arXiv subjects

Valentino Bianco

Publications and source records attributed to Valentino Bianco.

26 records · Page 2Linked to original sources

arXiv2017

Multi-scale approach for self-Assembly and protein folding

We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of water at bio-interfaces (e.g., proteins or membranes) and nano-interfaces (e.g., nanoparticles or graphene sheets) and coarse-grain models of hydration water for protein folding and protein design. We study protein self-assembly and crystallization, in bulk or under confinement, and the kinetics of protein adsorption onto nanoparticles, verify- ing our predictions in collaboration with several experimental groups. We try to find answers for fundamental questions (Why water is so important for life? Which properties make water unique for biological processes?) and applications (Can we design better drugs? Can we limit protein- aggregations causing Alzheimer? How to implement nanotheranostic?). Here we focus only on the two larger scales of our approach: (i) The coarse-grain description of hydrated proteins and protein folding at sub-nanometric length-scale and milliseconds-to-seconds time-scales, and (ii) the coarse-grain modeling of protein self-assembly on nanoparticles at 10-to-100 nm length-scale and seconds-to-hours time-scales.

cond-mat.soft↗

arXiv2017

How the stability of a folded protein depends on interfacial water properties and residue-residue interactions

Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule is denaturated. It is known that the extension and shape of the SR depend on i) the specific protein residue-residue interactions in the native state of the amino acids sequence and ii) the water properties at the hydration interface. Here we analyze by Monte Carlo simulations of different coarse-grained protein models in explicit water how changes in i) and ii) affect the SR. We show that the solvent properties ii) are essential to rationalize the SR shape at low T and high P and that our finding are robust with respect to parameter changes and with respect to different protein models. These results can help in developing new strategies for the design of novel synthetic biopolymers.

cond-mat.soft↗

arXiv2016

Liquid-Liquid Critical Point in 3D Many-Body Water Model

Many-body interactions can play a relevant role in water properties. Here we study by Monte Carlo simulations a coarse-grained model for bulk water that includes many-body interactions associated to water cooperativity. The model is efficient and allows us to equilibrate water at extreme low temperatures in a wide range of pressures. We find the line of temperatures of maximum density at constant pressure and, at low temperature and high pressure, a phase transition between high-density liquid and low-density liquid phases. The liquid-liquid phase transition ends in a critical point. In the supercritical liquid region we find for each thermodynamic response function a locus of weak maxima at high temperature and a locus of strong maxima at low temperature, with both loci converging at the liquid-liquid critical point where they diverge. Comparing our results with previous works for the phase diagram of a many-body water monolayer, we observe that the weak maxima of the specific heat are less evident in bulk and appear only at negative pressures, while we find those of compressibility and thermal expansion coefficient also at positive pressures in bulk. However, the strong maxima of compressibility and thermal expansion coefficient are very sharp for the bulk case. Our results clarify fundamental properties of bulk water, possibly difficult to detect with atomistic models not accounting for many-body interactions.

cond-mat.stat-mech↗

arXiv2016

Reentrant spinodals and the Speedy scenario in colloidal model systems

A re-entrant gas-liquid spinodal was proposed as a possible explanation of the apparent divergence of the compressibility and specific heat on supercooling water. Such a counter intuitive possibility, e.g. a liquid that becomes unstable to gas-like fluctuations on cooling at positive pressure, has never been observed, neither in real substances nor in off-lattice simulations. More recently, such re-entrant scenario has been dismissed on the premise that the re-entrant spinodal would collide with the gas-liquid binodal in the pressure-temperature plane. Here we study, numerically and analytically, two previously introduced one-component patchy particle models that both show (i) a re-entrant spinodal and (ii) a re-entrant binodal, providing a neat in silico (and in charta) realization of such unconventional thermodynamic scenario.

cond-mat.soft↗

arXiv2016

Universal criterion for designability of heteropolymers

Proteins are an example of heteropolymers able to self-assemble in specific target structures. The self-assembly of designed artificial heteropolymers is still, to the best of our knowledge, not possible with control over the single chain self-assembling properties comparable to what natural proteins can achieve. What artificial heteropolymers lacks compared to bio-heteropolymers that grants the latter such a versatility? Is the geometry of the protein skeleton the only a particular choice to be designable? Here we introduce a general criteria to discriminate which polymer backbones can be designed to adopt a predetermined structure. With our approach we can explore different polymer backbones and different amino acids alphabets. By comparing the radial distribution functions of designable and not-designable scenarios we identify as designability criteria the presence of a particular peak in the radial distribution function that dominates over the random packing of the heteropolymer. We show that the peak is a universal feature of all designable heteropolymers, as it is dominating also the radial distribution function of natural proteins. Our finding can help in understanding the key features that make proteins a highly designable system. The criteria that we present can be applied to engineer new types of self-assembling modular polymers that will open new applications for polymer based material science.

cond-mat.soft↗

arXiv2014

Critical behavior of a water monolayer under hydrophobic confinement

The properties of water can have a strong dependence on the confinement. Here, we consider a water monolayer nanoconfined between hydrophobic parallel walls under conditions that prevent its crystallization. We investigate, by simulations of a many-body coarse-grained water model, how the properties of the liquid are affected by the confinement. We show, by studying the response functions and the correlation length and by performing finite-size scaling of the appropriate order parameter, that at low temperature the monolayer undergoes a liquid-liquid phase transition ending in a critical point in the universality class of the two-dimensional (2D) Ising model. Surprisingly, by reducing the linear size L of the walls, keeping the walls separation h constant, we find a 2D-3D crossover for the universality class of the liquid-liquid critical point for L/h~50, i.e. for a monolayer thickness that is small compared to its extension. This result is drastically different from what is reported for simple liquids, where the crossover occurs for L/h ~ 5, and is consistent with experimental results and atomistic simulations. We shed light on these findings showing that they are a consequence of the strong cooperativity and the low coordination number of the hydrogen bond network that characterizes water.

cond-mat.soft↗

arXiv2010

Water at interface with proteins

Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of the hydration water and the dynamics of protein. These works have generated a large amount of data whose interpretation is debated. New experiments measure the dynamics of water at low temperature on the surface of proteins, finding a qualitative change (crossover) that might be related to the slowing down and stop of the protein's activity (protein glass transition), possibly relevant for the safe preservation of organic material at low temperature. To better understand the experimental data several scenarios have been discussed. Here, we review these experiments and discuss their interpretations in relation with the anomalous properties of water. We summarize the results for the thermodynamics and dynamics of supercooled water at an interface. We consider also the effect of water on protein stability, making a step in the direction of understanding, by means of Monte Carlo simulations and theoretical calculations, how the interplay of water cooperativity and hydrogen bonds interfacial strengthening affects the protein cold denaturation.

physics.bio-ph↗

arXiv2010

Effect of hydrogen bonds on protein stability

The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density fluctuations of surface water, or the destabilization of hydrophobic contacts because of the displacement of water molecules inside the protein, as proposed for high pressures. However, it is clear that water plays a fundamental role in the process. Here, we review some models that have been proposed to give insight into this problem. Next we describe a coarse-grained model of a water monolayer that successfully reproduces the complex thermodynamics of water and compares well with experiments on proteins at low hydration level. We introduce its extension for a homopolymer in contact with the water monolayer and study it by Monte Carlo simulations. Our goal is to perform a step in the direction of understanding how the interplay of cooperativity of water and interfacial hydrogen bonds affects the protein stability and the unfolding.

physics.bio-ph↗