SUPERFAMILY 1.75 including a domain-centric gene ontology method

Morais, David Anderson de Lima; Fang, Hai; Rackham, Owen J. L.; Wilson, Derek A.; Pethica, Ralph B; Chothia, Cyrus; Gough, Julian

doi:10.1093/nar/gkq1130

Cited by 156 publications

(162 citation statements)

References 33 publications

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“…Chemokines are small proteins, which activate different G protein-coupled receptors and cause migration of cells. They all belong to the same superfamily (35) and some of them exhibit high sequence and structural similarity. Our dataset consists of three tetramers (of which two are orthologues-human and bovine PF4), and one dimer.…”

Section: Geometric Comparisons Reveal Different Models Of Oligomeric mentioning

confidence: 99%

Evolution of oligomeric state through geometric coupling of protein interfaces

Perica

Chothia

Teichmann

2012

Proc. Natl. Acad. Sci. U.S.A.

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Oligomerization plays an important role in the function of many proteins. Thus, understanding, predicting, and, ultimately, engi-neering oligomerization presents a long-standing interest. From the perspective of structural biology, protein-protein interactions have mainly been analyzed in terms of the biophysical nature and evolution of protein interfaces. Here, our aim is to quantify the importance of the larger structural context of protein interfaces in protein interaction evolution. Specifically, we ask to what extent intersubunit geometry affects oligomerization state. We define a set of structural parameters describing the overall geometry and relative positions of interfaces of homomeric complexes with different oligomeric states. This allows us to quantify the contribution of direct sequence changes in interfaces versus indirect changes outside the interface that affect intersubunit geometry. We find that such indirect, or allosteric mutations affecting intersubunit geometry via indirect mechanisms are as important as interface sequence changes for evolution of oligomeric states.protein complex evolution | homomeric complexes | protein geometry D uring the course of evolution proteins are constrained by their stability, biochemical activity, and regulation. A specific level of evolutionary constraint is added by interactions with other proteins as a greater proportion of protein structure is involved in its function (1). The basic principles of protein recognition and interface formation have been understood for many years (2), and it has been clear for a long time that considerable differences exist between two functionally distinguishable groups-obligate and transient interfaces (3-5). The evolution of protein interfaces has been related to these two groups as well as other biophysical principles. For instance, Mintseris and Weng have, by appropriately grouping types of protein complexes, shown that protein interfaces are slightly more conserved than the surface but much less than the protein core (6). This makes sense in the light of the prediction where, on average, just two substitutions are sufficient to convert a patch on a protein surface into a protein interface (7). This in turn supports work on so-called hot spot (8-10) and anchor residues (11) or conserved residue clusters (12) in protein interfaces. The shared idea in all of these publications, that there are a few key interface residues, is in agreement with the nature of protein interface packing. Residues on the interface rim, which have more conformational freedom, can accommodate sequence changes more easily than ones in the interface core. More recently, there have been contributions to the field showing how interfaces can evolve through insertions of multiple residues forming so-called enabling loops (13,14).Interactions put additional constraints on protein sequences (15); however, in complexes where a subunit has multiple distinct surface regions that form interfaces (16), we would not expect the increase in evolutionary constraint ...

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Section: Geometric Comparisons Reveal Different Models Of Oligomeric mentioning

confidence: 99%

Evolution of oligomeric state through geometric coupling of protein interfaces

Perica

Chothia

Teichmann

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Knowledge of genes can be: their interacting networks [19], annotations by various ontologies (in dcGO database [27,28]), evolutionary ages [29], and residual domain superfamilies [30]. They are provided as RDataformatted files, and are maintained and updated using in-house Perl scripts.…”

Section: Data In the Dnet Packagementioning

confidence: 99%

The `dnet¿ approach promotes emerging research on cancer patient survival

Fang¹,

Gough²

2014

Genome Medicine

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We present the 'dnet' package and apply it to the 'TCGA' mutation and clinical data of >3,000 patients. We uncover the existence of an underlying gene network that at least partially controls cancer 'survivalness', with mutations that are significantly correlated with patient survival, yet independent of tumour origin and type. The survivalness network has natural community structure corresponding to tumour hallmarks, and contains genes that are potentially druggable in the clinic. This network has evolutionary roots in Deuterostomia identifying PTK2 and VAV1 as under-valued relative to more studied genes from that era. The 'dnet' R package is available at http://cran.r-project.org/package=dnet.

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“…PANTHER [18] signatures are based on sequences from 48 completed genomes. SUPERFAMILY [19] and Gene3D [20] also use completed genomes as a database source, but they classify the clusters based on the three-dimensional domains from the SCOP [21] and CATH [22] databases.…”

Section: Bioinformatics Tools and Www-based Databasesmentioning

confidence: 99%

Plant protein-coding gene families: emerging bioinformatics approaches

Martínez

2011

Trends in Plant Science

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Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is.

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SUPERFAMILY 1.75 including a domain-centric gene ontology method

Cited by 156 publications

References 33 publications

Evolution of oligomeric state through geometric coupling of protein interfaces

Evolution of oligomeric state through geometric coupling of protein interfaces

The `dnet¿ approach promotes emerging research on cancer patient survival

Plant protein-coding gene families: emerging bioinformatics approaches

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