44 research outputs found
Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state
An important step in a phospholipid membrane pore formation by melittin
antimicrobial peptide is a reorientation of the peptide from a surface into a
transmembrane conformation. In this work we perform umbrella sampling
simulations to calculate the potential of mean force (PMF) for the
reorientation of melittin from a surface-bound state to a transmembrane state
and provide a molecular level insight into understanding peptide and lipid
properties that influence the existence of the free energy barrier. The PMFs
were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We
observe that the free energy barrier is reduced when the P/L ratio increased.
In addition, we study the cooperative effect; specifically we investigate if
the barrier is smaller for a second melittin reorientation, given that another
neighboring melittin was already in the transmembrane state. We observe that
indeed the barrier of the PMF curve is reduced in this case, thus confirming
the presence of a cooperative effect
Entropy of Molecular Binding at Solvated Mineral Surfaces
We present thermodynamic integration simulations for the binding of mannose and methanoic acid onto the {10.4} calcite surface producing free energy of binding values of −2.89 and −1.64 kJ mol–1, respectively. We extract the entropy of binding from vacuum-based simulations and use these values to determine the entropy of binding for surface water molecules which is ∼6 J mol–1 K–1
Three Stages of Lysozyme Thermal Stabilization by High and Medium Charge Density Anions
Addition of high and medium charge density anions (phosphate, sulfate, and chloride) to lysozyme in pure water demonstrates three stages for stabilization of the protein structure. The first two stages have a minor impact on lysozyme stability and are probably associated with direct interaction of the ions with charged and partial charges on the protein’s surface. There is a clear transition between the second and third stages; in the case of sodium chloride, disodium sulfate and disodium hydrogen phosphate this is at 550, 210, and 120 mM, respectively. Stabilization of lysozyme can be explained by the free energy required to hydrate the protein as it unfolds. At low ion concentrations, the protein’s hydration layer is at equilibrium with the bulk water. After the transition, bulk water is depleted and the protein is competing for water with the ions. With competition for water between the protein and the ions at higher salt concentrations, the free energy required to hydrate the interior of the protein rises and it is this that stabilizes the protein structure
Water in Cavity−Ligand Recognition
We use explicit solvent molecular dynamics simulations to estimate free energy, enthalpy, and entropy changes along the cavity-ligand association coordinate for a set of seven model systems with varying physicochemical properties. Owing to the simplicity of the considered systems we can directly investigate the role of water thermodynamics in molecular recognition. A broad range of thermodynamic signatures is found in which water (rather than cavity or ligand) enthalpic or entropic contributions appear to drive cavity-ligand binding or rejection. The unprecedented, nanoscale picture of hydration thermodynamics can help the interpretation and design of protein-ligand binding experiments. Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models
Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods
We have used combined quantum mechanical and molecular mechanical free-energy perturbation
methods in combination with explicit solvent simulations to study the reaction mechanism of the
multicopper oxidases, in particular the regeneration of the reduced state from the native
intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states
of the copper ions and the protonation states of water- and O2-derived ligands, we have studied
redox potentials, acidity constants, isomerisation reactions, as well as water- and O2 binding
reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with
atomic detail. We also show that the two copper sites in the protein communicate so that redox
potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change
in the oxidation state of the other site
Hydrophobically Modified Sulfobetaine Copolymers with Tunable Aqueous UCST through Postpolymerization Modification of Poly(pentafluorophenyl acrylate)
Polysulfobetaines, polymers carrying highly polar zwitterionic side chains, present a promising research field by virtue of their antifouling properties, hemocompatibility, and stimulus-responsive behavior. However, limited synthetic approaches exist to produce sulfobetaine copolymers comprising hydrophobic components. Postpolymerization modification of an activated ester precursor, poly(pentafluorophenyl acrylate), employing a zwitterionic amine, 3-((3-aminopropyl)dimethylammonio)propane-1-sulfonate, ADPS, is presented as a novel, one-step synthetic concept toward sulfobetaine (co)polymers. Modifications were performed in homogeneous solution using propylene carbonate as solvent with mixtures of ADPS and pentylamine, benzylamine, and dodecylamine producing a series of well-defined statistical acrylamido sulfobetaine copolymers containing hydrophobic pentyl, benzyl, or dodecylacrylamide comonomers with well-controllable molar composition as evidenced by NMR and FT-IR spectroscopy and size exclusion chromatography.This synthetic strategy was exploited to investigate, for the first time, the influence of hydrophobic modification on the upper critical solution temperature (UCST) of sulfobetaine copolymers in aqueous solution. Surprisingly, incorporation of pentyl groups was found to increase solubility over a wide composition range, whereas benzyl groups decreased solubility—an effect attributed to different entropic and enthalpic contributions of both functional groups. While UCST transitions of polysulfobetaines are typically limited to higher molar mass samples, incorporation of 0–65 mol % of benzyl groups into copolymers with molar masses of 25.5–34.5 kg/mol enabled sharp, reversible transitions from 6 to 82 °C in solutions containing up to 76 mM NaCl, as observed by optical transmittance and dynamic light scattering. Both synthesis and systematic UCST increase of sulfobetaine copolymers presented here are expected to expand the scope and applicability of these smart materials
What can health inequalities researchers learn from an intersectionality perspective?:Understanding social dynamics with an inter-categorical approach
The concept of intersectionality was developed by social scientists seeking to analyse the multiple interacting influences of social location, identity and historical oppression. Despite broad take-up elsewhere, its application in public health remains underdeveloped. We consider how health inequalities research in the United Kingdom has predominantly taken class and later socioeconomic position as its key axis in a manner that tends to overlook other crucial dimensions. We especially focus on international research on ethnicity, gender and caste to argue that an intersectional perspective is relevant for health inequalities research because it compels researchers to move beyond (but not ignore) class and socioeconomic position in analysing the structural determinants of health. Drawing on these theoretical developments, we argue for an inter-categorical conceptualisation of social location that recognises differentiation without reifying social groupings – thus encouraging researchers to focus on social dynamics rather than social categories, recognising that experiences of advantage and disadvantage reflect the exercise of power across social institutions. Such an understanding may help address the historic tendency of health inequalities research to privilege methodological issues and consider different axes of inequality in isolation from one another, encouraging researchers to move beyond micro-level behaviours to consider the structural drivers of inequalities