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Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry
11:12

Organic Solvent-Based Protein Precipitation for Robust Proteome Purification Ahead of Mass Spectrometry

Published on: February 7, 2022

Solvent dramatically affects protein structure refinement.

Gaurav Chopra1, Christopher M Summa, Michael Levitt

  • 1Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA.

Proceedings of the National Academy of Sciences of the United States of America
|December 17, 2008
PubMed
Summary
This summary is machine-generated.

Implicit solvent models significantly improve protein structure refinement more effectively than knowledge-based potentials. This approach enhances homology models by guiding them toward native protein structures.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein structure refinement is crucial for improving homology models.
  • Traditional methods use in vacuo energy minimization with knowledge-based potentials.
  • Protein folding and function occur in aqueous environments, necessitating solvent consideration.

Purpose of the Study:

  • To investigate the role of solvent in protein structure refinement.
  • To compare the effectiveness of implicit and explicit solvent models against knowledge-based potentials.

Main Methods:

  • Performed molecular dynamics in explicit solvent.
  • Conducted energy minimization in both explicit and implicit solvent (Generalized Born Surface Area - GBSA).
  • Tested refinement on 75 native proteins and 729 near-native decoys per protein.

Main Results:

  • Implicit solvent (GBSA) provided greater refinement improvement for 24 of 75 proteins (>20% C(alpha) rmsd improvement).
  • Knowledge-based potentials showed improvement in only 7 proteins.
  • Molecular dynamics in explicit solvent moved structures away from native conformations.

Conclusions:

  • Implicit solvent models, particularly GBSA, are more effective for protein structure refinement than knowledge-based potentials.
  • Implicit solvent creates a stable energy landscape that favors native structures.
  • Explicit solvent molecular dynamics may not be optimal for refining near-native protein models.