Structure of human apolactoferrin at 2.0 angstrom resolution. Refinement and analysis of ligand-induced conformational change

The three-dimensional structure of a form of human apolactoferrin, in which one lobe (the N-lobe) :has an open conformation and the other lobe (the C- lobe) is closed, has been refined at 2.0 Angstrom resolution. The refinemen t, by restrained least-squares methods, used synchrotron radiation X-ray di ffraction data combined with a lower resolution diffractometer data set. Th e final refined model (5346 protein atoms from residues 1-691, two Cl- ions and 363 water molecules) gives a crystallographic R factor of 0.201 (R-fre e = 0.286) for all 51305 reflections in the resolution range 100-2.0 Angstr om, The conformational change in the N-lobe, which opens up the binding cle ft, involves a 54 degrees rotation of the N2 domain relative to the N1 doma in. This also results in a small reorientation of the two lobes relative to one another with a further similar to 730 Angstrom(2) of surface area bein g buried as the N2 domain contacts the C-lobe and the inter-lobe helix. The se new contacts also involve the C-terminal helix and provide a mechanism t hrough which the conformational and iron-binding status of the N-lobe can b e signalled to the C-lobe. Surface-area calculations indicate a fine balanc e between open and closed forms of lactoferrin, which both have essentially the same solvent-accessible surface. Chloride ions are bound in the anion- binding sites of both lobes, emphasizing the functional significance of the se sites. The closed configuration of the C-lobe, attributed in part to wea k stabilization by crystal packing interactions, has important implications for lactoferrin dynamics. It shows that a stable closed structure, essenti ally identical to that of the iron-bound form, can be formed in the absence of iron binding.