タンパク質の謎を解明する研究(Unfolding the secrets of proteins)

2025-11-06 イェール大学

<関連情報>

• https://engineering.yale.edu/news-and-events/news/unfolding-secrets-proteins
• https://journals.aps.org/pre/abstract/10.1103/9wf9-ywhw

折り畳まれたタンパク質の構造特性に対する立体化学的制約の影響 Effect of stereochemical constraints on the structural properties of folded proteins

Jack A. Logan, Jacob Sumner, Alex T. Grigas, Mark D. Shattuck, and Corey S. O’Hern
Physical Review E  Published: 6 November, 2025
DOI: https://doi.org/10.1103/9wf9-ywhw

Abstract

Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids ƒ_core, packing fraction ⟨Φ⟩ of core amino acids, and structure factor S(q) define the structure of folded proteins. It is well-known that folded proteins are compact with a radius of gyration R_g (N)∼N^v that obeys power-law scaling with the number of amino acids and v∼1/3, ƒ_core≈0.09, and ⟨Φ⟩≈0.55. We also investigate the internal scaling of the radius of gyration R_g(n) versus the chemical separation between amino acids for subchains of length and show that it does not obey simple power-law scaling with v∼1/3. Instead,R_g (n)∼n^v1,2 with a larger exponent v₁>1/3 for small and a smaller exponent  v₂<1/3 for large . To develop a minimal model for proteins that recapitulates these defining structural features, we carry out collapse simulations for a series of coarse-grained models with increasing complexity. We show that a model, which coarse-grains amino acids into a single spherical backbone bead and several variable-sized side-chain beads and enforces bend- and dihedral-angle constraints for the backbone, recapitulates R_g(n), ƒ_core, ⟨Φ⟩, and S(q) for more than 2500 x-ray crystal structures of proteins.