Abstract

The transport of water through aquaporins is a dynamic process that involves rapid movement of a chain of water molecules through the pore of the aquaporin. Structures of aquaporins solved using X-ray crystallography have provided some insights into how water is transported through these channels, and how certain structural features of the pore might help exclude other solutes from passing through the pore. However, such techniques provide only a static picture, and a dynamic picture of the transport and selectivity mechanism at work in aquaporins is possible with molecular dynamics (MD) simulations. In MD simulations, the forces between the different atoms in a system are computed, and the atoms are then allowed to move under the influence of these forces. This allows the sampling of different conformations of the molecule being studied, including conformations that are crucial in driving biological phenomena like water transport. Simulation studies have provided insights into a number of aspects of aquaporins, including the role of the asparagine-proline-alanine (NPA) motif and the aromatic/arginine (ar/R) constriction, water transport mechanism, mechanisms defining the selectivity of the channel, interaction with lipids, response to external electric field, and binding of putative drug molecules. This chapter provides a brief review of the current status of computational modeling of aquaporins using MD simulations. Initially, a brief account of force fields and MD simulations is presented followed by an account of how MD simulations have contributed to further our understanding of different aspects of aquaporins.

Abstract

Aqueous urea stabilizes the unfolded states of protein due to their ability to solvate both hydrophilic and hydrophobic residues favorably. The nature of interactions that stabilize different types of amino acid side chains in their solvent exposed state is still not understood. To gain insights into the molecular level details of urea interactions with proteins in their unfolded states, we have performed atomistic molecular dynamics simulations and free energy calculations using the thermodynamic integration method on model systems representing side chains of all amino acids in different solvent environments (water and varying concentrations of aqueous urea). A systematic analysis of structural, energetic and dynamic parameters has been done to understand the detailed atomistic mechanism. The main aim of the current study is to unravel the nature of urea-amino acid interactions by emphasizing on the chemical nature …

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

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

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

In recent times, our healthcare system is being challenged by many drug-resistant microorganisms and ageing-associated diseases for which we do not have any drugs or drugs with poor therapeutic profile. With pharmaceutical technological advancements, increasing computational power and growth of related biomedical fields, there have been dramatic increase in the number of drugs approved in general, but still way behind in drug discovery for certain class of diseases. Now, we have access to bigger genomics database, better biophysical methods, and knowledge about chemical space with which we should be able to easily explore and predict synthetically feasible compounds for the lead optimization process. In this chapter, we discuss the limitations and highlights of currently available computational methods used for protein–ligand binding affinities estimation and this includes force-field, ab initio electronic structure theory and machine learning approaches. Since the electronic structure-based approach cannot be applied to systems of larger length scale, the free energy methods based on this employ certain approximations, and these have been discussed in detail in this chapter. Recently, the methods based on electronic structure theory and machine learning approaches also are successfully being used to compute protein–ligand binding affinities and other pharmacokinetic and pharmacodynamic properties and so have greater potential to take forward computer-aided drug discovery to newer heights

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

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

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

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 …