Characterizing the folding core of the cyclophilin A - cyclosporin A complex I: hydrogen exchange data and rigidity analysis

TL;DR

This study combines experimental hydrogen exchange data and computational rigidity analysis to characterize the folding core of the cyclophilin A - cyclosporin A complex, revealing insights into structural dynamics and ligand effects.

Contribution

It integrates HDX NMR and rigidity analysis to compare folding cores of bound and unbound cyclophilin A, highlighting the method's predictive capabilities and limitations.

Findings

Rigidity analysis predicts the HDX folding core well.

Ligand binding effects are not fully captured by current rigidity analysis.

Comparison with previous data enhances understanding of protein-ligand interactions.

Abstract

The determination of a 'folding core' can help to provide insight into the structure, flexibility, mobility and dynamics, and hence, ultimately, function of a protein - a central concern of structural biology. Changes in the folding core upon ligand binding are of particular interest because they may be relevant to drug-induced functional changes. Cyclophilin A is a multi-functional ligand-binding protein and a significant drug target. It acts principally as an enzyme during protein folding, but also as the primary binding partner for the immunosuppressant drug cyclosporin A (CsA). Here, we have used hydrogen-deuterium exchange (HDX) NMR spectroscopy to determine the folding core of the CypA-CsA complex. We also use the rapid computational tool of rigidity analysis, implemented in FIRST, to determine a theoretical folding core of the complex. In addition we generate a theoretical folding core for the unbound protein and compare this with previously published HDX data. The FIRST method gives a good prediction of the HDX folding core, but we find that it is not yet sufficiently sensitive to predict the effects of ligand binding on CypA.