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
Mariusz Makowski , Józef Adam Liwo , Harold A. Scheraga
AbstractThe physics-based potentials of side-chain − side-chain inter- actions 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 fi tted 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 fi eld 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).
|Journal series||Journal of Physical Chemistry B, ISSN 1520-6106|
|Publication size in sheets||0.55|
|Score|| = 30.0, 20-12-2017, ArticleFromJournal|
= 30.0, 20-12-2017, ArticleFromJournal
|Publication indicators||: 2016 = 3.177 (2) - 2016=3.177 (5)|
|Citation count*||2 (2018-07-16)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.