Related papers: Functionality and Protein-Water Interactions
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
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)…
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,…
Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain.…
The peculiar structuring of liquid water stems from a fine-tuned molecular principle embodying the two different interaction demands of the water molecule: The formation of hydrogen bonds or the compensation for coordination defects. Here…
1. Role of inter-domain water clusters in large-scale dynamics of proteins; 2. Description of large-scale dynamics of proteins based on generalized Stokes-Einstein and Eyring-Polany equation; 3. Dynamic model of protein-ligand complexes…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
The ability of water to dissolve biomolecules is crucial for our life. It has been shown that protein has a profound effect on the behavior of water in its hydration shell, which in turn affects the structure and function of the protein.…
Water plays a major role in bio-systems, greatly contributing to determine their structure, stability and even function. It is well know, for instance, that proteins require a minimum amount of water to be functionally active. Since the…
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…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
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…
Water molecules and molecular chaperones efficiently help the protein folding process. Here we describe their action in the context of the energy and topological networks of proteins. In energy terms water and chaperones were suggested to…
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…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter…