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Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein.
TLDR
Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions.
A Mycobacterial Cyclic AMP Phosphodiesterase That Moonlights as a Modifier of Cell Wall Permeability*
TLDR
Rv0805 may play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.
Structural and conformational analysis of glycan moieties in situ on isotopically 13C, 15N-enriched recombinant human chorionic gonadotropin.
TLDR
The disposition of this glycan with respect to the protein backbone suggests that glycosylation maintains full biological activity of hCG either by interacting with a lectin-like region of the h CG receptor or by reducing the affinity of the hormone for the hCG receptor and preventing its down-regulation.
Structural models in the assessment of protein druggability based on HTS data
TLDR
This study uses high-throughput screening results on various targets, to obtain mathematical predictive models in which a minimal set of structural parameters significantly contributing to the hit rates or the affinity of the protein binding pockets for small molecular entities, is identified.
Catalytic significance of the specificity of divalent cations as KS* and kcat* cofactors for secreted phospholipase A2.
TLDR
It is proposed that the higher ground state stability of the E*CS complex with the inhibitory cations increases the effective activation energy, and considerable plasticity in the calcium binding and catalytic site environment is suggested.
Structure of a glycoconjugate in solution and in complex with an antibody Fv fragment.
TLDR
Quantitation of the NOE data with a full-relaxation matrix approach showed that the antibody selects a conformation from the solution repertoire which does not correspond with either of the two lowest energy conformations of the free glycan, and the internal energy of the glycan in the bound state is estimated to be at most approximately 15 kcal/mol higher than the global minimum energy conformation.
Methyl side-chain dynamics in proteins using selective enrichment with a single isotopomer.
TLDR
Chemical synthesis of amino acids containing a pure (13)CHD(2) isotopomer is described that overcomes the problem of loss of resolution and sensitivity in side-chain relaxation measurements on mouse major urinary protein selectively enriched with valine.
Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach.
TLDR
The dinucleotide substrate UpA is fitted into the active site of RNase A and several possible substrate conformations are investigated and the binding modes have been selected based on Contact Criteria, which ensure energy minimized in coordinate space and interactions.
Evaluation of CoA biosynthesis proteins of Mycobacterium tuberculosis as potential drug targets.
TLDR
It was found that coaD could only be inactivated in the presence of an additional gene copy, confirming it to be an essential gene and that CoaE was also essential for the survival of M. tuberculosis.
Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes.
TLDR
The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119 as well as guiding the ligand binding by forming a pocket.
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