Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES)Force Field

摘要

Three algorithms,namely,a replica exchange method (REM),a replica exchange multicanonical method (REMUCA),and a replica exchange multicanonical method with replica exchange (REMUCAREM),were implemented with the coarse-grained united-residue force field (UNRES)in both Monte Carlo and molecular dynamics versions.The MD algorithms use the constant-temperature Berendsen thermostat,with the velocity Verlet algorithm and a variable time step.The algorithms were applied to one peptide (20 residues of alanine with free ends;ala_(20))and two small proteins,namely,an alpha-helical protein of 46 residues (the B domain of the staphylococal protein A;1BDD)and an alpha+beta protein of 48 residues (the Escherichia coli Mltd Lysm Domain;1E0G).Calculated thermodynamic averages,such as canonical average energy and heat capacity,are in good agreement among all simulations for poly-L-alanine,showing that the algorithms were implemented correctly and that all three algorithms are equally effective for small systems.For protein A,all algorithms performed reasonably well,although some variability in the calculated results was observed,whereas for a more complicated alpha+beta protein (1E0G),only replica exchange was capable of producing reliable statistics for calculating thermodynamic quantities.Finally,from the replica exchange molecular dynamics results,we calculated free-energy maps as functions of the RMSD and radius of gyration for different temperatures.The free-energy calculations show correct folding behavior for poly-L-alanine and protein A,while for 1E0G,the native structure had the lowest free energy only at very low temperatures.Hence,the entropy contribution for 1E0G is larger than that for protein A at the same temperature.A larger contribution from entropy means that there are more accessible conformations at a given temperature,making it more difficult to obtain an efficient coverage of conformational space to obtain reliable thermodynamic properties.At the same temperature,ala20 has the smallest entropy contribution,followed by protein A,and then by 1E0G.