Nicholus Bhattacharjee

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The recently developed methods of constant pH molecular dynamics directly captures the correlation between protonation and conformation to probe protein structure, function, and dynamics. In this work, we investigate the effect of pH on the conformational properties of the protein human α-lactalbumin. Constant pH simulations at both acidic and alkaline(More)
Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a(More)
Hydration layer water molecules play important structural and functional roles in proteins. Despite being a critical component in biomolecular systems, characterizing the properties of hydration water poses a challenge for both experiments and simulations. In this context we investigate the local structure of hydration water molecules as a function of the(More)
The l,d-transpeptidases, Ldts, catalyze peptidoglycan cross-linking in β-lactam-resistant mutant strains of several bacteria, including Enterococcus faecium and Mycobacterium tuberculosis. Although unrelated to the essential d,d-transpeptidases, which are inactivated by the β-lactam antibiotics, they are nevertheless inhibited by the carbapenem antibiotics,(More)
This work is a first attempt to characterise the conformational preference of structurally ambivalent helices in terms of their backbone conformational entropy. Ambivalent sequences conform to two different secondary structures (helix-sheet or helix-random coil or sheet-random coil, etc.) in two different proteins. For variable ambivalent helices, the(More)
Analysis of known protein structures reveals that identical sequence fragments in proteins can adopt different secondary structure conformations. The extent of this conformational diversity is influenced by various factors like the intrinsic sequence propensity, sequence context and other environmental factors such as pH, site directed mutations or(More)
Water on a protein surface plays a key role in determining the structure and dynamics of proteins. Compared to the properties of bulk water, many aspects of the structure and dynamics of the water surrounding the proteins are less understood. It is interesting therefore to explore how the properties of the water within the solvation shell around the peptide(More)
The synthesis of all-cis amide (NtBu)-glycine oligomers up to 15 residues long by a blockwise coupling approach is reported. The structure and dynamical behavior of these peptoids have been studied by X-ray crystallography, NMR and molecular modeling. Analyses reveal that the folding of these oligomers is driven by weak CH···O=C hydrogen bonding along the(More)
Mutation of amino acid sequences in a protein may have diverse effects on its structure and function. Point mutations of even a single amino acid residue in the helices of the non-redundant database may lead to sequentially identical peptides which adopt different secondary structures in different proteins. However, various physico-chemical factors which(More)
Secondary structural elements like alpha-helix and beta-sheet constitute the major components of proteins. Here we present a systematic position wise analysis of the structural and sequence characteristics of alpha-helices and beta-sheets. Helix and sheet are found to follow a complementary distribution pattern along the protein chain length. We have(More)