相关论文: Influence of pH and sequence in peptide aggregatio…
In this work we study the tertiary structure of ionic surfactants when the pH in the system is modified using electrostatic dissipative particle dynamics simulations (DPD). The dependence with pH and kind of surfactant is presented. Our…
Specific interactions between cations and proteins have a strong impact on peptide and protein structure. We here shed light on the nature of the underlying interactions, especially regarding the effects on the polyamide backbone structure.…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
A significant part of the proteome is composed of intrinsically-disordered proteins (IDPs). These proteins do not fold into a well-defined structure and behave like ordinary polymers. In this work we consider IDPs which have the tendency to…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
The thermal and mechanical behaviors of powders are important for various additive manufacturing technologies. For powder bed fusion, capturing the temperature profile and the packing structure of the powders prior to melting is challenging…
The effect of rigid inclusions on the phase behavior of a film containing a mixture of lipid molecules is investigated. In the proposed model, the inclusion-induced deformation of the film, and the resulting energy cost are strongly…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…
Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales…
The formation and proliferation of protein aggregates play a central role in a number of devastating neuro-degenerative diseases. Many experimental studies indicate that the ability of existing aggregates to replicate is a key property in…
The aggregation of amyloid-forming peptides is a dynamic, complex process that underlies their diverse biological activities, from physiological functions to disease-associated dysfunctions. While the structure of fibrillar end-products is…
The supramolecular assembly of lipids into bilayer membranes is essential for cellular structure and function. However, the impact of lipid structural variations such as acyl chain length, degree of unsaturation, and headgroup type on…
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…
The effects of polymer concentration and chain length on aggregation in associative polymer solutions, are studied using self-consistent field lattice model. Only two inhomogenous morphologies, i.e. microfluctuation homogenous (MFH) and…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
Understanding the intertwined contributions of amino acid sequence and spatial structure is essential to explain protein behaviour. Here, we introduce INFUSSE (Integrated Network Framework Unifying Structure and Sequence Embeddings), a deep…
Numerical simulation of the dynamics of planar two- and three-layer molecular structures formed by $\beta$-sheets of polyglycine peptide chains and systems of parallel Kevlar (para-aramid) molecules placed on a graphene sheet has been…
The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show…