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Title: Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models

Abstract

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 onmore » interaction of various ligands in charged proteins in relation to isoelectric points. © 2016 Wiley Periodicals, Inc.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [1]
+ Show Author Affiliations
  1. Department of Physics and Astronomy University of Missouri–Kansas City Missouri 64110
  2. Department of Physics University of Massachusetts Amherst Massachusetts 01003, Department of Theoretical Physics J. Stefan Institute Ljubljana SI‐1000 Slovenia, Department of Physics Faculty of Mathematics and Physics University of Ljubljana SI‐1000 Ljubljana Slovenia
  3. Department of Biomedical Engineering Case Western Reserve University Cleveland Ohio 44106, Department of Radiology Case Western Reserve University Cleveland Ohio 44106, Department of Materials Science and Engineering Case Western Reserve University Cleveland Ohio 44106, Department of Macromolecular Science and Engineering Case Western Reserve University Cleveland Ohio 44106
  4. Department of Materials Science and Engineering Case Western Reserve University Cleveland Ohio 44106
  5. Department of Physics Faculty of Mathematics and Physics University of Ljubljana SI‐1000 Ljubljana Slovenia
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1401176
Grant/Contract Number:  
DE‐AC03‐76SF00098
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
International Journal of Quantum Chemistry
Additional Journal Information:
Journal Name: International Journal of Quantum Chemistry Journal Volume: 116 Journal Issue: 9; Journal ID: ISSN 0020-7608
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Eifler, Jay, Podgornik, Rudi, Steinmetz, Nicole F., French, Roger H., Parsegian, V. Adrian, and Ching, Wai‐Yim. Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models. United States: N. p., 2016. Web. doi:10.1002/qua.25089.
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Eifler, Jay, Podgornik, Rudi, Steinmetz, Nicole F., French, Roger H., Parsegian, V. Adrian, & Ching, Wai‐Yim. Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models. United States. https://doi.org/10.1002/qua.25089
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Eifler, Jay, Podgornik, Rudi, Steinmetz, Nicole F., French, Roger H., Parsegian, V. Adrian, and Ching, Wai‐Yim. Thu . "Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models". United States. https://doi.org/10.1002/qua.25089.
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@article{osti_1401176,
title = {Charge distribution and hydrogen bonding of a collagen α 2 ‐chain in vacuum, hydrated, neutral, and charged structural models},
author = {Eifler, Jay and Podgornik, Rudi and Steinmetz, Nicole F. and French, Roger H. and Parsegian, V. Adrian and Ching, Wai‐Yim},
abstractNote = {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. © 2016 Wiley Periodicals, Inc.},
doi = {10.1002/qua.25089},
journal = {International Journal of Quantum Chemistry},
number = 9,
volume = 116,
place = {United States},
year = {Thu May 05 00:00:00 EDT 2016},
month = {Thu May 05 00:00:00 EDT 2016}
}
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https://doi.org/10.1002/qua.25089
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