Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.

Human growth hormone (hGH) binds to its receptor (hGHr) in a three-body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone-receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821-825). In this paper, we model the recognition of hGH to the hGHr using shape complementarity of the three-dimensional structures and macromolecular docking to explore possible binding modes between the receptor and hormone. The method, reported previously (Hendrix DK, Kuntz ID, 1998, Pacific symposium on biocomputing 1998, pp 1234-1244), is based upon matching complementary-shaped strategic sites on the molecular surface. We modify the procedure to examine three-body systems. We find that the order of binding seen experimentally is also essential to our model. We explore the use of mutational data available for hGH to guide our model. In addition to docking hGH to the hGHr, we further test our methodology by successfully reproducing 16 macromolecular complexes from X-ray crystal structures, including enzyme-inhibitor, antibody-antigen, protein dimer, and protein-DNA complexes.

Surface solid angle-based site points for molecular docking.

We are developing a new site descriptor for the DOCK molecular modeling program suite. Sphgen, the current site description program for the DOCK suite, describes the pockets of a macromolecule by filling a volume with intersecting spheres. DOCK then identifies possible ligand orientations in the pocket by overlapping the atoms of proposed ligands with the sphere centers. Sphgen limits use of the DOCK program to concave binding regions, but macromolecular binding regions can be solvent-exposed rather than buried pockets. We present a more general site descriptor, based on the surface solid angle, which generates site points by determining the solid angle of exposure for points on the surface of the molecule, then identifying patches of surface with similar solid angle values which are then built into site points. We find possible ligand orientations by matching shape-based site points on the ligand and protein and demanding complementary solid angle values. Orientations are evaluated using the DOCK's force field-based score, which evaluates the Coulombic and van der Waals energy. The surface solid angle descriptor displays the complementary characteristics of the interfaces of our test systems: trypsin/trypsin inhibitor, chymotrypsin/turkey ovomucoid third domain, and subtilisin/chymotrypsin inhibitor. The solid angle site points can be used by DOCK to generate orientations within 1.5 A r.m.s.d. of the crystal structure orientation.

Effect of lymph composition on an in vitro preparation of the alligator lizard cochlea.

The effects of different artificial lymphs on the cochlear duct of the alligator lizard were studied in an in vitro preparation. The duct was dissected and cemented to the glass floor of a chamber that had been filled with an artificial lymph. The vestibular membrane was removed and latex beads (1-5 microns in diameter) were allowed to settle on the endolymphatic surface of the duct. During perfusion with an artificial lymph solution, the positions of beads were measured and video images of the duct were obtained. Artificial lymphs were isosmotic and included artificial endolymph (AE), artificial perilymph (AP), Leibovitz's L-15 culture medium, an AE solution whose calcium concentration was the same as that of AP, and AE and AP solutions in which gluconate was substituted for chloride ions. Results obtained in AE were consistently different from those in other lymphs. The displacements of beads, the projected area of the papilla, the occurrence of blebs, and direct observation of cells in the duct all indicated that the tissue swelled in AE (with or without 2 mmol/l Ca) but showed no consistent shrinking or swelling in any of the other artificial lymphs. Thus for the solutions we used, the presence of both potassium and chloride was required to elicit the swelling response to isosmotic artificial lymphs. There were some regional differences in the swelling response: the swelling of the endolymphatic surface of the tissue in a direction orthogonal to the basilar membrane surface was smaller on the free-standing region of the basilar papilla than either on the tectorial membrane or on the hyaline epithelial cells. The preparation was osmotically stable in AP and in both AE and AP solutions in which gluconate was substituted for chloride ions. After exposure to these solutions for as much as 300 min, the preparation showed no gross signs of deterioration visible with the light microscope, and continued to exhibit a highly specific osmotic response to the composition of the bathing medium.