Configurational temperature density of states simulations of proteins.
A novel method has been implemented to compute the density of states of proteins. A united atom representation and the CHARMM (Brooks et al., 1983) force-field parameters have been adopted for all the simulations. In this approach, an intrinsic temperature is computed based on configurational information about the protein. A random walk is performed in potential energy space and the configurational temperature is collected as a function of potential energy of the system. The density of states is then calculated by integrating the reciprocal of temperature. Unlike previously available methods, this approach does not involve calculations based on histograms of stochastic visits to distinct energy states. It is found that the proposed method is more efficient than earlier, related schemes for simulation of protein folding. Furthermore, it directly provides thermodynamic information, including free energies. The usefulness of the method is discussed by presenting results of simulations of the 16-residue beta-hairpin taken from the C-terminal fragment (41-56) of protein G.
Rathore
Nitin
N
Department of Chemical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Knotts
Thomas A
TA
de Pablo
Juan J
JJ
D000465:Algorithms; D001703:Biophysics / Q000379:methods; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013696:Temperature; D013816:Thermodynamics
D011506:Proteins