Structural studies on complexes. II. Crystal and molecular structure of a 1:1 caffeine and 5-chlorosalicyclic acid complex.
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Caffeine↗
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[Cooperative interaction of serum albumin with quaternized poly-4-vinyl pyridine and structure of the complexes].
Interaction of bovine serum albumin (BSA) with quaternized poly-4-vinyl pyridine (PE) in aqueous solutions at pH 7 was studied. It was shown that in a wide range of the ratios of the components (nBSA/nPE) soluble stable cooperative complexes were formed. At the same time a certain critical content of the protein exists at which the system loses its homogeneity. Complex formation is not accompanied by protein denaturation. At smaller nBSA/nPE ratios non-homogeneous distribution of protein globulas among polyelectrolite macromolecules was found; this corresponded to the "all or none" principle. Using ultracentrifugation technique viscosimetric measurements and electron microscopy it was shown that the soluble complexes exist in the form of rode-like particles consisting of protein globules stabilized by polycation chains. Such particle can be considered as a model of nucleoprotein complex. At certain crytical nBSA/nPE rations the rod-like particles aggregate with additional number of BSA-molecules and form more complicate soluble and insoluble cooperative complexes. Possible structural models of the complexes described were suggested and the thermodinamic and kinetic cryteria of their self-assembly were discussed.
Drug Stability↗
Molecular studies of mammalian branched-chain alpha-keto acid dehydrogenase complexes: domain structures, expression, and inborn errors.
We have cloned cDNAs encoding the E1b-alpha, E1b-beta, and E2b subunits of the bovine and human branched-chain alpha-keto acid complexes. The deduced primary structures indicate that the mammalian E2b contains a lipoyl-bearing, an E3-binding, and an inner core domain that are linked in series by two flexible hinge regions. The observed conservation among E2 proteins in each of the three folded domains strongly suggests that the structural cores of alpha-keto acid dehydrogenase complexes are evolutionarily related. We have expressed bovine pre-E2b in E. coli. The lipoate-free precursor protein is enzymatically active and appears to assemble into a 24-mer structure. Studies with deletion mutants support the proposal that the antigenicity in pre-E2b is associated with the flexible proline-rich hinge region. We have observed five distinct molecular phenotypes in maple syrup urine disease (MSUD) cells, according to the pattern of the branched-chain complex protein subunits and mRNAs present. The results have demonstrated a high degree of genetic heterogeneity in MSUD and have identified the affected genes which must be characterized.
3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗
Alkali and alkaline-earth metal ketyl complexes: isolation, structural diversity, and hydrogenation/protonation reactions
The use of hexamethylphosphoric triamide (HMPA) as a stabilizing ligand allowed successful isolation of a series of structurally characterizable alkali metal and calcium ketyl complexes. Reaction of lithium and sodium with one equivalent of fluorenone and reaction of sodium with one equivalent of benzophenone in THF, followed by addition of two equivalents of HMPA, yielded the corresponding ketyl complexes 1, 2, and 11, respectively, as microketyl-bridged dimers. If one equivalent of HMPA was used in the reaction of sodium with fluorenone, a further aggregated complex, the mu3-ketyl-bridged tetramer 3, was isolated, whereas analogous reaction of benzophenone with sodium afforded the trimeric ketyl complex 13, rather than a simple benzophenone analogue of 3. In the reaction of potassium with fluorenone, the use of two equivalents of HMPA gave the tetramer 4, rather than a dimeric complex analogous to 1 or 2. Compared to the tetrameric sodium complex 3, there is an extra HMPA ligand that bridges two of the four K atoms in 4. When 0.5 equiv of HMPA was used in the above reaction, complex 5, a THF-bridged analogue of 4, was isolated. In the absence of HMPA, the reaction of sodium with an excess of fluorenone yielded the tetrameric ketyl complex 6, in which two of the four Na atoms are each terminally coordinated by a fluorenone ligand, and the other two Na atoms are coordinated by a THF ligand. Two bridging THF ligands are also observed in 6. Reaction of 1,2-bis(biphenyl-2,2'-diyl)ethane-1,2-diol (7) with two equivalents of LiN(SiMe3)2 or NaN(SiMe3)2 in the presence of four equivalents of HMPA easily afforded 1 or 2, respectively, via C-C bond cleavage of a 1,2-diolate intermediate. The reaction of calcium with two equivalents of fluorenone or benzophenone in the presence of HMPA gave the corresponding complexes that bear two independent ketyl ligands per metal ion. In the presence of 3 or four equivalents of HMPA, the fluorenone ketyl complex was isolated in a six-coordinate octahedral form (10), while the benzophenone ketyl complex was obtained as a five-coordinate trigonal bipyramid (13). The radical carbon atoms in both benzophenone ketyl and fluorenone ketyl complexes are still in an sp2-hybrid state. However, in contrast with the planar configuration of the whole fluorenone ketyl unit, the radical carbon atom in a benzophenone ketyl species is not coplanar with any of the phenyl groups; this explains why benzophenone ketyl is more reactive than fluorenone ketyl. Hydrolysis of 2 or 11 with 2N HCI yielded the corresponding pinacol-coupling product, while treatment of 2 or 11 with 2-propanol, followed by hydrolysis, gave the pairs fluorenone and fluorenol or benzophenone and benzhydrol, respectively. A possible mechanism for these reactions is proposed.
Journal Article↗
The matrix method of metabolic control analysis: its validity for complex pathway structures.
The sensitivities of the variables of a metabolic system (such as fluxes and concentrations) to variations in enzyme concentration are expressed in metabolic control analysis as control coefficients. The matrix method is a system of writing matrix equations that generate expressions for the control coefficients in terms of the characteristics of the components (principally the enzymes). Previously, the matrix method has been considered in terms of simple pathway structures; here we justify its applicability to complex pathways, such as those with multiple branches. It is shown that this requires modification of the branch point relationship to take account of changes of flux along the limbs of the branch and of stoichiometric factors. The method of deriving the flux control coefficients with respect to different fluxes in the system is extended to cope with these circumstances.
Animals↗
Thermal stability of Rhizopus niveus lipase expressed in a kex2 mutant yeast.
Lipase from Rhizopus niveus (RNL) has a complex structure, and recombinant RNL, has even more complex structural properties in the yeast, Saccharomyces cerevisiae. These properties are due to the processing and to the size of the glycosylated sugar chain. The processing site was presumed to be that for the proteinase product of the KEX2 gene in yeast. We therefore, constructed an expression system in which the KEX2 gene was disrupted to produce a non-processed type of lipase with high thermal stability. This type of lipase was thermally stable to a temperature 15 degrees C higher than that of each processed type of lipase. This non-processed lipase had 50% residual activity after 2 h at 50 degrees C, while the residual activity of the processed lipases was only 10% after 30-45 min of incubation at 50 degrees C. The CD spectrum of the non-processed type of lipase at 222 nm was almost unchanged by heating, suggesting that this group of lipases had a very rigid structure and that the peptide bond between the A- and B-chain contributed to maintain this rigid structure. On the other hand, the length of the sugar chain bound to the lipase had no effect on the thermal stability.
Enzyme Stability↗
Gas phase, solution, and solid state alkali ion binding by the [NbE8](3-) (E = As, Sb) complexes: synthesis, structure, and spectroscopy.
Toluene solutions of Nb(toluene)(2) react with ethylenediamine solutions of K(3)E(7) (E = As, Sb) in the presence of 2,2,2-crypt to give [NbAs(8)](3-) (2) and [NbSb(8)](3-) (3) ions, respectively, in low yields. The (133)Cs NMR spectroscopy, ESIMS results (negative ion mode), and single-crystal X-ray structures of the ions are reported. The complexes have S(8)-like E(8) rings with Nb atoms in the center. The 1:1 complex of 2 with Cs+ was observed in solution and also in the gas phase as the oxidized ion [CsNbAs(8)](1-). The anion 2 selectively binds to Cs(+) in solution even in the presence of excess Na(+). Other gas-phase ions formed include [Cs(2)(NbAs(8))](1-), [KCs(NbAs(8))](1-), [KCs(NbAs(8))(2)](1-), [KNbAs(8)](1-), and [K(2)NbAs(8)](1-).
Journal Article↗
Identification of pathways controlling muscle protein metabolism in uremia and other catabolic conditions.
PURPOSE OF REVIEW: Major progress has been made in defining two key steps that mediate muscle protein degradation in kidney disease and other catabolic conditions. These advances are identified and discussed. RECENT FINDINGS: Activation of caspase-3 in muscle was discovered to be the initial step in breaking down the complex structure of myofibrils. Caspase-3 cleaves the complex structure, yielding substrate proteins and protein fragments that are degraded by the ubiquitin-proteasome system. Activation of caspase-3 occurs when insulin receptor substrate-1-associated phosphatidylinositol 3 kinase activity is suppressed in different models of catabolic conditions. The E3 ubiquitin ligases, MAFbx (also called atrogin-1) and MuRF1, were previously shown to play an essential role in muscle wasting. Several reports show that the insulin receptor substrate-1-associated phosphatidylinositol 3 kinase/Akt pathway activates forkhead transcription factors to increase expression of MAFbx/atrogin-1 and MuRF1. This response induces muscle protein wasting. In addition, chronic activation of the transcription factor, nuclear factor-kappaB, induces muscle atrophy. SUMMARY: The insulin-like growth factor-1/insulin receptor substrate-1-associated phosphatidylinositol 3 kinase/Akt cellular signaling pathway coordinately regulates two proteolytic pathways, caspase-3 and the ubiquitin ligases MAFbx/atrogin-1 and MuRF1 to control muscle protein degradation. These pathways represent therapeutic targets in diseases that cause muscle wasting.
Animals↗
eta1:eta2-Alkynyl-bridged W-Si complexes: formation, structure, and reaction with acetone.
Reactions of (eta5-C5Me4R)(CO)2(MeCN)WMe (R = Me, Et) with HPh2SiCCtBu gave the novel alkynyl-bridged W-Si complexes, (eta5-C5Me4R)(CO)2W(mu-eta1:eta2-CCtBu)(SiPh2) (R = Me, Et), whose alkynyl ligands bridge the tungsten and silicon atoms in an eta1:eta2-coordination mode. The structures of these complexes were fully characterized, including X-ray crystallography. Treatment of (eta5-C5Me5)(CO)2W(mu-eta1:eta2-CCtBu)(SiPh2) with acetone resulted in acetone insertion into the silicon-alkynyl linkage followed by intramolecular C-H activation of the tBu group to give the chelate-type alkyl-alkene complex, (eta5-C5Me5)(CO)2W(eta1:eta2-CH2CMe2C=CHSiPh2OCMe2).
Journal Article↗
The vertebrate nuclear pore complex: from structure to function.
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Active Transport, Cell Nucleus↗
Structural analysis of the active site of porcine pancreatic elastase based on the X-ray crystal structures of complexes with trifluoroacetyl-dipeptide-anilide inhibitors.
The X-ray crystal structures of two new (trifluoroacetyl)dipeptide p-(trifluoromethyl)anilide (TFA-dipeptide-TFM) inhibitors complexed to porcine pancreatic elastase are presented. TFA-Val-Ala-TFM and TFA-Phe-Ala-TFM both bind to elastase with the TFA group in the S1 subsite, Val or Phe in the S2 subsite, Ala in the S3 subsite, and the TFM group in the S4 subsite. Five other TFA-dipeptide-anilide/elastase crystal structures are available (two TFA-X-Ala-p-(trifluoromethyl)anilide, X = Lys, Leu, and three TFA-Lys-X-p-isopropylanilide, X = Pro, Leu, Phe). The four inhibitors with the trifluoromethyl substituent on the anilide ring bind in a single mode to elastase, whereas superposition of the three inhibitors with the isopropyl substituent on the anilide ring show three different modes of binding to the protein [Mattos, C., et al. (1994) Nature Struct. Biol. 1, 55-58]. The seven structures are taken together in a detailed analysis of the active site of porcine pancreatic elastase. The inhibition constants for the inhibitors are used in combination with the crystal structures to understand the specificity of the different elastase subsites.
Animals↗
The recombinant product of the Chryptomonas phi plastid gene hlpA is an architectural HU-like protein that promotes the assembly of complex nucleoprotein structures.
The HlpA protein which is encoded by the hlpA gene in the plastid genome of the cryptomonad alga Chryptomonas phi is structurally related to the non-sequence-specific DNA-binding and DNA-bending HU family of chromatin-associated proteins. The expression of the HlpA protein complements the mutant phenotype of Bacillus subtilis cells impaired in the Hbsu protein (B. subtilis HU), as measured by the resistance of the cells to methylmethane sulphonate. To analyse the interactions of HlpA with DNA, we expressed the protein in Escherichia coli and purified it to homogeneity. HlpA interacts preferentially with four-way junction DNA or DNA minicircles, when compared with linear DNA, recognising DNA structure. HlpA and E. coli HU display comparable affinities for all types of DNA tested; however, HlpA exhibits a stronger tendency to self-associate in the presence of DNA. Accordingly, HlpA oligomerises more readily than HU in protein crosslinking experiments. In the presence of topoisomerase I, HlpA constrains negative superhelical turns in closed circular plasmid DNA. The HlpA protein mediates the joining of distant recombination sites into a complex nucleoprotein structure, as judged by beta-mediated site-specific recombination. The results presented provide evidence that HlpA is a functional plastid equivalent of nuclear and mitochondrial HMG1-like proteins and bacterial HU proteins.
Bacillus subtilis↗
Crystal structure of the schiff base intermediate prior to decarboxylation in the catalytic cycle of aspartate alpha-decarboxylase.
l-Aspartate alpha-decarboxylase (ADC), encoded by the panD gene, catalyzes the conversion of l-aspartate into beta-alanine. In the microorganisms, beta-alanine is required for the synthesis of pantothenate (vitamin B(5)), which is the precursor of 4'-phosphopantetheine and coenzyme A. We have determined the crystal structure of Helicobacter pylori ADC, a tetrameric enzyme, in two forms: the apo structure at 2.0 A resolution and the isoasparagine complex structure at 1.55 A resolution. All subunits of the tetramer are self-processed at the Gly24-Ser25 linkage, producing the smaller beta chain (residues 1-24) and the larger alpha chain (residues 25-117). Each subunit contains nine beta-strands and three alpha-helices; it is folded into the double-psi beta-barrel structure. In the apo structure, the new amino terminus of the alpha chain, Ser25, is converted into a pyruvoyl group. In the isoasparagine complex structure, the substrate analog is covalently attached to the pyruvoyl group. This structure represents the enzyme-substrate Schiff base intermediate that was proposed to form prior to the decarboxylation step in the catalytic cycle of ADC. Thus our study provides direct structural evidence for the reaction mechanism of ADC.
Amino Acid Sequence↗
Electron microscopic identification of supercoiled regions in complex DNA structures.
When intracellular lambda replicative intermediates (theta structures) are intercalated with psoralen and then irradiated with long wavelength ultraviolet light (u.v.), interstrand crosslinks are produced. After purification and denaturation of these theta structures, a global difference in denaturation can be observed by electron microscopy; parental sections are essentially native whereas daughter segments are highly denatured. This difference can be explained if parental sections are covalently continuous (and therefore able to supercoil) and daughter segments are not. Due to the higher thermal stability of supercoiled DNA, parental DNA will remain native while daughter sections will denature. Because these structures are crosslinked, the thermal treatment does not lead to dissociation of the highly denatured daughter strands. Experiments with simple negatively supercoiled plasmid circles support the above conclusions. When circles are crosslinked with psoralen-u.v. and then denatured, they remain native because of the higher thermal stability of covalently closed structures. If the circles are linearized before heating but after the psoralen-u.v. treatment, the thermal stability effect is eliminated and the molecules become highly denatured. In this case, however, the crosslinking density is found to be higher than in samples linearized before psoralen-u.v. treatment. This, therefore, shows that crosslinking density also reflects the superhelical state of the molecule at the time of psoralen-u.v. treatment. Two different properties can be used to discriminate between supercoiled and covalently discontinuous domains in complex DNA structures. First, supercoiled regions remain native while covalently discontinuous segments denature following a thermal treatment. This effect requires that covalent continuity exists up to and during the heating treatment. Second, because negative superhelicity enhances psoralen intercalation, crosslinking density is higher in these regions. Even if supercoiled domains are destroyed after the psoralen-u.v. treatment, the imprint of superhelicity is retained and can be recognized as a higher than normal crosslinking density.
Bacteriophage lambda↗
Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA.
BACKGROUND: NF-kappa B/Rel transcription factors play important roles in immunity and development in mammals and insects. Their activity is regulated by their cellular localization, homo- and heterodimerization and association with other factors on their target gene promoters. Gambif1 from Anopheles gambiae is a member of the Rel family and a close homologue of the morphogen Dorsal, which establishes dorsoventral polarity in the Drosophila embryo. RESULTS: We present the crystal structure of the N-terminal specificity domain of Gambif1 bound to DNA. This first structure of an insect Rel protein-DNA complex shows that Gambif1 binds a GGG half-site element using a stack of three arginine sidechains. Differences in affinity to Dorsal binding sites in target gene promoters are predicted to arise from base changes in these GGG elements. An arginine that is conserved in class II Rel proteins (members of which contain a transcription activation domain) contacts the outermost guanines of the DNA site. This previously unseen specific contact contributes strongly to the DNA-binding affinity and might be responsible for differences in specificity between Rel proteins of class I and II. CONCLUSIONS: The Gambif1-DNA complex structure illustrates how differences in Dorsal affinity to binding sites in developmental gene promoters are achieved. Comparison with other Rel-DNA complex structures leads to a general model for DNA recognition by Rel proteins.
Amino Acid Sequence↗
Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.
We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric enzyme possesses eight distinct binding sites, and three different binding states are observed. The observation of these three states supports a mechanism in which precise conformational changes of a peptide loop and groups of active site residues modulate binding and specificity. The differences in protein conformation when one or two substrates are bound can be correlated with a condensation mechanism that leads productively to the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the progression from the apo form to a singly occupied "transitional binding" state and, subsequently, to a fully occupied, reactive state are revealed and indicate how the enzyme structure can be related to a plausible catalytic mechanism and, moreover, to favorable energetics of reaction.
Bacterial Proteins↗
Structures of complexes formed by HIV-1 reverse transcriptase at a termination site of DNA synthesis.
This study presents structural parameters associated with termination of human immunodeficiency virus, type 1 (HIV-1) reverse transcriptase (RT) at Ter2, the major termination site located in the center of the HIV-1 genome. DNA footprinting studies of various elongation complexes formed by RT around wild type and mutant Ter2 sites have revealed two major structural transformations of these complexes when the enzyme gets closer to Ter2. First, the interactions between RT and the DNA duplex are less extended, although the global affinity of the enzyme for this duplex is only decreased by 2-fold. Second, there is an atypical positioning of the RT RNase H domain on the DNA duplex. We interpret our data as indicating that the A(n)T(m) motif located upstream of Ter2 prevents a classical positioning of the enzyme on the double-stranded part of the DNA duplex at some precise positions of elongation downstream of this motif. Instead, novel species of binary and/or ternary complexes, characterized by atypical footprints, are formed. The new rate-limiting step of the reaction, characterized in the preceding paper (Lavigne, M., Polomack, L., and Buc, H. (2001) J. Biol. Chem. 276, 31429-31438), would be a transition leading from these new species to a catalytically competent ternary complex.
Base Sequence↗
Fourier-transform infrared spectroscopic studies on avidin secondary structure and complexation with biotin and biotin-lipid assemblies.
Fourier-transform infrared studies have been carried out to investigate the secondary structure and thermal stability of hen egg white avidin and its complexes with biotin and with a biotinylated lipid derivative, N-biotinyl dimyristoyl phosphatidylethanolamine (DMBPE) in aqueous dispersion. Analysis of the amide I stretching band of avidin yielded a secondary structural content composed of approximately 66% beta-sheet and extended structures, with the remainder being attributed to disordered structure and beta-turns. Binding of biotin or specific association with the biotinylated lipid DMBPE did not result in any appreciable changes in the secondary structure content of the protein, but a change in hydrogen bond stability of the beta-sheet or extended chain regions was indicated. The latter effect was enhanced by surface interactions in the case of the biotin-lipid assemblies, as was demonstrated by electrostatic binding to a nonspecific negatively charged lipid. Difference spectra of the bound biotin implicated a direct involvement of the ureido moiety in the ligand interaction that was consistent with hydrogen bonding to amino acid residues in the avidin protein. It was found that complexation with avidin leads to a decrease in bond length of the biotin ureido carbonyl group that is consistent with a reduction of sp3 character of the C-O bond when it is hydrogen bonded to the protein. Studies of the temperature dependence of the spectra revealed that for avidin alone the secondary structure was unaltered up to approximately 75 degrees C, above which the protein undergoes a highly cooperative transition to an unfolded state with concomitant loss of ordered secondary structure. The complexes of avidin with both biotin and membrane-bound DMBPE lipid assemblies display a large increase in thermal stability compared with the native protein.
Avidin↗