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Protein Dynamics in Living Cells

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Addressing Structural Heterogeneity in Real-time Tracking of Protein Dynamics Triggered by Caged Compounds.

Konstantinos Magkakis¹, Fredrik Orädd¹, Christian Pett¹

¹Department of Chemistry, Umeå University, Umeå, Sweden.

Journal of Molecular Biology

|October 8, 2025

Summary

This summary is machine-generated.

Researchers studied protein conformational changes using time-resolved X-ray solution scattering (TR-XSS) and molecular dynamics simulations. They developed a method to analyze complex protein dynamics, revealing intermediate states and unfolding during enzymatic reactions.

Keywords:

adenylate kinase ensemble optimization genetic algorithm protein dynamics time-resolved X-ray solution scattering

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Area of Science:

Biochemistry
Structural Biology
Biophysics

Background:

Proteins adopt multiple conformations, complicating structural studies.
Time-resolved X-ray solution scattering (TR-XSS) monitors protein dynamics.
Caged compounds trigger reactions, but release kinetics and equilibrium states pose interpretation challenges.

Purpose of the Study:

To address challenges in interpreting TR-XSS data due to non-instantaneous caged compound release.
To model and visualize protein structural heterogeneity during catalytic cycles.
To establish a framework for analyzing rapid protein conformational changes.

Main Methods:

Utilized Escherichia coli adenylate kinase (AdK) as a model system.
Employed synchrotron-based time-resolved X-ray solution scattering (TR-XSS).
Integrated molecular dynamics (MD) simulations for ensemble-based structural refinement.

Main Results:

Identified intermediate protein conformations at equilibrium, with partially open/closed domains.
Observed shifts towards fully closed/open conformations and partial unfolding upon ATP availability.
Demonstrated that non-instantaneous substrate release impacts transition kinetics.

Conclusions:

Ensemble-based structural refinement effectively tackles challenges from non-instantaneous substrate release.
Protein conformational changes follow a cracking model during enzymatic reactions.
The study provides a framework for dissecting rapid, caged-compound-induced protein dynamics.