A Simplified Model of Local Structure in Aqueous Proline Amino Acid Revealed by First-Principles Molecular Dynamics Simulations

Raphael Z. Troitzsch, Paul R. Tulip, Jason Crain, Glenn J. Martyna

Research output: Contribution to journalArticlepeer-review

Abstract

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.

Original languageEnglish
Pages (from-to)5014-5020
Number of pages7
JournalBiophysical Journal
Volume95
Issue number11
DOIs
Publication statusPublished - 1 Dec 2008

Keywords

  • CAR-PARRINELLO EQUATIONS
  • DENSITY-FUNCTIONAL THEORY
  • NEUTRON-DIFFRACTION
  • COLD-ACCLIMATION
  • PSEUDOPOTENTIALS
  • DEGRADATION
  • PROTEINS
  • STRESS

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