Related papers: Functionality and Protein-Water Interactions
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
So far, more than 82,000 protein structures have been reported in the Protein Data Bank, but the driving force and structures that allow for protein functions have not been elucidated at the atomic level for even one protein. We have been…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
A new statistical mechanics formulation of characterizing the structural fluctuation of protein correlated with that of water is presented based on the generalized Langevin equation and the 3D-RISM/RISM theory of molecular liquids. The…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
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…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
An all-atom model of proteins is used to show that the same sequence of amino acids can have many alternative structures, that are very distant from, and that can be as stable as, the corresponding native structure. Such alternative…
In addition to the biologically active monomer of the protein Insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The Insulin monomer contains two distinct surfaces, namely…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Thousands of plant and animal species have been observed to have superhydrophobic surfaces that lead to various novel behaviors [1-5]. These observations have inspired attempts to create artificial superhydrophobic surfaces, given such…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
Cells accomplish diverse functions using the same molecular building blocks, from setting up cytoplasmic flows to generating mechanical forces. In particular, transitions between these non-equilibrium states are triggered by regulating the…
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…