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Disallowed spots in protein structures.

Mayank Kumar1, R S Rathore1

  • 1Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar 824236, India.

Biochimica Et Biophysica Acta. General Subjects
|October 21, 2023
PubMed
Summary
This summary is machine-generated.

The Ramachandran map, used for protein structure analysis, shows no disallowed conformations in high-quality protein data. Disallowed spots in proteins are often due to interactions or short loops, not inherent residue properties.

Keywords:
Disallowed conformationFoldingProtein conformationProtein structureRamachandran (φ,ψ) mapSteric map

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • The Ramachandran (ϕ, ψ) steric map, established in 1963, defines available conformational space for protein structures.
  • Observations of protein residues in high-energy disallowed regions of the map prompted further investigation.

Purpose of the Study:

  • To unequivocally identify and characterize the locations of disallowed residue conformations in protein structures.
  • To investigate the factors contributing to the occurrence of residues in these high-energy states.

Main Methods:

  • Analysis of 36 high-resolution (≤1 Å, R ≤ 0.10) noise-free protein structures to identify disallowed conformations.
  • Examination of a larger dataset (≤1.5 Å) excluding model errors and disorders.
  • Conformational sampling and analysis of residue interactions.

Main Results:

  • No disallowed conformations were found in the high-quality, noise-free protein dataset.
  • Disallowed spots were identified in short loops (3-5 residues) and at interaction sites (disulfide bonds, intra/inter-molecular interactions).
  • Residues in interactions were relieved of strain upon interaction removal; short loops showed limited strain relief.

Conclusions:

  • High-energy disallowed conformations are not inherent to specific residues but arise from specific structural contexts like short loops or stabilizing interactions.
  • Residues like pre-Pro, Ser, Asp, trans-Pro, Val, Asn, and Gly may appear in disallowed regions due to conformational restrictions and stabilizing interactions.
  • The study refines the understanding of protein conformational space and the factors driving residues into high-energy states.