Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of found in experimental measurements. We show that as the hydrophobic interactions increase relative to the temperature, a novel jamming transition occurs when the core packing fraction exceeds . The model also recapitulates the global structure of proteins since it can accurately refold to native-like structures from partially unfolded states.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11118678 | PMC |
Publication Analysis
Top Keywords
Similar Publications
Jamming transition and normal modes of polydispersed soft particle packing.
Soft Matter
January 2025
Delft University of Technology, Process & Energy Laboratory, Leeghwaterstraat 39, 2628 CB Delft, The Netherlands.
The jamming transition of soft particles characterized by narrow size distributions has been well studied by physicists. However, polydispersed systems are more relevant to engineering, and the influence of polydispersity on jamming phenomena is still unexplored. Here, we numerically investigate jamming transitions of polydispersed soft particles in two dimensions.
View Article and Find Full Text PDFIntermittent Thermal Convection in Jammed Emulsions.
Phys Rev Lett
December 2024
Department of Physics and INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133 Rome, Italy.
We study the process of thermal convection in jammed emulsions with a yield-stress rheology. We find that heat transfer occurs via an intermittent mechanism, whereby intense short-lived convective "heat bursts" are spaced out by long-lasting conductive periods. This behavior is the result of a sequence of fluidization-rigidity transitions, rooted in a nontrivial interplay between emulsion yield-stress rheology and plastic activity, which we characterize via a statistical analysis of the dynamics at the droplet scale.
View Article and Find Full Text PDFTransitions between cooperative and crowding-dominated collective motion in non-jammed MDCK monolayers.
Cells Dev
December 2024
Department of Mechanical and Aerospace Engineering, University of Florida, Gainesville, FL 32605, United States of America; Department of Materials Science and Engineering, University of Florida, Gainesville, FL 32605, United States of America; J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32605, United States of America. Electronic address:
Transitions between solid-like and fluid-like states in living tissues have been found in steps of embryonic development and in stages of disease progression. Our current understanding of these transitions has been guided by experimental and theoretical investigations focused on how motion becomes arrested with increased mechanical coupling between cells, typically as a function of packing density or cell cohesiveness. However, cells actively respond to externally applied forces by contracting after a time delay, so it is possible that at some packing densities or levels of cell cohesiveness, mechanical coupling stimulates cell motion instead of suppressing it.
View Article and Find Full Text PDFOnsager variational principle for granular fluids.
Phys Rev E
November 2024
GRASP, Institute of Physics B5a, University of Liège, B4000 Liège, Belgium.
Granular fluids, as defined by a collection of moving solid particles, is a paradigm of a dissipative system out of equilibrium. Inelastic collisions between particles is the source of dissipation, and is the origin of a transition from a gas to a liquidlike state. This transition can be triggered by an increase of the solid fraction.
View Article and Find Full Text PDFUnjamming Transition as a Paradigm for Biomechanical Control of Cancer Metastasis.
Cytoskeleton (Hoboken)
December 2024
Applied Physics Program, University of Michigan, Ann Arbor, Michigan, USA.
Tumor metastasis is a complex phenomenon that poses significant challenges to current cancer therapeutics. While the biochemical signaling involved in promoting motile phenotypes is well understood, the role of biomechanical interactions has recently begun to be incorporated into models of tumor cell migration. Specifically, we propose the unjamming transition, adapted from physical paradigms describing the behavior of granular materials, to better discern the transition toward an invasive phenotype.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!