Related papers: Protein crystallization in vivo
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
We show that in experimental atomic force microscopy studies of the lifetime distribution of mechanically stressed folded proteins the effects of externally applied fluctuations can not be distinguished from those of internally present…
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to…
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number of different proteins (10%). These nucleoid proteins act as regulators of gene expression…
Recent experiments have revealed that cytoplasms become glassy when their metabolism is suppressed, while they maintain fluidity in a living state. The mechanism of this active fluidization is not clear, especially for bacterial cytoplasms,…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
In this article we describe the crystallization conjecture. It states that, in appropriate physical conditions, interacting particles always place themselves into periodic configurations, breaking thereby the natural translation-invariance…
Coagulation-fragmentation processes describe the stochastic association and dissociation of particles in clusters. Cluster dynamics with cluster-cluster interactions for a finite number of particles has recently attracted attention…
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…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of…
Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
Protein flotation is a process in which protein molecules are enriched by adsorption at rising bubbles. The bubbles then form a foam above the solution, where the liquid drains down and the dried foam, which is concentrated in protein, is…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Since the 1920s, packing arguments have been used to rationalize crystal structures in systems ranging from atomic mixtures to colloidal crystals. Packing arguments have recently been applied to complex nanoparticle structures, where they…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…