  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.
