中南大学生物化学考研课件蛋白质的二级、三级和四级结构ch6Proteins.ppt

Ch 6 Proteins: secondary, tertiary, and quaternary structure 蛋白质的二级、三级和四级结构,For Specialty of Bioengineering and Biotechnology at CSU Mr. Jinlan XIA,Overview on the Levels of Protein Structures 蛋白质结构级别纵览,1st : AA sequence (possibly with S-S-) 氨基酸序列(可能含双硫键) 2nd: Basic types: a-helix, b-sheet Less frequently: b-turn 转角, b-bulge凸起 Super 2nd超二级结构: aa, bb , bab 3rd: 3D shape of a folding polypeptide chain 单条折叠肽链的三维结构(形状) 4th: 3D organization of subunits 多亚基三维结构(组构),Key part,Content 内容,Forces influencing protein structure 影响蛋白质结构的作用力 Secondary structure in proteins 蛋白质的二级结构 Protein folding and tertiary structure 蛋白质折叠和三级结构 Subunit 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,Hydrogen 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）,The forces for each structural level of proteins 蛋白质每级结构对应的作用力,Basic forces for the 1st level Disulfide bond 双硫键（合力） Basic forces for the 2nd level Hydrogen bond 氢键（合力） Basic forces for the 3rd level and 4th level Hydrogen 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） Differences in forces between 3rd level and 4th level The 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,Characteristics of the Secondary structure in proteins 蛋白质二级结构的特点 Classes of Secondary Structures 二级结构的类型 Super secondary Structures 超二级结构,Characteristics of the Secondary structure in proteins 蛋白质二级结构的特点,The basic force for 2nd structures is hydrogen bond 二级结构的基本作用力是氢键 The basic types of secondary structures are a-helix and b-pleated sheet 二级结构的基本类型为a-螺旋和b-折叠片 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,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,Peptide 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) Rotate angles for Ca-N and Ca-C are f and y, respectively. (Ca-N 和 Ca-C 旋转角分别为f 和 y) Typcially, Rotation forbidden for 旋转禁止的典型情况： (f,y)=(0, 180), two carbonyl oxygens are too close; (f,y)=(180, 0), two amide groups are overlapping; (f,y)=(0, 0), carbonyl oxygen overlaps with amide group; Typical ranges of (f, w) for a-helix and b-sheet (a-螺旋和b-折叠片的典型旋转角范围): a-helix: (f, w) (-30 - 120, 0 -90) b-sheet: (f, w) (-90 - 180, 90 180),Peptide 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,Rotation of Amide Planes 酰胺平面的旋转,If (f,y) are known for all residues, the structure for the entire backbone is known. Some (f,y) are more likely than others in a folded protein Positive (f,y) values correspond to clockwise rotation around bonds when viewed from the Ca. Zero is defined when the C=O or N-H bond bisects the R-Ca-H angle.,f: phi, y: psi,Rotation of Amide Planes 酰胺平面的旋转,The typcial cases of rotation forbidden 旋转禁止的典型情况,=0, =180 two carbonyl oxygens are too close;,=0, =0 carbonyl oxygen overlaps with amide group,=180, =0 two amide groups are overlapping,Ramachandran Plot (图),f,y,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,f: 60 y: 45-50,Classes of Secondary Structures of Proteins 蛋白质的二级结构类型,a-Helix （a-螺旋） 3.613 helix (normal) 310, 4.416 (not often) b-(pleated) sheet （ b-折叠片） Parallel (normally 5 strands) 平行b-折叠片 （通常5 肽链） Anti-parallel (=2 strands) 反平行b-折叠片 （通常=2 肽链） b-Turn （b-转角） b-bulge （b-凸起）,The Alpha Helix （a-螺旋）,Right-handed 右手螺旋 H-bond patterns of the alpha helix （a-螺旋的氢键特征） H-bond （氢键） C=O (ith AA residue)- H-N (amide proton of the (i+4)th residue) Common a-helix （常见的a-螺旋） 3.613 helix No Proline except at the beginning of an a-helix 除非在螺旋起端，否则不含脯氨酸 Glu, Met, Ala, Leu more often occurred 常含有谷氨酸、蛋氨酸、丙氨酸和亮氨酸 Linus Pauling (Nobel Prize in Chemistry, 1954) figured out the structure of a-keratin helix,Secondary Structures,H-bond （氢键）,C=O (ith AA residue)- H-N (amide proton of the (i+4)th residue) 3.613 helix,a-helix (2nd),Four different graphic representations of the a-helix,Ribbon structure,Space-filling graphic,Showing peptide planes,Paulings model,Secondary Structures,b-Pleated sheet is formed from b-Strands (b折叠片是由b-肽链形成的),Two 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: Parallel b-sheet 平行b折叠片 Less extended (0.325 nm between two residues) 欠伸展 Larger (at least 5 strands) Anti-parallel b-sheet 反平行b折叠片 More extended (0.347 nm between two residues) 较伸展 Smaller size (=2 strands),The Beta Turn (b-转角),Beta 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 H-bond （氢键（特征） 310: C=O (ith residue) to H-N (amide proton of the (i+3)th residue) Pro, Gly more often occurred （常含脯氨酸和甘氨酸） Tight turn promotes formation of antiparallel beta sheets. （b-转角促使反平行b-片的形成）,Two kinds of b-turn,Secondary Structures,Beta Bulge (b凸起),Small, nonrepetitive （小，不具重复性） Much 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）,Leads to bending of the anti-parallel beta-strands,Secondary Structures,Three basic types of super secondary Structures 三种基本超二级结构,aa Coiled-coil 铰链式 Helix bundles 螺旋簇式 bb Hairpins 发夹式 bab Cross-overs 交叉式,Super Secondary Structures (I),aa Coiled-coil 铰链式 Common alpha helix structure Helix bundles 螺旋簇式 Refers to three or more helices packing together,Super secondary Structures (II),bb Hairpins 发夹式 Connect two antiparallel strands; bab Cross-overs 交叉式 Connect two parallel strands,To dive into the tertiary structure forms,Protein Folding and Tertiary Structure,Architecture of protein molecules 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),Review,Hydrophobic Structural role in nature Types Alpha-keratin Fibroin and beta-keratin Collagen, a triplex helix,Fibrous Proteins 纤维蛋白,Tertiary Structure,a-keratin 角蛋白,Basic structure: N-capping+Rod domain + C-capping,The rod domains form coiled coils right-handed a-helix, but left-handed twist,Tertiary Structure /Fibrous Proteins,Fibroin and b-keratin 蚕丝蛋白和b-角蛋白,Kind of b-sheet proteins Full of nonpolar amino acids, Gly, Ala,Tertiary Structure /Fibrous Proteins,A triple helix: poly(Gly-X-Y), X often Pro, Y often Pro or Hyp Gly of the 1st strand lies to X residue of the 2nd strand and to Y residue of the 3rd strand Fibrils Arrays of Tropocollagen molecules原胶原分子,Collagen 胶原蛋白,poly(Gly-Pro-Pro) right-handed triple helix left-handed helical chain,Tertiary Structure /Fibrous Proteins,Fibrils, Arrays of tropocollagen molecules,Hole zone has Sugars that Bind to 5-hydroxylysine or embeds hydoxyapatite,Tertiary Structure /Fibrous Proteins,Ca5(PO4)3OH Hydroxyapatite 羟基磷灰石,Hydroxylysine binds to sugar,Bone materials that embed in collagen:,Sugar may plays a role in organizing fibril assembly.,Tertiary Structure /Fibrous Proteins,Globular Proteins 球蛋白,Basic characteristics of globular proteins Physicochemical properties Basic types Molecular chaperones 分子陪伴蛋白 Protein domains 蛋白质域,Basic characteristics of globular proteins球蛋白的基本特征,Physicochemical properties 物理化学性质 Far more numerous, hydrophilic 大量，亲水 Substantially consisted of a-helices and b-sheets 基本上由a-螺旋和b-折叠片组成 H-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） Types Antiparallel a-helix proteins 反平行a-螺旋蛋白 Parallel or mixed b-sheet proteins 平行或混合b-折叠片蛋白 Antiparallel b-sheet proteins 反平行b-折叠片蛋白 Metal- and disulfide-rich proteins 金属和富含双硫键的蛋白,Three-dimensional structure of bovine ribonuclease A,Tertiary structure is substantially Consisted of a-helices and b-sheets.,Tertiary Structure /Globular Proteins,Tri-dimensional structure of bovine pancreatic trypsin inhibitor,Stabilized mainly by H-bonds,Electrostatic interaction Ligand binding,E-F hand structure, which forms Ca2+-binding sites in a variety of proteins,Tertiary Structure /Globular Proteins,Antiparallel a-Helix Proteins,Dominated by a-helices 主要由a-螺旋组成 Consist of bundles of antiparallel helices 由反平行a-螺旋簇组成 Simplest way to pack helices 组装方式最简单 Many 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 Many are regular, uniform structures 结构规则,Tertiary Structure /Globular Proteins,Examples of antiparallel a-proteins,TMV 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HA2,Tertiary Structure /Globular Proteins,Parallel or mixed b-sheet proteins,Parallel or mixed b-sheet Arrange hydrophobic residues on both sides of the sheet 折叠片两边为疏水性残基 Typically found as core structures (hydrophobic) 一般存在于核心结构里 Form sandwich structure 形成夹心结构 Parallel b-barrel 平行b-桶 b-a-b (i.e, two b-sheets linked by an antiparallel a-helix) Doubly wound parallel b-sheet 双绕平行b-片 Internal 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 Proteins,Diagram of this b-sheet arrangement in the Lipocalin family, which bind small molecules between the sheets of the sandwich b-片形成的夹心结构里键合了小分子,Tertiary Structure /Globular Proteins,Example: Lipocalin family 胞质中脂质键合蛋白家族,Example I : Porin 孔蛋白,Tertiary Structure /Globular Proteins,Example II : Parallel b-array proteins 平行b-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 view,Top view,Tertiary Structure /Globular Proteins,Hexokinase domain 1 己糖激酶蜮1,Flavodoxin 黄素氧还蛋白,Phosphoglycerate mutase 磷酸甘油酸变旋酶,Examples of several typical doubly wound parallel b-sheet proteins 典型双绕平行b-折叠片蛋白举例,Tertiary Structure /Globular Proteins,Antiparallel b-sheet proteins 反平行b-折叠片蛋白,Arrange hydrophobic residues on just one side of the sheet 折叠片两边为疏水性残基 Typical antiparallel topology modes 典型反平行拓扑模型 The Greek Key topology 希腊锁拓扑模型 The Jellyroll Topology 果冻卷拓扑模型,Tertiary Structure /Globular Proteins,With one face exposed to solvent, and the other face Covered by helices and random coils,Tertiary Structure /Globular Proteins,Gamma-crystallin fold g-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,Gamma-crystallin fold g-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,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-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A2,Ferredoxin 铁氧化还原蛋白,High-potential iron 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,Function: help fold globular proteins 功能：帮助折叠成球蛋白 Usually binds to the exposed hydrophobic regions of partially folded structures, and lead to less compact than the native fold structure Nature 特性 First identified as heat shock proteins 热激蛋白 Typical examples Hsp70: a 70-kD heat shock protein Hsp60s: a class of 60-kD