title: Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli.
abstract: Sub-terahertz (THz) vibrational modes of the protein thioredoxin in a water environment were simulated using molecular dynamics (MD) in order to find the conditions needed for simulation convergence, improve the correlation between experimental and simulated absorption frequencies, and ultimately enhance the predictive capabilities of computational modeling. Thioredoxin from E. coli was used as a model molecule for protocol development and to optimize the simulation parameters. The empirically parameterized software packages Amber 8 and 10 were used in this work. Using atomic trajectories from the constant energy and volume MD simulations, thioredoxin's sub-THz vibrational spectra and absorption coefficients were calculated in a quasi-harmonic approximation. An optimal production run length ~100 ps was found, in agreement with experimental data on thioredoxin relaxation dynamics. At the same time, a new procedure was developed for averaging correlation matrices of atomic coordinates in MD simulations. In particular, the open source package ptraj was edited to improve a matrix-analyzing function. Averaging only six matrices gave much more consistent results, with absorption peak intensities exceeding those from the individual spectra and a rather good correlation between simulated vibrational frequencies and experimental data.
authors.affiliation: Department of Electrical & Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA.
authors.forename: Naser
authors.initials: N
authors.lastname: Alijabbari
authors.forename: Yikan
authors.initials: Y
authors.lastname: Chen
authors.forename: Igor
authors.initials: I
authors.lastname: Sizov
authors.forename: Tatiana
authors.initials: T
authors.lastname: Globus
authors.forename: Boris
authors.initials: B
authors.lastname: Gelmont
mesh_terms: D000042:Absorption; D004926:Escherichia coli / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D012984:Software; D055068:Terahertz Spectroscopy; D013879:Thioredoxins / Q000737:chemistry*; D014584:User-Computer Interface; D014732:Vibration; D014867:Water / Q000737:chemistry*
chemical_list: D029968:Escherichia coli Proteins; D014867:Water; D013879:Thioredoxins