03蛋白质高级结构2013(1)

TEM image of collagen fibres.
Model of a collagen helix
Berisio R, Vitagliano L, Mazzarella L, Zagari A (2002). "Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3)". Protein Sci. 11 (2): 262–70.
27
310
3.613 (α) 4.416 (π)
Collagen 胶原蛋白 The collagen helix, or type 2 helix, consists of a triple helix made of the repetitious amino acid sequence glycine-proline-hydroxyproline. The three chains are hydrogen bonded to each other. The hydrogen bond donors are the NH groups of Gly. The hydrogen bond acceptors are the CO groups of residues on the other chains. The OH group of hydroxyproline also participates in hydrogen bonding. The rise of the collagen helix (superhelix) is 2.9 Å (0.29 nm) per residue.
coiled coil
β
Functional roles of alpha helix α helices have particular significance in DNA binding motifs, including helix-turn-helix motifs, leucine zipper motifs and zinc finger motifs. The diameter of the α helix is 12 Å, the same as the width of the major groove in B-form DNA.
Disallowed: Gly, Pro
二级结构的长度分布
一些典型的二级结构举例
α helix
a right-handed
Top viewSide viw肽平面Two key developments in the modeling of the modern α-helix were (1) the correct bond geometry, thanks to the crystal structure determinations of amino acids and peptides and Pauling‘s prediction of planar peptide bonds; and (2) the relinquishing (放弃) of the assumption of an integral number (整 数) of residues per turn of the helix. The pivotal moment came in the early spring of 1948, when Pauling caught a cold and went to bed. Being bored, he drew a polypeptide chain of roughly correct dimensions on a strip of paper and folded it into a helix, being careful to maintain the planar peptide bonds. After a few attempts, he produced a model with physically plausible hydrogen bonds. Pauling then worked with Corey and Branson to confirm his model before publication.
Omega (ω): Cα-C’-N- Cα, trans-180ºor cis-0º
trans is favored, except for X-P (cis configuration is preferred)
问题1：为何Omega角只能是0或180度？
主链
侧链
2, secondary structures
27
310
3.613 (α) 4.416 (π)
主链原子数加上形成氢键的氧和氢原子
A Ramachandran plot (拉氏图)
Ramachandran plot of the residues in bovine pancreatic trypsin inhibitor (BPTI).（牛胰蛋白酶抑制剂）
Psi-loop motif
This motif is rare as the process resulting in its formation seems unlikely to occur during protein folding. The Ψloop was first identified in the aspartic protease family.
310 helix
3 residues per turn and a 10 member loop
π helix 4.416 helix
Parameters of five actual or theoretical secondary structures:
Hydrogen bonding patterns for four helices
360º
Due to its double covalent nature, the peptide bond is rigid.
Rotation around the bonds in a polypeptide chain.
Dihedral angle: φ, ψ, ω Phi: the angle of rotation around the N-Cα bond (C’-N- Cα-C’) Psi: the angle of rotation around the Cα-C’ bond (N-Cα-C’-N)
羧基端
氨基端
Activation of amino acids for incorporation into proteins.
核糖体
peptide bond formation is coupled to the hydrolysis of ATP during translation
360º
β sheet
the backbone of the polypeptide chain is extended into a zigzag (锯齿形) structure.
β turns (转角)
β turns: connect the ends of two adjacent segments of an antiparallel β sheet.
■ The most common secondary structures are the α helix, the β conformation, and β turns. ■ The secondary structure of a polypeptide segment can be completely defined if the φ and ψ angles are known for all amino acid residues in that segment.
Greek key motif This type of structure forms easily during the protein folding process. It was named after a pattern common to Greek ornamental artwork (装 饰工艺品). 3 2 1 4
The λ repressor of bacteriophage lambda employs a helix-turnhelix to bind DNA
310 helix
27
310
3.613 (α) 4.416 (π)
π helix theoretically possible, but never found in the proteins
■ 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 way.
Refers to local folding of the backbone of a linear polymer to form a regular, repeating structure. For a polypeptide, the secondary structure is determined by the primary structure and the solvent environment in which it is located.
Ψ
β-meander motif （β 回曲）