Sayantan Mondal

What Gives an Insulin Hexamer Its Unique Shape and Stability? Role of Ten Confined Water Molecules

Self-assembly of proteins often gives rise to interesting quasi-stable structures that serve important biological purposes. Insulin hexamer is such an assembly. While monomer is the biologically active form of insulin, hexamer serves as the storehouse of the hormone. The hexamer also prevents the formation of higher order aggregates. While several studies explored the role of bivalent metal ions like Zn2+, Ca2+, etc., in the stabilization of the hexameric form, the role of water molecules has been ignored. We combine molecular dynamics simulations, quantum calculations, and X-ray analyses to discover that a team of approximately 10 water molecules confined inside a barrel-shaped nanocavity at the center of insulin hexamer is one of the major causes that account for the unusual stability of the biomolecular assembly. These cavity water molecules exhibit interesting dynamical features like intermittent escape and reentrance. We find that these water molecules are dynamically slower than the bulk and weave an intricate hydrogen bond network among themselves and with neighboring protein residues to generate a robust backbone at the center of the hexamer that holds the association strongly from inside and maintains the barrel shape.

Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20-80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.

Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves

There are certain small molecules that exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as an antidiabetic drug for type-two diabetes. Recent lines of evidence of its role in antitumor activities and increasing the survival rates of cancer patients (namely, colorectal, breast, pancreas, and prostate cancer) are emerging. However, theoretical studies of the structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three monoprotonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations, and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to those of the experimental findings. Energetics of proton transfer between two planar monoprotonated forms reveals a low energy barrier, which leads us to speculate a possible coexistence of them. Nevertheless, among the protonation states, we find that the nonplanar tautomeric form is the most stable. Our calculated values of the self-diffusion coefficient agree quantitatively with NMR results. Metformin forms strong hydrogen bonds with surrounding water molecules, and its solvation dynamics shows unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry, and metadynamics simulation. We find a nonintercalative mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT-rich domains. A significant decrease in the free energy of binding is observed when it binds to a minor groove of DNA.

DNA Solvation Dynamics

Experiments have revealed that DNA solvation dynamics is characterized by multiple time scales ranging from a few picoseconds to a few hundred nanoseconds and in some cases even up to several microseconds. The last part of decay is not only slow but can also be described by a power law (PL). The microscopic origin of this PL is yet to be clearly established. Here we present a theoretical study employing multiple approaches from time dependent statistical mechanics and computer simulations. The present study shows that water dynamics may not account for the slow PL decay because the longest time scales describing water dynamics could be at most of the order of 100 ps. We find that the DNA solvation dynamics is complex, due to multiple different contributions to solvation energy. Our investigations also show that the primary candidates for this exotic nature of solvation dynamics are the response of the counterions and ions of the buffer solution. We first employ the well-known Oosawa model of polyelectrolyte solution that includes effects of counterion fluctuations to construct a frequency dependent dielectric function. We use it in the continuum model of Bagchi, Fleming, and Oxtoby (BOF). We find that it fails to explain the slow PL decay of DNA solvation dynamics. We then extend the Oosawa model by employing the continuous time random walk technique developed by Scher, Montroll and Lax. We find that this approach could explain the long time PL decay, in terms of the collective response of the counterions. To check the nature of random walk of counterions along the phosphate backbone, we carry out atomistic molecular dynamics (MD) simulations with a long (38 base pair) DNA. We indeed find frequent occurrence of random walk of tagged counterions along the phosphate backbone. We next propose a generalized random walk model for counterion hopping on phosphate backbone (observed in our MD simulations) and carry out kinetic Monte Carlo simulations to show that the nonexponential contribution to solvation dynamics can indeed come from dynamics of such ions. We also employ a mode coupling theory (MCT) analysis to understand the slow relaxation that can originate from ions in solution due to the use of the buffer. Explicit evaluation suggests that buffer ion contribution could explain a logarithmic time dependence in the nanosecond time scale but not a power law. To further understand the nonexponentiality of solvation dynamics at relatively shorter times (less than 100 ps) we carry out atomistic MD simulations with explicit water molecules. Log-normal distributions of relaxation times of water dynamics inside the grooves may be responsible for the initial multiexponential decay of solvation dynamics. We find that the observed faster solvation of groove bound probe than that of the intercalated probe could arise from the self-motion of the probe.

Insulin dimer dissociation in aqueous solution: A computational study of free energy landscape and evolving microscopic structure along the reaction pathway

The dissociation of an insulin dimer to two monomers is an important life process. Although the monomer is the biologically active form of the hormone, it is stored in the β-cells of the pancreas in the hexameric form. The latter, when the need comes, dissociates to dimers and the dimers in turn to monomers to maintain the endogenous delivery of the hormone. In order to understand insulin dimer dissociation at a molecular level, we perform biased molecular dynamics simulations (parallel tempering metadynamics in the well-tempered ensemble) of the dissociation of the insulin dimer in water using two order parameters and an all-atom model of the protein in explicit water. The two order parameters selected (after appropriate studies) are the distance (RMM) between the center of mass of two monomers and the number of contacts (NMM) among the backbone-Cα atoms of the two monomers. We calculated the free energy landscape as a function of these two order parameters and determined the minimum free energy pathway of dissociation. We find that the pathway involves multiple minima and multiple barriers. In the initial stage of dissociation, the distance between the monomers does not change significantly but the NMM decreases rapidly. In the latter stage of separation, the opposite occurs, that is, the distance RMM increases at nearly a constant low value of NMM. The configurations of the two monomeric proteins so formed are found to be a bit different due to the entropic reasons. Water is seen to play a key role in the dissociation process stabilizing the intermediates along the reaction path. Our study reveals interesting molecular details during the dissociation, such as the variation in the structural and relative orientational arrangement of the amino acid residues along the minimum energy path. The conformational changes of monomeric insulin in the stable dimer and in the intermediate states during dimer dissociation have been studied in detail.

Enhancement of reaction rate in small-sized droplets: A combined analytical and simulation study

Several recent mass spectrometry experiments reveal a marked enhancement of the reaction rate of organic reactions in microdroplets. This enhancement has been tentatively attributed to the accumulation of excess charge on a surface, which in turn can give rise to a lowering of activation energy of the reaction. Here we model the reactions in droplets as a three-step process: (i) diffusion of a reactant from the core of the droplet to the surface, (ii) search by diffusion of the reactant on the surface to find a reactive partner, and finally (iii) the intrinsic reaction leading to bond breaking and product formation. We obtain analytic expressions for the mean search time (MST) to find a target located on the surface by a reactant in both two- and three-dimensional droplets. Analytical results show quantitative agreement with Brownian dynamics simulations. We find, as also reported earlier, that the MST varies as R2/D, where R is the radius of the droplet and D is the diffusion constant of the molecules in the droplet medium. We also find that a hydronium ion in the vicinity can substantially weaken the bond and hence lowers the activation barrier. We observe a similar facilitation of bond breaking in the presence of a static dipolar electric field along any of the three Cartesian axes. If the intrinsic reaction is faster compared to the mean search time involved, it becomes primarily a diffusion-controlled process; otherwise the reaction cannot be accelerated in the droplet medium. The air-droplet interface provides a different environment compared to the interior of the droplet. Hence, we might also expect a completely different mechanism and products in the case of droplet reactions.