Paper Citing NAMD - Abstract
Mernea, Maria; Calborean, Octavian; Petrescu, Livia; Dinca, Mihai P.; Leca, Aurel; Apostol, Dan; Dascalu, Traian; Mihailescu, Dan
The flexibility of hydrated bovine serum albumin investigated by THz spectroscopy and molecular modeling
ROMOPTO 2009: NINTH CONFERENCE ON OPTICS: MICRO- TO NANOPHOTONICS II, 7469 Art. No. 74690N, 2010
The native cellular environment represents a crowded system comprising high concentrations of soluble molecules that interact mostly in a nonspecific manner. Some of the macromolecular crowding effects occurring in biological media are conformational changes and macromolecular associations. Most of our knowledge on protein folding and protein-protein interactions was acquired from experiments on proteins in dilute solutions or from theoretical models of isolated proteins in either explicit or implicit solvent. Here we present a 50% w/w bovine serum albumin (BSA) solution model that comprises two solute molecules included in a single water box. We determined the vibration spectrum of the 50% w/w BSA solution using THz spectroscopy and we calculated the theoretical THz spectrum. We observed a good correlation between the experimental and theoretical spectra for the frequency range of 0.3 - 1.5 THz. We also investigated the contribution of each BSA molecule to the solution THz spectrum by simulating THz spectra of the two BSA molecules from the solution model and water, each accounting for a 50% w/w BSA solution. The spectra appear to be similar. As the two molecules in our solution model have different conformations, we investigated the importance of the apparently insignificant differences between simulated THz spectra of the two proteins. We found that the differences should be considered significant, as they reflect differences between the flexibility of the two BSA molecules.
