Paper Citing NAMD - Abstract
EzzEldin, Hussein M.; Solares, Santiago D.
CALCULATION OF ISOTHERMAL INTRINSIC COMPRESSIBILITY AND COMPRESSION OF GVPA PROTEIN IN HALOBACTERIUM SP. NRC-1 USING MOLECULAR MODELING AND DYNAMICS
DETC2009: PROCEEDINGS OF THE ASME INTERNATIONAL DESIGN ENGINEERING TECHNICAL CONFERENCES/COMPUTERS AND INFORMATION IN ENGINEERING CONFERENCE, 389-395, 2010
Gas vesicles are low-density, gas-filled protein organelles found inside various microorganisms. They have a lipid-free membrane with an average thickness of 2 nm and provide their hosts with buoyancy. In this study we characterized gas vesicle proteins synthesized by the Halobacterium sp. NRC-1 strain making use of molecular modeling methods and molecular dynamics (MD) simulations. The tertiary structure of GvpA protein, the major constituent of the gas vesicle membrane, was predicted using the De Novo computational design method available in the Rosetta Suite 2.3.1 software and was found to be in agreement with experimental data available from previous studies conducted by others and the consensus of different secondary structure prediction web servers. Optimization of the predicted structure was first carried out by energy minimization and simulated annealing. Subsequently, the mechanical properties of GvpA were investigated via constant pressure and temperature (NPT) aqueous MD simulations, in which two approaches were used to study the isothermal compressibility: quantification of the fluctuations in protein volume at constant pressure and temperature, and quantification of the volume changes induced through changes in the simulation pressure. Long term we plan to incorporate this information into multiscale models of whole gas vesicles.
