Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit water (Journal article)

Stavrakoudis, A.

Molecular dynamics simulations have been performed for the 104-117 alpha-helical fragment of apoliprotein A-I using the CHARMM22 force field and the NAMD simulation engine. Simulation ( 50 ns in explicit water) resulted in significant appearance of pi-helix conformation, which was totally diminished when the CMAP correction of the CHARMM force field was applied. This is consistent with other similar studies which suggest that the observation of pi-helix in peptide conformation was force field biased rather actually existed. This study suggests that the 104-117 fragment of apoliprotein A-I has a stable alpha-helical conformation in water. (C) 2008 Elsevier B.V. All rights reserved.
Institution and School/Department of submitter: Πανεπιστήμιο Ιωαννίνων. Σχολή Οικονομικών και Κοινωνικών Επιστημών. Τμήμα Οικονομικών Επιστημών
Keywords: microscopic view,alpha-helix,pi-helix,ewald,propagation,transitions,proteins
ISSN: 0009-2614
Link: <Go to ISI>://000258395300026
Appears in Collections:Άρθρα σε επιστημονικά περιοδικά ( Ανοικτά)

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