Related papers: Universal effects of solvent species on the stabil…
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…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
The aqueous solvent profoundly influences protein folding, yet its effects are relatively poorly understood. In this study, we investigate the impact of solvation on the folding of lattice proteins by using Monte Carlo simulations. The…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
Understanding the atomic level interactions and the resulting structural characteristics is required for developing beta-cyclodextrin ($\beta$CD) derivatives for pharmaceutical and other applications. The effect of four different solvents…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
Using molecular dynamics and thermodynamic integration, we report on the solvation process in water and in cyclohexane of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU). The polypeptides are selected to cover the full hydrophobic…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Despite the spontaneity of some in vitro protein folding reactions, native folding in vivo often requires the participation of barrel-shaped multimeric complexes known as chaperonins. Although it has long been known that chaperonin…
We study continuous finite element dicretizations for one dimensional hyperbolic partial differential equations. The main contribution of the paper is to provide a fully discrete spectral analysis, which is used to suggest optimal values of…
We consider a general incompressible finite model protein of size M in its environment, which we represent by a semiflexible copolymer consisting of amino acid residues classified into only two species (H and P, see text) following Lau and…