Vigneshwar Ramakrishnan

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Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation(More)
Sequence-specific binding of proteins to DNA is essential for almost all the cellular processes like transcription, translation, replication, etc. One among the various mechanisms that has been identified so far that contributes to the specificity in protein-DNA interaction is the DNA conformational change. Electrostatic neutralization of the phosphate(More)
Intracellular crowding in biological systems is usually mimicked in in vitro experiments by adding single crowders at high volume fractions, without taking into consideration the polydispersity of the crowders in the cellular environment. Here, we develop a molecular thermodynamic formalism to examine the effects of size-polydispersity of crowders on(More)
Protein-DNA interactions are an important class of biomolecular interactions inside the cell. Delineating the mechanisms of protein-DNA interactions and more specifically, how proteins search and bind to their specific cognate sequences has been the quest of many in the scientific community. Restriction enzymes have served as useful model systems to this(More)
Water plays an important role in protein-DNA interactions. Here, we examine using molecular dynamics simulations the differences in the dynamic and thermodynamic properties of water in the interfacial and intercalating regions of EcoRI bound to the cognate and to a minimally mutated noncognate DNA chain. The results show that the noncognate complex is not(More)
Human Serum Albumin (HSA) has been suggested to be an alternate biomarker to the existing Hemoglobin-A1c (HbA1c) marker for glycemic monitoring. Development and usage of HSA as an alternate biomarker requires the identification of glycation sites, or equivalently, glucose-binding pockets. In this work, we combine molecular dynamics simulations of HSA and(More)
The dynamics of a protein plays an important role in protein functionality. Here, we examine the differences in the dynamics of a minimally restructuring protein, EcoRI, when it is bound to its cognate DNA and to a noncognate sequence which differs by just a single basepair. Molecular dynamics simulations of the complexes and essential dynamics analyses(More)
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