Identification and Analysis of Novel Amino-Acid Sequence Repeats in<i>Bacillus anthracis</i>str.<i>Ames</i>Proteome Using Computational Tools

Hemalatha, G. R.; Rao, D. V. Sudhakar; Guruprasad, Lalitha

doi:10.1155/2007/47161

Cited by 2 publications

(2 citation statements)

References 33 publications

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“…The RADAR program is efficient for ab initio detection of repeats in the query sequence. Since repeats of larger lengths are domain repeats (Hemalatha, Rao, & Guruprasad, 2007), we considered the subset of proteins with repeat pairs of length >45 and having continuous PDB coordinates for the present analysis. These proteins were searched against pfam database (Punta et al, 2012) to assign their domains regions.…”

Section: Data-set and Identification Of Internal Repeatsmentioning

confidence: 99%

Conservation of inter-residue interactions and prediction of folding rates of domain repeats

Mary

Saravanan

Selvaraj

2014

Journal of Biomolecular Structure and Dynamics

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Domains are the main structural and functional units of larger proteins. They tend to be contiguous in primary structure and can fold and function independently. It has been observed that 10-20% of all encoded proteins contain duplicated domains and the average pairwise sequence identity between them is usually low. In the present study, we have analyzed the structural similarity between domain repeats of proteins with known structures available in the Protein Data Bank using structure-based inter-residue interaction measures such as the number of long-range contacts, surrounding hydrophobicity, and pairwise interaction energy. We used RADAR program for detecting the repeats in a protein sequence which were further validated using Pfam domain assignments. The sequence identity between the repeats in domains ranges from 20 to 40% and their secondary structural elements are well conserved. The number of long-range contacts, surrounding hydrophobicity calculations and pairwise interaction energy of the domain repeats clearly reveal the conservation of 3-D structure environment in the repeats of domains. The proportions of mainchain-mainchain hydrogen bonds and hydrophobic interactions are also highly conserved between the repeats. The present study has suggested that the computation of these structure-based parameters will give better clues about the tertiary environment of the repeats in domains. The folding rates of individual domains in the repeats predicted using the long-range order parameter indicate that the predicted folding rates correlate well with most of the experimentally observed folding rates for the analyzed independently folded domains.

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Section: Data-set and Identification Of Internal Repeatsmentioning

confidence: 99%

Conservation of inter-residue interactions and prediction of folding rates of domain repeats

Mary

Saravanan

Selvaraj

2014

Journal of Biomolecular Structure and Dynamics

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“…The folded domains can either serve as modules for building up large assemblies or provide specific catalytic enzyme functions or bindings of the proteins. It has been found that repeats of a length >50 residues often correspond to conserved regions that are present in proteins as single or multiple copies for the function of the proteins (Hemalatha et al, 2007). Our analysis of sequence repeats of the proteins with known 3D structures in the PDB (Berman et al, 2014) has shown that they retain similar folds in spite of divergences, in order to conserve the structure and function of the proteins and, repeats that are in the single/two domains from the same family contain conserved motifs for the function of the proteins (Mary Rajathei and Selvaraj, 2013).…”

Section: Introductionmentioning

confidence: 99%

Identification and Analysis of Long Repeats of Proteins at the Domain Level

Rajathei

Parthasarathy

Selvaraj

2019

Front. Bioeng. Biotechnol.

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Amino acid repeats play an important role in the structure and function of proteins. Analysis of long repeats in protein sequences enables one to understand their abundance, structure and function in the protein universe. In the present study, amino acid repeats of length >50 (long repeats) were identified in a non-redundant set of UniProt sequences using the RADAR program. The underlying structures and functions of these long repeats were carried out using the Gene3D for structural domains, Pfam for functional domains and enzyme and non-enzyme functional classification for catalytic and binding of the proteins. From a structural perspective, these long repeats seem to predominantly occur in certain architectures such as sandwich, bundle, barrel, and roll and within these architectures abundant in the superfolds. The lengths of the repeats within each fold are not uniform exhibiting different structures for different functions. We also observed that long repeats are in the domain regions of the family and are involved in the function of the proteins. After grouping based on enzyme and non-enzyme classes, we observed the abundant occurrence of long repeats in specific catalytic and binding of the proteins. In this study, we have analyzed the occurrence of long repeats in the protein sequence universe apart from well-characterized short tandem repeats in sequences and their structures and functions of the proteins at the domain level. The present study suggests that long repeats may play an important role in the structure and function of domains of the proteins.

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Identification and Analysis of Novel Amino-Acid Sequence Repeats inBacillus anthracisstr.AmesProteome Using Computational Tools

Cited by 2 publications

References 33 publications

Conservation of inter-residue interactions and prediction of folding rates of domain repeats

Conservation of inter-residue interactions and prediction of folding rates of domain repeats

Identification and Analysis of Long Repeats of Proteins at the Domain Level

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