Human steroid 5α-reductase 2 (SRD5A2) is an integral membrane enzyme in steroid metabolism and catalyzes the reduction of testosterone to dihydrotestosterone. Mutations in the SRD5A2 gene have been linked to 5α-reductase deficiency and prostate cancer. Finasteride and dutasteride, as SRD5A2 inhibitors, are widely used antiandrogen drugs for benign prostate hyperplasia. The molecular mechanisms underlying enzyme catalysis and inhibition for SRD5A2 and other eukaryotic integral membrane steroid reductases remain elusive due to a lack of structural information. Here, we report a crystal structure of human SRD5A2 at 2.8 Å, revealing a unique 7-TM structural topology and an intermediate adduct of finasteride and NADPH as NADP-dihydrofinasteride in a largely enclosed binding cavity inside the transmembrane domain. Structural analysis together with computational and mutagenesis studies reveal the molecular mechanisms of the catalyzed reaction and of finasteride inhibition involving residues E57 and Y91. Molecular dynamics simulation results indicate high conformational dynamics of the cytosolic region that regulate NADPH/NADP+ exchange. Mapping disease-causing mutations of SRD5A2 to our structure suggests molecular mechanisms for their pathological effects. Our results offer critical structural insights into the function of integral membrane steroid reductases and may facilitate drug development.

Water dynamics in the solvation shell around biomolecules plays a vital role in their stability, function, and recognition processes. Although extensively studied through various experimental and computational methods, dynamical time scales of water near DNA is highly debated. The residence time of water is one such dynamical quantity that has been probed rarely around DNA using computational methods. Moreover, the effect of local DNA sequence variation in water residence time has also not been addressed. Using 20 DNA systems with different sequences, we capture here the mean residence time (MRT) of water molecules around 360 different sites in the major and minor grooves of DNA. Thus, we show that a distribution of time scales exists even for a regular structure of DNA, reflecting the effect of chemistry, topography, and other factors governing dynamics of water. We used the stable state picture (SSP) formalism to calculate MRT that avoids the effect of transient recrossing. Results obtained from simulations agree well with experiments done on a few specific systems at a similar temperature. Most importantly, we find that although the groove width and depth influence water time scale, MRT of water is always longer in the middle of the DNA, in agreement with NMR experiments. We propose a simple kinetic model of water escape from DNA where water molecules move along the DNA and perpendicular to it in both the first and second solvation shell before it escapes to bulk. We show that this simple kinetic model captures both the time scale and the position dependence of MRT of water around DNA. This study thus portrays the origin and a measure of heterogeneity in water dynamics around DNA and provides a fresh perspective in the ongoing debate on water dynamical time scales around DNA.

Cytochrome c oxidase (CcO) is a redox-driven proton pump that powers aerobic respiratory chains. We show here by multi-scale molecular simulations that a protonated water cluster near the active site is likely to serve as the transient proton-loading site (PLS) that stores a proton during the pumping process. The pKa of this water cluster is sensitive to the redox states of the enzyme, showing distinct similarities to other energy converting proton pumps.

Despite Nipah virus outbreaks having high mortality rates (>70% in Southeast Asia), there are no licensed drugs against it. In this study, we have considered all 9 Nipah proteins as potential therapeutic targets and computationally identified 4 putative peptide inhibitors (against G, F and M proteins) and 146 small molecule inhibitors (against F, G, M, N, and P proteins). The computations include extensive homology/ab initio modeling, peptide design and small molecule docking. An important contribution of this study is the increased structural characterization of Nipah proteins by approximately 90% of what is deposited in the PDB. In addition, we have carried out molecular dynamics simulations on all the designed protein-peptide complexes and on 13 of the top shortlisted small molecule ligands to check for stability and to estimate binding strengths. Details, including atomic coordinates of all the proteins and their ligand bound complexes, can be accessed at http://cospi.iiserpune.ac.in/Nipah. Our strategy was to tackle the development of therapeutics on a proteome wide scale and the lead compounds identified could be attractive starting points for drug development. To counter the threat of drug resistance, we have analysed the sequences of the viral strains from different outbreaks, to check whether they would be sensitive to the binding of the proposed inhibitors.