Related papers: Long-range energy transfer in proteins

The anisotropic feature of charge transfer reactions in realistic proteins cannot be ignored, due to the highly complex chemical structure of bio-molecules. In this work, we have performed the first large-scale quantitative assessment of…

We study how the dynamic equilibrium of the reversible protein-protein binding network in yeast Saccharomyces cerevisiae responds to large changes in abundances of individual proteins. The magnitude of shifts between free and bound…

The efficiencies of light-harvesting complexes in biological systems can be much higher than the current efficiencies of artificial solar cells. In this paper, we therefore propose and analyse an energy transport mechanism which employs…

Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The protein sequences realizing a given function may largely…

Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…

Protein conformational changes are activated processes essential for protein functions. Activation in a protein differs from activation in a small molecule in that it involves directed and systematic energy flows through preferred channels…

All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes initiation, elongation, termination, and…

The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

The increasing interest in photoactivated proteins as natural replacement of standard inorganic materials in photocells drives to the compared analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the…

Allostery is a fundamental property of proteins that represents the functional coupling between distantly located sites. In different manifestations, this property underlies signal transduction, gene expression, and regulation -- elementary…

Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…

The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…

Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…

By using a Generalized Hubbard model for bosons, the energy transfer in a nonlinear quantum lattice is studied, with special emphasis on the interplay between local and nonlocal nonlinearity. For a strong local nonlinearity, it is shown…

Proteins are known to locate their specific targets on DNA up to two orders of magnitude faster than predicted by the Smoluchowski three-dimensional diffusion rate. One of the mechanisms proposed to resolve this discrepancy is termed…

Protein-protein interactions comprise both transport and reaction steps. During the transport step, anisotropy of proteins and their complexes is important both for hydrodynamic diffusion and accessibility of the binding site. Using a…

The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

We show how active transport of ions can be interpreted as an entropy facilitated process. In this interpretation, the pore geometry through which substrates are transported can give rise to a driving force. This gives a direct link between…

Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…