--forhisworkonribonuclease,especiallyconcerningtheconnectionbetweentheaminoacidsequenceandthebiologicallyactiveconformation"Thesequencedeterminesthestructure!Theinformationnecessarytospecifythestructureispresentinthesequence.Proteinsdonotsampleallpossibleconformations-rather,“partiallyfolded”states(“foldingintermediates”)withsomebutnotallpossiblebondsandinteractionsoccurduringthefoldingprocess.Thesequencealsospecifiesthefoldingpathway.Asmoreinteractionsform,thestructuregetscloserandclosertothefinalfoldedstate.Typicaltimesforproteinfoldingare~10-6secto102sec.ProteinFoldingPathwaysProteinFoldingPathwaysFreeEnergyLandscapeThecentraldogma中心法则FlowofinformationingeneexpressionThegeneticcodeThemRNAconsistsoffournucleotidesA,G,CandU.Threeconsecutivenucleotidesforma“codon”The64codonsencode20aminoacids,“Start”and“Stop”

SG’sfirsttask:Sequencethedomains(orfamilies)FromScience.2003Apr18;300(5618):445-52SCOPstatistics生物大分子结构与功能的关系：

功能=运动着的结构

生命是由蛋白复合物纳米机器运转着Somesay:Functionisstructure!Otherssay:Structureisfunction!!Isay:Functionsarestructuresinmotion!!!TheribosometranslatesthemRNAsequenceintoproteinsequenceRamakrishnan(2002),Cell108,557-572

ThestructureofthelargeandsmallribosomalsubunitSchematicsurfacerepresentationwithanimation23SRNA:orange5SRNA:yellowproteins:blueActivesite:greenBan,Nissen,Hansen,Moore&Steitz(2000)Nissen,Hansen,Ban,Moore&Steitz(2000)TheElongationCyclestudiedbyCryo-EM13452EPARHowdo~100RNAhelicesin6RNA