Hydration water dynamics around a protein surface: a first passage time approach

Preferential Ordering and Organization of Hydration Water Favor Nucleation of Ice by Ice-Nucleating Proteins over Antifreeze Proteins

Bacteria containing ice-nucleating proteins (INPs) evolved in nature to nucleate ice at the high sub-zero ambiance. The ability of the INPs to induce order in the hydration layer and their aggregation propensity appear to be key factors of their ice nucleation abilities. However, the mechanism of the process of ice nucleation by INPs is yet to be understood clearly. Here, we have performed all-atom molecular dynamics simulations and analyzed the structure and dynamics of the hydration layer around the proposed ice-nucleating surface of a model INP. Results are compared with the hydration of a topologically similar non-ice-binding protein (non-IBP) and another ice-growth inhibitory antifreeze protein (sbwAFP). We observed that the hydration structure around the ice-nucleating surface of INP is highly ordered and the dynamics of the hydration water are slower, compared to the non-IBP. Even the ordering of the hydration layer is more evident around the ice-binding surface of INP, compared to the antifreeze protein sbwAFP. Particularly with increasing repeat units of INP, we observe an increased population of ice-like water. Interestingly, the distances between the hydroxyl groups of the threonine ladder and its associated channel water of the ice-binding surface (IBS) of INP in the X and Y direction mimic the oxygen atom distances of the basal plane of hexagonal ice. However, the structural synergies between the hydroxyl group distances of the threonine ladder and its associated channel water of the IBS of sbwAFP and oxygen atom distances of the basal plane are less evident. This difference makes the IBS of the INP a better template for ice nucleation than AFP, although both of them bind to the ice surface efficiently.

Statistical physics of inhomogeneous transport: Unification of diffusion laws and inference from first-passage statistics

Characterization of composite materials, whose properties vary in space over microscopic scales, has become a problem of broad interdisciplinary interest. In particular, estimation of the inhomogeneous transport coefficients, e.g., the diffusion coefficient or the heat conductivity, which shape important processes in biology and engineering, is a challenging task. The analysis of such systems is further complicated because two alternative formulations of the inhomogeneous transport equations exist in the literature-the Smoluchowski and Fokker-Planck equations, which are also related to the so-called Ito-Stratonovich dilemma. Using the theory of statistical physics, we show that the two formulations, usually regarded as distinct models, are physically equivalent. From this result we develop efficient estimates for the transverse space-dependent diffusion coefficient in fluids near a phase boundary. Our method requires only measurements of escape probabilities and mean exit times of molecules leaving a narrow spatial region. We test our estimates in three case studies: (i) a Langevin model of a Büttikker-Landauer ratchet; atomistic molecular-dynamics simulations of liquid-water molecules in contact with (ii) vapor, and (iii) soap (surfactant) film which has promising applications in physical chemistry. Our analysis reveals that near the surfactant monolayer the mobility of water molecules is slowed down almost twice with respect to the bulk liquid. Moreover, the diffusion coefficient of water correlates with the transition from hydrophilic to hydrophobic parts of the film.

Analysis of the Passage Times for Unfolding/Folding of the Adenine Riboswitch Aptamer

The conformational transitions of the adenosine deaminase A-riboswitch aptamer both with and without ligand binding are investigated within the tenets of the generalized Langevin equation in a complex viscoelastic cellular environment. Steered molecular dynamics (SMD) simulations are performed to evaluate and compare the results of the first passage times (FPTs) with those obtained from the theory for the unfold and fold transitions of the aptamer. The results of the distribution of Kramers's FPT reveal that the unfold-fold transitions are faster and hence more probable as compared to the fold-unfold transitions of the riboswitch aptamer for both ligand-bound and -unbound states. The transition path time is lower than Kramers's FPT for the riboswitch aptamer as the transition path times for the unfold-fold transition of both without and with ligand binding are insensitive to the details of the exact mechanism of the transition events. However, Kramers's FPTs show varied distributions which correspond to different transition pathways, unlike the transition path times. The mean FPT increases with an increase in the complexity of the cellular environment. The results of Kramers's FPT, transition path time distribution, and mean FPT obtained from our calculations qualitatively match with those obtained from the SMD simulations. Analytically derived values of the mean transition path time show good quantitative agreement with those estimated from the single-molecule force spectroscopy experiments for higher barrier heights.

Effect of ligand binding on riboswitch folding: Theory and simulations

The effect of ligand binding on the conformational transitions of the add A-riboswitch in cellular environments is investigated theoretically within the framework of the generalized Langevin equation combined with steered molecular dynamics simulations. Results for the transition path time distribution provide an estimate of the transit times, which are difficult to determine experimentally. The time for the conformational transitions of the riboswitch aptamer is longer for the ligand bound state as compared to that of the unbound one. The transition path time of the riboswitch follows a counterintuitive trend as it decreases with an increase in the barrier height. The mean transition path time of either transitions of the riboswitch in the ligand bound/unbound state increases with an increase in the complexity of the surrounding environment due to the caging effect. The results of the probability density function, transition path time distribution, and mean transition path time obtained from the theory qualitatively agree with those obtained from the simulations and with earlier experimental and theoretical studies.