Symmetric Structures in the Universe of Protein Folds

Guerler, Aysam; Wang, Connie; Knapp, Ernst‐Walter

doi:10.1021/ci900185z

Cited by 15 publications

(19 citation statements)

References 21 publications

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“…Data for SymD 1.3hw3 and GANGSTA+, in addition to the list of SCOP domains, is taken from supplemental 3 of Kim et al [38]. The best-performing methods for each fold are in bold. 1 The number of superfamilies in the fold 2 CE-Symm using TM-score ≥ 0.4 and requiring order ≥ 2 3 CE-Symm using TM-score ≥ 0.4 4 SymD using Z-score ≥ 8 (recommended by authors) 5 SymD using Z-score ≥ 10 (recommended by authors) 6 The unpublished SymD version 1.5b using TM-score ≥ 0.4 7 GANGSTA+ using FSAR(fraction of sequentially aligned residues) ≥ 0.8, which the authors recommend [37] …”

Section: Figurementioning

confidence: 99%

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Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

Myers-Turnbull

Bliven

Rose

et al. 2014

Journal of Molecular Biology

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Symmetry is an important feature of protein tertiary and quaternary structure that has been associated with protein folding, function, evolution and stability. Its emergence and ensuing prevalence has been attributed to gene duplications, fusion events, and subsequent evolutionary drift in sequence. This process maintains structural similarity and is further supported by this study. To further investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed an algorithm, CE-Symm, to detect pseudosymmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than previous approaches. We use CE-Symm to build a census of symmetry among domain superfamilies in SCOP and note that 18% of all superfamilies are pseudo-symmetric. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail. Using the Enzyme Commission classification, symmetry was found to be enriched in some enzyme classes but depleted in others. CE-Symm thus provides a methodology for a more complete and detailed study of the role of symmetry in tertiary protein structure. Availability CE-Symm can be run from the web at http://source.rcsb.org/jfatcatserver/symmetry.jsp. Source code and software binaries are also available under the GNU Lesser General Public License (v. 2.1) at https://github.com/rcsb/symmetry. An interactive census of domains identified as symmetric by CE-Symm is available from: http://source.rcsb.org/jfatcatserver/scopResults.jsp.

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Section: Figurementioning

confidence: 99%

“… 7 GANGSTA+ using FSAR(fraction of sequentially aligned residues) ≥ 0.8, which the authors recommend [37] …”

Section: Figurementioning

confidence: 99%

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Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

Myers-Turnbull

Bliven

Rose

et al. 2014

Journal of Molecular Biology

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“…MASS (5), TOPOFIT (6), SCALI (7), GANGSTA (8,9) and others (10,11). Recently, GANGSTA+ (12) was introduced and we presented several applications such as the detection of non-sequential structural analogs for novel protein folds (12), the detection of symmetric (13) and circular permuted (14,15) protein structures in the protein databases and a large-scale evaluation of all-against-all sequence and structure alignments (16). …”

Section: Introductionmentioning

confidence: 99%

GIS: a comprehensive source for protein structure similarities

Guerler

Knapp

2010

Nucleic Acids Research

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A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. α-helices and β-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10 000 protein domains yielding about 55 × 106 possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

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“…Unfortunately, this is rarely the case (unless we are comparing backbone atoms) and thus some kind of atom mapping is required to establish atom equivalence. In the same context, frequently forgotten issues are resolving positional equivalence of atoms in side chains allowing symmetry ambiguity [1] or accounting for internal symmetry [2-7]. Another key issue is the comparison of proteins with flexible regions or partial overlap, where a direct RMSD calculation provides an unrealistic measure of the similarity.…”

Section: Introductionmentioning

confidence: 99%

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

et al. 2013

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BackgroundMost of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser.ResultsBioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin.ConclusionsBioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuper.

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Symmetric Structures in the Universe of Protein Folds

Cited by 15 publications

References 21 publications

Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

GIS: a comprehensive source for protein structure similarities

BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

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