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Related Experiment Videos

Spatial sign-alternating charge clusters in globular proteins.

Y N Chirgadze1, E A Larionova

  • 1Institute of Protein Research, Russian Academy of Sciences, Moscow.

Protein Engineering
|April 9, 1999
PubMed
Summary

Sign-alternating charge clusters are prevalent on globular protein surfaces, appearing in 85.8% of structures studied. These clusters, formed by charged amino acid residues, likely serve as a general functional factor on protein surfaces.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Protein Chemistry

Background:

  • Globular proteins feature charged amino acid residues and terminal groups.
  • The spatial arrangement and clustering of these charged groups influence protein structure and function.
  • Understanding charge distribution is crucial for deciphering protein-protein interactions and biological roles.

Purpose of the Study:

  • To investigate the prevalence and characteristics of sign-alternating charge clusters on globular protein surfaces.
  • To determine the relationship between cluster size, protein length, and molecular mass.
  • To propose a functional role for these charge clusters in protein interactions.

Main Methods:

  • Analysis of 274 non-homologous globular protein structures from the Protein Data Bank (resolution ≤ 2.5 Å, sequence similarity < 25%).

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  • Identification of charge clusters based on proximity criteria (2.4–7.0 Å) of charged N and O atoms.
  • Statistical analysis of cluster distribution, size, and correlation with protein properties (length, molecular mass).

    • Main Results:

    • Sign-alternating charge clusters were found in 85.8% (235/274) of the analyzed globular proteins.
    • The distribution of charged groups into isolated, small (2-3 groups), and large (≥4 groups) clusters was approximately equal (33%, 35%, 32%).
    • Large cluster occurrence correlated with protein length (1-3 clusters in small proteins, 4-6+ in large proteins; avg. 1.5 clusters/100 residues), but not molecular mass.

    Conclusions:

    • Sign-alternating charge clusters are a common and significant feature on the surfaces of globular proteins.
    • These clusters exhibit a size distribution independent of protein molecular mass.
    • The prevalence and distribution suggest a general functional role as local polar factors mediating protein interactions.