Back

Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes

Becker, L. M.; Fu, H.; Tatman, B. P.; Dreydoppel, M.; Kapitonova, A.; Weininger, U.; Engilberge, S.; Chipot, C.; Schanda, P.

2025-08-24 biophysics
10.1101/2025.08.20.671406 bioRxiv
Show 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 labeling 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 new crystal structure, reproduce these elevated barriers and reveal how the crystal restrains motions.

Published in Nature Chemistry (predicted rank #4) · training set

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
Nature Communications
○ 5641 papers in training set
Top 6%
22.6%
Similar papers in this journal
2
Journal of the American Chemical Society
● 217 papers in training set
Top 0.2%
15.3%
Similar papers in this journal
3
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 3%
9.9%
Similar papers in this journal
Nature Chemistry · published here
○ 42 papers in training set
Top 0.1%
5.6%
Similar papers in this journal
50% of probability mass above
5
JACS Au
● 43 papers in training set
Top 0.1%
4.9%
6
eLife
● 5828 papers in training set
Top 25%
4.9%
Similar papers in this journal
7
The Journal of Physical Chemistry Letters
● 63 papers in training set
Top 0.2%
3.3%
8
ACS Central Science
● 71 papers in training set
Top 0.3%
3.3%
9
Biophysical Journal
○ 631 papers in training set
Top 2%
3.2%
10
Science Advances
● 1243 papers in training set
Top 19%
1.8%
11
The Journal of Physical Chemistry B
● 167 papers in training set
Top 1%
1.8%
12
Angewandte Chemie International Edition
○ 93 papers in training set
Top 0.8%
1.8%
13
Structure
○ 193 papers in training set
Top 1%
1.7%
14
Protein Science
○ 246 papers in training set
Top 2%
1.5%
15
Biochemistry
● 148 papers in training set
Top 2%
1.5%
16
Chemical Science
● 73 papers in training set
Top 1%
1.1%
17
Communications Biology
○ 993 papers in training set
Top 24%
1.1%
18
Nature
○ 645 papers in training set
Top 9%
1.1%
19
Nature Structural & Molecular Biology
236 papers in training set
Top 3%
0.9%
20
Cell Reports
○ 1498 papers in training set
Top 26%
0.9%
21
ACS Nano
● 113 papers in training set
Top 2%
0.9%
22
PNAS Nexus
◐ 159 papers in training set
Top 4%
0.6%
23
Nucleic Acids Research
◐ 1281 papers in training set
Top 14%
0.6%
24
Journal of Molecular Biology
○ 232 papers in training set
Top 4%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.