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Bioinformatics Advance Access published online on November 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti128
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received June 18, 2004
Revised September 27, 2004
Accepted October 22, 2004

Article

Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins

Xin Yuan 1 and Christopher Bystroff 1*

1 Department of Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA

* To whom correspondence should be addressed.
Christopher Bystroff, E-mail: bystrc{at}rpi.edu


  Abstract

Motivation: Proteins of the same class often share a secondary structure packing arrangement but differ in how the secondary structure units are ordered in the sequence. We find that proteins that share a common core also share local sequence-structure similarities, and these can be exploited to align structures with different topologies. In this study, segments from a library of local sequence-structure alignments were assembled hierarchically, enforcing the compactness and conserved inter-residue contacts but not sequential ordering. Previous structure-based alignment methods often ignore sequence similarity, local structural equivalence, and compactness.

Results: The new program, SCALI (Structural Core ALIgnment), can efficiently find conserved packing arrangements, even if they are non-sequentially ordered in space. SCALI alignments conserve remote sequence similarity and contain fewer alignment errors. Clustering of our pairwise non-sequential alignments shows that recurrent packing arrangements exist in topologically different structures. For example, the 3-layer sandwich domain architecture may be divided into four structural subclasses based on internal packing arrangements. These subclasses represent an intermediate level of structure classification, more general than topology but more specific than architecture as defined in CATH. A strategy is presented for developing a set of predictive hidden Markov models based on multiple SCALI alignments.

Availability: An online topology independent SCALI structure comparison server is available at http://www.bioinfo.rpi.edu/~bystrc/scali.html.


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