1蛋白质二级结构

3, peptide bond

Peptide bonds form in the process of translation when the α-amino group of one amino acid residue forms a covalent bond (共价键) with the α-carboxyl group of another amino acid residue.

羧基端氨基端

Gly+AlaàGly-Ala (Glycylalanine)

Activation of amino acids for incorporation into proteins.

peptide bond formation is coupled to the hydrolysis of ATP during translation

核糖体

0.133nm

Rotation around the bonds in a polypeptide chain.

Dihedral angle: φ, ψ, ω

Phi: the angle of rotation around the N-Cαbond (C’-N-Cα-C’) Psi: the angle of rotation around the Cα-C’bond (N-Cα-C’-N)

Omega (ω): Cα-C’-N-Cα, trans-180ºor cis-0º

trans is favored, except for X-P (cis configuration is preferred)

pI: isoelectric point (Isoelectric focusing)

a distinct pH at which the net average charge of all the groups adds up to zero.The relative concentrations of the three forms of glycine as a function of pH

non-charged

Groups that may block N-or C-termini in proteins.

甲酰基

乙酰基

氨基

4, secondary structures

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.

Please enjoy a series of papers in PNAS 1951 to celebrate the 50th birthday of Dr. Pauling

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 way.

■The most common secondary structures are the αhelix, the βconformation, and βturns.

■The secondary structure of a polypeptide segment can be completely defined if the φand ψangles are known for all amino acid residues in that segment.

αhelix: the backbone of the

polypeptide chain is extended into

helical structure.

βsheet: the backbone of the

polypeptide chain is extended into a

zigzag (锯齿形)structure.

βturns:connect the ends of two

adjacent segments of an antiparallel βsheet.

310 helix

πhelix: theoretically possible,

but never found in the proteins

αhelix (3.6

13)

Four models of the helix, showing different aspects of its structure. (a) Formation of a right-handed αhelix. The planes of the rigid peptide bonds are parallel to the long axis of the helix, depicted here as a vertical rod. (b) Ball-and-stick model of a right-handed αhelix, showing the intrachain hydrogen bonds. The repeat unit is a single turn of the helix,

3.6 residues. (c) The helix as viewed from one end, looking down the longitudinal axis (derived from PDB ID 4TNC).Note the positions of the R groups, represented by purple spheres. This ball-and-stick model, used to emphasize the helical arrangement, gives the false impression that the helix is hollow, because the balls do not represent the van der Waals radii of the individual atoms. As the space-filling model (d) shows, the atoms in the center of the αhelix are in very close contact.