Alpha-helical stabilization by side chain shielding of backbone hydrogen bonds.

Abstract:

:We study atomic models of the thermodynamics of the structural transition of peptides that form alpha-helices. The effect of sequence variation on alpha-helix formation for alanine-rich peptides, Ac-Ala21-methyl amide (A21) and Ac-A5 (AAARA)3A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix-coil transition in explicit water. The simulations show that the guanidinium group in the Arg side chains in the Fs peptide interacts with the carbonyl group four amino acids upstream in the chain and desolvates backbone hydrogen bonds. This desolvation can be directly correlated with a higher probability of hydrogen bond formation. We find that Fs has higher helical content than A21 at all temperatures. A small modification in the amber force field reproduces the experimental helical content and helix-coil transition temperatures for the Fs peptide.

authors

García AE,Sanbonmatsu KY

doi

10.1073/pnas.042496899

keywords:

subject

Has Abstract

pub_date

2002-03-05 00:00:00

pages

2782-7

issue

5

eissn

0027-8424

issn

1091-6490

pii

042496899

journal_volume

99

pub_type

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