Molecular dynamics simulations study of hydrophilic and hydrophobic interactions between nanoscale particles

This dissertation presents our research on hydrophilic and hydrophobic interactions performed using molecular dynamics (MD) simulations with nanoscale model plates. Hydrophobic and hydrophilic interactions have been discussed in many places of chemistry and biology to explain water-involved phenomena such as solute aggregation and protein folding. However, until recently, the absence of appropriate methodology and insufficient computing power has prevented quantitatively detailed discussions of these phenomena. In this dissertation, we design model hydrophilic and hydrophobic plates and use MD methodology to study the nature of the hydrophobic and hydrophilic interactions. These plates are simple enough to be computationally accessible but still applicable for understanding the essence of hydrophobic and hydrophilic phenomena in nature. Since the hydrophobic and hydrophilic interactions are considered to be medium effects involving water molecules, we extract this medium contribution from the total interaction between two plates in water and analyze it. This analysis is applied to the case of two interacting model lipid plates across water and it demonstrates that the monotonic repulsive interaction between lipid bilayers, known as the hydration force, originates from the water-induced interaction, and not from the steric repulsions between the headgroups. Further detailed thermodynamic and hydrogen bonding analyses indicate that strong plate-water interaction is responsible for the repulsive water-mediated interaction. Interestingly, when we remove electric charges from the model lipid plate, the repulsive character due to water changes to the attractive character and the overall shape of the total interaction is very similar to typical hydrophobic interaction. We investigate the hydrophobic property of the charge-removed model lipid plate by comparing it with other hydrophobic plates based on the graphene plate model. From this comparison, we find that the roughness of the surface enhances the hydrophobic interaction. The graphene plates are also used to study the fluctuation of water between hydrophobic plates, which is considered to be a signature of the hydrophobic interaction

Enzyme Localization, Crowding, and Buffers Collectively Modulate Diffusion-Influenced Signal Transduction: Insights from Continuum Diffusion Modeling

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

A revisit to the one-form kinetic model of prothrombinase: A comment on the rebuttal

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

Molecular Dynamics Simulation Study of Interaction between Model Rough Hydrophobic Surfaces

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 figure

Comparison of the chemical compositions and nutritive values of various pumpkin (Cucurbitaceae) species and parts

Pumpkins have considerable variation in nutrient contents depending on the cultivation environment, species, or part. In this study, the general chemical compositions and some bioactive components, such as tocopherols, carotenoids, and β-sitosterol, were analyzed in three major species of pumpkin (Cucurbitaceae pepo, C. moschata, and C. maxima) grown in Korea and also in three parts (peel, flesh, and seed) of each pumpkin species. C. maxima had significantly more carbohydrate, protein, fat, and fiber than C. pepo or C. moschata (P < 0.05). The moisture content as well as the amino acid and arginine contents in all parts of the pumpkin was highest in C. pepo. The major fatty acids in the seeds were palmitic, stearic, oleic, and linoleic acids. C. pepo and C. moschata seeds had significantly more γ-tocopherol than C. maxima, whose seeds had the highest β-carotene content. C. pepo seeds had significantly more β-sitosterol than the others. Nutrient compositions differed considerably among the pumpkin species and parts. These results will be useful in updating the nutrient compositions of pumpkin in the Korean food composition database. Additional analyses of various pumpkins grown in different years and in different areas of Korea are needed

Diffusion-Limited Reaction Kinetics of a Reactant with Square Reactive Patches on a Plane

We present a simple reaction model to study the influence of the size, number, and spatial arrangement of reactive patches on a reactant placed on a plane. Specifically, we consider a reactant whose surface has an N &times; N square grid structure, with each square cell (or patch) being chemically reactive or inert for partner reactant molecules approaching the cell via diffusion. We calculate the rate constant for various cases with different reactive N &times; N square patterns using the finite element method. For N = 2, 3, we determine the reaction kinetics of all possible reactive patterns in the absence and presence of periodic boundary conditions, and from the analysis, we find that the dependences of the kinetics on the size, number, and spatial arrangement are similar to those observed in reactive patches on a sphere. Furthermore, using square reactant models, we present a method to significantly increase the rate constant by sequentially breaking the patches into smaller patches and arranging them symmetrically. Interestingly, we find that a reactant with a symmetric patch distribution has a power&ndash;law relation between the rate constant and the number of reactive patches and show that this works well when the total reactive area is much less than the total surface area of the reactant. Since our N &times; N discrete models enable us to examine all possible reactive cases completely, they provide a solid understanding of the surface reaction kinetics, which would be helpful for understanding the fundamental aspects of the competitions between reactive patches arising in real applications

Osmosis-Driven Water Transport through a Nanochannel: A Molecular Dynamics Simulation Study

In this work, we study a chemical method to transfer water molecules from a nanoscale compartment to another initially empty compartment through a nanochannel. Without any external force, water molecules do not spontaneously move to the empty compartment because of the energy barrier for breaking water hydrogen bonds in the transport process and the attraction between water molecules and the compartment walls. To overcome the energy barrier, we put osmolytes into the empty compartment, and to remove the attraction, we weaken the compartment-water interaction. This allows water molecules to spontaneously move to the empty compartment. We find that the initiation and time-transient behavior of water transport depend on the properties of the osmolytes specified by their number and the strength of their interaction with water. Interestingly, when osmolytes strongly interact with water molecules, transport immediately starts and continues until all water molecules are transferred to the initially empty compartment. However, when the osmolyte interaction strength is intermediate, transport initiates stochastically, depending on the number of osmolytes. Surprisingly, because of strong water-water interactions, osmosis-driven water transport through a nanochannel is similar to pulling a string at a constant speed. Our study helps us understand what minimal conditions are needed for complete transfer of water molecules to another compartment through a nanochannel, which may be of general concern in many fields involving molecular transfer