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We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
The purpose of this study was to report numerical validation of a 3D finite element model of contracting muscle. The model was based on continuum theory for fibre-reinforced composite materials. Here we simulated contractions for an…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins.…
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
Soft slender structures are ubiquitous in natural and artificial systems and can be observed at scales that range from the nanometric to the kilometric, from polymers to space tethers. We present a practical numerical approach to simulate…
We investigate the shear elastic modulus of soft polymer foams loaded with hard spherical particles and we show that, for constant bubble size and gas volume fraction, strengthening is strongly dependent on the size of those inclusions.…
Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps…
The folding dynamics of proteins at the single molecule level has been studied with single-molecule force spectroscopy (SMFS) experiments for twenty years, but a common standardized method for the analysis of the collected data and for the…
Protein activity is a significant characteristic for recombinant proteins which can be used as biocatalysts. High activity of proteins reduces the cost of biocatalysts. A model that can predict protein activity from amino acid sequence is…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Protein biologics hold immense potential in therapeutic applications, but their ephemeral nature has hindered their widespread application. The effects of different stressors on protein folding have long been studied, but whether these…
Mechanical strength of amyloid beta fibrils has been known to be correlated with neuronal cell death. Here, we resorted to steered molecular dynamics (SMD) simulations to mechanically stretch a single S-shape amyloid beta Abeta11-42…