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A Protocol for Computer-Based Protein Structure and Function Prediction
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PDBcor: An automated correlation extraction calculator for multi-state protein structures.

Dzmitry Ashkinadze1, Piotr Klukowski1, Harindranath Kadavath1

  • 1Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.

Structure (London, England : 1993)
|December 28, 2021
PubMed
Summary

PDBCor is a new method to detect protein dynamics and correlated motions from experimental structures without superposition. This tool analyzes protein conformers to reveal essential correlations for understanding protein mechanisms.

Keywords:
multi-state protein structureprotein correlationsprotein structurestatistical analysis of protein structures

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Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein dynamics are crucial for protein function and mechanism.
  • Understanding correlated motions links protein dynamics to function.
  • Existing methods may require structure superposition or are not unbiased.

Purpose of the Study:

  • To present PDBCor, an automated and unbiased method for detecting and analyzing correlated motions in proteins.
  • To enable the study of protein dynamics from experimental multi-state structures.
  • To provide a tool for elucidating the mechanisms of protein action.

Main Methods:

  • Utilizes torsion angle and distance statistics.
  • Employs clustering of protein conformers.
  • Applies information theory (mutual information) to extract correlations.
  • Does not require structure superposition.

Main Results:

  • Successfully detected correlated motions in the WW domain of PIN1, protein GB3, and cyclophilin.
  • Demonstrated the method's ability to reveal known correlated motion patterns.
  • Generated example protein structure ensembles illustrating different correlation levels.

Conclusions:

  • PDBCor is an effective tool for analyzing protein dynamics and correlated motions.
  • The extracted correlations can aid in nuclear magnetic resonance (NMR) structure optimization and validation.
  • PDBCor facilitates a deeper understanding of how protein dynamics relate to function.