Circular permuted proteins in the universe of protein folds

@article{SchmidtGoenner2010CircularPP,
  title={Circular permuted proteins in the universe of protein folds},
  author={Tobias Schmidt-Goenner and Aysam Guerler and Bjoern Kolbeck and Ernst-Walter Knapp},
  journal={Proteins: Structure},
  year={2010},
  volume={78}
}
Finding and identifying circular permuted protein pairs (CPP) is one of the harder tasks for structure alignment programs, because of the different location of the break in the polypeptide chain connectivity. The protein structure alignment tool GANGSTA+ was used to search for CPPs in a database of nearly 10,000 protein structures. It also allows determination of the statistical significance of the occurrence of circular permutations in the protein universe. The number of detected CPPs was… 
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TLDR
The non-sequential structure alignment algorithm GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), and the resulting protein structure alignments are provided as a public web-based service, named GANGstA+ Internet Services (GIS).
An Investigation into the Robustness of Algorithms Designed for Efficient Protein Structure Alignment across Databases
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It is argued that the dynamic programming framework has a natural affinity to accommodate studies of robustness under perturbations of the data, and numerical tests are reported to validate this observation.
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TLDR
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TLDR
The results suggest that MICAN is a highly effective tool for automatically detecting non-trivial structural relationships of proteins, such as circular permutations and segment-swapping, many of which have been identified manually by human experts so far.
Protein topology determines substrate-binding mechanism in homologous enzymes.
Non-sequential protein structure alignment based on variable length AFPs using the maximal clique
TLDR
A new non-sequential protein structure alignment method based on Aligned Fragment Pairs and the maximal clique and based on variable length AFPs which can better represent the local structure similarities and can also greatly speed up the computations is proposed.
Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust
TLDR
The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs) is robust against both parametric and structural variation.
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TLDR
Construction of a Thermotoga neapolitana adenylate kinase (AK) library using PERMUTE revealed that this approach produces vectors that express circularly permuted proteins with distinct sequence diversity from existing methods.
Fold Evolution before LUCA: Common Ancestry of SH3 Domains and OB Domains
TLDR
Relationships between SH3 and OB domains of ribosomal proteins, initiation, and elongation factors are explored using a combined sequence- and structure-based approach and it is demonstrated that an ancestral reconstruction of a permuted SH3 sequence folds into an OB structure, and an ancestral reconstructing of an permuted OB sequence folding into a SH3 structure.
Structure prediction and functional analysis of a non-permutated lectin from Dioclea grandiflora.
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References

SHOWING 1-10 OF 56 REFERENCES
Circularly permuted proteins in the protein structure database
  • J. Jung, B. Lee
  • Biology
    Protein science : a publication of the Protein Society
  • 2001
TLDR
A systematic search for all protein pairs in the SCOP 90% id domain database that become structurally superimposable when the sequence of one of the pairs is circularly permuted finds that 47% of all protein domains are superimposition to at least one other protein domain in the database after their sequence is circulary permuted.
Naturally occurring circular permutations in proteins.
TLDR
The small number of cases of circular permutation suggests that there is no mechanism of local genetic manipulation that can induce circular permutations; most examples observed seem to result from fusion of functional units.
Symmetric Structures in the Universe of Protein Folds
TLDR
The automated detection of rotational symmetries within a representative set of nearly 10,000 nonhomologous protein structures highlighted that the generation of symmetric, i.e., repetitive, protein structures is one of nature's major strategies to explore the universe of possible protein folds.
OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures
TLDR
This work has recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10−5), including structural permutations at all levels of complexity, which can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins.
Rapid motif-based prediction of circular permutations in multi-domain proteins
TLDR
An algorithm, RASPODOM, is developed, which is based on the classical recursive alignment scheme, and works several orders of magnitude faster than a reimplementation of the existing CP detection algorithm working on strings of amino acids, produces virtually no false positives and allows the discrimination of true CPs from 'intermediate' CPs (iCPs).
CPDB: a database of circular permutation in proteins
TLDR
CPDB is described, the first CP DataBase, a hierarchical categorization in which pairs of circular permutants are grouped into CP clusters, which are further grouped into folds and in turn classes that can be useful in protein folding and evolution studies.
SSAP: sequential structure alignment program for protein structure comparison.
Novel protein folds and their nonsequential structural analogs
TLDR
It is demonstrated that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three‐dimensional structure and newly determined protein structures that possess a new fold.
Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation
TLDR
The method, called FASE (flexible alignment of secondary structure elements), was tested on well-known data and various standard problems from the literature and shows that FASE is able to find remote and weak similarities consistently using a reasonable run time.
A simple algorithm for detecting circular permutations in proteins
TLDR
A simple and efficient algorithm that runs in time N2 is presented, based on duplicating one of the two sequences, and then performing a modified version of the standard dynamic programming algorithm, that performs very well.
...
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