Paper Citing NAMD - Abstract
Stavrakoudis, Athanassios
Conformational Studies of the 313-320 and 313-332 Peptide Fragments Derived from the alpha(IIb) Subunit of Integrin Receptor with Molecular Dynamics Simulations
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:263-272, DEC 2009
The peptide sequence YMESRADRKLAEVGRVYLFL, derived from 313-332 region of the alpha(IIb), has been identified as a potent inhibitor of platelet aggregation and fibrinogen binding to alpha(IIb)beta(3). More detailed studies have revealed that the Y(313)MESRADR(320) sequence is the shortest octapeptide with strong inhibitory activity. This work provides insight of the solution conformation of these peptides, by performing extensive molecular dynamics simulations of 100 ns. The 8mer peptide has no stable conformation in water while the 20mer peptide retains a relative conformational stability. Analysis of side chain orientation of the RAD fragment revealed the synplanar arrangement of guanidinium and beta-carboxylic groups providing a framework for explaining the similar biological activity of the two peptides, despite their differences in sequence and conformation.
