9I2I

X-ray structure of the B1 domain of streptococcal protein G triple mutant T2Q, N8D, and N37D (GB1-QDD).

Summary for 9I2I

• Entry DOI: 10.2210/pdb9i2i/pdb
• Descriptor: Immunoglobulin G-binding protein G, SODIUM ION (3 entities in total)
• Functional Keywords: gb1, crystallographic dimer, immune system
• Biological source: Streptococcus sp.
• Total number of polymer chains: 2
• Total formula weight: 12484.55

Authors

Engilberge, S.,Becker, L.M.,Kapitonova, A.,Schanda, P. (deposition date: 2025-01-20, release date: 2025-09-03, Last modification date: 2026-07-15)

Primary citation

Becker, L.M.,Fu, H.,Tatman, B.P.,Dreydoppel, M.,Kapitonova, A.,Balazs, D.M.,Weininger, U.,Engilberge, S.,Chipot, C.,Schanda, P.
Aromatic ring flips reveal reshaping of protein dynamics in crystals and complexes.
Nat.Chem., 18:1221-1230, 2026

PubMed Abstract: Protein conformational energy landscapes are shaped not only by intramolecular interactions but also by their environment. In protein crystals and protein-protein complexes, intermolecular contacts alter this energy landscape, but the exact nature of this alteration is difficult to decipher. Understanding how the crystal lattice affects protein dynamics is crucial for crystallography-based studies of motion, yet its influence on collective motions remains unclear. Aromatic ring flips in the hydrophobic core represent sensitive probes of such dynamics. Here, we compare the kinetics of aromatic ring flips in the protein GB1 in crystals, in complex with its binding partner IgG, and in solution, combining advanced isotope labelling with quantitative NMR methods. We show that rings in the core flip nearly a thousand times less frequently in crystals than in solution. Enhanced-sampling molecular dynamics simulations, based on a crystal structure of a GB1 variant reported in this work, reproduce these elevated barriers and reveal how the crystal restrains motions.

PubMed: 42271006
DOI: 10.1038/s41557-026-02155-0

Experimental method

X-RAY DIFFRACTION (1.08 Å)