Related papers: On Hydrophobicity Correlations in Protein Chains
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment. Using an exactly solvable lattice model, we design…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
Using a simple hydrophobic/polar protein model, we perform a Monte Carlo study of the thermodynamics and kinetics of binding to a target structure for two closely related sequences, one of which has a unique folded state while the other is…
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…
The tendency of amphiphilic molecules to form micelles in aqueous solution is a consequence of the hydrophobic effect. The fundamental difference between micelle assembly and macroscopic phase separation is the stoichiometric constraint…
In this manuscript, we present a general computational method for characterizing the molecular structure of liquid water interfaces as sampled from atomistic simulations. With this method, the interfacial structure is quantified based on…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Current major approaches to access surface hydrophobicity include directly introducing hydrophobic nonpolar groups/molecules into surface or elaborately fabricating surface roughness. Here, for the first time, molecular dynamics simulations…
We have studied the molecular scale hydrophobicity of an apolar solute, argon, confined between hydrophobic planar surfaces with different confinement widths. Specifically, we find that the hydrophobicity exhibits a non-monotonic behavior…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
We study statistical properties of DNA chains of thirteen microbial complete genomes. We find that the power spectrum of several of the sequences studied flattens off in the low frequency limit. This implies that the correlation length in…
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed…
This paper considers three kinds of length sequences of the complete genome. Detrended fluctuation analysis, spectral analysis, and the mean distance spanned within time $L$ are used to discuss the correlation property of these sequences.…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
We study the thermodynamic behavior of a model protein with 54 amino acids that is designed to form a three-helix bundle in its native state. The model contains three types of amino acids and five to six atoms per amino acid, and has the…
The distributions of many proteins in rod-shaped bacteria are far from homogenous. Often they accumulate at the cell poles or in the cell center. At the same time, the copy number of proteins in a single cell is relatively small making the…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…