iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/25577198
Evolutionary patterns in coiled-coils - PubMed Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Jan 10;7(2):545-56.
doi: 10.1093/gbe/evv007.

Evolutionary patterns in coiled-coils

Jaroslaw Surkont  1 , Jose B Pereira-Leal  2
Affiliations

Evolutionary patterns in coiled-coils

Jaroslaw Surkont et al. Genome Biol Evol. .

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).

Keywords: amino acid substitutions; coiled-coil; homology detection; phylogenetic inference; protein evolution; protein structure.

PubMed Disclaimer

Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Sequence conservation of protein regions. (a) Sequence conservation superimposed on the structure of SAS-6 homolog protein from Chlamydomonas reinhardtii (Protein Data Bank: 3Q0X; Kitagawa et al. 2011). Observed conservation ranges from 0.20 to 4.08 bit; blue indicates lowest and red highest conservation. (b) Average sequence conservation in human coiled-coil proteins.
F<sc>ig</sc>. 2.—
Fig. 2.—
Amino acid equilibrium frequencies (pi) in CC and LG models.
F<sc>ig</sc>. 3.—
Fig. 3.—
Amino acid exchangeability rates. (a) Symmetric matrix of amino acid exchangeability rates for coiled-coil regions in the CC model. The area of each bubble represents the value of exchangeability rij between amino acid i and j. (b) Heat map representation of the difference between amino acid substitution rates in CC and LG models. The value for each square is calculated as log⁡10qij(CC)qij(LG). For both plots, values are scaled so that the expected number of substitutions per site is 1.
F<sc>ig</sc>. 4.—
Fig. 4.—
Homology predictions (BLAST) of all human coiled-coil proteins containing at least one globular domain across all species present in the Ensembl database. Sensitivity, precision, and mcc are shown as cumulative plots of median values for each e value threshold. ☆+ denotes a significant difference (P < 0.01, Mann–Whitney U test) between full sequence and masked either coiled-coil regions or globular domains for a given threshold.
F<sc>ig</sc>. 5.—
Fig. 5.—
Homology search improvement under the CC model. Homology search comparison between CC140 and BLOSUM62 scoring matrix at the e value threshold of 1e-08. Statistical significance between samples was estimated with the Mann–Whitney U test (***P<0.001).
F<sc>ig</sc>. 6.—
Fig. 6.—
Human PBX4 (ENSP00000251203) orthology prediction against metazoan species with BLOSUM62 and CC140 scoring matrices. Blue/red—correctly/incorrectly assigned ortholog. Ensembl Pan-taxonomic Compara was used as the reference (REF).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Abascal F, Posada D, Zardoya R. MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol. 2007;24:1–5. - PubMed
    1. Adachi J, Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol. 1996;42:459–468. - PubMed
    1. Adachi J, Waddell PJ, Martin W, Hasegawa M. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol. 2000;50:348–358. - PubMed
    1. Akaike H. A new look at the statistical model identification. IEEE Trans Automat Contr. 1974;19:716–723.
    1. Altschul SF. Amino acid substitution matrices from an information theoretic perspective. J Mol Biol. 1991;219:555–565. - PMC - PubMed

Publication types