Paper Citing NAMD - Abstract
Mernea, Maria; Calborean, Octavian; Grigore, Oana; Dascalu, Traian; Mihailescu, Dan Florin
Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures
OPTICAL AND QUANTUM ELECTRONICS, 46:505-514, APR 2014
Terahertz (THz) spectroscopy is a promising technique for the study of protein structure and internal flexibility. Here, we used THz spectroscopy and molecular modeling for bovine serum albumin (BSA) structure investigation. BSA molecule was built using homology modeling methods and 30 different more relaxed models were obtained by molecular dynamics simulations of the hydrated protein. As the experimental and simulated THz spectra are linear, we compared them by comparing the slopes of the lines that fit them. Six BSA structures had slope values in the range given by the slope of the experimental spectrum 0.2 and a total of sixteen BSA structures had slope values in the 0.6 interval near the experimental slope value. BSA average structures were calculated over the six and the sixteen identified BSA molecules. Based on the similarity with the crystal structure of BSA, we validated the average structure calculated over the sixteen BSA conformations. The comparison with the crystal structure showed that the structure validated using THz spectroscopy is a coarse model of BSA, as its root-mean-square deviation relative to the crystal structure is 1.9 . The regions from our model that present the highest deviation from the crystal structure are exterior loops. The results presented here show that using THz spectroscopy and molecular modeling is a promising approach to determine the structure of proteins.
