Paper Citing VMD - Abstract
Aliaga, Alvaro E., Ahumada, Hernan, Sepulveda, Karen, Gomez-Jeria, Juan S., Garrido, Carlos, Weiss-Lopez, Boris E., Campos-Vallette, Marcelo M.
SERS, Molecular Dynamics and Molecular Orbital Studies of the MRKDV Peptide on Silver and Membrane Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:3982-3989, MAR 17 2011 2011
The MRKDV peptide, structurally associated with an immunomodulatory protein, was studied using surface enhanced Raman scattering (SERS), molecular dynamics (MD) simulations, and quantum chemical calculations. The SEAS spectrum of the MRKDV peptide adsorbed on the silver surface is dominated by signals coming from the guanidinium moiety of the arginine amino acid (R). Guanidinium is the intrinsic probe that drives the orientation of the peptide onto the silver surface. Molecular mechanics and extended Huckel calculations of a model of MRKDV interacting with a silver surface support the experimental results. MD calculations representing the evolution of the peptide toward a model membrane were also performed. The guanidinium moiety interacts with the phospholipidic membrane surface. A hydrophobic C-terminal modification favors the peptide membrane affinity.
