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Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins
N S Boutonnet1, M J Rooman, M E Ochagavia
1Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, France.
Protein Engineering
|July 1, 1995
Summary
This study introduces an automated method for aligning protein structures using root mean square (RMS) deviation. The procedure identifies common structural cores and detects rigid-body movements in protein families.
Area of Science:
- Structural bioinformatics
- Computational biology
- Protein structure analysis
Background:
- Accurate protein structure alignment is crucial for understanding protein function and evolution.
- Existing methods often require manual intervention or are limited in scope.
- Identifying conserved structural motifs across protein families remains a challenge.
Purpose of the Study:
- To develop a fully automatic procedure for optimal alignment of two protein structures.
- To leverage structural alignments for automatic definition of common structural cores within protein families.
- To enable automatic detection of rigid-body movements between structural elements.
Main Methods:
- Utilizes root mean square (RMS) deviation of superimposed backbone atoms (N, C alpha, C, O) as the sole similarity measure.
- Employs a two-step approach: segment identification based on conformational similarity, followed by a novel multiple linkage clustering algorithm for optimal global alignment.
- Applies automatic analysis of clustering trees to detect rigid-body movements.
Main Results:
- Successfully aligned distantly related protein families, including alpha+beta proteins (ubiquitin, ferredoxin, protein G) and beta-proteins (Greek key group, lipocalins, neuraminidases, lectins).
- Identified common structural motifs, such as a four beta-strand and one alpha-helix motif in alpha+beta proteins, and a five beta-strand motif in Greek key proteins.
- Revealed conserved structural elements and rigid-body movements, providing insights into evolutionary relationships within protein families.
Conclusions:
- The developed automatic procedure provides an efficient and objective method for protein structure alignment and analysis.
- The method aids in defining conserved structural cores and understanding evolutionary relationships within protein families.
- Findings offer new perspectives on the structural diversity and evolutionary connections among beta-proteins.