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The potential of mean force (PMF) is calculated to study the thermodynamics of water transport through a carbon nanotube.

Using molecular dynamics simulations, we study the equilibration of a system consisting of two nanoscale compartments connected by a carbon nanotube through which small mobile molecules can pass. The system is initially in a state where only one compartment is filled with molecules and the other is empty. When the molecules are allowed to move from the filled compartment to the empty one, the system starts equilibrating and finally reaches an equilibrium state where the molecules are distributed between the two compartments. In the absence of osmolytes, the equilibrium distribution of molecules is simply determined by the relative volumes of the compartments, but in the presence of osmolytes, the distribution is dependent on not only the relative compartment volumes but also the osmolyte properties. To systematically study the effect of osmolytes, we investigate how the number of osmolytes and the strength of the interaction between molecules and osmolytes affect the equilibrium state. Interestingly, we find that osmolytes strongly interacting with molecules can drain the initially filled compartment and induce the complete transfer of molecules to the initially empty compartment. We also study the kinetic and thermodynamic aspects of the equilibration processes.

Severe acute respiratory syndrome coronavirus (SARS-CoV-2) appeared as a new viral pathogen and caused the COVID-19 pandemic worldwide. Since the antiviral medicines effective for the treatment of COVID-19 are rare, it is necessary to identify the new candidate molecules for chemotherapy. The glycosylated Spike protein (S-protein) of SARS-CoV-2 plays a critical role in entering into the host cell through a direct interaction with human angiotensin-converting enzyme 2 (ACE2). For this reason, S-protein has served as one of the most effective therapeutic targets for discovering the antiviral medicines for COVID-19. In this work, we report the new small-molecule inhibitors of the interaction between the S-protein of SARS-CoV-2 and human ACE2, which were discovered through the structure-based virtual screening and in vitro biochemical binding assays. As a consequence of combining the computational and experimental validations, three novel inhibitors against the binding of S-protein and ACE2 were found with the associated IC

The selectivity and conduction specificity of the KcsA channel toward potassium ions is crucial to the activity of this protein and this channel is intricately associated with several osmotic regulation and neuronal signaling processes. Despite multi-ion characteristics, the selective conduction behavior of KcsA is controlled by the size and distance specific electrostatic interaction between the selected residues and the potassium ions. The mechanism describing the movement of potassium ions in the channel and the conformational changes to KcsA that facilitate ion movement were investigated by a molecular dynamics (MD) simulation. In this study, we analyze the movement of potassium ions and water molecules at various time intervals during a 90 ns molecular dynamics simulation in the high potassium ion concentration regime and in the absence of the voltage. Examination of specific (3.6, 17.3, 43.38 and 43.44 ns) simulation periods revealed that key residues in the selectivity filter of KcsA influence the movement of potassium ions in the channel.

The loss of electrode activity (referred to as electrode fouling) caused by an electropolymerized passive film of salicylic acid (SA), a major hydrolysis product of aspirin, significantly decreases the accuracy and the precision of indirect electrochemical detection of aspirin. However, the electrode fouling problem for electrochemical determination of SA and ways to remove the fouling film have been sparsely discussed. In addition, the electrochemical behavior of SA on a carbon-fiber electrode (CFE), widely used for the study of neurochemicals in vivo and in vitro, has not yet been studied. Herein, we report the electrochemical behavior of SA at CFEs using cyclic voltammetry and differential pulse voltammetry. The irreversible and pH dependent electrochemical oxidation of SA produced dihydroxybenzoic acids, SA dimeric products and poly-SA films that strongly adhered to the electrode surface and passivated further reactions. The electrode fouling caused by the SA films on a CFE decreased electrode sensitivity and reproducibility for the indirect determination of aspirin. In this study, the fouling effects were characterized with Fe(CN)64−/3−. Interestingly, we found that the poly-SA films on CFE can be removed by a strong base, undergoing the intramolecular base catalyzed hydrolysis of salicylate esters. This non-destructive cleaning method of poly-SA films on the electrode improved the linear dynamic range of SA as well as the accuracy and precision of SA measurements. This new cleaning method of CFEs was further applied to the indirect determination of aspirin in commercially available pharmaceutical tablets.

© 2014 Biophysical Society. We perform Brownian dynamics simulations and Smoluchowski continuum modeling of the bifunctional Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (P. falciparum DHFR-TS) with the objective of understanding the electrostatic channeling of dihydrofolate generated at the TS active site to the DHFR active site. The results of Brownian dynamics simulations and Smoluchowski continuum modeling suggest that compared to Leishmania major DHFR-TS, P. falciparum DHFR-TS has a lower but significant electrostatic-mediated channeling efficiency (∼15-25%) at physiological pH (7.0) and ionic strength (150 mM). We also find that removing the electric charges from key basic residues located between the DHFR and TS active sites significantly reduces the channeling efficiency of P. falciparum DHFR-TS. Although several protozoan DHFR-TS enzymes are known to have similar tertiary and quaternary structure, subtle differences in structure, active-site geometry, and charge distribution appear to influence both electrostatic-mediated and proximity-based substrate channeling.

A lattice model is proposed to explain the restructuring of an ionic surfactant absorbed on a charged surface. When immersed in water, an ionic mica plate initially covered by a monolayer of surfactants rearranges to a surface inhomogeneously covered by patches of surfactant bilayer and bare mica. The model considers four species that can cover lattice sites of a surface. These species include (i) a surfactant molecule with its headgroup down, (ii) surfactant molecule with the headgroup up, (iii) a surfactant dimer arranged in a tail-to-tail configuration, which is a part of a bilayer, and (iv) a mica lattice site covered by water. We consider that only nearest neighbors on the lattice interact and describe the interactions by an interaction matrix. Using this model, we perform Monte Carlo simulations and study how the structure of the inhomogeneous surface depends on the interaction between water covered lattice site and its neighboring surfactant species covered sites. We observe that when this interaction is absent, the system undergoes phase separation into a bilayer phase and mica surface covered with water. When this interaction is taken into account, patches of surfactant bilayer and water are present in our system. The interaction between mica surfaces covered by patches of ionic surfactants is studied in experiments to understand the nature of long-ranged "hydrophobic" forces.

Hydrophobic surfaces created by the adsorption of a monolayer of surfactants, such as CTAB or DODAB, to mica display long-range mutual attraction when placed in water. Initially, this attraction was considered to be due to hydrophobic interaction, but more careful measurements using AFM showed that the surfactant monolayer undergoes rearrangements to produce charged patches on the surface; therefore, the nature of the long-range interaction is due to the electrostatic interaction between patches. The monolayer rearrangement depends on the nature of the surfactant and its counterion. To study possible monolayer rearrangements in molecular detail, we performed detailed molecular dynamics computer simulations on systems containing a monolayer of surfactants RN(CH(3))(3)(+)Cl(-) (R indicates a saturated hydrocarbon chain) adsorbed on a mica surface and immersed in water. We observe that when chain R is 18 carbons long the monolayer rearranges into a micelle but it remains a monolayer when the chain contains 24 carbons.

© 2015 Wiley Periodicals, Inc. Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece and WW domain, was simulated via accelerated molecular dynamics (aMD). In comparison with hundred-of-microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2-2.1 Å of the native NMR or X-ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein-folding studies.

We present a simple theory that explains how surface curvature affects the reaction kinetics of diffusion-limited reactions on spherically curved surfaces. In this theory, we derive a quadratic equation under the conditions that the rate constant satisfies the Hill and Smoluchowski rate constants at the lowest and highest curvatures, respectively, and that at a certain intermediate curvature, there should be a maximum value of the rate constant, which was recently found in our previous work. We find that the result obtained from our theory is in good agreement with the corresponding one obtained from numerical calculation. In addition, we show that our theory can be directly applied to the Šolc-Stockmayer model of axially symmetric reactants, which can be considered as a spherical reactant with a single reaction site. Furthermore, we discuss using our theory to improve the formula for the rate constant in the Berg-Purcell ligand-binding model of a cell membrane covered by multiple receptors. Our simple theory yields insight into the effect of curvature on diffusion-influenced reactions and provides a useful formula for easily and quantitatively evaluating the curvature effect.

Thrombin is generated enzymatically from prothrombin by two pathways with the intermediates of meizothrombin and prethrombin-2. Experimental concentration profiles from two independent groups for these two pathways have been re-analyzed. By rationally combining the independent data sets, a simple mechanism can be established and rate constants determined. A structural model is consistent with the data-derived finding that mechanisms that feature channeling or ratcheting are not necessary to describe thrombin production.

© 2015 AIP Publishing LLC. Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion "barriers" arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to "compartments" of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways.

By using two different computer simulation methods, of which one produces exact results while the other is based on the Wilemski-Fixman closure approximation, we evaluate the utility of closure approximation in calculating the rates of diffusion-controlled reactions involving a reactant with multiple reaction sites. We find that errors in the estimates of steady-state rate constants due to closure approximation are not so large. We thus propose an approximate analytic expression for the rate constant based on the closure approximation.

Transcription factor IIS (TFIIS) is a protein known for catalyzing the cleavage reaction of the 3′-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II) to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound) states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound) state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS. © 2014 Eun et al.

We study models of two sequential enzyme-catalyzed reactions as a basic functional building block for coupled biochemical networks. We investigate the influence of enzyme distributions and long-range molecular interactions on reaction kinetics, which have been exploited in biological systems to maximize metabolic efficiency and signaling effects. Specifically, we examine how the maximal rate of product generation in a series of sequential reactions is dependent on the enzyme distribution and the electrostatic composition of its participant enzymes and substrates. We find that close proximity between enzymes does not guarantee optimal reaction rates, as the benefit of decreasing enzyme separation is countered by the volume excluded by adjacent enzymes. We further quantify the extent to which the electrostatic potential increases the efficiency of transferring substrate between enzymes, which supports the existence of electrostatic channeling in nature. Here, a major finding is that the role of attractive electrostatic interactions in confining intermediate substrates in the vicinity of the enzymes can contribute more to net reactive throughput than the directional properties of the electrostatic fields. These findings shed light on the interplay of long-range interactions and enzyme distributions in coupled enzyme-catalyzed reactions, and their influence on signaling in biological systems. © 2014 AIP Publishing LLC.

In cells, many enzyme-catalyzed reactions are coupled as a series of biochemical steps. Thus, the reaction rate is dependent on the kinetics of intermediate reaction steps. In this work, we study the case of two coupled enzyme reactions, where the product of the first reaction serves as the substrate of the second reaction. Using a diffusion-limited reaction model, we demonstrate that the overall kinetics is strongly dependent on the separation distance between two enzymes, although interestingly, we find that in some cases, the maximal rate occurs at a finite, non-smallest separation between enzymes. This is because the second enzyme in proximity can block the access of substrate for the first enzyme reaction, which leads to the decrease of product of the first reaction (substrate for the second reaction). We further demonstrate how this reaction rate is additionally dependent on the nature of electrostatic interactions between reactants and the two enzymes. We demonstrate the interplay of these concepts for the dihydrofolate reductase-thymidylate synthase (DHFR-TS) systems, whereby methylene tetrahydrofolate is converted to tetrahydrofoloate.Our study suggests the role of species-specific electrostatic and geometric factors in optimizing reaction rates of substrate-channeling systems.

We calculated the potential of mean force (PMF) for the interaction between a model zwitterionic bilayer and a model charged bilayer. To understand the role of water, we separated the PMF into two components: one due to direct interaction and the other due to water-mediated interaction. In our calculations, we observed that water-mediated interaction is attractive at larger distances and repulsive at shorter. The calculation of the entropic and enthalpic contributions to the solvent-mediated components of the PMF showed that attraction is entropically dominant, while repulsion is dominated by the enthalpy.

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes; it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in case of charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo, as the two plates are brought together., Comment: 27 pages, 9 figures

We performed molecular dynamics simulations on systems containing phosphatidycholine headgroups attached to graphene plates (PC−headgroup plates) immersed in water to study the interaction between phosphatidylcholine bilayers in water. The potential of mean force (PMF) between PC−headgroup plates shows that the interaction is repulsive. We observed three distinct regimes in the PMF depending on the interplate distances: the small distance regime, intermediate distance regime, and large distance regime. We believe that the repulsive interaction in the intermediate interplate distance regime is associated with the hydration force due to the removal of water molecules adjacent to the headgroups.

Competition between reactive species is commonplace in typical chemical reactions. Specifically the primary reaction between a substrate and its target enzyme may be altered when interactions with secondary species in the system are substantial. We explore this competition phenomenon for diffusion-limited reactions in the presence of neighboring particles through numerical solution of the diffusion equation. As a general model for globular proteins and small molecules, we consider spherical representations of the reactants and neighboring particles; these neighbors vary in local density, size, distribution, and relative distance from the primary target reaction, as well as their surface reactivity. Modulations of these model variables permit inquiry into the influence of excluded volume and competition on the primary reaction due to the presence of neighboring particles. We find that the surface reactivity effect is long-ranged and a strong determinant of reaction kinetics, whereas the excluded volume effect is relatively short-ranged and less influential in comparison. As a consequence, the effect of the excluded volume is only modestly dependent on the neighbor distribution and is approximately additive; this additivity permits a linear approximation to the many-body effect on the reaction kinetics. In contrast, the surface reactivity effect is non-additive, and thus it may require higher-order approximations to describe the reaction kinetics. Our model study has broad implications in the general understanding of competition and local crowding on diffusion-limited chemical reactions. © 2013 Author(s).

We generalize the Wilemski-Fixman-Weiss decoupling approximation to calculate the transient rate of absorption of point particles into multiple sinks of different sizes, shapes, and reactivities. As an application we consider the case involving two spherical sinks. We obtain a Laplace-transform expression for the transient rate that is in excellent agreement with computer simulations. The long-time steady-state rate has a relatively simple expression, which clearly shows the dependence on the diffusion constant of the particles and on the sizes and reactivities of sinks, and its numerical result is in good agreement with the known exact result that is given in terms of recursion relations.

Bacterial Microcompartments (BMCs) are proteinaceous organelles that sequester key metabolic reactions to increase enzymatic efficiency and prevent the loss of volatile or cytotoxic intermediates. 7 distinct BMC-type operons have been identified in 20-25% of bacteria, including BMCs involved in carbon fixation, propanediol catabolism, and ethanolamine catabolism. Ranging from 100 to 150 nm in width, BMCs are encapsulated in a protein shell consisting of hexagonal tiles of the conserved BMC-fold proteins. The BMC-fold proteins homo-oligomerize into hexameric or pseudo-hexameric assemblies with unique functionalities. High resolution X-ray determined structures have previously elucidated the organization and tiling interactions of several shell proteins from BMCs. However, it remains unknown how small molecule metabolites may enter or exit the BMC, passing through the protein shell; nor how intermediates may be trapped inside. Here, we present initial findings using current methods in Molecular Dynamics to investigate BMC shell pores, including: (1) Metadynamics and Umbrella Sampling to probe the free energy profile of small molecule metabolites at predicted routes through BMC shell protein hexamer pores; (2) Accelerated MD and Targeted MD to observe the conformational change between BMC shell protein pseudo-hexamers that have been solved in open and closed pore conformations. These experiments shed insight on BMC shell pore dynamics and function, furthering our understanding of BMC systems.