29 January 2001

Biol 6312

Helix capping

Hydrogen bonding patterns of residues at the ends of helices. Hydrophobic interactions can also be involved.

Helix capping (link to abstract only)

Rajeev Aurora, George D. Rose

Protein Science (1998) 7: 21-38

Periodicity in a-Helix Lengths and C-capping Preferences

Simon Penel, R. Gwilym Morrison, Russell J. Mortishire-Smith, Andrew J. Doig

J. Mol. Biol. (1999) 293: 1211-1219

In the paper by Aurora and Rose the propensities of the individual amino acids for all positions (+ or - 5 ) from the N-cap and the C-cap sites are calculated, using a database of protein structures.

Charts of these are linked below:

They found 7 distinct capping motifs: 3 at the N-terminus and 4 at the C-terminus.

At the N-terminus, amide Hydrogens are H-bonded predominantly to side chains of nearby residues.

At the C-terminus, carbonyl oxygens are H-bonded predominantly to backbone amides in the following turn.

In both cases hydrophobic residues at the termini of the helix make hydrophobic contacts with turn residues.

In a related study, Penel et al found a preference among a-helices to be an integral number of turns, rather than half-integral. Presumably, this allow the turns at both ends to be on the same side, as would be necessary for a surface helix.

Properties and Tendencies of the Individual Amino Acids

The actual torsional angles that each type of amino acid exhibits in a large database has been tabulated and provided by Gerald Kleywegt of Uppsala University. He hosts a website about the small molecules in protein crystal structures, so-called "hetero-compounds", called HIC-Up

They are in pdf format (requires Acrobat Reader) and are linked below:

3 others: all a.a., all (-gly), and all (-gly,pro)

Glycine, Gly, G

Positive phi values, outside of repeating secondar structure

Proline, Pro, P

Phi angle constrained to about 60 degrees, cis peptide bond common

Influence of Proline Residues on Protein Conformation

Malcolm W. MacArthur, Janet M. Thornton

J. Mol. Biol. (1991) 218: 397-412

Cysteine, Cys, C

3 forms, -SH, -S^-, -S-S-

Alanine, Ala, A

No conformational preferences

Valine, Isoleucine, Leucine, Methionine

Val, Ile, Leu, Met.

V, I, L, M

aliphatic chains

Serine, Ser, S and Threonine, Thr, T

Side chain -OH, surface, not a-helix

Asparagine, Asn, N and Glutamine, Gln, Q

Similar side chains, but conformationally Asn is special

Aspartate, Asp, D and Glutamate, Glu, E

Similar to difference between Asn ans Gln, but charge dominates

Lysine, Lys, K and Arginine, Arg, R

Same charge, but diffferent in H-bonding and flexibility

Histidine, His, H

Aromatic, sometimes positive charge

Tyrosine, Tyr, Y

Aromatic, sometimes negative charge

Phenylalanine. Phe, F

Aromatic, completely hydrophobic, except p-interactions with cations, H-bonds

Tryptophan, Trp, W

Largest, aromatice, hydrophobic, except p-interactions, 1 H-bond donor