Related papers: Conformational changes in glycine tri- and hexapep…
The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is…
We used for the first time the method of periodic orbit dividing surfaces in a non-integrable Hamiltonian system with three degrees of freedom. We have studied the structure of these four dimensional objects in the five dimensional phase…
The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the…
Glycans are structurally diverse and flexible biomolecules that play key roles in many biological processes. Their conformational variability makes the modeling of their interactions with proteins particularly challenging. This chapter…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Surface energies and surface elasticity largely affect the mechanical response of nanostructures as well as the physical phenomenon associated with surfaces such as evaporation and adsorption. Studying surface energies at finite…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
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…
Recent experimental studies have observed a surprisingly wide range of strengths in polycrystalline graphene. Previous computational investigations of graphene tilt boundaries have highlighted the role of interfacial topology in determining…
This work describes the development of a third-generation charge optimized many-body (COMB3) potential for Al-C and its application to the investigation of aluminum/graphene nanostructures. In particular, the new COMB3 potential was used to…
Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here, we show successful all-atom ab initio…
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…
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 systematically study phase transformations from one helical structure to another. Motivated in part by recent work that relates the presence of compatible interfaces with properties such as the hysteresis and reversibility of a phase…
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling…
We present a combination of the recently developed double incremental expansion of potential energy surfaces with the well-established adaptive density-guided approach to grid construction. This unique methodology is based on the use of an…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…