PROTEIN PHYSICS A. V. Finkelstein & O. B. Ptitsyn LECTURE 7 Secondary Structures ¾ Regular Secondary Structures - helices (not just α-) - β-sheet - superhelices ¾ Irregular Secondary Structure - β-turns - β-bulges Secondary Structures Helices - one continuous region of the polypeptide - stabilized by hydrogen bonds between carbonyl and amide groups and van der Waals interactions across the helical axis

(i,i+2) (i,i+3) (i,i+4) (i,i+5) L-handed

There are helices without any hydrogen bonds, stabilized only by van der Waals interactions ( synthetic: Poly(Pro)I-II, Poly(Gly)I-II) R-handed Structure Residues per Rise per Radius of Observed residue (Å) helix (Å)

310 - helix +3.0 2.0 1.9 Small pieces

αR -helix +3.6 1.5 2.3 Abundant

αL -helix -3.6 1.5 2.3 absent π-helix +4.3 1.1 2.8 absent β -2.3 3.2 1.0 Abundant β -2.3 3.4 1.0 Abundant helix -3 2.9 1.6 In fibers

αR – helix is the most abundant and the most stable Helices Alpha(R) - helix

• 4 – 100 components • average length ~10 residues, corresponding to 15Å • the helix is a long dipole; N-terminus is capped by negative phosphate groups C- • tendency to appear in an : Met, Ala, Leu, Lys, Gln

•– tends to bend/break helices, though often appears as the first residue of the helix

•– tends to disrupt the helix, it is entropically expensive state

N+ ALA, etc. GLY only Location of an α - helix Helical Wheel – axis view

11 11 11 7 7 7 4 10 4 4 10 3 3 10 3 8 1 8 1 1 8 6 6 2 6 2 5 2 5 5 9 9 9

K-E-D-A-K-G-K-S-E-E-E L-S-F-A-A-A-M-N-G-L-A totally buried I-N-E-G-F-D-L-L-R-S-G completely exposed partially buried

Branden C, Tooze J, Introduction to Protein Structure, 1991 Beta Sheet

• Pleated sheet - Cα atoms succesively a little above and below the plane

• Left-hand twist in the sheet

right-handed twist of each strand

viewed from the sheet’s edge Beta Sheet • Combination of several regions of the polypeptide chain, β-strands • β-strand – 5-10 residues in an almost fully extended conformation, lying adjacent to each other

Antiparallel Parallel Mixed

β↑↑, twisted β↓↑, twisted Mirror-asymmetric amino acids – mirror-asymmetric twist of β-sheets β-hairpin with turn turn I

turn I’

turn II β-bulge Irregular Secondary Structures

β – turns (I, II, III = ) o Bridge between neighboring β –strands o Hydrophilic chain - usually concentrated at the surface

β –turn(I) β –turn(II) β - bulge o H-bonding of 2 residues from one strand with 1 residue from the other strand Helices (Without) H-bonds • their tight arrangement is stabilized by van der Waals interactions only Collagen - o Right-handed helix with 3 left-handed helix running in parallel o Triplet: (Gly-X-Y); X, Y usually is Pro o 10 triplets per strand/superhelix turn o held together by van der Waals interactions and 1 H-bond/triplet o each helix is in a conformation similar to the L-handed Poly(Pro)II Helices (Without) H-bonds collagen Experimental study of secondary structure

X-ray crystallography

NMR spectroscopy (cross-peaks) Experimental study of secondary structure

Far UV CD spectra IR spectra (peptide groups) (amid I, C=O bond)