Related papers: Effect of hydrogen bonds on protein stability
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
For a model deca-alanine peptide the cavity (ideal hydrophobic) contribution to hydration favors the helix state in the coil-to-helix transition and the paired helix bundle in the assembly of two helices. The energetic contributions of…
We study ion pair dissociation in water at ambient conditions using a combination of classical and ab initio approaches. The goal of this study is to disentangle the sources of discrepancy observed in computed potentials of mean force. In…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Molecular dynamics results on water confined in a silica pore in the low hydration regime are presented. Strong layering effects are found due to the hydrophilic character of the substrate. The local properties of water are studied as…
We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We find that bond lifetime (``fast dynamics'') has Arrhenius temperature dependence. We also calculate the bond correlation function…
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through…
We present a coarse-grained model for ionic surfactants in explicit aqueous solutions, and study by computer simulation both the impact of water content on the morphology of the system, and the consequent effect of the formed interfaces on…
Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the…
Hydrogen bond symmetrization is a fundamental pressure-induced transformation in which the distinction between donor and acceptor sites vanishes, resulting in a symmetric hydrogen-bond network. While extensively studied in pure ice, most…
Hydrogen exhibits unusual behaviors at megabar pressures, with consequences for planetary science, condensed matter physics and materials science. Experiments at such extreme conditions are challenging, often resulting in hard-to-interpret…
Multivalent associative proteins with strong complementary interactions play a crucial role in phase separation of intracellular liquid condensates. We study the internal dynamics of such "bond-network" condensates comprised of two…
The zero point kinetic energy of protons in water is large on the scale of chemical interaction energies(29 Kj/mol in bulk room temperature water). Its value depends upon the structure of the hydrogen bond network, and can change as the…
The mechanism behind mutual recognition of homologous DNA sequences prior to genetic recombination is one of the remaining puzzles in molecular biology. Leading models of homology recognition, based on classical electrostatics, neglect the…
We investigate the effect of pressure on the carbon dioxide (CO$_{2}$) hydrate-water interfacial free energy along its dissociation line using advanced computer simulation techniques. In previous works, we have determined the interfacial…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
New experiments for water at the surface of proteins at very low temperature display intriguing dynamic behaviors. The extreme conditions of these experiments make it difficult to explore the wide range of thermodynamic state points needed…
Interfacial hydration structures are crucial in wide-ranging applications, including battery, colloid, lubrication etc. Multivalent ions like Mg2+ and La3+ show irreplaceable roles in these applications, which are hypothesized due to their…
Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine…
The hydrogen-bonded structure of methanol-water mixtures is investigated over the entire alcohol concentration range (from $x_{\mathrm{Methanol}}=$ 0.1 to 1.0) at several temperatures, from 300 K down to the freezing point of the given…