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SARFing the PDB

N N Alexandrov1

  • 1Laboratory of Mathematical Biology, NCI-NIH, Frederick, MD 21702, USA.

Protein Engineering
|September 1, 1996
PubMed
Summary
This summary is machine-generated.

A new program, SARF2, identifies non-topological protein structural similarities. This tool reveals hidden relationships between proteins, advancing comparative analysis and protein structure prediction.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational chemistry

Background:

  • The rapid increase in solved protein structures necessitates advanced comparative analysis methods.
  • Identifying structural similarities, even with different topological connections, is crucial for understanding protein function and evolution.

Purpose of the Study:

  • Introduce SARF2, a novel program for protein structure comparison.
  • Demonstrate SARF2's capability to detect non-topological structural resemblances.
  • Highlight new examples of significant, previously unnoticed structural similarities.

Main Methods:

  • Development of the SARF2 program for detecting spatial arrangements of secondary structure elements.
  • Analysis of protein structures to identify similar spatial arrangements despite differing topologies.

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  • Validation of structural similarities using similarity scores, aligned contact maps, and active site locations.

    • Main Results:

    • SARF2 successfully identified non-topological structural similarities between diverse protein pairs.
    • Examples include heme-binding proteins (cytochrome P450 and globin) sharing a six-alpha-helix arrangement.
    • Pectate lyase and snowdrop lectin exhibit similar beta-prism architecture via different topological routes.

    Conclusions:

    • Recurrent non-topological structural motifs suggest inherent energetic stability.
    • These findings open new avenues for protein sequence-structure alignment and threading methods.
    • SARF2 provides a valuable tool for exploring the structural diversity and relationships within the protein universe.