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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

Probing dynamic protein ensembles with atomic proximity measures.

Zoltán Gáspári1, Annamária F Angyán, Somdutta Dhir

  • 1Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary. szpari@chem.elte.hu

Current Protein & Peptide Science
|October 5, 2010
PubMed
Summary

Ubiquitin, though rigid, shows a diverse dynamic ensemble. Its atomic environments vary significantly across conformers, cautioning against single-structure analysis for function.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein dynamics are crucial for function, necessitating advanced analysis methods.
  • Understanding conformational ensembles is key to interpreting protein behavior.

Purpose of the Study:

  • To analyze the dynamic conformational ensemble of ubiquitin using proximity-based algorithms.
  • To evaluate the PRIDE-NMR algorithm's utility with NMR distance restraints.

Main Methods:

  • Analysis of ubiquitin's dynamically restrained conformational ensemble derived from residual dipolar coupling data.
  • Application of four proximity-based algorithms: CX, DPX, PRIDE, and PRIDE-NMR.
  • Examination of protruding/buried atoms and interatomic distances across conformers.

Main Results:

  • Ubiquitin exhibits a highly diverse dynamic ensemble despite its apparent rigidity.
  • Protruding atoms show high environmental variability, while only some buried atoms fluctuate.
  • PRIDE-NMR performance was evaluated on a broad dataset.

Conclusions:

  • Single ubiquitin conformers are insufficient for explaining functional phenomena due to ensemble variability.
  • The study provides insights into PRIDE-NMR's application with public NMR distance restraint sets.