Related papers: Protein Structure Parameterization via Mobius Dist…
Determining the 3D structures of proteins is essential in understanding their behavior in the cellular environment. Computational methods of predicting protein structures have advanced, but assessing prediction accuracy remains a challenge.…
Understanding complex biological macromolecules, especially proteins, is vital for grasping their diverse chemical functions with direct impact in biology and pharmacology. While techniques like X-ray crystallography and cryo-electron…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been…
In cell membranes, proteins and lipids are organized into sub-micrometric nanodomains of varying size, shape and composition, performing specific functions. Despite their biological importance, the detailed morphology of these nanodomains…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
Assessing the structural properties of large proteins is important to gain an understanding of their function in, e.g., biological systems or biomedical applications. We propose a method to examine the mechanical properties of proteins…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
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…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…