title: Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains.
abstract: The two-site coarse-grained model for the interactions of charged side chains, to be used with our coarse-grained UNRES force field for protein simulations proposed in the accompanying paper, has been extended to pairs of oppositely charged side chains. The potentials of mean force of four pairs of molecules modeling charged amino-acid side chains, i.e., propionate-n-pentylamine cation (for aspartic acid-lysine), butyrate-n-pentylamine cation (for glutamic acid-lysine), propionate-1-butylguanidine (for aspartic acid-arginine), and butyrate-1-butylguanidine (for glutamic acid-arginine) pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expression was fitted to the potentials of mean force. Compared to pairs of like-charged side chains discussed in the accompanying paper, an average quadrupole-quadrupole interaction term had to be introduced to reproduce the Coulombic interactions, and a multistate model of charge distribution had to be introduced to fit the potentials of mean force of all oppositely charged pairs well. The model reproduces all salt-bridge minima and, consequently, is likely to improve the performance of the UNRES force field.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland. momo@chem.univ.gda.pl
authors.forename: Mariusz
authors.initials: M
authors.lastname: Makowski
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D001224:Aspartic Acid / Q000737:chemistry; D018698:Glutamic Acid / Q000737:chemistry; D008239:Lysine / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins; D014867:Water; D001224:Aspartic Acid; D018698:Glutamic Acid; D001120:Arginine; D008239:Lysine