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Structure. 2015 Aug 4;23(8):1516-1525. doi: 10.1016/j.str.2015.05.022. Epub 2015 Jul 9.

SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets.

Author information

1
Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy. Electronic address: lponzoni@sissa.it.
2
Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
3
Institute for Computational Molecular Science, College of Science and Technology, Temple University, SERC, 1925 North 12th Street, Philadelphia, PA 19122, USA.

Abstract

Identifying dynamical, quasi-rigid domains in proteins provides a powerful means for characterizing functionally oriented structural changes via a parsimonious set of degrees of freedom. In fact, the relative displacements of few dynamical domains usually suffice to rationalize the mechanics underpinning biological functionality in proteins and can even be exploited for structure determination or refinement purposes. Here we present SPECTRUS, a general scheme that, by solely using amino acid distance fluctuations, can pinpoint the innate quasi-rigid domains of single proteins or large complexes in a robust way. Consistent domains are usually obtained by using either a pair of representative structures or thousands of conformers. The functional insights offered by the approach are illustrated for biomolecular systems of very different size and complexity such as kinases, ion channels, and viral capsids. The decomposition tool is available as a software package and web server at spectrus.sissa.it.

PMID:
26165596
DOI:
10.1016/j.str.2015.05.022
[Indexed for MEDLINE]
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