Abstract
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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Acknowledgments
Simulations were performed on the High-Performance Computing Cluster at Texas A&M University-Corpus Christi, which is supported by grant #0321218 from the National Science Foundation. This work was supported by a grant from Texas Research Development Fund.
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Walker, K.D., Causgrove, T.P. Contribution of arginine-glutamate salt bridges to helix stability. J Mol Model 15, 1213–1219 (2009). https://doi.org/10.1007/s00894-009-0482-5
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DOI: https://doi.org/10.1007/s00894-009-0482-5