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

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.