Evolutionary Patterns in Coiled-Coils

Surkont, J.; Pereira-Leal, J. B.

Publication

Evolutionary Patterns in Coiled-Coils

2015-01-10Journal article

dc.contributor.author	Surkont, J.
dc.contributor.author	Pereira-Leal, J. B.
dc.date.accessioned	2015-10-21T10:30:25Z
dc.date.available	2015-10-21T10:30:25Z
dc.date.issued	2015-01-10
dc.description.abstract	Models of protein evolution are used to describe evolutionary processes, for phylogenetic analyses and homology detection. Widely used general models of protein evolution are biased toward globular domains and lack resolution to describe evolutionary processes for other protein types. As three-dimensional structure is a major constraint to protein evolution, specific models have been proposed for other types of proteins. Here, we consider evolutionary patterns in coiled-coil forming proteins. Coiled-coils are widespread structural domains, formed by a repeated motif of seven amino acids (heptad repeat). Coiled-coil forming proteins are frequently rods and spacers, structuring both the intracellular and the extracellular spaces that often form protein interaction interfaces. We tested the hypothesis that due to their specific structure the associated evolutionary constraints differ from those of globular proteins. We showed that substitution patterns in coiled-coil regions are different than those observed in globular regions, beyond the simple heptad repeat. Based on these substitution patterns we developed a coiled-coil specific (CC) model that in the context of phylogenetic reconstruction outperforms general models in tree likelihood, often leading to different topologies. For multidomain proteins containing both a coiled-coil region and a globular domain, we showed that a combination of the CC model and a general one gives higher likelihoods than a single model. Finally, we showed that the model can be used for homology detection to increase search sensitivity for coiled-coil proteins. The CC model, software, and other supplementary materials are available at http://www.evocell.org/cgl/resources (last accessed January 29, 2015).	pt_PT
dc.description.sponsorship	FCT fellowship: (SFRH/BD/51880/2012).	pt_PT
dc.identifier	10.1093/gbe/evv007
dc.identifier.citation	Jaroslaw Surkont and Jose B. Pereira-Leal Evolutionary Patterns in Coiled-Coils Genome Biol Evol (2015) Vol. 7 545-556 first published online January 10, 2015 doi:10.1093/gbe/evv007	pt_PT
dc.identifier.doi	10.1093/gbe/evv007
dc.identifier.uri	http://hdl.handle.net/10400.7/419
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	Oxford University Press	pt_PT
dc.relation.publisherversion	http://gbe.oxfordjournals.org/content/7/2/545.long	pt_PT
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	coiled-coil	pt_PT
dc.subject	protein evolution	pt_PT
dc.subject	phylogenetic inference	pt_PT
dc.subject	homology detection	pt_PT
dc.subject	amino acid substitutions	pt_PT
dc.subject	protein structure	pt_PT
dc.title	Evolutionary Patterns in Coiled-Coils	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.citation.endPage	556	pt_PT
oaire.citation.issue	2	pt_PT
oaire.citation.startPage	545	pt_PT
oaire.citation.title	Genome Biology and Evolution	pt_PT
oaire.citation.volume	7	pt_PT
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT