Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.

Macromolecular crowding in the cellular cytoplasm can potentially impact diffusion rates of proteins, their intrinsic structural stability, binding of proteins to their corresponding partners as well as biomolecular organization and phase separation. While such intracellular crowding can have a large impact on biomolecular structure and function, the molecular mechanisms and driving forces that determine the effect of crowding on dynamics and conformations of macromolecules are so far not well understood. At a molecular level, computational methods can provide a unique lens to investigate the effect of macromolecular crowding on biomolecular behavior, providing us with a resolution that is challenging to reach with experimental techniques alone.

Computational investigation of the effects of polymer grafting on the effective interaction between silica nanoparticles in water.

Understanding and control of the effective interaction between nanoscale building blocks (colloids or nanoparticles) dispersed in a solvent is an important prerequisite for the development of bottom-up design strategies for soft functional materials. Here, we have employed all-atom molecular dynamics simulations to investigate the impact of polymer grafting on the solvent-mediated effective interaction between the silica nanoparticles (Si-NPs) in water, and in turn, on its bulk structural and thermodynamic properties. We found that the nature of the short grafting polymers [characterized by their interaction with water (hydrophobicity or hydrophilicity) and molecular weight] has a profound effect on the range and strength of the effective interaction between the Si-NPs.

Molecular mechanisms and energetics of lipid droplet formation and directional budding.

The formation and budding of lipid droplets (LDs) are known to be governed by the LD size and by membrane tensions in the endoplasmic reticulum (ER) bilayer and LD-monolayers. Using coarse-grained simulations of an LD model, we first show that ER-embedded LDs of different sizes can form through a continuous transition from wide LD lenses to spherical LDs at a fixed LD size. The ER tendency to relax its bilayer modulates the transition a subtle interplay between the ER and LD lipid densities.

Membrane curvature sensing by model biomolecular condensates.

Biomolecular condensates (BCs) are fluid droplets that form in biological cells by liquid-liquid phase separation. Their major components are intrinsically disordered proteins. Vast attention has been given in recent years to BCs inside the cytosol and nucleus.

Spherical Nanovesicles Transform into a Multitude of Nonspherical Shapes.

Nanovesicles are closed, bubblelike surfaces with a diameter between 20 and 200 nm, formed by lipid bilayers and biomembranes. Electron microscopy (EM) studies have shown that these vesicles can attain both spherical and nonspherical shapes. One disadvantage of EM methods is that they provide only a single snapshot of each vesicle.

Temperature Dependence of Static and Dynamic Heterogeneities in a Water-Ethanol Binary Mixture and a Study of Enhanced, Short-Lived Fluctuations at Low Concentrations.

Many aqueous binary mixtures, such as water-ethanol, are known to exhibit multiple structural transformations that are apparently driven by intermolecular hydrophobic interaction as well as hydrogen bonding. These interactions often cooperate to form special types of self-assembled structures. We study the effect of temperature on the formation of transient ethanol clusters as well as on the transient dynamic heterogeneity induced in the system due to such clustering.

Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy.

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface).

Multidimensional free energy surface of unfolding of HP-36: microscopic origin of ruggedness.

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular α-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution.

Solvent sensitivity of protein unfolding: dynamical study of chicken villin headpiece subdomain in water-ethanol binary mixture.

We carry out a series of long atomistic molecular dynamics simulations to study the unfolding of a small protein, chicken villin headpiece (HP-36), in water-ethanol (EtOH) binary mixture. The prime objective of this work is to explore the sensitivity of protein unfolding dynamics toward increasing concentration of the cosolvent and unravel essential features of intermediates formed in search of a dynamical pathway toward unfolding. In water-ethanol binary mixtures, HP-36 is found to unfold partially, under ambient conditions, that otherwise requires temperature as high as ∼600 K to denature in pure aqueous solvent.

Structural transformations, composition anomalies and a dramatic collapse of linear polymer chains in dilute ethanol-water mixtures.

Water-ethanol mixtures exhibit many interesting anomalies, such as negative excess partial molar volume of ethanol, excess sound absorption coefficient at low concentrations, and positive deviation from Raoult's law for vapor pressure, to mention a few. These anomalies have been attributed to different, often contradictory origins, but a quantitative understanding is still lacking. We show by computer simulation and theoretical analyses that these anomalies arise from the sudden emergence of a bicontinuous phase that occurs at a relatively low ethanol concentration of x(eth) ≈ 0.

Anomalous behavior of linear hydrocarbon chains in water-DMSO binary mixture at low DMSO concentration.

We find that at a mole fraction 0.05 of DMSO (x(DMSO) = 0.05) in aqueous solution, a linear hydrocarbon chain of intermediate length (n=30-40) adopts the most stable collapsed conformation.