Related papers: Estimation of protein folding probability from equ…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
Studies of how protein fold have shown that the way protein clumps form in the test tube is similar to how proteins form the so-called ``amyloid'' deposits that are the pathological signal of a variety of diseases, among them the memory…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
Proteins fold using a two-state or multi-state kinetic mechanisms, but up to now there isn't a first-principle model to explain this different behaviour. We exploit the network properties of protein structures by introducing novel…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
Determining the folding core of a protein yields information about its folding process and dynamics. The experimental procedures for identifying the amino acids which make up the folding core include hydrogen-deuterium exchange and…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
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…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
In this paper we present a method to study the folding structure of a simple model consisting of two kinds of monomers, hydrophobic and hydrophilic. This method has three main steps: an efficient simulation method to bring an open sequence…
We study the free energy landscape of the small peptide Met-enkephalin. Our data were obtained from a generalized-ensemble Monte Carlo simulation taking the interactions among all atoms into account. We show that the free energy landscape…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…