title: Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.
abstract: The physics-based potentials of side-chain-side-chain interactions corresponding to pairs composed of charged and polar, polar and polar, charged and hydrophobic, and hydrophobic and hydrophobic side chains have been determined. A total of 144 four-dimensional potentials of mean force (PMFs) of all possible pairs of molecules modeling these pairs were determined by umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation, and the analytical expressions were then fitted to the PMFs. Depending on the type of interacting sites, the analytical approximation to the PMF is a sum of terms corresponding to van der Waals interactions and cavity-creation involving the nonpolar sections of the side chains and van der Waals, cavity-creation, and electrostatic (charge-dipole or dipole-dipole) interaction energies and polarization energies involving the charged or polar sections of the side chains. The model used in this work reproduces all features of the interacting pairs. The UNited RESidue force field with the new side-chain-side-chain interaction potentials was preliminarily tested with the N-terminal part of the B-domain of staphylococcal protein A (PDBL 1BDD ; a three-α-helix bundle) and UPF0291 protein YnzC from Bacillus subtilis (PDB: 2HEP ; an α-helical hairpin).
authors.affiliation: Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Mariusz
authors.identifier: 0000-0002-7342-722X
authors.initials: M
authors.lastname: Makowski
authors.affiliation: Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland.
authors.forename: Adam
authors.initials: A
authors.lastname: Liwo
authors.affiliation: Baker laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.
authors.forename: Harold A
authors.initials: HA
authors.lastname: Scheraga
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001412:Bacillus subtilis; D002627:Chemistry, Physical; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D008958:Models, Molecular; D000072417:Protein Domains; D013205:Staphylococcal Protein A / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D013205:Staphylococcal Protein A; D014867:Water