<scp>PRDB</scp>: <scp>P</scp>rotein <scp>R</scp>epeat <scp>D</scp>ata<scp>B</scp>ase

Jorda, Julien; Baudrand, Thierry; Kajava, Andrey V.

doi:10.1002/pmic.201100534

Cited by 13 publications

(8 citation statements)

References 26 publications

(29 reference statements)

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“…A de novo approach was preferred over annotating domain repeats with profile hidden Markov models (HMMs) for known domain repeats, such as those provided by Pfam (Punta et al 2012) or SUPERFAMILY (Wilson et al 2009) for two reasons. First, the set of known domain repeats in these databases is not exhaustive and, accordingly, de novo approaches find many repeats that do not match any already known domain (Ponting et al 2001; Jorda et al 2012). Second, many HMMs provided by Pfam and SUPERFAMILY do not specifically match an individual repeat unit, but rather stretches of several repeat units in tandem.…”

Section: Resultsmentioning

confidence: 99%

Evolution of Protein Domain Repeats in Metazoa

Schüler

Bornberg‐Bauer

2016

Mol Biol Evol

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Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races.Key Words: protein evolution, domain rearrangements, protein repeats, concerted evolution.

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Section: Resultsmentioning

confidence: 99%

Evolution of Protein Domain Repeats in Metazoa

Schüler

Bornberg‐Bauer

2016

Mol Biol Evol

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“…Repeat proteins play key roles in biological processes ranging from adhesion to signaling to defense mechanisms [1]. These proteins consist of adjacent series of usually non-identical repeated amino acid sequences; in most cases, these repeated units fold cooperatively into either a solenoid-shaped or a toroid-shaped structure [2–4].…”

Section: Introductionmentioning

confidence: 99%

A General Computational Approach for Repeat Protein Design

Parmeggiani

Huang

Vorobiev

et al. 2015

Journal of Molecular Biology

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Repeat proteins have considerable potential for use as modular binding reagents or biomaterials in biomedical and nanotechnology applications. Here we describe a general computational method for building idealized repeats that integrates available family sequences and structural information with Rosetta de novo protein design calculations. Idealized designs from six different repeat families were generated and experimentally characterized; 80% of the proteins were expressed and soluble and more than 40% were folded and monomeric with high thermal stability. Crystal structures determined for members of three families are within 1 Å root-mean-square deviation to the design models. The method provides a general approach for fast and reliable generation of stable modular repeat protein scaffolds.

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“…Widely used structural classifications such as CATH (35) and SCOP (36) also do not explicitly annotate repeats in protein structures, although it may be possible to leverage individual annotations to find similar repeats. Some databases exist for the detection of repeats from sequence (37–39), but usually these are limited to short tandem repeats and do not take into account divergent repeats, such as solenoids or toroids. The main domain sequence databases such as Pfam (40) and SMART (41) do not excel at the annotation of these repeat types either, as coverage is rather low and many repeat units go undetected.…”

Section: Introductionmentioning

confidence: 99%

RepeatsDB: a database of tandem repeat protein structures

et al. 2013

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RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services.

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PRDB: Protein Repeat DataBase

Cited by 13 publications

References 26 publications

Evolution of Protein Domain Repeats in Metazoa

Evolution of Protein Domain Repeats in Metazoa

A General Computational Approach for Repeat Protein Design

RepeatsDB: a database of tandem repeat protein structures

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