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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
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Patterns of Dynamics Comprise a Conserved Evolutionary Trait.

F Zsolyomi1, V Ambrus1, M Fuxreiter1

  • 1MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.

Journal of Molecular Biology
|November 30, 2019
PubMed
Summary
This summary is machine-generated.

Protein dynamics, or patterns of dynamics (PODs), are evolutionarily conserved, offering insights into protein function and relationships beyond sequence or structure. These dynamic patterns are important for both structured and disordered proteins.

Keywords:
Divergent sequencesEvolutionary relationshipIntrinsically disordered proteinsProtein dynamicsStructure conservation

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Evolutionary Biology

Background:

  • Protein dynamics significantly influence protein function, suggesting evolutionary pressure on large-scale protein motions.
  • Understanding protein dynamics is crucial for deciphering protein function and evolutionary history.

Purpose of the Study:

  • To systematically investigate the dynamic characteristics of protein domains within the Pfam database.
  • To define and analyze patterns of dynamics (PODs) and their evolutionary conservation.
  • To explore the utility of PODs for inferring evolutionary relationships, especially in challenging cases like disordered regions.

Main Methods:

  • Analysis of 2221 protein domains (58477 sequences) from the Pfam database.
  • Definition of patterns of dynamics (PODs) using estimated NMR order parameters and predicted degree of disorder.
  • Comparative analysis of POD conservation against sequence conservation, hydropathy, and interaction potential.

Main Results:

  • A significant correlation was found between NMR order parameters and the degree of disorder across protein families.
  • Conservation of dynamic patterns often exceeds sequence conservation and is comparable to other biophysical properties.
  • POD similarity shows weak correlation with structural similarity and degree of disorder, highlighting their unique information content.

Conclusions:

  • Patterns of dynamics (PODs) represent a conserved evolutionary trait.
  • PODs can be effectively applied to analyze sequentially divergent and intrinsically disordered protein regions.
  • PODs offer a valuable alternative to sequence and structure for inferring evolutionary relationships.