Related papers: Osmolyte-Induced Protein Stability Changes Explain…
The strength of the lithosphere is typically modelled based on constitutive equations for steady-state flow. However, models of lithospheric flexure reveal differences in lithospheric strength that are difficult to reconcile based on such…
Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…
We study cold denaturation of proteins at high pressures. Using multicanonical Monte Carlo simulations of a model protein in a water bath, we investigate the effect of water density fluctuations on protein stability. We find that above the…
Two types of osmolytes, i.e., trimethylamin N-oxide (TMAO) and urea, demonstrate dramatically different properties in a protein folding process. Even with the great progresses in revealing the potential underlying mechanism of these two…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
The current work analyses the onset characteristics of buoyancy and thermocapillary-driven instabilities in two-layer binary fluid systems near their upper critical solution temperature (UCST). The dynamics of the binary fluids are modelled…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
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…
The Fenna Mathews Olson (FMO) complex of green sulphur bacteria is an example of a photosynthetic pigment protein complex, in which the electronic properties of the pigments are modified by the protein environment to promote efficient…
Despite being used for decades as stabilizers, amino acids (AAs) remain mysterious components of many medical and biological formulations. Hypotheses on their role vary ranging from hydrotropic to protein-specific effects (stabilization…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
The protein-polysaccharide combinations that lead to electrostatic complex and coacervates formation are the object of extensive research using both layer-by-layer and mixed emulsion approaches. The protein-polysaccharide conjugates…
To date, the instability of prognostic predictors in a sparse high dimensional model, which hinders their clinical adoption, has received little attention. Stable prediction is often overlooked in favour of performance. Yet, stability…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
It has recently been demonstrated that many biological networks exhibit a scale-free topology where the probability of observing a node with a certain number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has been…
Functional proteins must fold with some minimal stability to a structure that can perform a biochemical task. Here we use a simple model to investigate the relationship between the stability requirement and the capacity of a protein to…
The field of molecular excitons and related supramolecular systems has largely focused on aggregates where nearest-neighbour couplings dominate. We propose that radically different states can be produced by moving beyond that paradigm. In…
We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…