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Dynamic protein domains: identification, interdependence, and stability.

ABSTRACT: Existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. However, this information is vital for many areas of protein research. The recently developed hierarchical clustering of correlation patterns (HCCP) technique provides machine-based domain identification in a computationally simple and physically consistent way. Here we present the modification of this technique, which not only allows determination of the most plausible number of dynamic domains but also makes it possible to estimate the degree of their independence (the extent of correlated motion) and stability (the range of environmental conditions, where domains remain intact). With this technique we provided domain assignments and calculated intra- and interdomain correlations and interdomain energies for >2500 test proteins. It is shown that mean intradomain correlation of motions can serve as a quantitative criterion of domain independence, and the HCCP stability gap is a measure of their stability. Our data show that the motions of domains with high stability are usually independent. In contrast, the domains with moderate stability usually exhibit a substantial degree of correlated motions. It is shown that in multidomain proteins the domains are most stable if they are of similar size, and this correlates with the observed abundance of such proteins.

SUBMITTER: Yesylevskyy SO

PROVIDER: S-EPMC1483087 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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Dynamic protein domains: identification, interdependence, and stability.

Yesylevskyy Semen O SO Kharkyanen Valery N VN Demchenko Alexander P AP

Biophysical journal 20060421 2

Existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. However, this information is vital for many areas of protein research. The recently developed hierarchical clustering of correlation patterns (HCCP) technique provides machine-based domain identification in a computationally simple and physically consistent way. Here we present the modification of this technique, which not only allows determination of the mo ...[more]

PMID: 16632509

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Project description:BackgroundProteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational methodologies for large-scale determination of protein domains and their boundaries. We provide and rigorously evaluate a novel set of domain families that is automatically generated from sequence data. Our domain family identification process, called EVEREST (EVolutionary Ensembles of REcurrent SegmenTs), begins by constructing a library of protein segments that emerge in an all vs. all pairwise sequence comparison. It then proceeds to cluster these segments into putative domain families. The selection of the best putative families is done using machine learning techniques. A statistical model is then created for each of the chosen families. This procedure is then iterated: the aforementioned statistical models are used to scan all protein sequences, to recreate a library of segments and to cluster them again.ResultsProcessing the Swiss-Prot section of the UniProt Knoledgebase, release 7.2, EVEREST defines 20,230 domains, covering 85% of the amino acids of the Swiss-Prot database. EVEREST annotates 11,852 proteins (6% of the database) that are not annotated by Pfam A. In addition, in 43,086 proteins (20% of the database), EVEREST annotates a part of the protein that is not annotated by Pfam A. Performance tests show that EVEREST recovers 56% of Pfam A families and 63% of SCOP families with high accuracy, and suggests previously unknown domain families with at least 51% fidelity. EVEREST domains are often a combination of domains as defined by Pfam or SCOP and are frequently sub-domains of such domains.ConclusionThe EVEREST process and its output domain families provide an exhaustive and validated view of the protein domain world that is automatically generated from sequence data. The EVEREST library of domain families, accessible for browsing and download at 1, provides a complementary view to that provided by other existing libraries. Furthermore, since it is automatic, the EVEREST process is scalable and we will run it in the future on larger databases as well. The EVEREST source files are available for download from the EVEREST web site.

Project description:Proteins convey the majority of biochemical and cellular activities in organisms. Over the course of evolution, proteins undergo normal sequence mutations as well as large scale mutations involving domain duplication and/or domain shuffling. These events result in the generation of new proteins and protein families. Processes that affect proteome evolution drive species diversity and adaptation. Herein, change over the course of metazoan evolution, as defined by birth/death and duplication/deletion events within protein families and domains, was examined using the proteomes of 9 metazoan and two outgroup species.In studying members of the three major metazoan groups, the vertebrates, arthropods, and nematodes, we found that the number of protein families increased at the majority of lineages over the course of metazoan evolution where the magnitude of these increases was greatest at the lineages leading to mammals. In contrast, the number of protein domains decreased at most lineages and at all terminal lineages. This resulted in a weak correlation between protein family birth and domain birth; however, the correlation between domain birth and domain member duplication was quite strong. These data suggest that domain birth and protein family birth occur via different mechanisms, and that domain shuffling plays a role in the formation of protein families. The ratio of protein family birth to protein domain birth (domain shuffling index) suggests that shuffling had a more demonstrable effect on protein families in nematodes and arthropods than in vertebrates. Through the contrast of high and low domain shuffling indices at the lineages of Trichinella spiralis and Gallus gallus, we propose a link between protein redundancy and evolutionary changes controlled by domain shuffling; however, the speed of adaptation among the different lineages was relatively invariant. Evaluating the functions of protein families that appeared or disappeared at the last common ancestors (LCAs) of the three metazoan clades supports a correlation with organism adaptation. Furthermore, bursts of new protein families and domains in the LCAs of metazoans and vertebrates are consistent with whole genome duplications.Metazoan speciation and adaptation were explored by birth/death and duplication/deletion events among protein families and domains. Our results provide insights into protein evolution and its bearing on metazoan evolution.

Dataset Information

Dynamic protein domains: identification, interdependence, and stability.

Publications

Dynamic protein domains: identification, interdependence, and stability.

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