Related papers: Evolution and Function of SMC Proteins
Protein aggregates exhibit diverse morphology, exemplified by amyloid fibrils, gel-like structures, and liquid-like condensates. Differences in the morphologies in identical proteins play important functional roles in several diseases.…
Recently we have shown experimental evidence for a fragile-to-strong dynamic crossover (FSC) phenomenon in hydration water around a globular protein (lysozyme) at ambient pressure. In this letter we show that when applying pressure to the…
Self-organized criticality (SOC) is a popular concept that has been the subject of more than 3000 articles in the last 25 years. Here we show that SOC may enable theory to connect standard Web-based (BLAST) short-range amino acid (aa)…
The conformational dynamics of a single protein molecule in a shear flow is investigated using Brownian dynamics simulations. A structure-based coarse grained model of a protein is used. We consider two proteins, ubiquitin and integrin, and…
Molecular diffusion measurements are widely used to probe microstructure in materials and living organisms noninvasively. The precise relation of diffusion metrics to microstructure remains a major challenge: In complex samples, it is often…
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in…
The eukaryotic cell nucleus harbors the DNA genome that is organized in a dynamic chromatin network and embedded in a viscous crowded fluid. This environment directly affects enzymatic reactions and target search processes that access the…
A tight-binding model together with a novel statistical method are used to investigate the relation between the sequence-dependent electric transport properties and the sequences of protein-coding regions of complete genomes. A correlation…
A highly diluted aqueous solution of histamine was studied by molecular dynamics using the TIP3P and SPC/E water models. It was shown that the local structure of the solution around histamine is determined by local Coulomb interactions and…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
Random walks on multidimensional nonlinear landscapes are of interest in many areas of science and engineering. In particular, properties of adaptive trajectories on fitness landscapes determine population fates and thus play a central role…
We study the low-frequency, long-wavelength dynamics of liquid crystal elastomers, crosslinked in the smectic-$A$ phase, in their smectic-$A$, biaxial smectic and smectic-$C$ phases. Two different yet related formulations are employed. One…
Using molecular dynamics simulations we investigate the relaxation dynamics of a supercooled liquid close to a rough as well as close to a smooth wall. For the former situation the relaxation times increase strongly with decreasing distance…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
Composed of amino acid chains that influence how they fold and thus dictating their function and features, proteins are a class of macromolecules that play a central role in major biological processes and are required for the structure,…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
The supra-molecular structure of a liquid is strongly connected to its dynamics which in turn controls macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential…