Journal
JOURNAL OF MOLECULAR MODELING
Volume 15, Issue 10, Pages 1213-1219Publisher
SPRINGER
DOI: 10.1007/s00894-009-0482-5
Keywords
alpha-helix; Molecular dynamics; Peptide folding; Salt bridge interactions
Categories
Funding
- National Science Foundation [0321218]
- Texas Research Development Fund
- Direct For Computer & Info Scie & Enginr
- Division Of Computer and Network Systems [0321218] Funding Source: National Science Foundation
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Peptide side chain interactions were studied by molecular dynamics simulation using explicit solvent on a peptide with the sequence AAARAAAAEAAEAAAARA. Three different protonation states of the glutamic acid side chains were simulated for four 20 ns runs each, a total simulation time of 240 ns. Two different salt bridge geometries were observed and the preferred geometry was found to depend on Glu - Arg residue spacing. Stable charge clusters were also observed, particularly in the fully charged peptide. Salt bridges were selectively interrupted upon protonation, with concomitant changes in secondary structure. The fully charged peptide was highly helical between residues 9 and 13, although protonation increased helicity near the N-terminus. The contribution of salt bridges to helix stability therefore depends on both position and relative position of charged residues within a sequence.
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