Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose

In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose. We find that the presence of trehalose causes global retardation of the dynamics of water. Comparing aqueous solutions of lysozyme with/without trehalose, we observe that the dynamics of water in the hydration layers close to the protein is dramatically slower when trehalose is present in the system. We also analyze the structure of water and trehalose around the lysozyme and find that the trehalose molecules form a cage surrounding the protein that contains very slow water molecules. We conclude that the transient cage of trehalose molecules that entraps and slows the water molecules prevents the crystallisation of protein hydration water upon cooling.DC, EGS, and HES thank the NSF chemistry Division for support (Grants CHE-1213217, CHE-0911389, and CHE-0908218). PG gratefully acknowledges the computational support reveived by the INFN RM3-GRID at Roma Tre University. (CHE-1213217 - NSF chemistry Division; CHE-0911389 - NSF chemistry Division; CHE-0908218 - NSF chemistry Division)Published versio

Large Decrease of Fluctuations for Supercooled Water in Hydrophobic Nanoconfinement

Using Monte Carlo simulations, we study a coarse-grained model of a water layer confined in a fixed disordered matrix of hydrophobic nanoparticles at different particle concentrations c . For c = 0 , we find a first-order liquid-liquid phase transition (LLPT) ending in one critical point at low pressure P . For c > 0 , our simulations are consistent with a LLPT line ending in two critical points at low and high P . For c = 25 % , at high P and low temperature, we find a dramatic decrease of compressibility, thermal expansion coefficient, and specific heat. Surprisingly, the effect is present also for c as low as 2.4%. We conclude that even a small presence of hydrophobic nanoparticles can drastically suppress thermodynamic fluctuations, making the detection of the LLPT more difficult

Confinement of Anomalous Liquids in Nanoporous Matrices

Using molecular dynamics simulations, we investigate the effects of different nanoconfinements on complex liquids-e.g., colloids or protein solutions-with density anomalies and a liquid-liquid phase transition (LLPT). In all the confinements, we find a strong depletion effect with a large increase in liquid density near the confining surface. If the nano confinement is modeled by an ordered matrix of nanoparticles (NPs), we find that the anomalies are preserved. On the contrary, if the confinement is modeled by a disordered matrix of NPs, we find a drastically different phase diagram: the LLPT shifts to lower pressures and temperatures, and the anomalies become weaker, as the disorder increases. We find that the density heterogeneities induced by the disordered matrix are responsible for the weakening of the LLPT and the disappearance of the anomalies

Cluster Monte Carlo and numerical mean field analysis for the water liquid--liquid phase transition

By the Wolff's cluster Monte Carlo simulations and numerical minimization within a mean field approach, we study the low temperature phase diagram of water, adopting a cell model that reproduces the known properties of water in its fluid phases. Both methods allows us to study the water thermodynamic behavior at temperatures where other numerical approaches --both Monte Carlo and molecular dynamics-- are seriously hampered by the large increase of the correlation times. The cluster algorithm also allows us to emphasize that the liquid--liquid phase transition corresponds to the percolation transition of tetrahedrally ordered water molecules.Comment: 6 pages, 3 figure

Effects of confinement on the thermodynamics of supercooled water

Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.The main focus of this thesis is to understand how confinement alters the phase diagram of supercooled liquid water by employing methods of statistical mechanics and numerical simulations. Water is very complex and anomalous when compared to simple liquids. For example, experimental data for liquid water reveals the presence of a temperature of maximum density (TMD) below which the density decreases under isobaric cooling. Another anomaly is the hypothesized liquid- liquid phase transition (LLPT) between two types of liquid water with different densities. In this thesis we study how confinement affects such anomalies as TMD and LLPT in supercooled liquid water. This thesis is separated into three parts: (i) Monte Carlo simulations of a 2D coarsegrained model of a water layer confined in a fixed disordered matrix of hydrophobic nanoparticles, (ii) molecular dynamics simulations of a Jagla ramp model of liquid confined in fixed ordered and disordered matrices of hydrophobic nanoparticles, and (iii ) all-atom simulations of trehalose and maltose in aqueous solut ion of lysozyme. In Part (i), we perform Monte Carlo simulations and find that a nanoparticle concentration as small as 2.4% is enough to destroy the LLPT for pressure P > 0.14 GPa. Moreover, we find a substantial (more t han 90%) decrease of compressibility, t hermal expansion coefficient and specific heat at high P and low temperature T upon increase of nanoparticle concentration from 0% to 25%. In Part (ii), we ask how, for single component systems interacting via a soft-core isotropic potential with two characteristic length scales, t he geometry of hydrophobic confinement affects the phase diagram. We use molecular dynamics simulations to study particles interacting through a ramp potential and a shoulder potential, each confined in a fixed matrix of nanoscopic particles with a fixed volume fraction. We find a substantial weakening of the LLPT and the disappearance of TMD upon the increase of disorder in the confining geometry. In Part (iii), we study aqueous systems with all-atom simulations. We are currently investigating the mechanism of water-trehalose-protein and water-maltose-protein interaction upon supercooling for its relevance to bioprotection.2031-01-0

Understanding CNS Effects of Antimicrobial Drugs Using Zebrafish Models

Antimicrobial drugs represent a diverse group of widely utilized antibiotic, antifungal, antiparasitic and antiviral agents. Their growing use and clinical importance necessitate our improved understanding of physiological effects of antimicrobial drugs, including their potential effects on the central nervous system (CNS), at molecular, cellular, and behavioral levels. In addition, antimicrobial drugs can alter the composition of gut microbiota, and hence affect the gut–microbiota–brain axis, further modulating brain and behavioral processes. Complementing rodent studies, the zebrafish (Danio rerio) emerges as a powerful model system for screening various antimicrobial drugs, including probing their putative CNS effects. Here, we critically discuss recent evidence on the effects of antimicrobial drugs on brain and behavior in zebrafish, and outline future related lines of research using this aquatic model organism

Understanding CNS Effects of Antimicrobial Drugs Using Zebrafish Models

Antimicrobial drugs represent a diverse group of widely utilized antibiotic, antifungal, antiparasitic and antiviral agents. Their growing use and clinical importance necessitate our improved understanding of physiological effects of antimicrobial drugs, including their potential effects on the central nervous system (CNS), at molecular, cellular, and behavioral levels. In addition, antimicrobial drugs can alter the composition of gut microbiota, and hence affect the gut–microbiota–brain axis, further modulating brain and behavioral processes. Complementing rodent studies, the zebrafish (Danio rerio) emerges as a powerful model system for screening various antimicrobial drugs, including probing their putative CNS effects. Here, we critically discuss recent evidence on the effects of antimicrobial drugs on brain and behavior in zebrafish, and outline future related lines of research using this aquatic model organism