Molecular modeling of the neurophysin I/oxytocin complex.
Neurophysins I and II (NPI and NPII) act in the neurosecretory granules as carrier proteins for the neurophyseal hormones oxytocin (OT) and vasopressin (VP), respectively. The NPI/OT functional unit, believed to be an (NPI/OT)2 heterotetramer, was modeled using low-resolution structure information, viz. the C alpha carbon atom coordinates of the homologous NPII/dipeptide complex (file 1BN2 in the Brookhaven Protein Databank) as a template. Its all-atom representation was obtained using standard modeling tools available within the INSIGHT/Biopolymer modules supplied by Biosym Technologies Inc. A conformation of the NPI-bound OT, similar to that recently proposed in a transfer NOE experiment, was docked into the ligand-binding site by a superposition of its Cys1-Tyr2 fragment onto the equivalent portion of the dipeptide in the template. The starting complex for the initial refinements was prepared by two alternative strategies, termed Model I and Model II, each ending with a approximately 100 ps molecular dynamics (MD) simulation in water using the AMBER 4.1 force field. The free homodimer NPI2 was obtained by removal of the two OT subunits from their sites, followed by a similar structure refinement. The use of Model I, consisting of a constrained simulated annealing, resulted in a structure remarkably similar to both the NPII/dipeptide complex and a recently published solid-state structure of the NPII/OT complex. Thus, Model I is recommended as the method of choice for the preparation of the starting all-atom data for MD. The MD simulations indicate that, both in the homodimer and in the heterotetramer, the 3(10)-helices demonstrate an increased mobility relative to the remaining body of the protein. Also, the C-terminal domains in the NPI2 homodimer are more mobile than the N-terminal ones. Finally, a distinct intermonomer interaction is identified, concentrated around its most prominent, although not unique, contribution provided by an H-bond from Ser25 O gamma in one NPI unit to Glu81 O epsilon in the other unit. This interaction is present in the heterotetramer (NPI/OT)2 and absent or weak in the NPI2 homodimer. We speculate that this interaction, along with the increased mobility of the 3(10)-helices and the carboxy domains, may contribute to the allosteric communication between ligand binding and NPI dimerization.
Kaźmierkiewicz
R
R
Faculty of Chemistry, University of Gdańsk, Poland.
Czaplewski
C
C
Lammek
B
B
Ciarkowski
J
J
D000494:Allosteric Regulation; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003198:Computer Simulation; D019281:Dimerization; D008024:Ligands; D046911:Macromolecular Substances; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009481:Neurophysins / Q000737:chemistry* / Q000235:genetics; D010121:Oxytocin / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D013816:Thermodynamics
D008024:Ligands; D046911:Macromolecular Substances; D009481:Neurophysins; D010121:Oxytocin