Related papers: Local Interactions and Protein Folding: A Model St…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
In a recent work we proposed a coarse-grained methodology for studying the response of peptides when simulated at different values of pH; in this work we extend the methodology to analyze the pH-dependent behavior of coiled coils. This…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We study a model lipid bilayer composed of a mixture of two incompatible lipid types which have a natural tendency to segregate in the absence of membrane fluctuations. The membrane is mechanically characterized by a local bending rigidity…
We use the Random Phase Approximation (RPA) to compute the structure factor, S(q), of a solution of chains interacting through a soft and short range repulsive potential V. Above a threshold polymer concentration, whose magnitude is…
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form clusters, interconnected via neutral networks, in the space…
The formation of colloidal gels is strongly dependent on the volume fraction of the system and the strength of the interactions between the colloids. Here we explore very dilute solutions by the means of numerical simulations, and show…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
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…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
We investigate the ground state of a one-dimensional lattice system that hosts two different kinds of excitations (species) which interact with a power-law potential. Interactions are only present between excitations of the same kind and…
We investigate the mechanisms underlying selective molecular recognition of single heteropolymers at chemically structured planar surfaces. To this end, we study systems with two-letter (HP) lattice heteropolymers by exact enumeration…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
A theory for sequence dependent liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) in the study of biomolecular condensates is formulated by extending the random phase approximation (RPA) and field-theoretic…
Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…
Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the…
Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone, or by non-local tertiary interactions? To answer this question we have measured the entropy densities…
A typical protein structure is a compact packing of connected alpha-helices and/or beta-strands. We have developed a method for generating the ensemble of compact structures a given set of helices and strands can form. The method is tested…
I explore the form of the effective interaction in harmonic-oscillator-based effective theory (HOBET) in next-to-next-to-next-to-leading order (N3LO). As the included space in a HOBET (as in the shell model) is defined by the oscillator…