Scrutinising the Conformational Ensemble of the Intrinsically Mixed-Folded Protein Galectin-3

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Galectin-3 is a protein implicated in various cellular processes and serves as a biomarker for heart disease, kidney disease, and cancer.
• The protein consists of a carbohydrate recognition domain (CRD) and an unstructured N-terminal domain (NTD) with collagen-like repeats.
• While the CRD structure is known, the full-length galectin-3 conformations remain poorly understood.

Purpose of the Study:

• To investigate the conformational ensemble of full-length galectin-3 using molecular dynamics (MD) simulations.
• To refine the Martini 3 force field for accurate simulation of galectin-3 by matching SAXS experimental data.
• To elucidate the structural dynamics and interactions within full-length galectin-3.

Main Methods:

• Performed all-atom molecular dynamics (MD) simulations of full-length galectin-3.
• Systematically re-scaled solute-solvent interactions in the Martini 3 force field.
• Validated simulation results against experimental data from SAXS and NMR.

Main Results:

• MD simulations generated a diverse set of galectin-3 conformations, showing significant fluctuations in radius of gyration (2-5 nm).
• Observed transient contacts within the NTD, frequently involving aromatic residues.
• Identified contacts between CRD and NTD that do not involve the carbohydrate-binding site, consistent with NMR data.
• Demonstrated NTD-mediated formation of dynamic, unspecific complexes.

Conclusions:

• This study provides a comprehensive view of the full-length galectin-3 conformational landscape.
• The findings offer molecular-level insights into galectin-3's biological functions.
• The refined simulation methodology can be applied to other intrinsically disordered proteins.