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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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Updated: Feb 17, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

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Improving Protein Structure Determination by Integrating Ensemble-Driven Molecular Dynamics with Chemical Shift-Based

Márton Gadanecz^1,2, Zsolt Fazekas¹, Dóra K Menyhárd^1,3

¹Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter Stny. 1/A, Budapest H-1117, Hungary.

Journal of Chemical Information and Modeling

|February 16, 2026

Summary

We introduce ensemble-driven molecular dynamics (EDMD) to refine protein structures determined using nuclear magnetic resonance (NMR) chemical shifts. This method improves accuracy and enhances the incorporation of experimental data for better structural models.

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Area of Science:

Biophysics
Structural Biology
Computational Chemistry

Background:

Nuclear magnetic resonance (NMR) spectroscopy is crucial for determining molecular structures.
Chemical shift data provides valuable information for structure determination.
Existing methods may require refinement for complex systems.

Purpose of the Study:

To present a novel protocol for NMR chemical shift-based structure determination.
To refine protein structures using ensemble-driven molecular dynamics (EDMD).
To improve the accuracy and reliability of experimentally derived structural models.

Main Methods:

Application of Chemical-Shift-Rosetta (CS-Rosetta) followed by EDMD.
Development of continuous, differentiable potential energy functions (PEFs) for EDMD.
Incorporation of measurement temperature and dihedral angle distributions into force fields.
Benchmarking EDMD against known protein structures.

Main Results:

EDMD consistently improved backbone root-mean-square deviation (RMSD) compared to CS-Rosetta ensembles.
Enhanced fulfillment of nuclear Overhauser effect (NOE)-derived distance restraints.
Improved NOE-RASREC-Rosetta models and maintained correct protein-ligand conformations.
Successful refinement of nonconverged CS-Rosetta structure calculations.

Conclusions:

EDMD offers a robust method for refining NMR-based protein structure determination.
The approach accurately reincorporates nonprotein moieties and refines structural ensembles.
EDMD can be generalized for various ensembles with scoring information, advancing structural biology.