• B Jayaram

      Articles written in Journal of Biosciences

    • Free energy simulations: Applications to the study of liquid water, hydrophobic interactions and solvent effects on conformational stability

      D L Beveridge M Mezei G Ravishanker B Jayaram

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      Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed to identify stabilizing factors. Implications of result with respect to the structural chemistry of proteins and nucleic acids is considered.

    • ProRegIn: A regularity index for the selection of native-like tertiary structures of proteins

      Lipi Thukral Sandhya R Shenoy Kumkum Bhushan B Jayaram

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      Automated protein tertiary structure prediction from sequence information alone remains an elusive goal to computational prescriptions. Dividing the problem into three stages viz. secondary structure prediction, generation of plausible main chain loop dihedrals and side chain dihedral optimization, considerable progress has been achieved in our laboratory (http://www.scfbio-iitd.res.in/bhageerath/index.jsp) and elsewhere for proteins with less than 100 amino acids. As a part of our on-going efforts in this direction and to facilitate tertiary structure selection/rejection in containing the combinatorial explosion of trial structures for a specified amino acid sequence, we describe here a web-enabled tool ProRegIn (Protein Regularity Index) developed based on the regularity in the 𝛷, Ψ dihedral angles of the amino acids that constitute loop regions. We have analysed the dihedrals in loop regions in a non-redundant dataset of 7351 proteins drawn from the Protein Data Bank and categorized them as helix-like or sheet-like (regular) or irregular. We noticed that the regularity thus defined exceeds 86% for 𝛷 barring glycine and 70% for Ψ for all the amino acid side chains including glycine, compelling us to reexamine the conventional view that loops are irregular regions structurally. The regularity index is presented here as a simple tool that finds its application in protein structure analysis as a discriminatory scoring function for rapid screening before the more compute intensive atomic level energy calculations could be undertaken. The tool is made freely accessible over the internet at www.scfbio-iitd.res.in/software/proregin.jsp.

    • Editorial: Nucleic acids in disease and disorder: Understanding the language of life emerging from the `ABC' of DNA

      Manju Bansal B Jayaram Aditya Mittal

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    • DNA-energetics-based analyses suggest additional genes in prokaryotes

      Garima Khandelwal Jalaj Gupta B Jayaram

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      We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.

    • A possible molecular metric for biological evolvability

      Aditya Mittal B Jayaram

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      Proteins manifest themselves as phenotypic traits, retained or lost in living systems via evolutionary pressures. Simply put, survival is essentially the ability of a living system to synthesize a functional protein that allows for a response to environmental perturbations (adaptation). Loss of functional proteins leads to extinction. Currently there are no universally applicable quantitative metrics at the molecular level for either measuring ‘evolvability’ of life or for assessing the conditions under which a living system would go extinct and why. In this work, we show emergence of the first such metric by utilizing the recently discovered stoichiometric margin of life for all known naturally occurring (and functional) proteins. The constraint of having well-defined stoichiometries of the 20 amino acids in naturally occurring protein sequences requires utilization of the full scope of degeneracy in the genetic code, i.e. usage of all codons coding for an amino acid, by only 11 of the 20 amino acids. This shows that the non-availability of individual codons for these 11 amino acids would disturb the fine stoichiometric balance resulting in non-functional proteins and hence extinction. Remarkably, these amino acids are found in close proximity of any given amino acid in the backbones of thousands of known crystal structures of folded proteins. On the other hand, stoichiometry of the remaining 9 amino acids, found to be farther/distal from any given amino acid in backbones of folded proteins, is maintained independent of the number of codons available to synthesize them, thereby providing some robustness and hence survivability.

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