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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

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Published on: September 17, 2017

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

Jianhan Chen1, Wonpil Im, Charles L Brooks

  • 1Department of Molecular Biology, Center for Theoretical Biological Physics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Journal of the American Chemical Society
|December 9, 2004
PubMed
Summary
This summary is machine-generated.

Implicit solvent models significantly improve protein NMR structure refinement quality, especially with limited experimental data. Combining these models with replica exchange (REX) methods rapidly guides structures toward their native state.

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15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Published on: April 19, 2021

Area of Science:

  • Structural Biology
  • Computational Chemistry
  • Biophysics

Background:

  • Nuclear Magnetic Resonance (NMR) biomolecular structure calculations rely on simulated annealing for conformational sampling.
  • High redundancy in experimental restraints is typically required for accurate three-dimensional structure determination.
  • Generalized Born (GB) implicit solvent models offer potential to integrate experimental data with empirical force fields for improved NMR structures.

Purpose of the Study:

  • To investigate the influence of implicit solvent on the refinement of protein NMR structures.
  • To identify an optimal protocol for utilizing implicit solvent models and advanced sampling techniques in NMR structure refinement.
  • To assess the efficacy of the proposed protocol across proteins of varying sizes and data redundancy levels.

Main Methods:

  • Structure refinement experiments were conducted on model proteins with published NMR structures, using full and subsets of NMR restraints.
  • Implicit solvent effects were studied, alongside the application of advanced sampling techniques like replica exchange (REX).
  • An optimal protocol was developed involving initial structure generation with conventional NMR software and subsequent refinement using implicit solvent and REX.

Main Results:

  • Implicit solvent had minimal impact on refinement when sufficient experimental restraints were available.
  • Refinement with implicit solvent substantially improved structure quality when experimental data were limited.
  • Combining implicit solvent with the REX method rapidly guided near-native structures toward the native basin, providing enhanced sampling and automatic selection of low-energy structures.

Conclusions:

  • An optimal protocol combining initial structure generation with experimental data and subsequent refinement using implicit solvent and REX significantly improves NMR structure quality, especially with limited restraints.
  • This protocol is particularly beneficial in early stages of NMR structure determination and for biomolecules with limited redundant data, such as large multidomain proteins and in solid-state NMR.
  • The proposed method expedites the overall NMR structure determination process by providing a reliable estimate of the native fold from limited data.