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S Gore
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Volume 32 Issue 5 August 2007 pp 921-928 Articles
V S Gowri K Anamika S Gore N Srinivasan
Protein structural alignments are generally considered as ‘golden standard’ for the alignment at the level of amino acid residues. In this study we have compared the quality of pairwise and multiple structural alignments of about 5900 homologous proteins from 718 families of known 3-D structures. We observe shifts in the alignment of regular secondary structural elements (helices and strands) between pairwise and multiple structural alignments. The differences between pairwise and multiple structural alignments within helical and 𝛽-strand regions often correspond to 4 and 2 residue positions respectively. Such shifts correspond approximately to “one turn” of these regular secondary structures. We have performed manual analysis explicitly on the family of protein kinases. We note shifts of one or two turns in helix-helix alignments obtained using pairwise and multiple structural alignments. Investigations on the quality of the equivalent helix-helix, strand-strand pairs in terms of their residue side-chain accessibilities have been made. Our results indicate that the quality of the pairwise alignments is comparable to that of the multiple structural alignments and, in fact, is often better. We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis.
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Journal of Biosciences
Volume 48, 2023
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Journal of Biosciences | News
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To trigger further research on plant mitochondria, the Journal of Biosciences is bringing out a special issue titled "Plant Mitochondria: Properties and Interactions with Other Organelles".
Plant mitochondria are quite distinct and have unique features, such as a cyanide-insensitive alternate pathway. They also interact with chloroplasts to optimize photosynthetic carbon assimilation.
Submissions are welcome until 30 July 2023. The contributions can be original articles, short communications, reviews, or mini-reviews on any topic related to plant mitochondria.
Authors can submit their articles online at https://www.editorialmanager.com/jbsc/default2.aspx
Posted on April 12, 2023< -
Editorial Note on Continuous Article Publication
Posted on July 25, 2019Click here for Editorial Note on CAP Mode
Forthcoming Special issue.
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