Protein folding as a jamming transition
arXiv:2405.09646 · doi:10.1103/PRXLife.3.013018
Abstract
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.
5 pages, 4 figures
References in corpus (34)
- Canonical sampling through velocity-rescaling
- Jamming at Zero Temperature and Zero Applied Stress: the Epitome of Disorder
- Jamming of Soft Particles: Geometry, Mechanics, Scaling and Isostaticity
- FreeSASA: An open source C library for solvent accessible surface area calculations
- Effects of compression on the vibrational modes of marginally jammed solids
- Vibrations and diverging length scales near the unjamming transition
- Jamming of frictional spheres and random loose packing
- Hypoconstrained Jammed Packings of Nonspherical Hard Particles: Ellipses and Ellipsoids
- Jamming transitions in amorphous packings of frictionless spheres occur over a continuous range of volume fractions
- Jamming in Systems Composed of Frictionless Ellipse-Shaped Particles
- Excess Vibrational Modes and the Boson Peak in Model Glasses
- Jamming in finite systems: stability, anisotropy, fluctuations and scaling
- Understanding the Frequency Distribution of Mechanically Stable Disk Packings
- Universal non-Debye scaling in the density of states of amorphous solids
- Exploring the jamming transition over a wide range of critical densities
- Constraints and vibrations in static packings of ellipsoidal particles
- Protocol dependence of the jamming transition
- Jamming of semiflexible polymers
- A simple effective rule to estimate the jamming packing fraction of polydisperse hard spheres
- The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions
- Detection of boson peak and fractal dynamics of disordered system using terahertz spectroscopy
- The Inherent Structure Landscape Connection Between Liquids, Granular materials and the Jamming Phase Diagram
- Random close packing in protein cores
- Packing in Protein Cores
- Calibrated Langevin dynamics simulations of intrinsically disordered proteins
- Void distributions reveal structural link between jammed packings and protein cores
- The response of jammed packings to thermal fluctuations
- RFOT theory for glassy dynamics in a single condensed polymer
- Reliable protein folding on non-funneled energy landscapes: the free energy reaction path
- Effects of spherical confinement and backbone stiffness on flexible polymer jamming
- Densest vs. jammed packings of 2D bent-core trimers
- Densest versus jammed packings of bent-core trimers
- Dynamic Gardner crossover in a simple structural glass
- The connection between polymer collapse and the onset of jamming