title: The low-energy conformations of gonadotropin-releasing hormone in aqueous solution.
abstract: Using the chain-build-up method based on Empirical Conformational Energies of Peptides Program including solvation, we have computed, the low energy conformations of gonadotrpin-releasing hormone, GnRH, whose sequence is Pyro-Glu(PG)-His-Trp-Ser-Tyr-Gly-Leu-Arg-Pro-Gly-NH2. We have found 5,077 solvated conformations with conformational energies that were within 5 kcal/mole of that of the global minimum. These minima were found to occur in 802 distinct conformational classes of which 25 represented 70 % of the Boltzmann energy-weighted structures. Virtually all of these structures adopted bend conformations from Tyr 5-Leu 8, and 3,861 structures adopted bend conformations at residues 4-7. However, these structures differed significantly from one another, indicating that GnRH does not adopt a well-defined structure in aqueous solution consistent with the absence of a well-defined NMR structure of GnRH in water. A total of 300 of these structures were found to be superimposable on possible NMR structures for GnRH in DMSO with a combined statistical weight of 1.6 %. We found that Gly 6 adopts low energy "starred" states, e.g., C* and D*, that are energetically forbidden to L-amino acids but are low energy for D-amino acids, with a statistical weight of 43 %. This can explain why substitutions of L-amino acids for Gly 6 are known to inactivate GnRH while D-amino acid substitutions enhance its activity. Using these findings, in the accompanying manuscript, we compute the low energy conformations for the substituted GnRHs that enable inference of possible receptor-bound conformations.
authors.affiliation: Department of Pathology, SUNY Downstate Medical Center, 450 Clarkson Avenue, Brooklyn, NY, 11203, USA, matthew.pincus2@va.gov.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Pincus
authors.forename: Jannie
authors.initials: J
authors.lastname: Woo
authors.forename: Regina
authors.initials: R
authors.lastname: Monaco
authors.forename: Jack
authors.initials: J
authors.lastname: Lubowsky
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Avitable
authors.forename: Robert P
authors.initials: RP
authors.lastname: Carty
mesh_terms: D000595:Amino Acid Sequence; D007987:Gonadotropin-Releasing Hormone / Q000737:chemistry* / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D011487:Protein Conformation; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D007987:Gonadotropin-Releasing Hormone