Catalytic conformation of carboxypeptidase A. The structure of a true reaction intermediate stabilized at subzero temperatures

The structure of the mixed anhydride, acyl-enzyme intermediate of the esterolytic reaction of carboxypeptidase A is characterized by application of cryoenzymologic, magnetic resonance, and molecular graphics methods with use of the Co²⁺-substituted enzyme and the specific spin-label ester substrate O-3-(2,2,5,5-tetra-methylpyrrolinyl-1-oxyl)-propen-2-oyl-l-β-phenyllactate. A radial separation of 7·7 Å between the active site Co²⁺ and the nitroxide group in the low temperature-stabilized acyl-enzyme intermediate is determined on the basis of their spin-spin (dipole-dipole) interactions. Application of molecular graphics techniques shows that the only configuration of the substrate that is sterically accommodated by the active site yields a calculated metal ion-to-nitroxide distance of 7·8 Å. Steric accommodation of the spin-label in the active site requires severe torsional distortion around the aliphatic double bond of the propenoyl side-chain. Examination of the structure of the enzyme: spin-label intermediate reveals that the distortion arises from steric interactions of the pyrrolinyl group with the protein at a position that corresponds to the site occupied by the penultimate amide residue of an oligopeptide substrate from the site of cleavage. Together with kinetic data showing that hydrolysis of the spin-label is governed by rate-limiting deacylation, the results indicate that geometric distortion of substrates by secondary interactions with the enzyme, in general, is an obligatory part of the catalytic action of carboxypeptidase A. When viewed with respect to requirements for stereoelectronic control of bond cleavage in tetrahedral adducts of esters and amides (Deslongchamps, 1975) the results suggest that torsional distortion during catalysis results in rotation around the scissile bond of the substrate, and that this rotation is required to form the mixed anhydride reaction intermediate. These findings further support the interpretation that the hydrolysis of esters and amides catalyzed by carboxypeptidase A proceeds according to similar mechanisms except that formation of the mixed anhydride is rate-determining in peptide hydrolysis while deacylation of the mixed anhydride is rate-limiting in ester hydrolysis.Additionally, in this study application of the extension of the theory of the Solomon-Bloembergen-Morgan equations derived by Lindner (1965) for paramagnetic metal ions with S ≥ 1 demonstrates that the zero-field splitting of the high-spin Co²⁺ in the metal-substituted enzyme has no significant influence in determination of the relaxation enhancement of solvent protons by the active site metal ion.     

Crystal structure of ferric Aplysia limacina myoglobin at 2 X 0 A resolution

The three-dimensional structure of ferric myoglobin from the mollusc Aplysia limacina has been refined at 2 X 0 A resolution. The crystallographic R factor, calculated at this stage, is 0 X 194. Despite its high content of apolar residues (both aromatic and aliphatic), Aplysia limacina myoglobin, which contains only one histidine residue (at the proximal position), has a structure that conforms to the common eight-helices globin fold observed in other phyla.     

Studies on the metal—amide bond. XVII. The crystal and molecular structure of the α-form of aqua[N,N′-bis(2′-pyridinecarboxamido)-1,3-propane] copper(II) dihydrate

α-Aqua[N,N′-bis(2′-pyridinecarboxamido)-1,3-propane]copper(II) dihydrate, C₁₅H₂₀N₄O₅Cu, is monoclinic, space group P2₁/c, with a = 11.719(2), b = 13.092(2), c = 12.663(2) Å, β = 119.56(1)°, Z = 4. The structure was refined to R = 0.026 for 2398 diffractometer data using full-matrix least-squares methods. The copper atom is five-coordinate with the N₄-tetradentate ligand encompassing the base of a distorted square-based pyramid which is appreciably distorted towards a trigonal bipyramid [average Cu-N(amide) 1.950(2), Cu-N(pyridine) 2.043(2) Å, N(amide)-Cu-N(amide) 94.5(1), N(pyridine)-Cu-N(pyridine) 100.2(1)°] and with the copper atom lying 0.27 Å above the N₄ plane towards the apical water molecule [Cu-O 2.236(2) Å]. The central six-membered chelate ring adopts a skewed boat conformation and the enforced strain in the molecule results in non-planar distortions in the pyridine rings with only small distortions in the amide groups. The molecules pack in sheets parallel to (10$\text{1}$) and the hydrogen-bonding network involves the water molecules and the amide oxygen atoms of the ligand.     

Synthesis of a branched pentasaccharide sequence of "bisected" structure of N-glycoproteins

For the synthesis of the threefold-branched pentasaccharide, O-alpha-D-mannopyranosyl-(1----3)-O-[(2-acetamido-2-deoxy-beta-D- glucopyranosyl)-(1----4)]-O-[alpha-D-mannopyranosyl-(1----6)]-O-beta-D- mannopyranosyl-(1----4)-2-acetamido-2-deoxy-D-glucopyranose (20), which is a part of the structure of the N-glycoproteins, the disaccharide 4-O-(4-O-acetyl-3,6-di-O-allyl-2-O-benzyl-beta-D-mannopyranosyl) -1,6-anhydro-2-azido-3-O-benzyl-2-deoxy-beta-D-glucopyranose was synthesized as a key compound by use of the silver silicate-catalyst procedure. After elimination of the 4-O-acetyl group, a 2-acetamido-2-deoxy-beta-D-glucopyranosyl group was attached according to the phthalimido method. Further elimination of the allyl groups allowed the linkage of two alpha-D-mannopyranosyl groups in the presence of mercury salt. A deblocking sequence consisting of four steps gave 20.     

Further sequence analysis of the phage lambda receptor site. Possible implications for the organization of the lamB protein in Escherichia coli K12

We present the DNA sequence alterations due to seven lamB missense mutations yielding resistance to phages lambda and K10. They reveal five different amino acid positions in the LamB protein. Three positions (245, 247 and 249) define a new region required for phage adsorption. The two other positions (148 and 152) belong to a region where mutations to phage resistance has already been detected. These two regions are hydrophilic and could belong to turns of the protein located at the surface of the cell. All the missense mutational alterations to phage resistance sequenced in the LamB protein correspond to 10 sites located in four different segments of the polypeptide chain. We discuss their location in terms of the notion of phage receptor site and of a working model for the organization of this protein in the outer membrane of Escherichia coli.     

How does limited trypsinization influence the surface structure and binding of calcium to lipoprotein (a): a spin-labeling study

Enzyme kinetic studies are presented which demonstrate the activating effect of phosphate on the conversion of pyruvate to lactate by rabbit muscle lactate dehydrogenase. A simple method of active enzyme gel chromatography is used to preclude the possibility that this effect is due to redistribution of enzyme between tetrameric and dissociated states as the result of preferential binding of phosphate to the tetrameric enzymatic form. By analysis of the kinetic results in terms of an ordered two-substrate mechanism, the source of the activation is traced to enhancement of the strength of the enzyme-NADH interaction, primarily because of an increase in the rate constant for the formation of the binary enzyme-coenzyme complex. Preliminary estimates of the relevant equilibrium constants from the kinetic data indicate that the binding of phosphate to rabbit muscle lactate dehydrogenase leads to a two- to fourfold increase in the intrinsic association constant for the interaction between NADH and the enzyme under the conditions (pH 7.4, I = 0.15) used to study the activation phenomenon.     

The complete amino acid sequence of bovine liver catalase and the partial sequence of bovine erythrocyte catalase

The data upon which the sequence of the 506 residues in the subunit of bovine liver catalase (BLC) is based are presented in detail. A partial sequence of bovine erythrocyte catalase (BEC) which accounts for 493 residues shows complete concordance with the BLC data. On the other hand, BEC has at least 517 residues, that is, an extension beyond the C terminus of the BLC data. Although normally BLC has only 506 residues, there is evidence that, at some point in its history, it also had the C-terminal extension. It is speculated that this extension is lost in BLC either through a different processing of the molecule in liver than in erythrocytes or by partial degradation in the first stages of catabolism.     

Histone H1: Ultracentrifugation studies of the effects of ionic strength and denaturants on the solution conformation

The conformation of histone H1 has been examined under native and denaturing conditions in the absence of DNA or chromatin. Sedimentation coefficients were determined for Histone H1 in 0.1 m KCl and in 6 m guanidine hydrochloride solutions at pH 7.4. The influence of ionic strength on the conformation of histone H1 has been determined by measurement of the sedimentation coefficient in tetramethylammonium chloride solutions of up to 2.5 m and extrapolated to infinite ionic strength. Results from these experiments suggest that the native conformation of histone H1 is very asymmetric in shape. The molecule is best described as a prolate ellipsoid with axes of 312 Å (2a) and 16 Å (2b) in low ionic strength media and also as a prolate ellipsoid with axes of 202 Å (2a) and 20 Å (2b) at high ionic strength or when associated with polyanions, e.g., DNA. Denaturation of histone H1 by guanidine hydrochloride was found to be completely reversible. In 6 m guanidine hydrochloride, the H1 molecule collapses to a sphere but the original extended conformation of the protein is readily restored on dialysis. This suggests rigid conformational requirements for the H1 molecule as incorporated into chromatin. The shape and dimensions for the H1 molecule at high ionic strength are not sufficiently conclusive to locate H1 in the chromatin structure. It is proposed, however, that viable models for chromatin architecture must be consistent with the histone H1 solution dimensions obtained here.     

Biosynthesis of monoterpenes: preliminary characterization of bornyl pyrophosphate synthetase from sage (Salvia officinalis) and demonstration that Geranyl pyrophosphate is the preferred substrate for cyclization.

Previous studies with soluble enzyme preparations from sage (Salvia officinalis) demonstrated that the monoterpene ketone (+)-camphor was synthesized by the cyclization of neryl pyrophosphate to (+)-bornyl pyrophosphate followed by hydrolysis of this unusual intermediate to (+)-borneol and then oxidation of the alcohol to camphor (R. Croteau, and F. Karp, 1977, Arch. Biochem. Biophys.184, 77–86). Preliminary investigation of the (+)-bornyl pyrophosphate synthetase in crude preparations indicated that both neryl pyrophosphate and geranyl pyrophosphate could be cyclized to (+)-bornyl pyrophosphate, but the presence of high levels of phosphatases in the extract prevented an accurate assessment of substrate specificity. The competing phosphatases were removed by combination of gel filtration on Sephadex G-150, chromatography on hydroxylapatite, and chromatography on O-(diethylaminoethyl)-cellulose. In these fractionation steps, activities for the cyclization of neryl pyrophosphate and geranyl pyrophosphate to bornyl pyrophosphate were coincident, and on the removal of competing phosphatases, the synthetase was shown to prefer geranyl pyrophosphate as substrate ($\text{V}\text{K}{}_{\mathrm{m}}$ for geranyl pyrophosphate was 20-fold that of neryl pyrophosphate). No interconversion of geranyl and neryl pyrophosphates was detected. The partially purified bornyl pyrophosphate synthetase had an apparent molecular weight of 95,000, and required Mg²⁺ for catalytic activity (K_m for Mg²⁺ ~ 3.5 mm). Mn²⁺ and other divalent cations were ineffective in promoting the formation of bornyl pyrophosphate. The enzyme exhibited a pH optimum at 6.2 and was strongly inhibited by both p-hydroxymercuribenzoate and diisopropylfluorophosphate. Bornyl pyrophosphate synthetase is the first monoterpene synthetase to be isolated free from competing phosphatases, and the first to show a strong preference for geranyl pyrophosphate as substrate. A mechanism for the cyclization of geranyl pyrophosphate to bornyl pyrophosphate is proposed.     

The activation of bovine Factor X by bovine Factor Xa

A steady-state kinetic analysis of the activation of bovine Factor X, by bovine Factor X_a, was undertaken. The activation was found to be dependent on the presence of divalent cations; Ca²⁺ showing the greatest stimulatory effect and Mn²⁺ exhibiting a lower degree of activity for this reaction. Although Sr²⁺ and Mg²⁺ were ineffective when present alone, each contributed synergistically to the activation rate at suboptimal levels of Ca²⁺. The effect of phospholipid (phosphatidylcholine:phosphatidylserine, 4:1, w:w) on the rate of activation and on the activation pathway was investigated. Phospholipid (PL) concentrations of up to 40 μm had no effect on the activation rate; whereas, concentrations of 40–180 μm were slightly inhibitory. In the absence of PL, the major product of the activation was Factor α-X_a, while in the presence of PL, lower-molecular-weight forms of Factor X (Factor β-X) and Factor X_a (Factor β-X_a were produced. At saturating levels of Ca²⁺, the K_{m app} for the activation, at pH 7.4 and 37 °C, in the absence of PL, was found to be 0.6 ± 0.1 μm and the V was 1.7 ± 0.3 mol Factor X cleaved min^?1 mol^?1 Factor X_a. The corresponding values, in the presence of 90 μm PL, were 1.4 ± 0.2 μm and 2.2 ± 0.2 mol Factor X cleaved min^?1 mol^?1 Factor X_a.     

Evidence for sub-families of actin genes in Dictyostelium as determined by comparisons of 3' end sequences

We have sequenced the 3′ end of five actin genomic clones and three actin complementary DNA clones from Dictyostelium. Comparison of the sequences shows that the protein coding regions are highly conserved, while the region corresponding to the 3′ untranslated regions are divergent. Additional analysis indicates regions of homology in the 3′ untranslated region between sets of actin genes. Southern DNA blot hybridization studies using labeled 3′ ends suggest that there are sub-families of actin genes that are related within the 3′ untranslated regions. No homology is found in the sequences outside the messenger RNA encoding regions. Analysis of the sequence data has shown that the difference in length between the ~1.25 × 10³ and ~1.35 × 10³ base actin messenger RNAs is in the lengths of the 3′ untranslated region.     

Nuclear magnetic resonance studies on pyridine dinucleotides. Carbon-13 assignments and structure determination of NADHX and the primary acid product of NADH.

The ¹³C spectra of β-NADH, NADHX, and the primary acid product of NADH were obtained and assigned. The conversion of the NADHX isomers to the two isomers of NADH acid product is demonstrated through the use of ¹³C-enriched compounds. The structure of NADHX is assigned as β-6-hydroxy-1,4,5,6-tetrahydronicotinamide adenine dinucleotide and the structures of the primary acid products of NADH are assigned as α-O^2′-6B-cyclotetrahydronicotinamide adenine dinucleotide and α-O^2′-6A-cyclotetrahydronicotinamide adenine dinucleotide.The structures of NADHX and the major isomer of the primary acid product, derived from studies of model compounds, are consistent with those proposed by Oppenheimer and Kaplan [Biochemistry (1974) 13, 4675, 4685]. However, the spectra of ¹³C-enriched primary acid product also demonstrated the existence of the A isomer which was not observed in the latter ¹H study. The A and B isomers were found to exist in the same ratio even when the primary acid product was formed directly from NADHX. This observation is discussed in terms of the previously proposed mechanism for the acid decomposition of NADH.     

Spectroscopy and crystal structure of neodymium coordination compound with glycine: Nd2(Gly)6·(ClO4)6·9H2O

Neodymium complex compound with glycine: Nd₂(Gly)₆·(ClO₄₆·9H₂O was synthesized and obtained in the form of monocrystals. Absorption spectra recorded in the region of 8000–35 000 cm^-1 were measured along the crystallographic axes. Intensities of the f-f transitions were analysed on the basis of the Judd theory. The X-ray crystal structure determination of the complex is reported. Crystals are triclinic, space group P$\text{I}$, with a = 11.554(4) Å, b = 14.108(1) Å, c = 15.660(3) Å, α = 97.14(1)°, β = 102.82(2)°, γ = 105.28(1)°, V = 2355.25 ų Z = 2, M.W. = 1495.4, D_c = 2.129)(3) g cm^-3, D^m = 2.103(1) g cm^-3. The structure was solved by Patterson's method and successive Fourier syntheses giving the locations of all nonhydrogen atoms. The final R factor was 0.062 and R_w = 0.073 for 12869 reflections with |F_o| > 5σ|(F_o)|. The asymmetric unit consists of a dimeric formula unit. The coordination polyhedron of Nd atoms comprises seven oxygen atoms from glycine and two from water molecules. The neodymium-glycine bonding mode is compared with that of the calcium-glycine complex.     

Effects of butyric acid on cell cycle regulation and induction of histone H1(0) in mouse cells and tissue culture. Inducibility of H1 (0)in the late S-G2 phase of the cell cycle

We have examined the regulation of the synthesis of histone H1(0) in cultured mammalian cells treated with butyric acid. Treatment of cells with the inducer results in the arrest of synthesis of DNA and the other histones, while increasing the synthesis of H1(0) by a factor of 11. The induction of H1(0) by butyric acid occurs in a pulse with a peak at six hours, followed by a decrease to negligible levels. This pulse-like induction appears to be due to the fact that the cells are inducible for H1(0) only in the late S or G2 phases of the cell cycle. This, coupled with the fact that butyric acid blocks cells in G1, results in the burst of H1(0) synthesis after addition of the inducer. The G1 block provoked by butyric acid does not appear to result from the accumulation of H1(0). Removal of butyric acid from G1-blocked cells resulted in the resumption of cellular proliferation without prior loss of H1(0), demonstrating that the presence of this histone is not sufficient to prevent cellular proliferation.     

Complexation of Pd(II) with nucleosides. Evidence for a strong interaction Pd⋯HN by NMR

Bis-derivatives of phenylantimony(III) with some monothio-β-diketones have been synthesized and characterized as five coordination species by elemental analyses, molecular weight and spectral data. The stereochemistry of the complexes having asymmetrical ligands is discussed.     

Copper(II) halide complexes of 2-aminobenzophenone. Crystal and molecular structure of bis(2-aminobenzophenone)dichlorocopper(II)

The complexes CuX₂L₂ (X = Cl, Br; L = 2-aminobenzophenone) were prepared and characterized by means of magnetic and spectroscopic measurements. For the Cl compound the crystal structure was also determined. Crystals are triclinic, space group P$\text{1}$, with a = 13.397(3), b = 10.752(2), c = 9.205(2) Å, α = 72.26(1)°, β = 91.58(1)°, γ = 106.86(1)°, and Z = 2. The structure was solved by the heavy-atom method and refined by least-squares calculations to R = 0.034 for 2581 counter data. It consists of discrete CuX₂L₂ monomers showing distorted trigonal bipyramidal coordination geometry about the copper ion. The amino nitrogens are axial ligands, with the equatorial positions occupied by two chlorine atoms and a carbonyl oxygen from one L molecule acting as a bidentate ligand. Infrared and ligand field spectroscopies and magnetic measurements, interpreted on the basis of the known crystal structure, also suggest a similar structure for the related Br compound.     

Base sequence studies of 300 nucleotide renatured repeated human DNA clones

A band of 300 nucleotide long duplex DNA is released by treating renatured repeated human DNA with the single strand-specific endonuclease S₁. Since many of the interspersed repeated sequences in human DNA are 300 nucleotides long, this band should be enriched in such repeats. We have determined the nucleotide sequences of 15 clones constructed from these 300 nucleotide S₁-resistant repeats. Ten of these cloned sequences are members of the Alu family of interspersed repeats. These ten sequences share a recognizable consensus sequence from which individual clones have an average divergence of 12.8%. The 300 nucleotide Alu family consensus sequence has a dimeric structure and was evidently formed from a head to tail duplication of an ancestral monomeric sequence. Three of the remaining clones are variations on a simple pentanucleotide sequence previously reported for human satellite III DNA. Two of the 15 clones have distinct and complex sequences and may represent other families of interspersed repeated sequences.     

Crystal structure of (theophyllinato)methylmercury(II) monohydrate

The title compound belongs to space group P2₁/c, a = 10.884 Å, b = 9.187 Å, c = 14.458 Å, β = 131.02°, Z = 4. The structure was refined on 1355 nonzero reflections to an R factor of 0.059. The crystal contains discrete [CH₃Hg(theophyllinate)] molecules in which the proton initially bound to N7 is replaced by the CH₃Hg⁺ ion. The water molecule forms hydrogen bonds with both carbonyl oxygens, whereas an intermolecular contact of 2.98 Å is established between mercury and N9. The intramolecular Hg?O6 distance of 3.18 Å is consistent with the absence of significant Hg?carbonyl bonding interactions in the present structure.