中南大学生物化学考研蛋白质二级三级和四级结构ch6Proteins06.pptx

Ch 6 Proteins:secondary,tertiary,and quaternary structure蛋白质的二级、三级和四级结构蛋白质的二级、三级和四级结构For Specialty of Bioengineering and Biotechnology at CSUMr.Jinlan XIAOverview on the Levels of Protein Structures蛋白质结构级别纵览蛋白质结构级别纵览n1st:nAA sequence(possibly with S-S-)氨基酸序列(可能含双硫键)n2nd:nBasic types:a-helix,b-sheetnLess frequently:b-turn 转角,b-bulge凸起nSuper 2nd超二级结构:aa,bb,babn3rd:n3D shape of a folding polypeptide chain 单条折叠肽链的三维结构(形状)n4th:n3D organization of subunits 多亚基三维结构(组构)Key partContent 内容内容nForces influencing protein structure 影响蛋白质结构的作用力nSecondary structure in proteins 蛋白质的二级结构nProtein folding and tertiary structure 蛋白质折叠和三级结构nSubunit interactions and quaternary structure 亚基相互作用和四级结构Forces influencing protein structure影响蛋白质结构的作用力nHydrogen bond 氢键（合力）nHydrophobic interaction 疏水作用nElectrostatic bond（静）电键或离子键（合力）nVan der Waals force 范德华力nDisulfide bond 双硫键（合力）The forces for each structural level of proteins 蛋白质每级结构对应的作用力蛋白质每级结构对应的作用力nBasic forces for the 1st level nDisulfide bond 双硫键（合力）nBasic forces for the 2nd levelnHydrogen bond 氢键（合力）nBasic forces for the 3rd level and 4th levelnHydrogen bond 氢键（合力）；Hydrophobic interaction 疏水作用；Electrostatic bond（静）电键或离子键（合力）；Van der Waals force 范德华力；Disulfide bond 双硫键（合力）nDifferences in forces between 3rd level and 4th level nThe 4th level of protein is compacted from the 3rd levels of subunits mainly by hydrophobic interaction and Van der Waals force 四级蛋白质结构主要依靠疏水作用力和范德华力将三级结构的亚基紧密堆积而成Secondary structure in proteins 蛋白质的二级结构蛋白质的二级结构nCharacteristics of the Secondary structure in proteins 蛋白质二级结构的特点nClasses of Secondary Structures 二级结构的类型nSuper secondary Structures 超二级结构超二级结构Characteristics of the Secondary structure in proteins 蛋白质二级结构的特点蛋白质二级结构的特点nThe basic force for 2nd structures is hydrogen bond 二级结构的基本作用力是氢键二级结构的基本作用力是氢键nThe basic types of secondary structures are aa-helix and bb-pleated sheet 二级结构的基本二级结构的基本类型为类型为aa-螺旋和螺旋和b b-折叠片折叠片nSecondary structures are related to the orientations of the amide plane 二级结构与（肽二级结构与（肽键）酰胺平面的取向有关键）酰胺平面的取向有关Secondary structures are related to the orientations of the amide plane 二级结构与（肽键）酰胺平面的取向有关二级结构与（肽键）酰胺平面的取向有关nPeptide units are planar and rigid，but they can rotate with rotation of Ca-N and Ca-C bonds(肽单元是刚性平面，但它们可随着Ca-N 和 Ca-C 键旋转而转动)nRotate angles for Ca-N and Ca-C are and,respectively.(Ca-N 和 Ca-C 旋转角分别为 和)nTypcially,Rotation forbidden for 旋转禁止的典型情况：n(,)=(0,180),two carbonyl oxygens are too close;n(,)=(180,0),two amide groups are overlapping;n(,)=(0,0),carbonyl oxygen overlaps with amide group;nTypical ranges of(f,wf,w)for aa-helix and bb-sheet (a-螺旋和b-折叠片的典型旋转角范围):na-helix:(f,w)(-30 -120,0 -90)nb-sheet:(f,w)(-90 -180,90 180)Peptide units are planar and rigid，but they can rotate with rotation of Ca a-N and Caa-C bonds 肽单元是刚性平面，但它们可随着肽单元是刚性平面，但它们可随着Ca a-N 和和 Caa-C 键键旋转而转动旋转而转动Rotation of Amide Planes 酰胺平面的旋转酰胺平面的旋转nIf(,)are known for all residues,the structure for the entire backbone is known.nSome(,)are more likely than others in a folded proteinnPositive(,)values correspond to clockwise rotation around bonds when viewed from the Ca.Zerois defined when the C=O or N-H bond bisects the R-Ca-H angle.:phi,:psiRotation of Amide Planes 酰胺平面的旋转酰胺平面的旋转Peptide bondPeptide bond=180,=180Amide plane酰胺平面a-carbonThe typcial cases of rotation forbidden 旋转禁旋转禁止的典型情况止的典型情况=0,=180two carbonyl oxygens are too close;=0,=0carbonyl oxygen overlaps with amide group=180,=0two amide groups are overlappingRamachandran Plot(图)Antiparallel b-sheet反平行b-折叠片Parallel b-sheet平行b-折叠片a:a-helix (right-handed+)右手a-螺旋（+）aL:a-helix(left-handed-)左手a-螺旋（-）C:collagen triple helix 胶原三股螺旋p:4.416 helix(closed ring)4.416螺旋（闭合环）n:Number of AA residues/turn of helix 氨基酸残基数/螺旋圈:60:45-50Classes of Secondary Structures of Proteins 蛋白质的蛋白质的二二级结构类型级结构类型na-Helix （a-螺旋）n3.613 helix(normal)n310,4.416(not often)nb-(pleated)sheet （b-折叠片）nParallel(normally 5 strands)平行b-折叠片（通常5 肽链）nAnti-parallel(=2 strands)反平行b-折叠片（通常=2 肽链）nb-Turn（b-转角）nb-bulge（b-凸起）3.613 helix每个螺旋含3.6个氨基酸残基每个氢键相隔的原子数 The Alpha Helix（a-螺旋）nRight-handed 右手螺旋nH-bond patterns of the alpha helix（a-螺旋的氢键特征）nH-bond（氢键）nC=O(ith AA residue)-H-N(amide proton of the(i+4)th residue)nCommon a-helix（常见的a-螺旋）n3.613 helixnNo Proline except at the beginning of an a-helix 除非在螺旋起端，否则不含脯氨酸nGlu,Met,Ala,Leu more often occurred 常含有谷氨酸、蛋氨酸、丙氨酸和亮氨酸nLinus Pauling(Nobel Prize in Chemistry,1954)figured out the structure of a-keratin helix Secondary StructuresH-bond（氢键）n C=O(ith AA residue)-H-N(amide proton of the(i+4)th residue)n3.613 helix5.4 (3.6 amino acid residues per each turn)1.5 (each amino acid residue)Hypothesized axisa a-helix(2nd)Residues per turn:3.6Rise per residue:1.5 Rise per turn:5.4(,)=(-60,-45)C=O N-H side chainTotal dipole moment Four different graphic representations of the a a-helixRibbon structureSpace-fillinggraphicShowingpeptide planesPaulings modelSecondary Structuresb b-Pleated sheet is formed from b-b-Strands(b b折叠片是由折叠片是由b-b-肽链形成的肽链形成的)Due to the planarity of the peptide bond that forces the formation of the b b-pleated sheet由于肽键的平面性促使形成由于肽键的平面性促使形成b b-折叠片折叠片Side-view of one peptide chainb-b-Strandsb b-Pleated sheetnTwo types of b-sheets and their H-bond characteristics 两种类型b折叠片和它们的氢键特征:nParallel b-sheet 平行b折叠片nLess extended(0.325 nm between two residues)欠伸展nLarger(at least 5 strands)nAnti-parallel b-sheet 反平行b折叠片nMore extended(0.347 nm between two residues)较伸展nSmaller size(=2 strands)The Beta Turn(b-转角)nBeta turns connect beta strands and reverse the direction of beta strands b-转角连接b-肽链，并使b-肽链改变方向nH-bond （氢键（特征）n310:C=O(ith residue)to H-N(amide proton of the(i+3)th residue)nPro,Gly more often occurred（常含脯氨酸和甘氨酸）nTight turn promotes formation of antiparallel beta sheets.（b-转角促使反平行b-片的形成）Two kinds of b b-turn Secondary StructuresBeta Bulge(b b凸起凸起)nSmall,nonrepetitive（小，不具重复性）nMuch less occurs,and few irregularly in antiparallel b-structures（很少见，有时不规则地出现在反平行b-结构中）Classic bulgeC-1 bulgeWide bulgeLeads to bending of the anti-parallel beta-strandsSecondary StructuresThree basic types of super secondary Structures 三种基本超二级结构三种基本超二级结构naa nCoiled-coil 铰链式铰链式nHelix bundles 螺旋簇式螺旋簇式nbb nHairpins 发夹式发夹式nbabnCross-overs 交叉式交叉式Super Secondary Structures (I)naaaanCoiled-coil 铰链式nCommon alpha helix structure nHelix bundles 螺旋簇式nRefers to three or more helices packing togetherSuper secondary Structures(II)nbb nHairpins 发夹式发夹式nConnect two antiparallel strands;nbabnCross-overs 交叉式交叉式nConnect two parallel strandsRight-handed Cross-overTo dive into the tertiary structure formsProtein Folding and Tertiary StructureArchitecture of protein molecules 蛋白分子构造蛋白分子构造Three global classes based on shape and solubility:Fibrous proteins 纤维蛋白(hydrophobic 疏水)Globular proteins 球蛋白(Hydrophilic 亲水)Membrane proteins 膜蛋白(hydrophobic 疏水)Collagen,afibrous proteinMyoglobin,aglobular proteinBacteriorhodopsin,amembrane proteinReviewnHydrophobicnStructural role in naturenTypesnAlpha-keratinnFibroin and beta-keratinnCollagen,a triplex helixFibrous Proteins 纤维蛋白纤维蛋白Tertiary Structurea a-keratin 角蛋白角蛋白Basic structure:N-capping+Rod domain+C-cappingThe rod domains form coiled coilsright-handed a-helix,but left-handed twistTertiary Structure/Fibrous ProteinsFibroin and b b-keratin 蚕丝蛋白和蚕丝蛋白和b b-角蛋白角蛋白 Kind of b b-sheet proteins Full of nonpolar amino acids,Gly,AlaTertiary Structure/Fibrous ProteinsnA triple helix:npoly(Gly-X-Y),X often Pro,Y often Pro or HypnGly of the 1st strand lies to X residue of the 2nd strand and to Y residue of the 3rd strandnFibrils nArrays of Tropocollagen molecules原胶原分子Collagen 胶原蛋白胶原蛋白poly(Gly-Pro-Pro)right-handed triple helixleft-handed helical chainTertiary Structure/Fibrous ProteinsFibrils,Arrays of tropocollagenmoleculesHole zone hasSugars thatBind to 5-hydroxylysineor embeds hydoxyapatite5dd:distance300nmTertiary Structure/Fibrous ProteinsCa5(PO4)3OHHydroxyapatite羟基磷灰石Hydroxylysine binds to sugarBone materials thatembed in collagen:Sugar may plays a role in organizing fibrilassembly.Tertiary Structure/Fibrous ProteinsGlobular Proteins 球蛋白球蛋白nBasic characteristics of globular proteinsnPhysicochemical propertiesnBasic types nMolecular chaperones 分子陪伴蛋白nProtein domains 蛋白质域Basic characteristics of globular proteins球蛋白的基本特征球蛋白的基本特征nPhysicochemical properties 物理化学性质nFar more numerous,hydrophilic 大量，亲水nSubstantially consisted of a-helices and b-sheets 基本上由a-螺旋和b-折叠片组成nH-bonds may the main force,(other forces may be electrostatic interactions,ligand binding,etc.)主要作用力为氢键，其它力可能包括电性作用、配位键合，等）nTypesnAntiparallel a-helix proteins 反平行a-螺旋蛋白nParallel or mixed b-sheet proteins 平行或混合b-折叠片蛋白nAntiparallel b-sheet proteins 反平行b-折叠片蛋白nMetal-and disulfide-rich proteins 金属和富含双硫键的蛋白Three-dimensional structure of bovine ribonuclease ATertiary structure is substantiallyConsisted of a a-helices and b b-sheets.Tertiary Structure/Globular ProteinsTri-dimensional structure of bovinepancreatic trypsin inhibitorStabilized mainly by H-bondsElectrostatic interactionLigand bindingE-F hand structure,whichforms Ca2+-binding sites ina variety of proteinsTertiary Structure/Globular ProteinsAntiparallel a a-Helix ProteinsnDominated by a-helices 主要由a-螺旋组成nConsist of bundles of antiparallel helices 由反平行a-螺旋簇组成nSimplest way to pack helices 组装方式最简单nMany exhibit a slight(15)left-handed twist of the helix bundle很多情况下是倾斜15角的左手扭曲的螺旋簇nMany are regular,uniform structures 结构规则Tertiary Structure/Globular ProteinsExamples of antiparallel a a-proteinsTMV Protein烟草花叶病病毒蛋白Myohemerythrin肌血红球素Uteroglobin子宫珠蛋白Influenza virus hemagglutinin HA2流感病毒血凝素HA2Tertiary Structure/Globular ProteinsParallel or mixed b b-sheet proteinsnParallel or mixed b-sheetnArrange hydrophobic residues on both sides of the sheet 折叠片两边为疏水性残基nTypically found as core structures(hydrophobic)一般存在于核心结构里nForm sandwich structure 形成夹心结构nParallel b-barrel 平行b-桶nb-a-b(i.e,two b-sheets linked by an antiparallel a-helix)nDoubly wound parallel b-sheet 双绕平行b-片nInternal twister wall of parallel or mixed b-sheet protected on both sides by helices or other substructures 内部结构由外部螺旋或其它亚结构所保护Tertiary Structure/Globular ProteinsDiagram of this b-sheet arrangement in the Lipocalin family,which bind small molecules between the sheets of the sandwichb-片形成的夹心结构里键合了小分子Tertiary Structure/Globular ProteinsExample:Lipocalin family 胞质中脂质键合蛋白家族胞质中脂质键合蛋白家族Example I:Porin 孔蛋白孔蛋白Tertiary Structure/Globular ProteinsExample II:Parallel b b-array proteins 平行平行b b-阵列蛋白阵列蛋白8-stranded b-barrels of triose phosphate isomerase三糖磷酸异构酶的8股链构成的b-桶Pyruvate kinase丙酮酸激酶Side viewTop viewTertiary Structure/Globular ProteinsHexokinase domain 1己糖激酶蜮1Flavodoxin黄素氧还蛋白Phosphoglycerate mutase 磷酸甘油酸变旋酶Examples of several typical doubly wound parallel b b-sheet proteins 典型双绕平行典型双绕平行b b-折叠片蛋白举例折叠片蛋白举例Tertiary Structure/Globular ProteinsAntiparallel b b-sheet proteins反平行反平行b b-折叠片蛋白折叠片蛋白nArrange hydrophobic residues on just one side of the sheet 折叠片两边为疏水性残基nTypical antiparallel topology modes 典型反平行拓扑模型nThe Greek Key topology 希腊锁拓扑模型nThe Jellyroll Topology 果冻卷果冻卷拓扑模型Tertiary Structure/Globular ProteinsSoybean trypsin inhibitor豆芽胰蛋白酶抑制素Rubredoxin红素氧还蛋白Papain domain 2木瓜蛋白酶域2With one face exposed to solvent,and the other faceCovered by helices and random coilsTertiary Structure/Globular ProteinsGamma-crystallin foldg g-晶体蛋白折叠晶体蛋白折叠Topology of the Greek Key and the folding examples希腊锁的拓扑学及其折叠举例希腊锁的拓扑学及其折叠举例Gamma-crystallin foldg g-晶体蛋白折叠晶体蛋白折叠Globular Proteins/Folding质体蓝素折叠希腊锁拓扑结构希腊锁拓扑结构Jellyroll fold example果冻卷折叠示例果冻卷折叠示例Globular Proteins/Folding星状烟草坏疽病毒衣壳蛋白的果冻折叠Metal-and Disulfide-rich proteins富含金属富含金属-和双硫键蛋白和双硫键蛋白Relatively small(100 residues)Highly dependent on the content of metal or disulfide bonds(a)Disulfide-rich protein 富含双硫键蛋白(b)Metal-rich protein 富含金属蛋白Insulin胰岛素Phospholipase A2磷酸酯酶A2Ferredoxin铁氧化还原蛋白High-potentialiron protein高势铁蛋白Distorted a-helix cluster扭曲a-螺旋簇Distorted b-barrel structure扭曲b-桶结构Crambin海甘蓝素No standard structure无标准结构Molecular chaperones分子陪伴蛋白分子陪伴蛋白nFunction:help fold globular proteins 功能：帮助折叠成球蛋白nUsually binds to the exposed hydrophobic regions of partially folded structures,and lead to less compact than the native fold structurenNature 特性nFirst identified as heat shock proteins 热激蛋白nTypical examplesnHsp70:a 70-kD heat shock proteinnHsp60s:a class of 60-kD heat shock proteinA model for the stepsinvolved in the foldingof globular proteinsChaperone proteinsMay assist in theInitiation of theFolding process1.The rapid and reversible formation of local secondary structures 快速和可逆形成局部二级结构2.Formation of domains through the cooperative aggregation of folding nuclei通过折叠核的协同堆积形成结构域3.“Molten globule”formation of the assembled domains 组装好的结构域形成熔态球4.An adjustment in the conformation of the domains 结构域构象的调整5.Final protein monomer 最终蛋白单体Protein domains 蛋白质域蛋白质域nStructural domain(or domain结构域,SD)nsubunit of protein 蛋白质的亚基nFunctional domain(功能域 FD)nFunctional unit in the protein 蛋白质中的功能单元nMotif 基序nA small structural domain that can be recognized in a variety of proteinsnThe relationship among SD,FD,and motifnFD may 1SD or several SDsnMotif may a part of SDSubunit interactions and quaternary structure Self-studynQuestionsnWhat are the forces driving quaternary association?维系四级结构的力是什么？nPlease explain the typical structure of immunoglobulin molecule.请解释免疫球蛋白分子的典型结构。nWhat are the main types of oligomeric associations of protein subunits?蛋白亚基寡肽的相互作用的主要类型是什么？nWhat are the structural and functional advantages of quaternary association?四级结构(比其它级别)的结构的结构和功能性优点有哪些？Homework p207nProblems 1-9