Biology subjects

Dubey, K. D.

Publications and source records attributed to Dubey, K. D..

3 recordsLinked to original sources

bioRxiv2022

Unravelling Key Interactions and the Mechanism of Demethylation during hAGT mediated DNA Repair via Simulations

Alkylating agents possess the biggest threat to the genomic integrity of cell by damaging DNA bases through regular alkylation. Such damages are repaired by several automated machinery inside cell. O6-alkylguanine-DNA alkyltransferase (AGT) is such an enzyme which performs the direct repair of an alkylated guanine base by transferring the alkyl group to a Cysteine residue. In the present study using extensive MD simulations and hybrid QM/MM calculations, we have investigated the key interactions between the DNA lesion and the hAGT enzyme and elucidated the mechanisms of the demethylation of the guanine base. Our simulation shows that the DNA lesion is electrostatically stabilized by the enzyme and the Arg135 of hAGT enzyme provides the main driving force to flip the damaged base into the enzyme. The QM/MM calculations show demethylation of damaged base as a three step in thermodynamically feasible and irreversible manner. Our calculations show that the final products forms via Tyr114 in a facile way in contrast to the previously proposed Lys-mediated route.

biochemistry↗

bioRxiv2022

Combined MD and QM/MM Calculations reveal Allostery Driven Promiscuity in Dipeptide Epimerases of Enolase Family

The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in the enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a new way to enhance the promiscuity, i.e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.

biochemistry↗

bioRxiv2019

Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD Simulation

CD4-mimetic HIV-1 entry inhibitors are small sized molecules which imitate similar conformational flexibility in gp120 as CD4 receptor, the mechanism of the conformational flexibility instigated by these small sized inhibitors, however, is little known. Likewise, the effect of the antibody on the function of these inhibitors is also less studied. In this study, we present a thorough inspection of the mechanism of the conformational flexibility induced by a CD4-mimetic inhibitor, NBD-557, using Molecular Dynamics Simulations and free energy calculations. Our result shows a functional importance of Asn239 in substrate instigated conformational dynamics in gp120. The MD simulations of Asn239Gly mutant provide a less dynamic gp120 in the presence of NBD-557 without incapacitating the binding enthalpy of NBD-557. The MD simulations of complex with the antibody clearly shows the enhanced affinity of NBD-557 due to the presence of the antibody which is in good agreement with experimental Isothermal Titration Calorimetry results (Biochemistry 2006, 45, 10973-10980).

biochemistry↗