相关论文: Influence of pH and sequence in peptide aggregatio…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH…
Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the…
Based on a newly developed contact-density chain-growth algorithm, we have simulated a nongrafted peptide in the vicinity of different attractive substrates. We analyzed the specificity of the peptide adsorption by focussing on the…
A multiphysics modeling approach for heat conduction in metal hydride powders is presented, including particle shape distribution, size distribution, granular packing structure, and effective thermal conductivity. A statistical geometric…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
Peptides are biomolecules comprised of amino acids that play an important role in our body. In recent years, peptides have received extensive attention in drug design and synthesis, and peptide prediction tasks help us better search for…
We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
The primary structures of peptides, originating from food proteins, affect their taste. Connecting primary structure to taste, however, is difficult because the size of the peptide sequence space increases exponentially with increasing…
This paper summarizes previous work linking protein aggregation to the heterozygosity of organisms. It also cites the literature showing a correlation between species' morphological complexity and the lengths of their proteins. These two…
We present a simulation method that allows us to calculate the titration curves for systems undergoing protonation/deprotonation reactions -- such as charged colloidal suspensions with acidic/basic surface groups, polyelectrolytes,…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
By integrating various simulation and experimental techniques, we discovered that antimicrobial peptides (AMPs) may achieve synergy at an optimal concentration and ratio, which can be caused by aggregation of the synergistic peptides. On…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
We present and study a minimal structure-based model for the self-assembly of peptides into ordered beta-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and…
Peptide compounds demonstrate considerable potential as therapeutic agents due to their high target affinity and low toxicity, yet their drug development is constrained by their low membrane permeability. Molecular weight and peptide length…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…