Inhibition of trypsin and thrombin by amino(4-amidinophenyl)methanephosphonate diphenyl ester derivatives: X-ray structures and molecular models.

X-ray structures of trypsin from bovine pancreas inactivated by diphenyl [N-(benzyloxycarbonyl)amino](4-amidinophenyl)methanephosphonate [Z-(4-AmPhGly)P(OPh)2] were determined at 113 and 293 K to 1.8 angstrom resolution and refined to R factors of 0.211 (113 K) and 0.

Mechanism-based isocoumarin inhibitors for blood coagulation serine proteases. Effect of the 7-substituent in 7-amino-4-chloro-3-(isothioureidoalkoxy)isocoumarins on inhibitory and anticoagulant potency.

A series of 7-amino-4-chloro-3-(3-isothioureidopropoxy)isocoumarin (NH2-CiTPrOIC) derivatives with various substituents at the 7- and 3-positions have been synthesized as inhibitors of several blood coagulation enzymes. Isocoumarins substituted with basic groups such as guanidino or isothioureidoalkoxy groups were previously shown to be potent irreversible inhibitors of blood coagulation enzymes [Kam et al. Biochemistry 1988, 27, 2547-2557].

X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 A resolution.

The x-ray crystal structure of pea lectin, in complex with a methyl glycoside of the N-linked-type oligosaccharide trimannosyl core, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside, has been solved by molecular replacement and refined at 2.6-A resolution. The R factor is 0.

Inhibition of porcine pancreatic elastase by 7-substituted 4-chloro-3-ethoxyisocoumarins: structural characteristics of modeled noncovalent complexes relate to the measured inhibition kinetics.

Kinetic measurements for the inhibition of porcine pancreatic elastase by 7-substituted 4-chloro-3-ethoxyisocoumarins were performed. To obtain possible explanations for the kinetic results, structures resulting from energy minimizations of inhibitor-enzyme complex structures where each inhibitor was initially positioned in 64 locations within the active site were obtained. In keeping with solution NMR studies, a positive-charged His-57 was employed.

Michaelis complexes of porcine pancreatic elastase with 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins: translational sampling of inhibitor position and kinetic measurements.

A step leading to the formation of the covalent complexes between porcine pancreatic elastase (PPE) and 7-[(alkylcarbamoyl)amino]-4-chloro-3-ethoxyisocoumarins (alkylHNCO-EICs) is the formation of the noncovalent Michaelis complex. No average structures are available for the Michaelis complexes of PPE with alkylHNCO-EICs. We present the results of an initial step in obtaining these structures and have determined kinetic constants as well.

Design, expression, and crystallization of recombinant lectin from the garden pea (Pisum sativum).

The propeptide form of the lectin from the garden pea (Pisum sativum agglutinin) has been expressed in Escherichia coli by attaching its cDNA to an inducible promoter. By a number of criteria, including the ability to form dimers, hemagglutination titer, Western blot, and enzyme-linked immunosorbent assay, the resulting propeptide molecule is virtually indistinguishable from the mature proteolytically processed lectin isolated from peas. Preliminary crystallization experiments using the recombinant propeptide lectin yield crystals in space group P2(1)2(1)2(1) with a = 64.

Preliminary crystallographic study of the alpha-D-galactose-specific lectin from jack fruit (Artocarpus integra) seeds.

Crystals of the alpha-D-galactose-specific lectin from Jack fruit (Artocarpus integra) have been obtained from polyethylene glycol 400 solutions. The crystals are orthorhombic, space group P2(1)2(1)2 with a = 77.09 A, b = 123.

The crystal structure of pea lectin at 3.0-A resolution.

The structure of pea lectin has been determined to 3.0-A resolution based on multiple isomorphous replacement phasing to 6.0-A resolution and a combination of single isomorphous replacement, anomalous scattering, and density modification to 3.

Preliminary X-ray investigation of variant-2 scorpion toxin from Centruroides sculpturatus Ewing. Evidence of a reversible transition between crystal forms.

Crystals of Variant-2 scorpion toxin have been grown using seeding techniques from 30% 2-methyl-2,4-pentanediol at pH 9.2 and T = 4 degrees C. These crystals display a temperature-dependent, reversible phase transition near room temperature.

Structure of variant-3 scorpion neurotoxin from Centruroides sculpturatus Ewing, refined at 1.8 A resolution.

The three-dimensional structure of the variant-3 protein neurotoxin from the scorpion Centruroides sculpturatus Ewing has been determined by X-ray diffraction data. The initial model for the 65-residue protein was obtained at 3 A resolution by multiple-isomorphous-replacement methods. The structure was refined at 1.

The crystal structure of pea lectin at 6-A resolution.

The three-dimensional crystal structure of the mitogenic lectin from the green pea (Pisum sativum) has been determined at 6-A resolution by x-ray diffraction methods. Pea lectin was isolated by use of affinity chromatography and was crystallized from polyethylene glycol solutions. Crystals of pea lectin are orthorhombic, space group P212121, and diffract to at least 1.

The three-dimensional structure of scorpion neurotoxins.

The crystal and molecular structure of a toxin from the scorpion Centruroides sculpturatus has been solved by standard x-ray crystallographic methods at 3 A resolution. Subsequently the 3 A model has been refined and the resolution has been extended to 1.8 A using the gradient-curvature method.

Three-dimensional structure of a protein from scorpion venom: a new structural class of neurotoxins.

The three-dimensional crystal structure of variant-3 toxin from the scorpion Centruroides sculpturatus Ewing has been determined at 3 A resolution. Phases were obtained by use of K2PtCl4 and K2IrCl6 derivatives. The most prominent secondary structural features are two and a half turns of alpha-helix and a three-strand stretch of antiparallel beta-sheet, which runs parallel to the alpha-helix.

Hydrogen bonding in yeast phenylalanine transfer RNA.

Further analysis of the three-dimensional electron density map of yeast phenylalanine tRNA is presented. Attention is focused on the several types of unique hydrogen bonding that are found in the molecule and a number of sections of the electron density map are presented. These sections are compared with an electron density map of a dinucleoside phosphate.

Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles.

The atomic coordinates of yeast phenylalanine transfer RNA (tRNA) as well as the torsion angles of the polynucleotide chain are presented as derived from an x-ray diffraction analysis of orthorhombic crystals. A comparison is made between the coordinates obtained from analysis of monoclinic crystals of the same material. It is concluded that the molecule has substantially the same form in the orthorhombic and the monoclinic lattices, except for differences found between residues at the 3' end of the polynucleotides chain.

The general structure of transfer RNA molecules.

The three-dimensional structure of yeast phenylalanine tRNA serves as a useful basis for understanding the tertiary structure of all tRNAs. A large number of tRNA sequences have been surveyed and some general conclusions are drawn. There are only a few regions in the molecule in which there are differences in the number of nucleotides; and the structure of yeast phenylalanine tRNA can accommodate these differences by forming or enlarging protuberances on the surface of the basic framework molecule.

Three-dimensional tertiary structure of yeast phenylalanine transfer RNA.

The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule. The overall features of the molecule are virtually the same as those seen at a resolution of 4 angstroms except that many additional details of tertiary structure are now visualized. Ten types of hydrogen bonding are identified which define the specificity of tertiary interactions.

The molecular structure of yeast phenylalanine transfer RNA in monoclinic crystals.

The molecular structure of monoclinic crystals of yeast phenylalanine tRNA is analyzed by comparing it to the orthorhombic crystals of the same material whose structure has been determined. Changing the packing of the molecule from the head-to-head, tail-to-tail arrangement in the orthorhombic lattice to a head-to-tail packing makes it possible to generate a proposed structure for the monoclinic unit cell. The structure factors for the proposed arrangement have been calculated and compared with those experimentally observed from monoclinic crystals.