Abstract

Hydroxymethylbilane synthase (HMBS), the third enzyme in the heme biosynthesis pathway, catalyzes the formation of 1-hydroxymethylbilane (HMB) by a stepwise polymerization of four molecules of porphobilinogen (PBG) using the dipyrromethane (DPM) cofactor. The mechanism by which HMBS polymerizes four units of PBG has not been elucidated to date. In vitro and in silico studies on HMBS have suggested certain residues with catalytic importance, but their specific role in the catalysis is unclear. To understand the catalytic mechanism of HMBS, quantum mechanical (QM) calculations were performed on model systems obtained from the active site of the human HMBS enzyme. The addition of one molecule of PBG to the DPM cofactor is carried out in four steps: (1) protonation of the substrate, PBG; (2) deamination of PBG; (3) electrophilic addition of the deaminated substrate to the terminal pyrrole ring of the enzyme-bound DPM cofactor and (4) deprotonation of the carbon atom at the a-position of the second ring of DPM. Based on the energy profiles from the QM calculations on cluster models, R26 is proposed to be the best suitable proton donor to the PBG moiety, which aids in the deamination of the substrate. During the electrophilic addition step, the intermediate formed is stabilized by the carboxylate side chain of the D99 residue. In the final deprotonation step, an extra proton from the second ring of DPM is transferred to R26 via the carboxylate side chain of D99, thus completing one cycle of the catalytic mechanism. The residues in the cluster model seem to play an important role in obtaining accurate energy barriers. All the stationary points along the reaction pathway have been characterized using QM calculations. The rate limiting step for the complete mechanism is found to be the deamination of the PBG moiety. The results of this study provide a detailed understanding of the catalytic mechanism and would help design future studies aimed at modulating the activity of HMBS

Abstract

Understanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.

Abstract

Understanding synergistic effect by calculating electronic structure is essential to fine-tune the catalytic properties of bimetallic nanoalloy clusters which might be used for design of novel efficient catalysts. Density functional theory PBE0 calculations were performed to investigate the structure and energetics of various intermediates involved in the CO oxidation reaction catalyzed by Au3-xYx (x= 0–3 and Y denotes Ag or, Pt or, Pd) trimeric clusters through two possible pathways: Eley-Rideal (ER) and Langmuir-Hinshelwood (LH). The results of this investigation show that the catalytic behavior of the nanocluster highly depends on its composition and the reaction site taken into consideration. The most active reaction centres of goldsilver, gold-palladium, gold-platinum clusters are gold, palladium and platinum atoms respectively. The gold-silver clusters and AuPt2 prefer ER mechanism whereas, gold-palladium and Au2Pt selectively favour LH mechanism in comparison to the other. Bimetallic clusters, in general, are more efficient in comparison to their pristine mono-metallic counterparts, in activating the OO bond for the reaction and have relatively easy CO2 dissociation. Overall results indicate that the alloyed clusters could potentially have a better catalytic activity as compared to pure gold clusters for CO oxidation at low temperatures.

Abstract

We developed a set of conformationally locked molecules each of which makes a single CH⋯O H-bond/short contact and has different electron density at the acceptor oxygen atom. The downfield shift of the 1H NMR signals due to the hydrogen involved in the CH⋯O H-bond varied from 0.93–1.6 ppm, and the magnitude of Δδ is in correlation with the hybridization state of the acceptor oxygen and with the CH⋯O H-bond strengths quantified using a computational method.

Abstract

Urea-assisted denaturation of protein and RNA has been shown to be a valuable tool to study their stabilities and folding phenomena. It has been shown that stacking interactions between nucleobases and urea are one of the driving forces of denaturation. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated by performing high-level quantum calculations (RI-MP2/aug-ccpVDZ level) on a few thousands of model systems. Four systems were considered based on the RNA nucleobases (GUA, ADE, CYT, and URA) for the investigation. For each system, a set of models were designed to study the role of hetero-atoms/groups of the nucleobases on stacking interactions with urea moiety with respect to every possible pair. Several plane-parallel complexes were generated with urea on top of aromatic systems to exhaustively study all possible factors for urea-nucleobases stacking interactions. Energy decomposition analysis (EDA), atoms in molecules (AIM) and natural bond orbital (NBO) analysis were performed to gain better insights on non-covalent stacking interactions. Dispersion component was found to be heavily stabilizing, while the EHF was found to be repulsive for all the four systems indicating lack of hydrogen bonding (HB) type interactions and presence of dispersion type interactions. Amide and carbonyl groups of urea molecule were found to play a major role in favourable stacking interactions. We demonstrate that along with functional groups present on the nucleobases, the orientation of urea molecules plays a vital role in stabilizing the urea-nucleobase non-covalent interactions. The proposed study quantifies and provides a comprehensive theoretical description of urea nucleobase unconventional stacking interactions which helps to unravel urea driven RNA unfolding mechanism.

Abstract

An understanding of the determinants of the thermal stability of thermostable proteins is expected to enable design of enzymes that can be employed in industrial biocatalytic processes carried out at high temperatures. A major factor that has been proposed to stabilize thermostable proteins is the high occurrence of salt bridges. The current study employs free energy calculations to elucidate the thermodynamics of the formation of salt bridge interactions and the temperature dependence, using acetate and methylguanidium ions as model systems. Three different orientations of the methylguanidinium approaching the carboxylate group have been considered for obtaining the free energy profiles. The association of the two ions becomes more favorable with an increase in temperature. The desolvation penalty corresponding to the association of the ion pair is the lowest at high temperatures. The occurrence of …

Abstract

Gold clusters are currently regarded as new-generation catalysts owing to their exceptional efficiency in accelerating several classes of reactions. Density functional theory (DFT) is the method of choice for the investigation of energy pathways of reactions assisted by metal nanoparticles due to their computational efficiency. However, the reliability of such theoretical studies depends to a large extent on the choice of the DFT functional used. In the present work, the performance of a series of DFT-based functionals to accurately model the prototypical CO oxidation reaction catalyzed by a cluster has been examined by comparing the results with those obtained from high-level ab initio CCSD(T) method. This comparison study has been carried along the two possible pathways [Eley–Rideal (ER) and the Langmuir–Hinshelwood (LH)]. No significant differences among the DFT functionals were observed in …

Abstract

Multidrug resistance in Mycobacterium tuberculosis (M. Tb) and its coexistence with HIV are the biggest therapeutic challenges in anti-M. Tb drug discovery. The current study reports a Virtual Screening (VS) strategy to identify potential inhibitors of Mycobacterial cyclopropane synthase (CmaA1), an important M. Tb target considering the above challenges. Five ligand-based pharmacophore models were generated from 40 different conformations of the cofactors of CmaA1 taken from molecular dynamics (MD) simulations trajectories of CmaA1. The screening abilities of these models were validated by screening 23 inhibitors and 1398 non-inhibitors of CmaA1. A VS protocol was designed with four levels of screening i.e., ligand-based pharmacophore screening, structure-based pharmacophore screening, docking and absorption, distribution, metabolism, excretion and the toxicity (ADMET) filters. In an …

Abstract

Bimetallic nanoparticles (NPs) have been shown to exhibit certain advantages over pure NPs in catalysis due to a synergistic effect. It is common to disperse NPs in a polymer matrix such as polyvinylpyrrolidone (PVP) to prevent flocculation, which imparts considerable electronic effects on the NPs. In the present study, the interactions between aqueous solutions of N-ethylpyrrolidone (EP, system chosen to model the monomeric form of PVP) and Au/Pd bimetallic NPs, which are relevant in catalysis, have been investigated using molecular dynamics simulations and density functional theory (DFT) method. The adequacy of the force fields used was assessed based on their ability to reproduce the structures and adsorption energies obtained using DFT calculations. The interactions of NPs with the environment were studied at various concentrations of aqueous solutions of EP to examine the strength of NP–EP and NP …

Abstract

Urea transporters are membrane proteins that selectively allow urea molecules to pass through. It is not clear how these transporters allow rapid conduction of urea, a polar molecule, in spite of the presence of a hydrophobic constriction lined by aromatic rings. The current study elucidates the mechanism that is responsible for this rapid conduction by performing free energy calculations on the transporter dvUT with a cumulative sampling time of about 1.3 μs. A parallel arrangement of aromatic rings in the pore enables stacking of urea with these rings, which, in turn, lowers the energy barrier for urea transport. Such interaction of the rings with urea is proposed to be a conserved mechanism across all urea-conducting proteins. The free energy landscape for the permeation of multiple urea molecules reveals an interplay between interurea interaction and the solvation state of the urea molecules. This is for the first time …