title: SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets.
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.
authors.affiliation: Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy. Electronic address: lponzoni@sissa.it.
authors.forename: Luca
authors.initials: L
authors.lastname: Ponzoni
authors.affiliation: Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Guido
authors.initials: G
authors.lastname: Polles
authors.affiliation: Institute for Computational Molecular Science, College of Science and Technology, Temple University, SERC, 1925 North 12th Street, Philadelphia, PA 19122, USA.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Carnevale
authors.affiliation: Molecular and Statistical Biophysics, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Cristian
authors.initials: C
authors.lastname: Micheletti
mesh_terms: D000263:Adenylate Kinase / Q000737:chemistry*; D002213:Capsid / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology; D020407:Internet; D007473:Ion Channels / Q000737:chemistry*; D008958:Models, Molecular; D058011:Multifactor Dimensionality Reduction / Q000379:methods*; D017434:Protein Structure, Tertiary; D012984:Software; D013816:Thermodynamics; D019400:Tobacco mosaic satellite virus / Q000737:chemistry
chemical_list: D007473:Ion Channels; D000263:Adenylate Kinase