Related papers: Simultaneous identification of multiple binding si…

Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…

Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes of proteins in different salt solutions. We demonstrate the existence of ion-specific attractive…

The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…

Hydrogen bonding is modeled in terms of virtual exchange of protons between water molecules. A simple lattice model is analyzed, using ideas and techniques from the theory of correlated electrons in metals. Reasonable parameters reproduce…

Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…

We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…

We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each…

We present an overview of the recent progress that has been made in understanding the origin of hydrophobic interactions. We discuss the different character of the solvation behavior of apolar solutes at small and large length scales. We…

We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of…

We introduce an exactly solvable statistical-mechanical model of the hydration of non-polar compounds, based on grouping water molecules in clusters where hydrogen bonds and isotropic interactions occur; interactions between clusters are…

Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic tendencies of sequence and structure…

We have theoretically studied the uptake of a non-uniformly charged biomolecule, suitable to represent a globular protein or a drug, by a charged hydrogel carrier in the presence of a 1:1 electrolyte. Based on the analysis of a physical…

Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…

Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…

A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…

Elastic netwok models coarse grain proteins into a network of residue beads connected by springs. We add dissipative dynamics to this mechanical system by applying overdamped Langevin equations of motion to normal-mode vibrations of the…

A model of protein-ligand binding kinetics in which slow solvent dynamics results from hydrophobic drying transitions is investigated. Molecular dynamics simulations show that solvent in the receptor pocket can fluctuate between wet and dry…