Eifler, Jay; Podgornik, Rudi; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Ching, Wai-Yim
Charge distribution and hydrogen bonding of a collagen (2)-chain in vacuum, hydrated, neutral, and charged structural models

A challenging task in computational biophysics is to ascertain the solvent effect on the electronic structure and interatomic bonding at the atomistic level. Simulations must be carried out on reasonably large biomolecules for accurate calculations to yield valid results. We report the results of a calculation on collagen model in the form of a peptide under three different environments: vacuum, solvated and with neutral and charged sites. Quantitative results and analysis of the partial charge (PC) distribution on each amino acid are discussed. A significant charge transfer of more than 1 electron from protein to water molecules is found with similar results when the model contains charged sites. The main contributions to the interatomic bonding are from hydrogen bonds (HBs) between water-water and water-protein pairs. A connection between PC and HBs can be established since the nonpolar amino acids form no HBs and have the smallest PC and vice versa. The ab initio PC obtained are used in the NAMD simulation showing significant improvement over the default values as reflected in the root mean square deviation of atomic positions in the MD steps and the total free energy in energy minimization. These results could facilitate the interpretation of data on interaction of various ligands in charged proteins in relation to isoelectric points. (c) 2016 Wiley Periodicals, Inc.


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