ArticleBMC bioinformatics2014
Identifying tandem Ankyrin repeats in protein structures.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 29 citations in OpenAlex.
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- Diversity and features of proteins with structural repeats.Biophysical reviews · 2023Review
- Sequence and Structure-Based Analyses of Human Ankyrin Repeats.Molecules (Basel, Switzerland) · 2022Article
- DbStRiPs: Database of structural repeats in proteins.Protein science : a publication of the Protein Society · 2022Article
- Understanding structural variability in proteins using protein structural networks.Current research in structural biology · 2022Article
- Search for Highly Divergent Tandem Repeats in Amino Acid Sequences.International journal of molecular sciences · 2021Article
- ANKRD22, a novel tumor microenvironment-induced mitochondrial protein promotes metabolic reprogramming of colorectal cancer cells.Theranostics · 2020Article
- PRIGSA2: Improved version of protein repeat identification by graph spectral analysis.Journal of biosciences · 2020Article
- ANKRD22 is involved in the progression of prostate cancer.Oncology letters · 2019Article
- NAPS update: network analysis of molecular dynamics data and protein-nucleic acid complexes.Nucleic acids research · 2019Article
- ANKRD22 promotes progression of non-small cell lung cancer through transcriptional up-regulation of E2F1.Scientific reports · 2017Article
- AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking.BMC bioinformatics · 2017Article
- In silico SNP analysis of the breast cancer antigen NY-BR-1.BMC cancer · 2016Article
- NAPS: Network Analysis of Protein Structures.Nucleic acids research · 2016Article
- Structural and Energetic Characterization of the Ankyrin Repeat Protein Family.PLoS computational biology · 2015Article
- Functional Analysis of the Pepper RING-Type E3 Ligase CaANKR1 Involved in Drought Stress Tolerance via Modulation of Abscisic Acid Signaling.Physiologia plantarumArticle
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTandem repetition of structural motifs in proteins is frequently observed across all forms of life. Topology of repeating unit and its frequency of occurrence are associated to a wide range of structural and functional roles in diverse proteins, and defects in repeat proteins have been associated with a number of diseases. It is thus desirable to accurately identify specific repeat type and its copy number. Weak evolutionary constraints on repeat units and insertions/deletions between them make their identification difficult at the sequence level and structure based approaches are desired. The proposed graph spectral approach is based on protein structure represented as a graph for detecting one of the most frequently observed structural repeats, Ankyrin repeat.
resultsIt has been shown in a large number of studies that 3-dimensional topology of a protein structure is well captured by a graph, making it possible to analyze a complex protein structure as a mathematical entity. In this study we show that eigen spectra profile of a protein structure graph exhibits a unique repetitive profile for contiguous repeating units enabling the detection of the repeat region and the repeat type. The proposed approach uses a non-redundant set of 58 Ankyrin proteins to define rules for the detection of Ankyrin repeat motifs. It is evaluated on a set of 370 proteins comprising 125 known Ankyrin proteins and remaining non-solenoid proteins and the prediction compared with UniProt annotation, sequence-based approach, RADAR, and structure-based approach, ConSole. To show the efficacy of the approach, we analyzed the complete PDB structural database and identified 641 previously unrecognized Ankyrin repeat proteins. We observe a unique eigen spectra profile for different repeat types and show that the method can be easily extended to detect other repeat types. It is implemented as a web server, AnkPred. It is freely available at 'bioinf.iiit.ac.in/AnkPred'.
conclusionsAnkPred provides an elegant and computationally efficient graph-based approach for detecting Ankyrin structural repeats in proteins. By analyzing the eigen spectra of the protein structure graph and secondary structure information, characteristic features of a known repeat family are identified. This method is especially useful in correctly identifying new members of a repeat family.
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