Paper Citing NAMD - Abstract
Stavrakoudis, Athanassios
A disulfide linked model of the complement protein C8 gamma complexed with C8 alpha indel peptide
JOURNAL OF MOLECULAR MODELING, 15:165-171, FEB 2009
In a recent study C8 gamma (complement protein) with Cys40Ala substitution and a C8 alpha derived peptide with Cys164Ala substitution were co-crystallized and their binding mode was revealed. Computer modeling and molecular dynamics simulations were performed in order to check the hypothesis that the residues Ala164 of C8 alpha and Ala40 of C8 gamma occupied the right position if cysteine residues were in their place for disulfide bonding. Substitution of these two alanine residues with cysteine along with disulfide bond creation via molecular modeling and subsequent molecular dynamics simulation of the complex corroborated the hypothesis, which was also confirmed from recent crystallographic data. Average RMSD between backbone atoms of the indel peptide during the MD trajectory in comparison with the corresponding sequence of crystal structure of the C8 alpha/gamma complex was found only 0.085 nm.
