相关论文: Molecular Mechanics of Chitin-Protein Interface

Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…

Proteins need to selectively interact with specific targets among a multitude of similar molecules in the cell. But despite a firm physical understanding of binding interactions, we lack a general theory of how proteins evolve high…

Chemical bonding governs how atoms interact to form compounds, thereby determining their physicochemical properties. Despite being an elusive concept, chemical bonding has led to the development of models and tools to explain and predict…

Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction…

Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…

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…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…

Proteins are intricate molecular machines whose complexity arises from the heterogeneity of the amino acid building blocks and their dynamic network of many-body interactions. These nanomachines gain function when put in the context of a…

There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the…

The cytoplasm and biomembranes in biological cells contain large numbers of proteins that cyclically change their shapes. They are molecular machines that can function as molecular motors or carry out many other tasks in the cell. We…

Proteins are macromolecules which hardly act alone; they need to make interactions with some other proteins to do so. Numerous factors are there which can regulate the interactions between proteins [4]. Here in this present study we aim to…

Water contained within biological membranes plays a critical role in maintaining the separation between intracellular and extracellular environments and facilitating biochemical processes. Variations in membrane composition and temperature…

Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…

We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…

Elastin is a structural protein with outstanding mechanical properties (e.g., elasticity and resilience) and biologically relevant functions (e.g., triggering responses like cell adhesion or chemotaxis). It is formed from its precursor…

We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…

Soft materials, such as colloidal suspensions, polymer solutions, and biological systems, are typically multicomponent mixtures of macromolecules and simpler components (e.g., microions, monomers, solvent) that can assemble into complex…

All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…