Analysis of sequence repeats of proteins in the PDB

Rajathei, David Mary; Selvaraj, Samuel

doi:10.1016/j.compbiolchem.2013.09.001

Cited by 15 publications

(12 citation statements)

References 44 publications

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“…It has been shown that the presence of Shine-Dalgarno-like sequence in mRNA causes translational pause with deleterious consequences (Li et al, 2012). Other possible underlying biology of longer-range correlation and periodicity include the nucleosome positioning within exons (Andersson et al, 2009), and periodicity/repeats in protein sequences (Marcotte et al, 1998;Korotkova et al, 1999;Heger and Holmm, 2000;Rajathei and Selvaraj, 2013).…”

Section: Within-frame Correlation In Cds Subsequencesmentioning

confidence: 98%

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes

Cocho

Miramóntes

Mansilla

et al. 2014

Computational Biology and Chemistry

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Section: Within-frame Correlation In Cds Subsequencesmentioning

confidence: 98%

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes

Cocho

Miramóntes

Mansilla

et al. 2014

Computational Biology and Chemistry

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“…Homology modeling was performed using the Swiss-Model (Arnold et al, 2006), and PDBeFold server (Mary Rajathei and Selvaraj, 2013) was used for the structural superimposition.…”

Section: Structural Modelingmentioning

confidence: 99%

Bacillus subtilis SalA is a phosphorylation‐dependent transcription regulator that represses scoC and activates the production of the exoprotease AprE

Derouiche

Shi

Bidnenko

et al. 2015

Molecular Microbiology

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SummaryBacillus subtilis Mrp family protein SalA has been shown to indirectly promote the production of the exoprotease AprE by inhibiting the expression of scoC, which codes for a repressor of aprE. The exact mechanism by which SalA influences scoC expression has not been clarified previously. We demonstrate that SalA possesses a DNA-binding domain (residues 1-60), which binds to the promoter region of scoC. The binding of SalA to its target DNA depends on the presence of ATP and is stimulated by phosphorylation of SalA at tyrosine 327. The B. subtilis protein-tyrosine kinase PtkA interacts specifically with the C-terminal domain of SalA in vivo and in vitro and is responsible for activating its DNA binding via phosphorylation of tyrosine 327. In vivo, a mutant mimicking phosphorylation of SalA (SalA Y327E) exhibited a strong repression of scoC and consequently overproduction of AprE. By contrast, the nonphosphorylatable SalA Y327F and the ΔptkA exhibited the opposite effect, stronger expression of scoC and lower production of the exoprotease. Interestingly, both SalA and PtkA contain the same ATP-binding Walker domain and have thus presumably arisen from the common ancestral protein. Their regulatory interplay seems to be conserved in other bacteria.

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“…A complete analysis of PDB sequences using RADAR is reported in Rajathei and Selvaraj ( 2013 ), where a good correlation among PTR, structural similarity, and functionally involved residues is highlighted.…”

Section: Correlation Of Protein-tr With Other Protein Propertiesmentioning

confidence: 99%

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

Pellegrini

2015

Front. Bioeng. Biotechnol.

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Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR.

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Analysis of sequence repeats of proteins in the PDB

Cited by 15 publications

References 44 publications

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: The role of mixing statistics and frame shift of neighboring genes

Bacillus subtilis SalA is a phosphorylation‐dependent transcription regulator that represses scoC and activates the production of the exoprotease AprE

Tandem Repeats in Proteins: Prediction Algorithms and Biological Role

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