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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Forging tools for refining predicted protein structures.

Xingcheng Lin1,2,3, Nicholas P Schafer1,4, Wei Lu1,2

  • 1Center for Theoretical Biological Physics, Rice University, Houston, TX 77030.

Proceedings of the National Academy of Sciences of the United States of America
|April 20, 2019
PubMed
Summary
This summary is machine-generated.

Mechanical deformation strategies inspired by blacksmithing accelerate protein structure refinement. This computational method uses collective variables to guide simulations, improving predicted protein models efficiently.

Keywords:
mechanical deformationsprincipal component analysisprotein blacksmithingprotein structure refinementside-chain isomerization

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Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Refining predicted protein structures computationally is crucial for understanding protein function.
  • All-atom molecular dynamics simulations are a powerful tool but are limited by slow conformational changes in folded proteins.
  • Current methods struggle with routine refinement of predicted structures due to computational expense.

Purpose of the Study:

  • To develop an efficient computational method for refining predicted protein structures.
  • To overcome the limitations of slow rearrangements in standard molecular dynamics simulations.
  • To improve the quality of computationally derived protein models.

Main Methods:

  • A two-step refinement procedure inspired by mechanical deformation techniques.
  • Identification of collective variables for mechanical deformation using coarse-grained models.
  • Sampling along identified deformation modes in all-atom simulations, focusing on low-frequency collective modes that alter the protein contact map.

Main Results:

  • The method successfully refined 20 protein structures from the CASP12 competition.
  • Simulations induced significant structural rearrangements, improving accuracy compared to experimental structures within 50 ns.
  • Aromatic side-chain reorientation was identified as a slow process even with global deformations.

Conclusions:

  • Mechanical deformation strategies can significantly accelerate the refinement of predicted protein structures.
  • The developed method enhances the quality of computational protein models.
  • Further improvements can be achieved by reducing side-chain isomerization barriers in force fields.