Protein folding as a jamming transition

Alex T Grigas; Zhuoyi Liu; Jack A Logan; Mark D Shattuck; Corey S O'Hern

Protein folding as a jamming transition

ArXiv [Preprint]. 2024 May 15:arXiv:2405.09646v1.

Authors

Alex T Grigas^{1

2}, Zhuoyi Liu^{3

2}, Jack A Logan³, Mark D Shattuck⁴, Corey S O'Hern^{3

1

2

5

6}

Affiliations

¹ Graduate Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, 06520, USA.
² Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA.
³ Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut, 06520, USA.
⁴ Benjamin Levich Institute and Physics Department, The City College of New York, New York, New York 10031, USA.
⁵ Department of Physics, Yale University, New Haven, Connecticut, 06520, USA.
⁶ Department of Applied Physics, Yale University, New Haven, Connecticut, 06520, USA.

PMID: 38800654
PMCID: PMC11118678

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 $ϕ_{c} = 0.55$ 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 $ϕ_{c}$ . The model also recapitulates the global structure of proteins since it can accurately refold to native-like structures from partially unfolded states.

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Preprint

Abstract

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