Paper Citing NAMD - Abstract
Tatsis, Vasileios A.; Tsoulos, Ioannis G.; Stavrakoudis, Athanassios
Molecular Dynamics Simulations of the TSSPSAD Peptide Antigen in Free and Bound with CAMPATH-1H Fab Antibody States: The Importance of the beta-Turn Conformation
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:1-9, MAR 2009
Humanized CAMPATH-1H antibody has been found to have biological applications through the recognition of the CD52 antigen. A peptide mimotope of the CD52 antigen with the sequence T(1)SSPSAD(7) has been co-crystallized with the CAMPATH-1H antibody. A plethora of hydrogen bond interactions were found to mediate antigen recognition. An important feature of peptide's bound conformation was the type I beta-turn found in the S(3)PSA(6) peptide's fragment. Paradoxically, this fact has been underestimated from other researchers. In order to further investigate the importance of this structural feature and its significance in antibody/antigen binding we have performed molecular dynamics simulations in explicit water of the T1SSPSAD7 peptide in both antibody free and bound states. We have found that the turn structure has been perfectly retained in the bound state but it was eliminated in the free state. This fact implies that the turn structure of the peptide is unstable in aqueous environment and it is induced upon antibody binding. Analysis of the trajectories revealed also several other important features of the antibody/antigen binding mode.
