PROTEIN PHYSICS LECTURE 2 Protein chain regular backbone

PROTEIN PHYSICS LECTURE 2

Protein chain: regular backbone & gene-encoded sequence of side chains

Protein chain Covalent bond lengths: 0. 9 – 1. 8 Å Covalent bond angles: 109 o – 120 o Atom radii: 1– 2Å

Side chains

Protein chain Side chains: Lamino acids ___ Main-chain peptide group: flat & rigid ______

STEREO: CROSS your eyes; fix right eye at the left picture, and left eye at the right picture. Bring images together. See 3 D image! ____________________

Gly Ala _L_ Ala -D-

Two amino acids have asymmetric side chains: THR ILE Chemical S-S bond of two CYS side chains:

Peptide group: flat & rigid sp 2 + p Covalent bonding

Main-chain: f (N-Ca) , y (Ca-C’), w (C’=N) Side-chain: c 1, c 2, . . .

Counting angles: 120 o 180 o 0 o _______________________

sp 2 - sp 2 (w) w = 180 o w = 0 o

Potentials: from IR spectra of vibrations _______________________ ¼ e. V

Potentials: from IR spectra of vibrations _______________________ QUANTUM EFFECTS: Covalent bond lengths: l 0 = 0. 9 – 1. 8 Å No thermal vibrations of bonds at T~300 o. K quantum Covalent bond angles: 109 o – 120 o Thermal vibrations of angles just begin at T~300 o. K semiclassical

Potentials: from IR spectra of vibrations classical _______________________ sp 2 - sp 2 (w) Pro All, but Pro sp 3 – sp 3 (c) CH 3 -CH 3 C-CH 2 -C sp 2 – sp 3 (f, y)

“Partial” double bond: sp 2 + p “Resonance” of bonds: