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The determination of a 'folding core' can help to provide insight into thestructure, flexibility, mobility and dynamics, and hence, ultimately, functionof a protein - a central concern of structural biology. Changes in the foldingcore upon ligand binding are of particular interest because they may berelevant to drug-induced functional changes. Cyclophilin A is amulti-functional ligand-binding protein and a significant drug target. It actsprincipally as an enzyme during protein folding, but also as the primarybinding partner for the immunosuppressant drug cyclosporin A (CsA). Here, wehave used hydrogen-deuterium exchange (HDX) NMR spectroscopy to determine thefolding core of the CypA-CsA complex. We also use the rapid computational toolof rigidity analysis, implemented in FIRST, to determine a theoretical foldingcore of the complex. In addition we generate a theoretical folding core for theunbound protein and compare this with previously published HDX data. The FIRSTmethod gives a good prediction of the HDX folding core, but we find that it isnot yet sufficiently sensitive to predict the effects of ligand binding onCypA.

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