Solution structure of RP 71955, a new 21 amino acid tricyclic peptide active against HIV-1 virus.

The structure of RP 71955, a new tricyclic 21 amino acid peptide active against human immunodeficiency virus 1, was determined. Its amino acid composition was inferred from the results of fast atom bombardment mass spectrometry, nuclear magnetic resonance, Raman spectroscopy, and amino acid analysis. Its sequence could not be determined classically, using Edman degradation, given the lack of a free terminal NH2. It was deduced from the interpretation of interresidue nuclear Overhauser effects and confirmed by the sequencing of peptides obtained by limited chemical hydrolysis. It was found to be CLGIGSCNDFAGCGYAVVCFW. An internal amide bond between the NH2 of C1 and the gamma-COOH of D9 was observed, as well as two disulfide bridges, one between C1 and C13 and one between C7 and C19. The three-dimensional structure of RP 71955 was determined from nuclear magnetic resonance derived constraints using distance geometry, restrained molecular dynamics, nuclear Overhauser effect back calculation, and an iterative refinement using a full relaxation matrix approach. Analogies between the structure of RP 71955 and some functional domains of gp41, the transmembrane protein of human immunodeficiency virus 1, suggest hypotheses concerning the mode of action of RP 71955.

Refinement of the C222(1) crystal form of oxidized uteroglobin at 1.34 A resolution.

The structure of uteroglobin, a progesterone binding protein from rabbit uterine fluid, was determined and refined at 1.34 A resolution to a conventional R-factor of 0.229. The accuracy of the co-ordinates is estimated to be 0.15 A. The isotropic temperature factor of individual atoms was refined and its average value is 11.9 A2 for the 548 non-hydrogen atoms of the protein monomer. A total of 83 water molecules was located in difference electron density maps and refined, first using a constant occupancy factor of 1 and then variable occupancy, the final (Q) being 0.63. The mean temperature factor of the water oxygen atoms is 26.4 A2. Uteroglobin is a dimer and its secondary structure consists of four alpha-helices per monomer that align in an anti-parallel fashion. There is one beta-turn between helix 2 and helix 3 (Lys26 to Glu29); 76% of the residues are part of the alpha-helices. In the core of the dimeric protein molecule, between the two monomers that are held together by two disulfide bridges, we have observed a closed cavity. Its length is 15.6 A and its width is 9 A; 14 water molecules could be positioned inside. In the "bottom" part of the protein, near the C terminus, we have observed a smaller cavity, occupied by two water molecules. The calculation of the molecular surface revealed four surface pockets whose possible functional implications are discussed below.

Crystallization and preliminary X-ray diffraction results of trichorzianine A 1, a peptide with nineteen residues from Trichoderma harzianum.

Trichorzianine A 1 is one of the main components of a mixture of related antibiotic peptides (trichorzianines) produced by the fungus Trichoderma harzianum. Good crystals were obtained and allowed X-ray diffraction up to 0.8 A resolution. The space group is orthorhombic, C222(1), Z = 8, a = 64.8 (1) A, b = 9.33 (3) A, c = 39.9 (1) A. The solvent content is only 12%, preventing a heavy ion diffusion. So, we are trying to obtain the structure by direct methods.

Additional conformational data for the mapping of the progestin binding site: crystal structures of 21-(phenylseleno)progesterone and 17 alpha-(phenylseleno)progesterone.

The crystal structures of 21-(phenylseleno)progesterone (1), which binds with moderate affinity to the progestin receptor, and 17 alpha-(phenylseleno)progesterone (2), which binds hardly at all, have been studied in an attempt to explain these differences in affinity and to obtain further information on the location of the progestin receptor binding site with respect to the progesterone molecule. The crystal structures were refined by isotropic thermal approximation to R values of 0.082 for 1 and 0.084 for 2. The unusual 17 beta side-chain orientation of 2 with a C16-C17-C20-O20 torsion angle of +13 degrees compared to -7 degrees for progesterone would seem to preclude hydrogen bonding with the progestin receptor binding site and provides strong supporting evidence for the contention that this site is located above the beta face of the molecule. Any rotation of the C21 methyl group into a more appropriate position is furthermore impeded by the presence of the 17 alpha-phenylseleno substituent. On the other hand, some hydrogen bonding can occur in the case of 1 (C16-C17-C20-O20 = 31 degrees) despite the fact that the difference in torsion angle (24 degrees) with respect to progesterone is, in absolute values, greater than that for 2 (20 degrees). This is because the orientation of the 17 beta-acetyl side chain of 1 is directed above the beta face closer to the progestin binding site, as previously defined on the basis of data on a large number of molecules, and because the 21-phenylseleno substituent constitutes only limited steric hindrance to binding. Thus, the difference in affinity of these two compounds is entirely consistent with observations that the H-bond donor is located toward O20 in the beta region of C16.