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Similarities between protein 3-D structures

U Lessel¹, D Schomburg

¹Gesellschaft für Biotechnologische Forschung, Department of Molecular Structure Research, Braunschweig, Germany.

Protein Engineering

|October 1, 1994

Summary

A new method systematically evaluates protein structural similarity by matching C alpha atoms in superimposed fragments. This approach classifies proteins into 182 structural families, revealing relationships within protein folds.

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Area of Science:

Structural biology
Bioinformatics
Computational chemistry

Background:

Evaluating protein structural similarity is crucial for understanding protein function and evolution.
Existing methods may lack systematic approaches for comprehensive structural comparison.

Purpose of the Study:

To develop a novel, systematic method for assessing protein structural similarity.
To quantify protein fold similarity and identify optimal superpositions.
To systematically analyze the Protein Data Bank for structural relationships.

Main Methods:

A new method detects and superimposes similar protein fragments.
Iterative refinement maximizes matching C alpha atoms within a distance threshold.
The number of matching C alpha atoms quantifies structural similarity.

Main Results:

The method successfully quantifies protein fold similarity.
A systematic search identified 182 distinct structural protein families.
Relationships between members of identified structural classes were estimated.

Conclusions:

The developed method provides a robust and systematic way to evaluate protein structural similarity.
This classification into structural families aids in understanding protein evolution and function.
The findings offer a framework for exploring large-scale protein structural databases.

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