生物大分子结构与功能第2章相互作用力第3节第4节

1、2.3 蛋白质的二级结构（3学时） 2.4 蛋白质的高级结构（3学时） 1, the protein secondary structures 2, Super secondary structures and domains 3,Tools to investigate the protein conformation 4, globular proteins and SCOP 5, fibrous proteins,第一章： 蛋白质的结构层次,1, the secondary structures 2, Super secondary structures and domains 3,To

2、ols to investigate the protein conformation 4, globular proteins and SCOP 5, fibrous proteins,Protein Secondary Structure Secondary structure is the regular arrangement of amino acid residues in a segment of a polypeptide chain, in which each residue is spatially related to its neighbors in the same

3、 way. The most common secondary structures are the helix, the conformation, and turns. The secondary structure of a polypeptide segment can be completely defined if the and angles are known for all amino acid residues in that segment.,10 papers from Linus Pauling and colleagues published in PNAS, 19

4、51, helix 310 helix helix: theoretically possible, but never found in the proteins sheet: parallel and anti-parallel, helix, sheet,3.613 helix,Parameters of five actual or theoretical secondary structures:,helix: the backbone of the polypeptide chain is extended into helical structure Which Is built

5、 up from one continuous region.,helix, angle pair approximately -60 and -50. The length rang from 4 or 5 to 44 residues.The average length is around 10 residues,3.6 residues per turn with hydrogen bonds between C=O of residues n and NH of residues n+4. The end of helices are polar and are almost at

6、the surface of protein molecules,310 helix, helix 4.416 helix N+5,3 residues per turn and a 10 atoms between the hydrogen bond donor and acceptor, N+3,Idealized helices:,Hydrogen bonding patterns for four helices,27 310 3.613 4.414,The helix has a dipole moment,1.The overall effect is a significant

7、net dipole for the helix. That gives a partial positive charge at the amino end a partial negative charge at the Carboxyl end (0.5-0.7 unit charge) 2. Unit charge at each end attract ligands of opposite charge. Phosphate groups frequently bind at the N-terminal of helix. In contrast, positive charge

8、 ligands rarely bind at C-teminal.,Some amino acids are preferred in helix: Ala (A), Glu (E), Leu (L), and Met (M) are good helices formers. 2) Pro(P), Gly(G), Tyr (Y) and Ser (S) are very Poor formers 3) The most common location for an helix in a protein structure is along the outside of the protei

9、n, with one side facing the solution and the other side facing the hydrophobic interior of the protein. 4) helices that across membran are in a Hydrophobic environment, most of their side Chains are hydrophobic,Saccharomyces cerevisiae mitochondrial thioredoxin3,Bao et al.,Membrane Protein,J.Deisenh

10、ofer, H.Michel Science (245):1463,1989 J.Dersenhofer, O.Epp, K.Miki, R.Huber, H.Michel, Nature (318):618,1985 J.Deisenhofer, O.Epp, K.Miki, R.Huber, H.Michel, J.Mol.Biol.(180):385,1984 H.Michel J.Mol.Biol.(158):567,1982,First Membrane Protein Structure: Photosynthetic Reaction Center of Rhodopseudom

11、onas virdis 红假单胞菌 Complex (four subunits) solved in 1985 (1PRC) Nobel Chemistry Prize was awarded to J.Deisenhofer, R.Huber, H.Michel in 1988.,1) sheet: the backbone of the polypeptide chain is extended into a zigzag structure. 2) sheet is built up from a combination of several regions of the polype

12、ptide chain. 3) The length rang from 5 to 10 residues., sheet,The amino acide can all run in the same biochemical direction, amio terminal to carboxy terminal,The amino acid can have alternating directions, the N-terminal to C-terminal follow by C-terminal to N-terminal,Two forms have a distinctive

13、pattern of hydrogen-bonding,Parallel,Antiparallel,The sheet that are formed from several strands are “pleated”, sheet can also combine into mixed sheet (About 20% of known protein structures are mixed),Almost all the sheet have twist strands.This twist has the same handedness (right-handed), angles

14、within the broad structurally allowed region,the Double-headed Arrowhead Protease Inhibitor A,Bao et al.,Loop region frequently participate in forming binding sites and enzyme active sites,Loop regions are at the surface of protein molecules,Hairpin loops,Hydrogen bond between the oxygen of 1st carb

15、oxyl group and hydrogen of the 4th amino group,-turns: connect the ends of two adjacent segments of an antiparallel sheet.,Products of 13 genes involved in peptidyl-prolyl cis-trans isomerase activity,the common presence of Pro and Gly residues in turns, turns, turn,Hydrogen bond between the oxygen

16、of 1st carboxyl group and hydrogen of the 3rd amino group,A Ramachandran plot,Schematic pictures of proteins highlight secondary structure,Simplify Facilitate seeing similarity between proteins Helices sometimes cylinders,Topology diagrams are useful for classification of protein structures,Show the

17、 direction of each strand and the way the strands are connected to each other along the polypeptide chain,1, The secondary structures 2, Super secondary structures and domains 3,Tools to investigate the protein conformation 4, globular proteins and SCOP 5, fibrous proteins,Supersecondary structures,

18、 also called motifs or simply folds, are particularly stable arrangements of several elements of secondary structure and the connections between them.,Two helices that are connected by a short loop region. A: helix-turn-helix motif is specific for DNA binding B: the calcium binding motif is present

19、in many proteins Whose function is regulated by calcium.,The calcium-binding motif is symbolized by right hand Example: the calcium is bound to the motif in the troponin-C,The calcium-binding motif is symbolized by a right hand.This motif is called an EF hand because the fifth and sixth helices from

20、 the amino terminus in structure Of paravalbumin (in muscle relaxation found in 1973) which a labeled E and F ,are parts of the structure that were original used to illustrate calcium binding by this motif. The loop region between the two a helices binds the calcium atom. Carboxyl side chains from A

21、sp and Glu, main-chain C=O and H2O from ligands to metal atom. The helix-loop-helix motif provides a scaffold That holds the calcium ligand in proper position to bend and release calcium. c) The structure of troponin-C is built up from four EF motifs.,Hairpin motif (No specific function),The strong

22、preference for strands to be adjacent in sheets when they are adjacent in the amino acid Sequence and thus to form a hairpin motif. The length of the loop region between the strands very but are generally from 2 to 5 residues long. There is no specific function associated with this motif.,Two exampl

23、es: a) bovin trypsin inhibitor;b) snake venom erabutoxin,The Greek key motif,Example: the enzyme Staphylococcus nuclease, an enzyme that degrades DNA The Greek key motif is not associated with any specific function, But it occurs frequently in protein structures.,The - motif contains two parallel st

24、rands,The loop regions can be of very different lengths, from 1 or 2 residues to over 100. The two loops have Different functions. The loop that connects the carboxyl end of the strand with amino end of helix is often involved in forming the functional binding site, or active site, of these structur

25、es. These loop regions thus usually have conserved amino acid sequences in homologous proteins. In contrast, the other loop has not yet found to contribute to an active site.,Connections between strands in layered sheets,Two arrangements of strands stabilized by the tendency of the strands to twist.

26、,Hemolysin (a pore-forming toxin that kills a cell by creating a hole in its membrane) from the bacterium Staphylococcus aureus (PDB 7AHL).,photolyase (a protein that repairs certain types of DNA damage) from E. coli (PDB 1DNP).,氨基酸顺序相邻的花样通常在三维结构上也靠近,RNA结合蛋白(ROP)的四个 -螺旋折叠为一个四螺旋束,-螺旋的球状折叠,反平行的 -链形成桶结

27、构,上-下-回折桶结构,反平行- 结构中的希腊图案花样,果冻卷饼状桶(jelly roll barrels) 结构花样, / TIM桶结构 开放扭曲的 / 结构,开放扭曲的/结构中的结合部位形成裂缝,Protein molecules are organized in a structural hierarchy(等级） Primary structure Secondary structure Tertiary structure (domains) Quaternary structure,Large polypeptide chains fold into several domains

28、,EGF: domains that are homologous to epidermal (表皮细胞） growth factor (53 amino acids),Constructing large motifs from smaller ones,1, re-visit of the secondary structures 2, Super secondary structures and domains 3, Tools to investigate the protein conformation 4, globular proteins and SCOP 5, fibrous

29、 proteins,Helpful websites: 1, PDB (Protein Data Bank) /pdb/index.html 2, SCOP (Structural Classification of Proteins) http:/scop.mrc-lmb.cam.ac.uk/scop/ 3, comparison of protein structures in 3D http:/www.ebi.ac.uk/dali/index.html,A, X-ray crystallography B, NMR (nuclear magnetic

30、resonance) C, CD (circular dichroism) D, ,Computer programs,3D structure comparison: http:/www.ebi.ac.uk/dali/index.html,1, re-visit of the secondary structures 2, Tools to investigate the protein conformation 3, Super secondary structures and domains 4, globular proteins and SCOP 5, fibrous protein

31、s,In considering these higher levels of structure, it is useful to classify proteins into two major groups: fibrous proteins, having polypeptide chains arranged in long strands or sheets, and globular proteins, having polypeptide chains folded into a spherical or globular shape.,The two groups differ functionally from each other: fibrous proteins provide support, shape, and external protection to vertebrates globular proteins: most enzymes and regulatory proteins,The two groups are structura