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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method.

Juyong Lee1, Benjamin T Miller1, Ana Damjanović1,2

  • 1Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.

Journal of Chemical Theory and Computation
|November 18, 2015
PubMed
Summary
This summary is machine-generated.

We developed a new 2D replica exchange method for enhanced sampling in constant-pH simulations. This method improves protonation state transitions and conformational sampling, converging faster than previous techniques.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Constant-pH simulations are crucial for understanding biomolecular behavior.
  • Existing methods like 1D EDS-HREM have limitations in sampling efficiency.
  • Accurate simulation of protonation states is essential for biological function.

Purpose of the Study:

  • To introduce a novel two-dimensional (2D) enhanced sampling method for constant-pH simulations.
  • To extend the capabilities of enveloping distribution sampling (EDS) coupled with Hamiltonian exchange (HREM).
  • To improve the efficiency and accuracy of sampling protonation states and conformations.

Main Methods:

  • Developed a 2D EDS-HREM scheme incorporating external pH as an additional dimension.
  • Implemented exchanges on a lattice of Hamiltonians varying in pH and smoothness parameters.
  • Validated the method by simulating aspartic acid, glutamic acid, lysine, a peptide, and snake cardiotoxin.

Main Results:

  • The 2D EDS-HREM method accurately reproduces semigrand canonical ensemble properties.
  • Demonstrated faster convergence and enhanced sampling of protonation states and conformations compared to the 1D method.
  • Observed improved sampling of wider conformational space with equivalent computational resources.

Conclusions:

  • The 2D EDS-HREM method offers significant advantages for constant-pH simulations.
  • This approach enhances efficiency in sampling protonation dynamics and conformational landscapes.
  • The method provides a powerful tool for studying protonation-dependent processes in biomolecules.