Analysis of sequence repeats of proteins in the PDB |
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| Institution: | 1. Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico;2. Industrial Biotechnology, CIATEJ AC, Zapopan Unit, CONACYT, Camino Arenero 1227, Col. El Bajío del Arenal, CP 45019 Zapopan, Jalisco, Mexico;3. The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, 350 Community Dr. Manhasset, NY 11030, USA;4. Molecular Biology Laboratory, Biosafety Area, Medical and Pharmaceutical Biotechnology, Guadalajara Unit, CIATEJ AC, CONACYT, Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico;1. Department of Entomology, Faculty of Science, Cairo University, P. O. Box 12613, Giza, Egypt;2. Key Lab for Biological Control of the Ministry of Agriculture, Department of Entomology, China Agricultural University, Beijing, 100193, PR China;3. Unité DGIMI UMR INRA-UM 1333, Université Montpellier, Place Eugène Bataillon, Montpellier, France;1. International Institute of Physics, Universidade Federal do Rio Grande do Norte, Campus Universitário, Lagoa Nova, Natal-RN 59078-970, Brazil;2. Departamento de Ciencias Físicas, Universidad Andres Bello, Sazié 2212, Santiago, Chile;3. Departamento de Física, Universidade Federal da Paraíba, Caixa Postal 5008, 58051-970, Joao Pessoa, PB, Brazil;1. Department of Pharmacy, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, India;2. School of Pharmaceutical Sciences, Bahra University, Waknaghat, Solan, Himachal Pradesh, India;1. School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK;2. Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA 92521, USA |
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| Abstract: | Internal repeats in protein sequences play a significant role in the evolution of protein structure and function. Applications of different bioinformatics tools help in the identification and characterization of these repeats. In the present study, we analyzed sequence repeats in a non-redundant set of proteins available in the Protein Data Bank (PDB). We used RADAR for detecting internal repeats in a protein, PDBeFOLD for assessing structural similarity, PDBsum for finding functional involvement and Pfam for domain assignment of the repeats in a protein. Through the analysis of sequence repeats, we found that identity of the sequence repeats falls in the range of 20–40% and, the superimposed structures of the most of the sequence repeats maintain similar overall folding. Analysis sequence repeats at the functional level reveals that most of the sequence repeats are involved in the function of the protein through functionally involved residues in the repeat regions. We also found that sequence repeats in single and two domain proteins often contained conserved sequence motifs for the function of the domain. |
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| Keywords: | Sequence repeats PDB Structure Function Domain |
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