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Exploring Protein Conformational Diversity.

Alexander Miguel Monzon1, Maria Silvina Fornasari1, Diego Javier Zea2

  • 1Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina.

Methods in Molecular Biology (Clifton, N.J.)
|October 10, 2018
PubMed
Summary
This summary is machine-generated.

Proteins exist in multiple dynamic shapes, known as conformational diversity. The CoDNaS database analyzes these variations and their impact on protein function and modeling.

Keywords:
CoDNaS databaseConformational diversityConformersNative stateProtein dynamicsProtein evolution

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Proteins exist as an ensemble of dynamic conformations in their native state.
  • Understanding protein conformational diversity is crucial for comprehending biological function.
  • Existing databases may not fully capture the extent of native-state structural variations.

Purpose of the Study:

  • To explore issues related to protein conformational diversity in the native state.
  • To introduce and utilize the CoDNaS database for analyzing conformational ensembles.
  • To investigate the relationship between conformational diversity, sequence divergence, and homology modeling.

Main Methods:

  • Utilized the CoDNaS database, a curated collection of redundant protein structures for identical sequences.
  • Employed global and local structural similarity measures to quantify conformational diversity.
  • Analyzed how structural differences correlate with various structural features and sequence divergence.

Main Results:

  • CoDNaS provides a framework for estimating and exploring the degree of protein conformational diversity.
  • Structural differences among conformers vary significantly and can be linked to specific structural features.
  • A relationship was observed between protein conformational diversity and sequence divergence.

Conclusions:

  • Protein conformational diversity is a measurable and significant aspect of the native state.
  • The CoDNaS database serves as a valuable resource for studying protein structural ensembles.
  • High conformational diversity in proteins may present challenges and require specific considerations in homology modeling techniques.