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  • Biochemistry and Biotechnology  (16.218)
  • Heterocycles
  • 1
    Digitale Medien
    Digitale Medien
    Novel Fluorescent Dyes by the Extension of the Core of Perylenetetracarboxylic Bisimides (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 365-380 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Fluorescent dyes ; Perylenes ; Heterocycles ; NIR dyes ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Core-extended perylenetetracarboxylic bisimides were prepared by Diels-Alder reaction followed by reduction, or by nitration followed by cyclisation. Highly fluorescent dyes were obtained with absorption regions from the visible to the NIR. Applications for solar energy harvesting, and quantum counters were suggested.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 2
    Digitale Medien
    Digitale Medien
    Synthesis of 5-Methylbenzo[b]thieno[2,3-c]isoquinolines and5-Methylbenzo[b]seleno[2,3-c]isoquinolines (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1353-1357 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Rearrangements ; C-C coupling ; C-C coupling ; Cyclizations ; Isoquinolines ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -5-Methylbenzo[b]thieno[2,3-c]isoquinolines and 5-methylbenzo[b]seleno[2,3-c]isoquinolines 11b,c have been prepared by Bischler-Napieralski cyclization of 2-acetamido-3-phenylbenzo[b]heteroarenes.
    Zusätzliches Material: 4 Tab.
    Materialart: Digitale Medien
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  • 3
    Digitale Medien
    Digitale Medien
    Oxidative Heterocyclization of 2-Alkynylbenzaldehydes with 1,2-Phenylenediamine (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1433-1441 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Alkynes ; Annelation reactions ; Carbonyl compounds ; Heterocycles ; Polycycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Upon condensation of ortho-phenylenediamine (2) with ortho-alkynylbenzaldehydes in nitrobenzene, oxidative cyclizations are observed, which result in benzimidazo[2,1-a]isoquinolines (8) or isoindolo[2,1-a]quinoxalines (9) depending on the influence of additional substituents at the alkyne.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 4
    Digitale Medien
    Digitale Medien
    Calculated Properties and Ring-Chain Rearrangements of Triphosphirane (P3H3) (2000)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 2000 (2000), S. 103-112 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Ab initio calculations ; Ionization potentials ; Phosphorus ; Heterocycles ; Small ring systems ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Ab initio quantum chemical calculations have been used to explore the P3H3 potential energy surface focussing on the ring-chain rearrangements of the three-membered ring in (PH)3 (1), the parent triphosphirane. Relative energies between stationary points were estimated using the QCISD(T)/6-311G(d,p) method based on MP2/6-31G(d,p) geometries and corrected for zero-point contributions. Ring strain, proton affinities, ionization and excitation energies and heats of formation have been evaluated using larger basis sets, e.g. 6-311++G(3df,2p). The cyclic trans-triphosphirane (1a) is the most stable P3H3 isomer and lies about 40 kJ/mol below the open-chain phosphanyldi-phosphene (H2P-P=PH). The decrease of ring strain in three-membered rings when CH2 is replaced by PH is confirmed. Triphosphirane 1a is a virtually strain-free ring and even gains some stabilization relative to three separate P-P single bonds. The reduced ring strain also helps diminish the phosphorus inversion barrier to 224 kJ/mol compared to the monocyclic isomers of (CH2)(PH)2 and (CH2)2(PH). Compound 1a follows a pure ring-opening or a 1,2-hydrogen shift rather than a combined motion pathway, in fundamental contrast with corresponding processes of diphosphirane and phosphirane. This is due to the existence of an open-chain P3H3 phosphorane intermediate stabilized by allylic conjugation. The pericyclic ring-opening of 1a is the most favored process but the energy barrier in the gas phase is about 180 kJ/mol high. Electron density is largely delocalized within the three-membered P3 ring not only in the C3v-symmetric 1b (all-cis) but also in 1a (Cs). The proton affinity of 1a is similar to that of PH3. The proton affinities decrease with n in cyclo-(CH3)3 -n(PH)n and their values were obtained: PA(1a) = 777 ±10, PA(diphosphirane) = 799 ±10 and PA(phosphirane) = 802 ±10 kJ/mol. Heats of formation are evaluated as follows (ΔH°f0 at 0 K in kJ/mol): 1a, 70 ±10; cyclo-(PH)2(PH2)+ (protonated 1a), 821 ±10; diphosphirane, 85 ±10; cyclo-(CH2)(PH)(PH2)+ (protonated diphosphirane), 814 ±10; phosphirane, 86 ±10; and protonated phosphirane, 812 ±10 kJ/mol. All P rings remain cyclic following ionization to the radical cations. Adiabatic ionization energies (IEa) are estimated as: 1a and diphosphirane, 9.3 ±0.3 eV and phosphirane 9.5 ±0.3 eV. The first UV absorption band shifts toward the longer wavelength region on going from phosphirane to 1a. The GIAO/B3LYP computed magnetic shieldings for 1a and related molecules reveal a clear relationship between the narrow bond angles in the rings and their unusually strong magnetic shielding. The similarity of the predicted 31P-NMR signals in 1a and its heteroanalog diphosphirane, (CH2)(PH)2, can be rationalized in terms of a compensation of the carbon-substituent effect (downfield shift) and the bond-bending effect imposed by the ring (upfield shift).
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 5
    Digitale Medien
    Digitale Medien
    1-Alkyl- and Azeto[1,2-a][1,5]benzodiazepine Derivatives in the Reaction of o-Phenylenediamine with 3-(Dimethylamino)propiophenones (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1973-1976 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Benzodiazepines ; Heterocycles ; Azeto[1,2-a]-1,5-benzodiazepines ; Cyclizations ; Cycloadditions ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---The reaction of o-phenylenediamine (4) with one, two or three equivalents of p-substituted 3-dimethylaminopropiophenone hydrochlorides 5a-e was studied. 4-Aryl-2,3-dihydro-1H-1,5-benzodiazepine derivatives 6a-e were obtained in good yields, along with the 1:2-adducts 7c-e and the unexpected 1:3-adducts rac-8c-e. The type of adduct formed is determined by the molar ratio of the reactants 4 and 5 and by the nature of the substituent in the para position of the propiophenone 5.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 6
    Digitale Medien
    Digitale Medien
    Preparation and Characterization of Cyanovinyl-Substituted 2-Aminothiophenes and 2-Aminothiazoles and Some of Their Heterooligomers (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1327-1334 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Thiophenes ; Solvatochromism ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -The reaction of 2,2-dicyanoethenyl- and 1,2,2-tricyanoethenyl-substituted bromoalkanes, bromomethyl benzenes, thiophenes, and furans 19-22 with 3-aminothioacrylamides and their 2-azaanalogues 23 and 24 gives a series of 5-dicyanoethenyl- and 5-tricyanoethenyl-substituted 2-aminothiophenes, 2-aminothiazoles and their (hetero)benzologous analogues 25-32. The solvatochromism, which is a characteristic feature of these donor-acceptor substituted heterocyclic compounds, was studied in detail and correlated with the Kamlet-Taft solvent parameters.
    Zusätzliches Material: 4 Tab.
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  • 7
    Digitale Medien
    Digitale Medien
    Proximate, syn-Periplanar Bisdiazene Skeletons: Syntheses, Structures, Homoconjugate Reactivity and Photochemistry (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 763-785 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Bisdiazenes ; Homoconjugation ; Photochemistry ; Heterocycles ; Diazenes ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Rigid N=N/N=N (diazene/diazene) systems (F) consisting of more or less alkylated DBH and DBO chromophoric units (1, 2, X-ray structures), with very short π,π distances [d = 2.849 (1a, av.), 2.822 Å (2)] and almost perfect syn-periplanar π,π alignments [ω = 168.6 (1a), 174.2° (2)] as well as the more flexible, less “proximate” metathesis isomers (3a,c, 27a,c, d 〉4.6 Å, ω = 90-100°) have been synthesized. Homoconjugate π,π interaction (in 1, 2, not in 3, 27) is deduced from UV spectroscopic measurements [π → π* maxima at 239 (234) nm (sh, 260)], while PE analyses furnished only small interaction parameters (1a: 〈0.3 eV). The potential of the novel syn-periplanar N=N/N=N motif in 1 and 2 for the synthesis of somewhat exotic polyheterocycles has been explored by calculation (B3LYP) as well as experimentally: i.a. kinetically stabilized, all-cis-peralkylated tetrazolidines (38, 44) and perhydro-1,2,4,5-tetrazines (41, 47) have become accessible (i.a. via novel azomethine/diazene and azomethine/azomethine cycloadditions). In 1a with its unreactive DBO chromophoric subunits, in the “buttressed” derivatives 1b-d, as well as in the DBH/DBO combination 2, and likewise in more ‘distant’ 27 (differently from the analogous C=C/C=C and N=N/C=C systems), irrespective of the excitation conditions employed (light of λ ≥≥ 280, 254 nm, low temperature matrix irradiation, acetone sensitization) no [2+2]photocycloaddition was observed. Instead exclusively N2-elimination took place. It is argued that unproductive N=N/N=N photocycloaddition would have become observable through metathesis isomerization of the respective tetrazetidines.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 8
    Digitale Medien
    Digitale Medien
    Proximate, syn-Periplanar, Rigid Imine(Nitrone)/Ene-, and Diazene(Diazeneoxy)/Ene Systems: Syntheses, Homoconjugate Reactivity and Photochemistry (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 743-762 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Chromophores ; Photochemistry ; Heterocycles ; Diazenes ; Imines ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---The chances for intramolecular imine/ene (→ azetidines), diazene/ene (→ 1,2-diazetidines), diazeneoxy/ene (→ 1,2-diazetidine oxides) and diazenedioxiene (→ 1,2-diazetidine dioxides) [2+2]photocycloadditions and for the isolation of the respective photoproducts, have been probed with specifically designed substrates. Upon direct or sensitized excitation, [2+2]cycloaddition was found to be the exclusive or at least dominant chemical process for the C=N/C=C, N=N/C=C and ON=N(O)/C=C systems featuring very small π,π-distances of 2.8-3.0 Å and large π,π-interorbital angles of 160-170° (7 → 51, 17 → 55, 33 → 58 (competing N2 elimination), 22 → 62). This is not the case, however, in ON=NO/C=C (23, where electron transfer is a possibility), or in the more flexible, less “proximate” C=N/C=N (57) and C=NO/C=N (63) systems (π,π-distances of 〉3.8 Å). While the corseted 1,2-diazetidine photoadducts (55, 58) proved to be thermally stable, their N-oxides (62, 65) were thermally too labile to be directly observable above -65 °C. For the latter's only fleeting existence, electronic rather than strain effects are held responsible (B3LYP/6-31G* calculations). Very facile C=NO/C=C (12 → 13) and N=NO/C=C (22 → 24) [3+2]cycloadditions, homoconjugate addition of H2 and of dienophiles ([2+2+2]) to the diazene/ene 17 (→ 39, 41, 45) are manifestations of “proximity” in these bichromophoric skeletons.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 9
    Digitale Medien
    Digitale Medien
    Polyol Peptidomimetics (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1113-1120 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Peptidomimetics ; Reverse turn mimetics ; Glycomimetics ; Heterocycles ; Lactams ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -D-Glucurono-3,6-lactone and L-cysteine combine in a highly stereoselective manner to give the 7,5-bicyclic thiazolidinlactam 2. The α-hydroxy group of the D-glucurono-3,6-lactone was exchanged for an amino function (to give 13) and, after condensation with L-cysteine methyl ester, the polyol dipeptide 7 was obtained. Peptide couplings proceed without the need to protect the three secondary hydroxy groups of the seven-membered ring. The amino group of 7 was deprotected and selectively elongated to the pseudo-tripeptide 16. The depsipeptide 17 was obtained by condensation of Boc-Ala-OH with the polyol 2. Elongation at the carboxy terminus yielded 19 and 20. The bicyclic scaffold populates a well-defined solution conformation; the hydroxy groups mimic the side chains of hydrophilic amino acids and can be further functionalized.
    Zusätzliches Material: 1 Ill.
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  • 10
    Digitale Medien
    Digitale Medien
    Substituted Tetraoxa[8]circulenes - New Members of the Liquid Crystal Family (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1637-1640 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Circulenes ; Heterocycles ; Liquid crystals ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---A general method for the synthesis of substituted tetraoxa[8]circulenes based on alkylation of 2,3-bis(bromomethyl)-1,4-dimethoxybenzene with acetylides is reported. Four of the compounds shows LC behavior, and the tetraoxa[8]circulenes are thus new candidates for discotic mesogens.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 11
    Digitale Medien
    Digitale Medien
    Nucleophilic Substitution of 4H-Imidazoles - A Key Step in the Synthesis of Fused Imidazoles and New Chromophores (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1661-1668 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Imidazoles ; Nucleophilic substitutions ; Fulvenes ; Pseudo-azulenes ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---The electrophilic properties of the 4H-imidazoles 1 and their protonated derivatives 2 permit the introduction of nucleophilic building blocks, as illustrated by reactions of 1 with selected amines. Depending on the nature of the amine and the substituents R1 on the heterocycle 1, single (3) or double (4) transamination is observed. The 1H-NMR spectra of the products, as well as X-ray structure analyses of compounds 3f and 4c, confirm that the residues at the 4- and/or 5-positions of 1 are exchanged. The tautomerism between 3e-h and 3e′-h′ seems to be central to the chemistry of these mixed substituted derivatives. Using orthoesters and acetophenone dimethylacetal as cyclization partners, the imidazo[4,5-d]imidazoles 5 and the 4H-imidazo[4,5-b]pyrazines 6 are obtained, respectively. Reduction of 3e with Zn/HCl or H2S leads to the air-sensitive, strongly fluorescent leuco compounds 8. Quenching of 8 by addition of aromatic aldehydes results in a condensation reaction and, coupled with the subsequent redox disproportionation, this conversion constitutes an alternative route to imidazo[4,5-d]imidazoles of type 11. The unexpected reaction of 3e-h with Lawesson's reagent allows synthesis of the 6-azapentafulvenes 14. The relevant spectral data show 14 to be members of a new chromophoric system, in which an electron-rich five-membered ring is coupled with an electron-deficient ring.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 12
    Digitale Medien
    Digitale Medien
    Reaction of 1,3-Disubstituted Acetone Derivatives with Pseudohalides: A Simple Approach to Spiro[4.4]nonane-Type Bis-Oxazolidines and -Imidazolidines (Bicyclic Carbamates, Thiocarbamates, Ureas, and Thioureas) (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 205-209 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Carbohydrates ; Imidazolidines ; Oxazolidines ; Spiro compounds ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Prochiral 1,3-dihydroxyacetone forms racemic oxazolidine- and oxazoline-type spiro[4.4]nonanes upon reactions with potassium (thio)cyanate and cyanamide. In contrast, 1,3-diaminoacetone yields only the corresponding spiro-bisimidazolidinethione under similar conditions together with monocyclic by-products, but the spiro-bisimidazolidinone is accessible by reaction of 1,3-dichloroacetone with urea. The resolution of the racemic spiro-bisoxazolidinethione 2a was achieved by using brucine as the resolving agent.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
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  • 13
    Digitale Medien
    Digitale Medien
    Synthesis and Absolute Configuration of Hongoquercin A, an Antibacterial Sesquiterpene-Substituted Orsellinic Acid Isolated as a Fungal Metabolite (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 297-302 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Antibiotics ; Configuration determination ; Heterocycles ; Hongoquercin A ; Terpenoids ; Total synthesis ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---(±)-Hongoquercin A (1), the racemate of an antibacterial fungal metabolite, has been synthesized starting from geranylacetone (2) and ethyl orsellinate (ethyl 2,4-dihydroxy-6-methylbenzoate, 5). The structure (±)-1 has been confirmed by X-ray analysis of its ethyl ester (±)-10. Synthesis of the naturally occurring (+)-hongoquercin A from (-)-sclareol (11) established its configuration as depicted in 1.
    Zusätzliches Material: 1 Ill.
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  • 14
    Digitale Medien
    Digitale Medien
    The Effect of the Carbon Ligand on the Reaction of Organozinc Reagents in the Synthesis of Substituted 2,5-Dihydrofurans: A Rare Example of An Uncatalysed Allylic-Substitution Reaction Involving Alkyl Zinc Halides (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1711-1718 
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    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Zinc ; Palladium ; Catalysts ; Sulfur ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Organozinc halides derived from Grignard reagents behave differently in their reaction with ethyl (±±)-(2RS,3SR)-tetrahydro-4-methylene-2-phenyl-3-(phenylsulfonyl)furan-3-carboxylate (3) according to the hybridisation of the carbon ligand. During the development of short multi-component reactions for the synthesis of diverse functionalized ethyl 2,5-dihydrofuran-3-carboxylates it was discovered that aryl and vinyl zinc halides undergo clean reaction with 3 in the presence of Pd(PPh3)4. In contrast, when alkyl zinc halides are reacted with 3 in the presence of Pd(PPh3)4, reductive desulfonation of 3 is observed. Remarkably, in the absence of a transition metal catalyst, the allylic substitution of 3 with alkyl zinc halides proceeds cleanly and in moderate to good yield.
    Zusätzliches Material: 2 Ill.
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  • 15
    Digitale Medien
    Digitale Medien
    A Simple Stereoselective Synthesis of Enantiopure 2-Substituted Pyrrolidines and Piperidines from Chiral (R)-Phenylglycinol-Derived Bicyclic 1,3-Oxazolidines (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 1719-1726 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Asymmetric synthesis ; Nitrogen heterocycles ; Heterocycles ; Pyrrolidines ; Piperidines ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Chiral, nonracemic 2-substituted pyrrolidines and piperidines were prepared in high ee and moderate to good chemical yields in three steps from (R)-phenylglycinol and γ- or δ-chloroketones. The key step of the synthesis was the stereoselective reductive ring-opening of chiral bicyclic 1,3-oxazolidines prepared by condensation of (R)-phenylglycinol and the corresponding ketones.
    Zusätzliches Material: 1 Ill.
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  • 16
    Digitale Medien
    Digitale Medien
    Proximate, syn-Periplanar Diazene/Diazene(di)oxy, Diazeneoxy/Diazene(di)oxy, and Diazenedioxy/Diazenedioxy Skeletons: Syntheses, [2+2]Photocycloadditions, Metathesis (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 787-806 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Photochemistry ; Heterocycles ; Diazenes ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Of two very proximate syn-periplanar bisdiazenes (1,2) mono-, di-, tri- and tetra-N-oxides were prepared, representing six combinations of the individual N=N/N=NO/ON=NO chromophores. According to DFT calculations (B3LYP/6-31G*), [2+2]photocycloaddition to the respective oxidized tetrazetidines is significantly to moderately endothermic. The metathesis isomerization of the oxidized tetrazetidines is generally highly exothermic and kinetically increasingly favorable with increasing oxidation state. In practice, four out of the six bichromophoric combinations undergo selectively, in competition with N2 elimination from a DBH unit (13) still partially, metathesis isomerization upon π → π* excitation (monochromatic 254 nm light). In the case of the syn-N=NO/N=NO combinations (5/6, 14), the photoaddition is thermally reversed. For a ON=NO/N=N combination (30), internal electron transfer is responsible for a complex reaction pattern. The preparative value of the metathesis reactions, though, is limited: The metathesis-derived bis[diazene mono(di)oxides] undergo relatively fast secondary photoreactions, while the tri(tetra)oxides undergo rapid thermal transformations. For the N=N/N=NO systems (12), of three potential pathways for its metathesis isomerization, the one that takes place via σ-symmetric intermediates (63, 64) is excluded by virtue of the retention of optical purity in the photometathesis of a highly enriched enantiomer [(-)-12]. Matrix irradiation experiments (12 K, IR control) with 12 result in the appearance of a kinetically highly labile transient. Supported by DFT calculations it is concluded that in the metathesis reactions, the respective tetrazetidine oxides (increasingly destabilized by interactions between oxygen lone pairs and NNσ* orbitals) function as vibrationally excited transients. That thermal reversion of these transients might be a general, nonproductive competition, is suggested by the experimental verification of a “reversed photometathesis” (51 → 15) and by the generally low rates in product formation upon irradiation. The question remains to be answered why in structurally analogous molecular skeletons, [2+2]photocycloaddition occurs in the C=C/N=N and variously oxidized N=N/N=N, and not, however, in the parent N=N/N=N combinations.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 17
    Digitale Medien
    Digitale Medien
    Synthesis of Ascididemine and an Isomer (2000)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 2000 (2000), S. 849-855 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Marine alkaloids ; Heterocycles ; Natural products ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: ---Ascididemine (9H-quino[4,3,2-de][1,10]phenanthrolin-9-one) (1) and an isomer (9H-quino[4,3,2-de][1,7]phenanthrolin-9-one) (4) have been synthesized starting from 1,4-dimethoxyacridone (7). The acridone was converted into 1,4-dimethoxy-9-ethynylacridine (11) by a triflate coupling. The ethynylacridine was converted in one-pot into 3H-6-methoxypyrido[2,3,4-kl]acridine (15) by reaction with sodium diformylamide; the mechanism of this key transformation is discussed. Conversion into 6H-4-bromopyrido[2,3,4-kl]acridin-6-one (19) and 6H-pyrido[2,3,4-kl]acridin-6-one (17), followed by reaction of each of these under high pressure conditions with acrolein N,N-dimethylhydrazone, gave ascididemine and its isomer, respectively.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 18
    Digitale Medien
    Digitale Medien
    Synthesis Mediated by Ring-Closing Metathesis - Applications in the Synthesis of Azasugars and Alkaloids (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 959-968 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Alkaloids ; Castanospermine ; Metathesis ; Azasugars ; Manzamine A ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -The application of the ring-closing metathesis (RCM) reaction to the construction of a wide variety of nitrogen-containing ring systems is described. The examples include pyrrolizidine, indolizidine, and quinolizidine derivatives related to azasugars. A formal total synthesis of castanospermine (5) is presented. The utilisation of two RCM steps in the synthetic sequence leading to the multicyclic ABCDE nucleus 7 of the complex alkaloid manzamine A (6) is discussed.
    Zusätzliches Material: 3 Ill.
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  • 19
    Digitale Medien
    Digitale Medien
    Intramolecular Copper- and Rhodium-Mediated Carbenoid Reactions of α-(Propargyloxy)silyl-α-diazoacetates (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1213-1221 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Diazo compounds ; Carbenes ; Carbenoids ; Silicon ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -Copper(I) triflate catalyzes the transformation of α-[(2-alkynyl)oxy]silyl-α-diazoacetates 1a-g into 1,2-bis(2,5-dihydro-1,2-oxasilol-4-yl)ethenes 2 and/or 2H-1,2-oxasilines 3. With rhodium(II) perfluorobutyrate as catalyst, 1a-e furnish only 3 but no 2. Bicyclic 2-methoxyfurans 6 are formed when 1a,c,e (containing terminal alkyne functions) are treated with catalytic amounts of copper(I) chloride. The experimental observations are explained in terms of metal-mediated intramolecular cyclopropenation and subsequent metal-assisted ring-opening of the strained bicyclic cyclopropene leading to vinylcarbene-metal complexes. An unusual autoxidation of 2H-1,2-oxasilines 3a,c,e is also described.
    Zusätzliches Material: 1 Ill.
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  • 20
    Digitale Medien
    Digitale Medien
    Synthesis of the Enantiomers of 2-sec-Butyl-4,5-dihydrothiazole and (1R,5S,7R)-3,4-Dehydro-exo-brevicomin, Pheromone Components of the Male Mouse, Mus musculus (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2167-2173 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Acetals ; Heterocycles ; Mouse ; Mus musculus/ Pheromones ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Two components [2-sec-butyl-4,5-dihydrothiazole (1) and 3,4-dehydro-exo-brevicomin (2)] of a male-produced pheromone of the mouse Musmusculus have been synthesized in optically active forms. The enantiomers of 1 were obtained with an enantiomeric purity of ca. 92% ee and were found to be readily racemizable. Asymmetric dihydroxylation was employed as the key reaction (15→16) allowing the preparation of (1R,5S,7R)-2 with ca. 94% ee.
    Zusätzliches Material: 1 Tab.
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  • 21
    Digitale Medien
    Digitale Medien
    The Synthesis of Novel Cyclic β-Amino Acids as Intermediates for the Preparation of Bicyclic β-Lactams (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2433-2441 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Amino acids ; Lactams ; Schiff bases ; Nitrogen heterocycles ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Several derivatives of homopipecolic acid are prepared by α-amino alkylation of malonic acid with cyclic imines 6 and 7. These are prepared on a large scale and with different substitution patterns. The β-amino acids 8 and 9 were formed in high yield and with remarkable diastereoselectivity if chiral imines are used as starting materials. The diastereoselectivity of the amino alkylation leading to homopipecolic acid analogues is compared to those of thiazolidineacetic acids by epimerisation experiments. A method for resolution of the obtained racemic β-amino acids by diastereomeric salt formation is described. The β-amino acids 9 and 15 were converted into their corresponding carbacepham analogues 14 and isopenam 16. The isopenam endo-16 was selectively epimerised by mild basic treatment of the N/S-acetal to give an exo-configured precursor of isopenicillin G.
    Zusätzliches Material: 2 Tab.
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  • 22
    Digitale Medien
    Digitale Medien
    Pd-Catalyzed Asymmetric Allylic Alkylation of 3-Acetoxy-N-(tert-butyloxycarbonyl)-1,2,3,6-tetrahydropyridine - Preparation of Key Intermediates for Natural Product Synthesis (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2515-2521 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Asymmetric synthesis ; Heterocycles ; Palladium ; Alkylations ; Allyl complexes ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: A convenient synthesis of racemic tetrahydropyridine 1 was developed. Pd-catalyzed allylic alkylation of 1 with malonate and dimethylacetoxymalonate as nucleophiles with the phosphanylcarboxylic acid L1 and the dihydrooxazol L2 as ligands, were carried out and gave enantiomeric excesses of up to 98%. Absolute configurations were determined for all compounds described. From the alkylation products (+)- and (-)-2a, and (+)- and (-)-2b a variety of versatile, nonracemic chiral intermediates were prepared.
    Zusätzliches Material: 1 Tab.
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  • 23
    Digitale Medien
    Digitale Medien
    New Heterocycles from the Reaction between Some Natural α-Amino Acid Hydrazides and Formaldehyde (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2943-2948 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Amino acids ; α-Amino acid phenylhydrazides ; Heterocycles ; Cyclization reactions ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The ring forming condensation between some natural α-amino acid phenylhydrazides (1) and aqueous formaldehyde (2) has opened a novel synthetic route to hexahydro-1,2,4-triazin-6-one derivatives (3). Polycyclic systems were obtained from the same reaction carried out with L-aspartic acid 1,4-bis(2-phenylhydrazide) (1d), L-histidine phenylhydrazide (1e) and L-tryptophan phenylhydrazide (1f) which gave perhydro-4,6-dioxo-2,8-diphenyl[1,2,4]triazino[4,5-d][1,2,4]triazepine (5) perhydro-1-oxo-3-phenylimidazo[5,4-d][1,2,4]triazino[4,5-a]pyridine (7) and 1,2,3-H-3-(2-phenylcarbazoyl)-β-carboline (8), respectively. Substrates 1 were conveniently obtained by direct reaction of phenylhydrazine with L-α-amino acid esters retaining the original chirality.
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  • 24
    Digitale Medien
    Digitale Medien
    Intramolecular Donor-Assisted Cyclization of Organotin Compounds (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 887-898 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Tin ; Phosphorus ; Intramolecular coordination ; O ligands ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: New intramolecularly coordinated organotin compounds containing the monoanionic O,C,O-coordinating ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- have been synthesized by substitution reactions starting from organotin halides. In view of the enhanced reactivity of the intramolecularly coordinated compounds {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}SnR2R′ (2, R = Ph, R′ = CH2SiMe3; 3, R = R′ = Ph; 6, R = R′ = Cl), cationic tin species are suggested to occur as intermediates in the formation of the heterocyclic compounds [1(Sn),3(P)-Ph2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (8), [1(Sn), 3(P)-Ph(Me3SiCH2)SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)2]C6H2 (15), and {[1(Sn),3(P)-Cl2SnOP(O)(OEt)-5-tert-Bu-7-P(O)(OEt)]C6H2}2 (16). The latter compounds are formed by intramolecular cyclizations of pentacoordinate cationic tin species under elimination of ethyl halide. Furthermore, the synthesis of [1(Sn),3(P)-Ph2SnOP(O)(OH)-5-tert-Bu-7-P(O)(OH)2]C6H2 (13) is described. Reaction of 8 with an excess of Me3SiBr leads to the unexpected formation of {2-[P(O)(OEt)(OSiMe3)]-4-tert-Bu-6-[P(O)(OEt)2]C6H2}SnPhBr2 (9) as a result of an O-Sn bond cleavage initiated by Me3SiBr and subsequent reaction of the intermediate with further Me3SiBr under Sn-C bond cleavage. The high donor capacity and the rigidity of the new ligand {4-tert-Bu-2,6-[P(O)(OEt)2]2C6H2}- are demonstrated by X-ray diffraction analyses of the tetraorganotin compound 2 and the monoorganotin trichloride 6. Furthermore, the molecular structures of the 2,3,1-oxaphosphastannoles 8 and 16 are discussed.
    Zusätzliches Material: 5 Ill.
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  • 25
    Digitale Medien
    Digitale Medien
    Synthesis, Structure and Reactivity of 3,4-Dihydro-2H-1,2,4,3-triazaboroles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1193-1198 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Boron ; Triazaboroles ; Heterocycles ; Halogens ; Cyanides ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 3,4-Dihydro-2,4-diphenyl-2H-1,2,4,3-triazaboroles 3a, 3b, and 4 were synthesized by cyclocondensation of N1,N3-diphenylformamidrazone (1) with dibromophenylborane, dibromomethylborane, and boron trichloride. 3-Chloro-3,4-dihydro-2,4-diphenyl-2H-1,2,4,3-triazaborole (4) was converted into 3,4-dihydro-2,4-diphenyl-2H-1,2,4,3-triazaborole (5) by treatment with LiAlH4. The corresponding 3-cyanato and 3-cyano derivatives 6 and 7 resulted from the reaction of 4 with AgOCN and AgCN, respectively. Compound 7 was transformed into the bis(1,2,4,3-triazaborolyl)oxane 8 by silver oxide. Compounds 1-8 were characterized by elemental analyses and spectroscopic methods (1H, 11B, and 13C NMR; IR; MS). The molecular structure of 8 was established by single-crystal X-ray diffraction analysis.
    Zusätzliches Material: 2 Ill.
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  • 26
    Digitale Medien
    Digitale Medien
    New Inorganic Metallacycles and the First Six-Membered Covalent “True” Heterocycle - Oxidation of RC(E)NHPPh2 (E = O or S; R = H2N, Ph, or Py) with O, S, or Se to Give RC(E)NHP(E′)Ph2 (E′ = O, S, Se) and Their Coordination Chemistry (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1445-1452 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Metallacycles ; Solid-state structures ; Heterocycles ; Oxidations ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Direct oxidation of PhC(O)NHPPh2, H2NC(S)NHPPh2, (C5H4N)C(S)NHPPh2 with O2, S8, or Se gives [PhC(O)NHP(O)Ph2] (1), [H2NC(S)NHP(S)Ph2] (2), [H2NC(O)NHP-(S)Ph2] (3), [PhC(O)NHP(S)Ph2] (4), [(C5H4N)C(S)NHP(S)Ph2] (5), and [H2NC(S)NHP(Se)Ph2] (6). Deprotonation of 1, 2, 4-6 with potassium tert-butoxide gives K[PhC(O)NP(O)Ph2] (7), K[H2NC(S)NP(S)Ph2] (8), K[PhC(O)NP(S)Ph2] (9), K[(C5H4N)C(S)NP(S)Ph2] (10), and K[H2NC(S)NP(Se)Ph2] (11). Reaction of 4with KOBu and [Cu(Ph3P)2][NO3] gives [Cu(Ph3P)(PhC(O)NP(S)Ph2)] (12) which is the first crystallographically characterised example of a non-ionic six-membered “true” heterocycle (i.e. a ring in which every heterocatom is different). 9 and 10 were treated with [PdCl2(COD)] to give [Pd{PhC(O)NP(S)Ph2}2] (13) and [Pd{(C5H4N)C(O)NP(S)Ph2}2] (14), respectively The anion of 8 coordinates to zinc forming [Zn{H2NC(S)NP(S)Ph2}2] (15). Treatment of 2 or 8 with [PtCl2(COD)] gives [Pt{H2NC(S)NP(S)Ph2}{H2NC(S)NHP(S)Ph2}]+Cl- (16) and [Pt{H2NC(S)NP(S)Ph2}2] (17), respectively. The X-ray structures of 12, 15-17are reported.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 27
    Digitale Medien
    Digitale Medien
    Borane Insertion into Group-4 Metal-to-Carbon Bonds: The Reaction of HB(C6F5)2 with (η2-Formaldehyde)zirconocene Dimer and with (Butadiene)zirconocene (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2243-2247 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Metallaoxirane ; HBR2 addition ; (Formaldehyde)zirconocene ; (Butadiene)zirconocene ; Heterocycles ; Boron ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: (η2-Formaldehyde)zirconocene dimer (8) cleanly adds one or two molar equivalents of the borane HB(C6F5)2 by insertion of the H-[B] unit into the zirconium-carbon bond of the metallaoxirane moieties to form the mono- and bis-insertion products 16 and 17, respectively. These systems contain five-membered heterocyclic rings that are built up by connecting five different elements, namely H, B, C, O, and Zr. The bis(borane) insertion product 17 was characterized by an X-ray crystal structure analysis. (Butadiene)zirconocene reacts with HB(C6F5)2 in a similar way by insertion of the H-[B] unit into the (butadiene)C4-Zr linkage to form the metallacycle 18.
    Zusätzliches Material: 1 Ill.
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  • 28
    Digitale Medien
    Digitale Medien
    Synthesis and 1H-, 15N-, 31P-, 183W-Multinuclear Magnetic Resonance Study of the Cyclotriphosphazenes [N3P3(dobp)2(OC5H4N-4)2] and [N3P3(dobp)(OC5H4N-4)4] and Their W(CO)5 Complexes (dobp = 2,2′-dioxybiphenyl) (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1015-1020 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Cyclotriphosphazenes ; Oxypyridine ; Carbonyltungsten compounds ; NMR spectroscopy ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The reactions of [N3P3(dobp)2Cl2] and [N3P3(dobp)Cl4] with a mixture of HOC5H4N-4 and K2CO3 in acetone give the cyclotriphosphazenes [N3P3(dobp)2(OC5H4N-4)2] and [N3P3(dobp)(OC5H4N-4)4], respectively. These compounds react with [W(MeOH)(CO)5] in methanol to give mixtures of the polymetallic complexes [N3P3(dobp)2(OC5H4N-4)2{W(CO)5}x] (x = 1, 2) and [N3P3(dobp)(OC5H4N-4)4{W(CO)5}x] (x = 1-4), which are unstable in solution, slowly undergoing loss of the pentacarbonyl moiety. A complete characterization by multinuclear 1H, 15N, 31P, 183W magnetic resonance has revealed that the complexation of the N atom of one 4-oxypyridine ligand by the W(CO)5 fragment has a measurable effect on other parts of the phosphazene molecule very far away from the coordination site. The changes observed in δ183W have been used to identify the components in mixtures of compounds incorporating different numbers of tungsten atoms in the molecule. The characterization of less sensitive nuclei has been accomplished by means of indirect detection methods.
    Zusätzliches Material: 3 Ill.
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  • 29
    Digitale Medien
    Digitale Medien
    Novel Condensed Thionated Bis(phosphonic) Acid Salts with a Rigid Naphthalene-1,8-diyl Backbone (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2327-2333 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Heterocycles ; Organo-phosphorus compounds ; Dithiadiphosphetane disulfides ; Phosphonates ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: New salts of thionated (naphthalene-1,8-diyl)bis(phosphonic) acid monoanhydrides [PPh4+]2[C10H6PS2(μ-S)PS22-] (2) and [K+]2[C10H6PS2(μ-S)POS2-]·H2O (3) both containing the C3P2S ring, were prepared in high yields by the reaction of 2,4-(naphthalene-1,8-diyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide (1) with NaHS and PPh4Cl, or KOH, respectively, in water. The derivative 3, containing a P=O terminal bond as well as P-S-P bridge, undergoes, in acid conditions, a rearrangement reaction leading to the O,S-symmetrically substituted derivative [K+]2[C10H6PS2(μ-O)PS22-] (4) containing a C3P2O heterocycle. Dipotassium salt 4 was converted into the bis(tetraphenylphosphonium) salt 5 by the treating with PPh4Cl. Hydrolysis of [PyH+][C10H6P(S)(NHMe)(μ-S)PS22-] (15) led to [CH3NH3+][PyH+][C10H6POS(μ-O)POS2-]·1.5 Py (6). New compounds were characterised by 31P{1H}-, 1H- and 13C{1H}-NMR, FT-IR, ES-MS and in the cases 2-6 by X-ray structure determination. The 31P{1H}-NMR spectra of these mixed O,S-derivatives are briefly discussed.
    Zusätzliches Material: 5 Ill.
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  • 30
    Digitale Medien
    Digitale Medien
    Syntheses of Batzelline A, Batzeline B, Isobatzelline A, and Isobatzelline B (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1173-1183 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Marine alkaloids ; Pyrroloquinoline ; Total synthesis ; Heterocycles ; Alkaloids ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -Batzellines A and B (1a, b) and isobatzellines A and B (2a, b) are 1,3,4,5-tetrahydropyrrolo[4,3,2-de]quinoline-containing marine alkaloids characterized by the presence of a methylthio substituent at C-2 of the tricyclic system. We describe here the total synthesis of these natural compounds following the synthetic strategy that we have used previously for the synthesis of damirones A and B, batzelline C, isobatzelline C, discorhabdin C, and makaluvamines A, B, C, and D. The introduction of the methylthio group by electrophilic substitution of a pyrrolo[4,3,2-de]quinoline, appropriately substituted and in a suitable oxidation state, is the key step in the success of these syntheses.
    Zusätzliches Material: 2 Ill.
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  • 31
    Digitale Medien
    Digitale Medien
    The Preparation of 2,3,5-Tri- and 2,3-Disubstituted Furans by Regioselective Palladium(0)-Catalyzed Coupling Reactions: Application to the Syntheses of Rosefuran and the F5 Furan Fatty Acid (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2045-2057 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Homogenous catalysis ; Palladium ; Cross-coupling ; Heterocycles ; Synthetic methods ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The 5-acceptor-substituted 2,3-dibromofurans 1 and 2 underwent a regioselective Pd0-catalyzed coupling reaction at the C-2 carbon atom. With alkynes the corresponding 2-alkynylfurans 4 and 5 were accessible (49-97% yield). Alkyl-, aryl-, and alkenylzinc reagents gave the 2-substituted furans 8 starting from compound 2 (66-84% yield). The 2-allylfurans 8e and 8f were obtained by a regioselective Stille coupling in 79% and 73% yield. The latter reaction was also applied to the parent 2,3-dibromofuran (27) and yielded the substitution product 28 (60% yield). Subsequent Pd0-catalyzed reactions to introduce a methyl group in 3-position by a methyldebromination were successfully conducted for 2-alkynyl-3-bromofurans with MeZnCl and PdCl2(PPh3)2 as the catalyst in THF (reflux) to yield compounds 13-16 and 24 (67-76%) and with SnMe4 and PdCl2[P(o-Tol)3]2 as the catalyst in DMA (90 °C) for the 2-allyl-3-bromofuran 8e to yield 18 (70%). The more facile reaction of the 2-alkynylfurans relative to those of furans bearing an sp3-carbon atom at C-2 appears to be due to steric reasons. Studies on the 2-alkyl-3-bromofuran 20 supported this notion. With the regioselective coupling methodology the terpene rosefuran (22) was prepared in four steps starting from furan 2 (35% yield overall). The F5 furan fatty acid (26) was synthesized from furan 1 in five steps (29% yield overall).
    Zusätzliches Material: 4 Tab.
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  • 32
    Digitale Medien
    Digitale Medien
    Umpolung of Reactivity of Lithium Trimethylsilyldiazomethane at the C-5 Position of 6-Substituted Uracil Derivatives (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2751-2755 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Lithium ; Lithium trimethylsilyldiazomethane ; Heterocycles ; Uracil derivatives ; Pyrazolo[4,3-d]pyrimidindiones ; Pyrazolo[4,3-d]pyrimidindiones ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The nucleophilic addition of TMSC(Li)N2 at the low reactive C-5 position of the uracil ring of C-6 substituted uracil derivatives is reported. The ratio of C-5 versus C-6 nucleophilic addition of TMSC(Li)N2 dramatically depends on the stereoelectronic properties of the C-6 substituent. In particular, substituents characterized both by sterically bulky and/or electron-withdrawing (EWG) effects appear to direct the nucleophile mainly (methyl, chloromethyl or halogen) or completely (isopropyl) toward the C-5 position. The fine-tuned substituent selectivity found in the nucleophilic addition of TMSC(Li)N2 to C-6 substituted uracils plays a leading role in the synthesis of new trimethylsilyl-1H-[4,3-d]pyrimidin-5,7-dione derivatives, which can in turn be easily modified through known silicon chemistry.
    Zusätzliches Material: 1 Ill.
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  • 33
    Digitale Medien
    Digitale Medien
    A New Strategy for the Asymmetric Synthesis of 1,3-Oxathiolane-Based Nucleoside Analogues (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1455-1458 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Nucleoside analogues ; 1,3-Oxathiolanes ; Chiral sulfoxides ; Heterocycles ; Antiviral agents ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: -A ready asymmetric synthesis of 3′-oxathionucleosides has been accomplished in three main steps from benzoyloxyethanal. The synthesis is characterized by high overall yield and considerable enantiomeric excesses. It represents a general synthetic path to prepare a wide range of heterosubstituted sulfur-containing nucleoside analogues.
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  • 34
    Digitale Medien
    Digitale Medien
    Novel Stereoelectronic Behavior of Bicyclic Glycosyl Donors: Application to the Synthesis of Both 2-Deoxy-α- and -β-Glycosides (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1869-1874 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Carbohydrates ; Heterocycles ; Electrostatic interactions ; Glycosylation ; Glycosides ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Two pairs of novel stereoisomeric, cyclic glycosyl donors exhibit different behaviors in glycosylation processes. In the pair of α-gluco (1) and β-manno (2), the former exhibits reversability with its glycoside product whereas the latter does not. In the α-gluco (3) and β-manno (4) set, the former undergoes glycosyl transfer via an isolable intermediate whereas the latter does not. The differing anomeric effects exerted in the ground states are proposed as the force which explains the differences in behavior.
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  • 35
    Digitale Medien
    Digitale Medien
    Silicon-Oxygen Heterocycles from Thermal, Photochemical, and Transition-Metal-Catalyzed Decomposition of α-(Alkoxysilyl and Alkenyloxysilyl)-α-diazoacetates (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 1939-1946 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Diazo compounds ; Carbenes ; Carbenoids ; Silicon ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Photolysis of (ethoxy)silyl-, (propyloxy)silyl-, and (isopro-pyloxy)silyl-substituted diazoacetates 1a-c leads to tetrahydro-1,2-oxasiloles 2a-c by intramolecular C-H insertion of a carbene intermediate. Photochemical or catalytic decomposition of (allyloxysilyl)diazoacetates 3a-e results in intramolecular cyclopropanation which provides 3-oxa-2-silabicyclo[3.1.0]hexane systems 5a-e. In contrast, the thermal reaction of 3b-d gives rise to 2,5-dihydro-1,2-oxasiloles 4b-d, which are likely to be formed on a pyrazoline rather than a carbene route. For (3-butenyloxysilyl)diazoacetate 3f, all modes of decomposition generate the 3-oxa-2-silabicyclo[4.1.0]heptane system 7. Fluoride-induced cleavage of the bicyclic systems 5b-d provides trans-2-hydroxyalkyl-1-cyclopropanecarboxylates 9 diastereospecifically.
    Zusätzliches Material: 1 Tab.
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  • 36
    Digitale Medien
    Digitale Medien
    An Easy Access to 1-Azaspiropentane-2-carboxamides - The First Derivatives of a New Type of Amino Acids (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2017-2024 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Amino acids ; Azaspiropentanes ; Heterocycles ; Peptides ; Strained molecules ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Azaspiropentanecarboxamides 10 and 12 are formed with remarkable ease in two steps in a one-pot operation from methyl 2-chloro-2-cyclopropylideneacetate (4) by addition of a primary amine in tetrahydrofuran and subsequent treatment with sodium hydride/triethylamine in the presence of another equivalent of a primary amine or ammonia. Achievable yields of the amides 10, 12 were moderate to good (27-59%, 12-48%), while the corresponding esters 9 could only be obtained in poor yields (4-14%). The new α-amino acid amides are surprisingly stable, and they can be incorporated into small peptides as demonstrated with the preparation of the glycine 13e and the spirocyclopro-paneoxazoline derivative 14e.
    Zusätzliches Material: 2 Ill.
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  • 37
    Digitale Medien
    Digitale Medien
    2-Substituted 5-Acetyl-4-Thiazolyl Triflates as Useful Building Blocks for the Preparation of Functionalized Thiazoles (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 3117-3126 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Heterocycles ; Thiazoles ; Pyrido[3,4-c]thiazoles ; Triflates ; Palladium ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The readily available 2-substituted 5-acetyl-4-thiazolyl triflates 2are useful building blocks for the preparation of functionalised thiazoles by means of palladium-catalysed cross-coupling reactions with organometallic reagents and alkoxycarbonylation and deoxygenation reactions. The combination of palladium-catalysed coupling of 2 together with 1-alkynes/6-endo-dig annulation reactions in the presence of ammonia leads to functionalised pyrido[3,4-c]thiazoles in satisfactory yields. The utilisation of uncatalysed displacement reactions of the triflate group represents a very simple method for the synthesis of 4-N-,4-O-, and 4-S-substituted thiazoles.
    Zusätzliches Material: 2 Tab.
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  • 38
    Digitale Medien
    Digitale Medien
    Syntheses, Structures, and Coordination of Diborylbipyridines and Bipyridinediborates (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 393-398 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Boranes ; Bipyridine ; Crystal structures ; Donor-acceptor interaction ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 6,6′-Bis(diethylboryl)-2,2′-bipyridine (1a) was obtained in low yield by in situ deprotonation of 2,2′-bipyridine in the presence of diethyl(methoxy)borane. 6,6′-Dilithio-2,2′-bipyridine reacts with various alkoxyboranes leading to bipyridinediborates 2 in good yields. The derivatives 2b and 2c allow the formation of the free diborylbipyridines 1b and 1c. The coordination properties of the diboryl-bipyridines as tetrafunctional donor-acceptor compounds have been used for the formation of the copper complex 4 and of the adduct 5 which is built from diborylbipyridine and a dihydroxydiboroxan derivative. The composition of the products follows from spectroscopic data and from X-ray structure analyses for 2f, 4, and 5.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 39
    Digitale Medien
    Digitale Medien
    Insights into the Staudinger Reaction: Experimental and Theoretical Studies on the Stabilization of cis-Phosphazides (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1659-1664 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Phosphorus ; Iminophosphorane ; Staudinger reaction ; Heterocycles ; Ab initio calculations ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The Staudinger-model reaction H3P (1) + HN3 (2) → H3P=NH (5) + N2 (6) has been investigated at the CCSD(T)/6-31G**//MP2(Full)/6-31G* level. Primary products formed in this reaction are the phosphazides H3P=N-N=NH (3) which exist as trans and cis isomers. In contrast to some previous assumptions, cis -3is 8.2 kcal mol-1 more stable than trans -3 but decomposes rather easily into the expected products H3P=NH and N2. This decomposition can be effectively hampered by intramolecular donor-acceptor interactions as shown by calculations on model compounds as well as by experiments. Thus the reaction of a methylene-σ3,λ3-phosphanyl-σ5,λ5-phosphorane with PhN3 led to a new four-membered heterocycle containing a thermally remarkable stable cis-phosphazide moiety.
    Zusätzliches Material: 4 Ill.
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  • 40
    Digitale Medien
    Digitale Medien
    Synthesis of N-Acetylglucosaminyl and Diacetylchitobiosyl Amides of Heterocyclic Carboxylic Acids as Potential Chitinase Inhibitors (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2293-2297 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Carboxylic acid amides ; Chitinase ; Chitobiose ; Heterocycles ; Enzyme inhibitors ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 2-(Dimethylamino)oxazoline-4-carboxylic acids 5 were prepared by condensation of binucleophilic amino acids 4and O-ethyl-N,N-dimethylisourea 3. New heterocyclic N-acetylglucosaminyl amides and chitobiosyl amides 8 were obtained by the coupling of tetraacetylglucosamine 6a or heptaacetylchitobiosylamine 6b with acid chlorides of heterocyclic carboxylic acids 2 or 5a and subsequent deacetylation. Based on their substitution patterns, compounds 8were expected to have inhibitory activity towards chitinases. Enzyme assays showed that glycosyl amides 8 indeed were moderate inhibitors of chitinases, the diacetylchitobiosyl amides 8d-f generally having higher inhibitory activities than the N-acetylglucosaminyl amide derivatives 8a-c. Inhibitory activities depended on the chitinase tested.
    Zusätzliches Material: 2 Tab.
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  • 41
    Digitale Medien
    Digitale Medien
    Synthesis of (-)-Cytoxazone, a Novel Cytokine Modulator Isolated from Streptomyces sp. (1999)
    Weinheim : Wiley-Blackwell
    Liebigs Annalen 1999 (1999), S. 2965-2967 
    Details
    ISSN: 1434-193X
    Schlagwort(e): Amino alcohol ; Asymmetric synthesis ; Cell signaling ; Dihydroxylations ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Cytoxazone [(4R,5R)-(-)-5-hydroxymethyl-4-(4-methoxyphenyl)-2-oxazolidinone, 1], a new immunosuppressant, was synthesized by starting from p-methoxycinnamyl alcohol (2) employing the Sharpless asymmetric dihydroxylation as the key reaction in 26% overall yield (7 steps).
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  • 42
    Digitale Medien
    Digitale Medien
    Cyclic Ketiminoboranes (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 7-9 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Boranes ; Diazaboroles ; Heterocycles ; Ketiminoboranes ; Crystal Structures ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The cyclocondensation reaction of benzil-bis(trimethylsilylimin) (3) and Cl2B-NiPr2 via silicon-boron exchangeresults in the solvent-dependent formation of the 1,3,2-diazaborole 1a or the 1,3,6,8,2,7-tetraazadiborecin 2a. Using the more rigid 9,10-bis(trimethylsilylimino)phenanthrene instead of 3 only the five-membered heterocycle 4,5-biphenylene-2-diisopropylamino-1,3,2-diazaborole (1b) is formed. The cyclic ketiminoboranes are characterized by NMR and X-ray diffraction data. The 1,3,2-diazaborole ring is almost planar, while the conformation of the 1,3,6,8,2,7-tetraazadiborecin has the shape of a figure-eight loop.
    Zusätzliches Material: 2 Ill.
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  • 43
    Digitale Medien
    Digitale Medien
    Synthesis and Structure of 2-Hydro-, 2-Alkyl-, 2-Alkynyl-, and 2-Stannyl-2,3-dihydro-1H-1,3,2-diazaboroles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 491-497 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Boron ; Diazaboroles ; Hydrides ; Tin ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 1,3-Di-tert-butyl-2,3-dihydro-1H-1,3,2-diazaborole (4a) and 1,3-bis(2,6-dimethylphenyl)-2,3-dihydro-1H-1,3,2-diazaborole (4b) were formed by the reaction of the corresponding 2-bromo or 2-iodo derivatives 1a and 2b with LiAlH4. Treatment of 1a with n-butyllithium afforded 2-n-butyl-1,3-di-tert-butyl-2,3-dihydro-1H-1,3,2-diazaborole (5a), whereas 1,3-di-tert-butyl-2-cyano-2,3-dihydro-1H-1,3,2-diazaborole (3a) was converted into the 2-tert-butyl derivative 6a or the 2-ethynyl-1,3,2-diazaborole 7a by means of tert-butyllithium or by the ethylenediamine adduct of lithium acetylide. Similarly, 1,3-di-tert-butyl-2-trimethylstannyl-2,3-dihydro-1H-1,3,2-diazaborole (8a) and 1,3-bis(2,6-dimethylphenyl)-2-trimethylstannyl-2,3-dihydro-1H-1,3,2-diazaborole (8b) were accessible from 1a or 2b and trimethylstannyllithium. In the complex 9a the compound 3a serves as an η1 ligand towards the [Cr(CO)5] unit via the cyano group. These novel compounds were characterized by 1H-, 11B-, 13C-, and 119Sn-NMR spectroscopy, as well as by X-ray structure analyses of 4b, 8a, and 9a.
    Zusätzliches Material: 3 Ill.
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  • 44
    Digitale Medien
    Digitale Medien
    Reactions of 1,8-Diheterocyclotetradeca-4,11-diynes with (η4-Cycloocta-1,5-diene)(η5-cyclopentadienyl)cobalt (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 499-504 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Alkynes ; Heterocycles ; Cyclizations ; Cobalt ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The following monocyclic and bicyclic 14-membered diynes were treated with [CpCo(cod)]: 1-oxacyclotetradeca-4,11-diyne (2), 1,8-dioxacyclotetradeca-4,11-diyne (3), cyclotetradeca-4,11-diynone (4), cyclotetradeca-4,11-diyne-1,8-dione (5), 1,1,8,8-tetramethyl-1,8-disilacyclotetradeca-4,11-diyne (6), 1-allyl-1-azacyclotetradeca-4,11diyne (7), 1,8-dipropyl-1,8-diazacyclotetradeca-1,11-diyne (8), 1,8-diallyl-1,8-diazacyclotetradeca-4,11-diyne (9), 1,8-diazabicyclo[6.6.4]octadeca-4,11-diyne (10), 1,8-diazabicyclo[6.6.6]eicosa-4,11-diyne (11), 1,10-diazabicyclo[8.6.6]docosa-13,19-diyne (12) and 1,12-diazabicyclo[10.6.6]tetracosa-15,21-diyne (13). In all cases we obtained an intramolecular cyclobutadiene complex stabilized with a CpCo fragment (15-26). For 3 we could isolate, besides the cyclobutadiene complex 16, the trimerization product 28. In the cases of 15, 16, 18, 20, 23, 25, and 26 the structure of the cylobutadiene complexes could be confirmed by X-ray studies. Common to all structures is a boat-like conformation of the tricyclic unit containing the cyclobutadiene ring. The two cycloheptene units adopt a chair conformation in which the heteroatom is removed from the metal center.
    Zusätzliches Material: 1 Ill.
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  • 45
    Digitale Medien
    Digitale Medien
    Nucleophilic Substitution Reactions with the 3-Borane-1,4,5-trimethylimidazol-2-ylidene Anion. - Unexpected Formation of an Imidazabole Isomer (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 789-793 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Boranes ; Carbenes ; Heterocycles ; Imidazoles ; X-ray structures ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The nucleophilic carbene 3-borane-1,4,5-trimethylimidazol-2-ylidene anion (1-) reacts with the electrophiles CH3I, (CH3)3SiCl, (CH3)3SnCl, and the bromodiazaboroline 7 to form the 2-substituted imidazoles 4, 5, 6, and 8. With triethylborane, the anionic carbene borane adduct 9- is obtained. An unexpected result was achieved when chlorodimethoxyborane and HBCl2 · S(CH3)2 were used as electrophiles. In both cases only the imidazabole 14a could be isolated. Imidazole 5, the imidazole borane adduct 3a and the imidazabole 14a were characterized by X-ray structure analyses.
    Zusätzliches Material: 3 Ill.
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  • 46
    Digitale Medien
    Digitale Medien
    Carbon=Carbon Hydrogenation of Silicon-Functionalized Silaheterocycles (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 1095-1102 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Silanorbornenes ; Silanorbornanes ; Silicon-functionalized olefins ; Silacyclobutanes ; Hydrogenations ; Heterocycles ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Catalytic hydrogenation of olefins containing functionalized silicon groups affords the saturated products in good yields. Chloro and alkoxy substituents at the silicon atom remain unaffected and, in the case of heterocyclic compounds, the cyclic or bicyclic moieties remain intact. The 2-silanorbornanes 4, 5, and 6 were synthesized from the corresponding 2-silanorbornenes 1, 2, and 3, and organosilanes 13 and 14 possessing the cyclopentyl group, were prepared from the cyclopentenyl-substituted precursors 10 and 12. The 3-vinyl-substituted silacyclobutanes 15, 17, and 18 were also hydrogenated in a simple apparatus with diethyl ether or THF as solvent, and Pd/C as a recoverable catalyst system. A basic organosilicon compound, trichloro(vinyl)silane, is hydrogenated in a nearly quantitative yield to form the saturated trichloro(ethyl)silane; this emphasizes the general applicability of this method.
    Zusätzliches Material: 2 Ill.
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  • 47
    Digitale Medien
    Digitale Medien
    Synthesis, X-ray Crystal Structures and Reactivity Towards Alkynes of Gold(I)-Phosphinine Complexes (1999)
    Weinheim : Wiley-Blackwell
    Berichte der deutschen chemischen Gesellschaft 1999 (1999), S. 2233-2241 
    Details
    ISSN: 1434-1948
    Schlagwort(e): Phosphorus ; Heterocycles ; Phosphinines ; Gold ; Cycloadditions ; Chemistry ; General Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The coordination behaviour of 2,6-disilyl-substituted phosphinines towards gold(I) has been examined. The reaction of the bis(trimethylsilyl)phosphinine 1 with [AuCl(SMe2)] gives the corresponding AuCl derivative 2. X-ray crystal structure analysis reveals that the aromaticity of the phosphinine ring is slightly reduced as a result of the poor π-back bonding ability of the AuCl fragment. The same phenomenon is observed in the cationic complex [Au(1)2][GaCl4] (3) which was readily prepared by reaction of two equivalents of 1 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. Reaction of 2,6-bis(phenylethynyldimethylsilyl)phosphinine (4) with the same precursor leads similarly to the complex [AuCl(4)] (5). Interestingly, this complex dimerizes upon crystallization to give the bis(phosphabarrelene) complex 6, also structurally characterized. The formation of 6 results from a [4 + 2] cycloaddition between one alkynyl group of each phosphinine with the other phosphinine subunit. The formation of the cationic complex [Au(4)][GaCl4] (8) occurs under classical conditions but it disproportionates to give the cationic complex [Au(4)2][GaCl4] (9) and colloidal gold deposition. The formation of 9 has been ascertained by treating 8 with one equivalent of ligand 4. Additionally, 9 can also be obtained in a straightforward fashion by treating two equivalents of 4 with [AuCl(SMe2)] followed by treatment with GaCl3 at low temperature. The structure of 9 has been elucidated. Despite a particular arrangement of the alkyne groups which encapsulate the gold coordination sphere, no gold-alkyne interactions are visible.
    Zusätzliches Material: 5 Ill.
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  • 48
    Digitale Medien
    Digitale Medien
    Characterization of receptors with a new negative image: Use in molecular docking and lead optimization (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 321-336 
    Details
    ISSN: 0887-3585
    Schlagwort(e): surface characterization ; DOCK ; structure-based molecular design ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The characterization of receptor binding sites is an important aspect of molecular docking, molecular recognition, and the structure-based design process. This characterization can take several forms: the receptor surface itself can be delineated or described, the space adjacent to the surface can be chemically mapped, or a negative image of the protein binding region can be generated. In this report, we describe a new method of constructing a negative image through generation of a set of spheres. These spheres lie along the receptor surface, and their centers represent possible ligand atom positions. By the method in which they are constructed, these spheres carry a limited amount of energetic and chemical information in addition to their primary geometric information. We test the accuracy of the image by comparing sphere positions to the positions of bound ligand atoms and propose a figure of merit for such tests. Then, we use the spheres to orient ligands in enzyme active sites and show how they can be used to generate low scoring configurations more efficiently than other approaches that search orientation space. In addition, two novel applications of these spheres are described: they are used to help identify structural differences among families of enzymes and to suggest points for ligand modification in analog design. Proteins 30:321-336, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 49
    Digitale Medien
    Digitale Medien
    Nitric oxide myoglobin: Crystal structure and analysis of ligand geometry (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 352-356 
    Details
    ISSN: 0887-3585
    Schlagwort(e): myoglobin ; nitric oxide ; ligand binding ; X-ray crystallography ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The structure of the ferrous nitric oxide form of native sperm whale myoglobin has been determined by X-ray crystallography to 1.7 Å resolution. The nitric oxide ligand is bent with respect to the heme plane: the Fe-N-O angle is 112°. This angle is smaller than those observed in model compounds and in lupin leghemoglobin. The exact angle appears to be influenced by the strength of the proximal bond and hydrogen bonding interactions between the distal histidine and the bound ligand. Specifically, the Nε atom of histidine64 is located 2.8 Å away from the nitrogen atom of the bound ligand, implying electrostatic stabilization of the FeNO complex. This interpretation is supported by mutagenesis studies. When histidine64 is replaced with apolar amino acids, the rate of nitric oxide dissociation from myoglobin increases tenfold. Proteins 30:352-356, 1998. © 1998 Wiley-Liss, Inc.
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  • 50
    Digitale Medien
    Digitale Medien
    A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 372-380 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein modeling ; crystal structure ; conformation change ; prediction ; mechanism ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The occurrence of large domain motions associated with the mechanism of action of many proteins is well established. We present a general method of predicting domain closure applicable to proteins containing domains separated by an apparent hinge. The method attempts to allow for natural directional bias within the closing protein by repeatedly applying a weak pulling force over a short distance between pairs of atoms chosen at random in the two domains in question. Appropriate parameters governing the pulling function were determined empirically. The method was applied to the bi-lobal protein PGK and a closed-form activated ternary complex generated for Bacillus stearothermophilus PGK. This model was compared with the recently determined crystal structure of closed-form Trypanosoma brucei PGK. The model predicts the correct hinge regions, although the magnitude of movement at one hinge point was overestimated, and provides a reasonable representation of the closed-form ternary complex. Proteins 30:372-380, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 51
    Digitale Medien
    Digitale Medien
    Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 388-400 
    Details
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; free energy perturbation ; thermodynamics integration ; spherical solvent boundary potential ; cell multipole method ; Nosé-Hoover equation ; component analysis ; chymotrypsin inhibitor 2 ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, ΔΔG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed. Proteins 30:388-400, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 52
    Digitale Medien
    Digitale Medien
    Proteolysis as a probe of thermal unfolding of cytochrome C (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 435-441 
    Details
    ISSN: 0887-3585
    Schlagwort(e): cytochrome c ; thermal unfolding ; proteolysis ; proteinase K ; thermolysin ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recent hydrogen exchange experiments on native cytochrome c implicate a sequential unfolding pathway in contrast to a simple two-state process. We have studied the heat-induced unfolding of this protein by using spectroscopic measurements to detect changes in conformation and proteolytic enzyme digestion to identify regions of the protein that are labile. Several spectroscopic profiles were monitored: CD at 222 nm, a measurement of secondary structure change in the protein, the absorbance at 280 nm, involving the local environment of Trp 59, and absorbance at 420 nm, the Soret band of the heme. The apparent Tm values for these probes differ, consistent with an unfolding pathway containing intermediates. The limited digestion by proteinase K is consistent with population of an intermediate state in unfolding. We find a single strong region of cleavage at low temperature with retention of structure in each fragment. Proteins 30:435-441, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 53
    Digitale Medien
    Digitale Medien
    Crystallographic and spectroscopic characterization of a molecular hinge: Conformational changes in bothropstoxin I, a dimeric Lys49-phospholipase A2 homologue (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 442-454 
    Details
    ISSN: 0887-3585
    Schlagwort(e): venom toxin ; protein-membrane interaction ; X-ray diffraction ; spectroscopy ; quaternary structural change ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Bothropstoxin I (BthTX-I) from the venom of Bothrops jararacussuis a myotoxic phospholipase A2 (PLA2) homologue which, although catalytically inactive due to an Asp49→Lys substitution, disrupts the integrity of lipid membranes by a Ca2+-independent mechanism. The crystal structures of two dimeric forms of BthTX-I which diffract X-rays to resolutions of 3.1 and 2.1 Å have been determined. The monomers in both structures are related by an almost perfect twofold axis of rotation and the dimer interfaces are defined by contacts between the N-terminal α-helical regions and the tips of the β-wings of partner monomers. Significant differences in the relative orientation of the monomers in the two crystal forms results in “open” and “closed” dimer conformations. Spectroscopic investigations of BthTX-I in solution have correlated these conformational differences with changes in the intrinsic fluorescence emission of the single tryptophan residues located at the dimer interface. The possible relevance of this structural transition in the Ca2+-independent membrane damaging activity is discussed. Proteins 30:442-454, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 54
    Digitale Medien
    Digitale Medien
    Structure-based design of model proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 10-20 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein design ; lattice model ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with the target structure in being low energy conformations. The decoy structures are chosen to have strong overlaps in contacts with the putative native state. The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact energies to both the native and nonnative contacts. The design procedure is also successfully applied to the two-dimensional HP model. Proteins 31:10-20, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 55
    Digitale Medien
    Digitale Medien
    Modelling repressor proteins docking to DNA (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 535-549 
    Details
    ISSN: 0887-3585
    Schlagwort(e): docking ; protein-DNA ; prediction ; structure ; base recognition ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The docking of repressor proteins to DNA starting from the unbound protein and model-built DNA coordinates is modeled computationally. The approach was evaluated on eight repressor/DNA complexes that employed different modes for protein/ DNA recognition. The global search is based on a protein-protein docking algorithm that evaluates shape and electrostatic complementarity, which was modified to consider the importance of electrostatic features in DNA-protein recognition. Complexes were then ranked by an empirical score for the observed amino acid /nucleotide pairings (i.e., protein-DNA pair potentials) derived from a database of 20 protein/DNA complexes. A good prediction had at least 65% of the correct contacts modeled. This approach was able to identify a good solution at rank four or better for three out of the eight complexes. Predicted complexes were filtered by a distance constraint based on experimental data defining the DNA footprint. This improved coverage to four out of eight complexes having a good model at rank four or better. The additional use of amino acid mutagenesis and phylogenetic data defining residues on the repressor resulted in between 2 and 27 models that would have to be examined to find a good solution for seven of the eight test systems. This study shows that starting with unbound coordinates one can predict three-dimensional models for protein/DNA complexes that do not involve gross conformational changes on association. Proteins 33:535-549, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 56
    Digitale Medien
    Digitale Medien
    Influence of protein structure databases on the predictive power of statistical pair potentials (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 139-149 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein structure ; statistical potentials ; protein structure database ; assessing protein models ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139-149, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 57
    Digitale Medien
    Digitale Medien
    Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: Conformational influence of an engineered disulfide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 128-138 
    Details
    ISSN: 0887-3585
    Schlagwort(e): antibody ; antitumor ; single chain Fv ; variable domains ; X-ray crystallography ; protein structure ; protein stability ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A recombinant Fv construct of the B1 monoclonal antibody that recognizes the LewisY-related carbohydrate epitope on human carcinoma cells has been prepared. The Fv is composed of the polypeptide chains of the VH and VL domains expressed independently and isolated as inclusion bodies. The Fv is prepared by combining and refolding equimolar amounts of guanidine chloride solubilized inclusion bodies. The Fv is stabilized by an engineered interchain disulfide bridge between residues VL100 and VH44. This construct has a similar binding affinity as that of the single-chain construct (Benhar and Pastan, Clin. Cancer Res. 1:1023-1029, 1995). The B1 disulfide-stabilized Fv (B1dsFv) crystallizes in space group P6122 with the unit cell parameters a = b = 80.1 Å, and c = 138.1 Å. The crystal structure of the B1dsFv has been determined at 2.1-Å resolution using the molecular replacement technique. The final structure has a crystallographic R-value of 0.187 with a root mean square deviation in bond distance of 0.014 Å and in bond angle of 2.74°. Comparisons of the B1dsFv structure with known structures of Fv regions of other immunoglobulin fragments shows closely related secondary and tertiary structures. The antigen combining site of B1dsFv is a deep depression 10-Å wide and 17-Å long with the walls of the depression composed of residues, many of which are tyrosines, from complementarity determining regions L1, L3, H1, H2, and H3. Model building studies indicate that the LewisY tetrasaccharide, Fuc-Gal-Nag-Fuc, can be accommodated in the antigen combining site in a manner consistent with the epitope predicted in earlier biochemical studies (Pastan, Lovelace, Gallo, Rutherford, Magnani, and Willingham, Cancer Res. 51:3781-3787, 1991). Thus, the engineered disulfide bridge appears to cause little, if any, distortion in the Fv structure, making it an effective substitute for the B1 Fab. Proteins 31:128-138, 1998. Published 1998 Wiley-Liss, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
    Zusätzliches Material: 10 Ill.
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  • 58
    Digitale Medien
    Digitale Medien
    Interaction of transmembrane helices by a knobs-into-holes packing characteristic of soluble coiled coils (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 150-159 
    Details
    ISSN: 0887-3585
    Schlagwort(e): photosynthetic reaction center ; bacteriorhodopsin ; cytochrome C oxidase ; zipper ; packing ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Membrane-embedded protein domains frequently exist as α-helical bundles, as exemplified by photosynthetic reaction centers, bacteriorhodopsin, and cytochrome C oxidase. The sidechain packing between their transmembrane helices was investigated by a nearest-neighbor analysis which identified sets of interfacial residues for each analyzed helix-helix interface. For the left-handed helix-helix pairs, the interfacial residues almost exclusively occupy positions a, d, e, or g within a heptad motif (abcdefg) which is repeated two to three times for each interacting helical surface. The connectivity between the interfacial residues of adjacent helices conforms to the knobs-into-holes type of sidechain packing known from soluble coiled coils. These results demonstrate on a quantitative basis that the geometry of sidechain packing is similar for left-handed helix-helix pairs embedded in membranes and coiled coils of soluble proteins. The transmembrane helix-helix interfaces studied are somewhat less compact and regular as compared to soluble coiled coils and tolerate all hydrophobic amino acid types to similar degrees. The results are discussed with respect to previous experimental findings which demonstrate that specific interactions between transmembrane helices are important for membrane protein folding and/or oligomerization. Proteins 31:150-159, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 59
    Digitale Medien
    Digitale Medien
    Protein folding in the landscape perspective: Chevron plots and non-arrhenius kinetics (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 2-33 
    Details
    ISSN: 0887-3585
    Schlagwort(e): chevron plot ; energy landscape ; folding funnel ; kinetic trap ; lattice models ; non-Arrhenius behavior ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple-exponential and two-state (single-exponential) kinetics. Experiments show that two-state relaxation times have “chevron plot” dependences on denaturant and non-Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple-exponental behavior, whereas the HP+ model gives more smooth funnels and two-state behavior. Multiple-exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two-state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2-33, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 35 Ill.
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  • 60
    Digitale Medien
    Digitale Medien
    Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 49-60 
    Details
    ISSN: 0887-3585
    Schlagwort(e): kohonen network ; mitochondrial processing peptidase (MPP) ; mitochondrial intermediate peptidase (MIP) ; neural network ; protein import ; sequence motif ; mitochondrial targeting ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps. Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs. Neural networks were used to define local sequence features around precursor cleavage sites. Proteins 30:49-60, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 61
    Digitale Medien
    Digitale Medien
    Don Caspar, TMV, and protein-protein interactions (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 109-112 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
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  • 62
    Digitale Medien
    Digitale Medien
    A hybrid sequence approach to the paracelsus challenge (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 136-143 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein design ; protein structure ; circular dichroism ; trifluoroethanol ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Inspired by the Paracelsus Challenge of Rose and Creamer (Proteins 19:1-3, 1994), we have designed a protein sequence that is 50% identical to an all-helical protein but is intended to fold into a largely β-sheet structure. Rather than attempt a de novo design, our strategy was to construct a hybrid sequence based on a helical “parent” protein (434 Cro) and a “target” protein with the desired fold (the B1 domain of protein G). The hybrid sequence (Crotein-G) is 50% identical to 434 Cro but is also 62% identical to the B1 domain of protein G. We also created a variant of Crotein-G (ZCrotein-G) that contains a potential His3Cys1 zinc binding site. At low protein concentrations and in the presence of 20% 2,2,2-trifluoroethanol (TFE) (v/v), the circular dichroism spectra of the designed proteins are distinct from that of 434 Cro and similar to that of the B1 domain of protein G. However, the proteins fail to denature in a cooperative manner. Furthermore, aggregation occurs at moderate protein concentrations or in the absence of TFE. Addition of zinc to ZCrotein-G does not promote structure formation. In summary, 434 Cro has been altered to something that may resemble the B1 domain of protein G, but the protein does not adopt a native structure. Proteins 30:136-143, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 63
    Digitale Medien
    Digitale Medien
    Monte Carlo simulation of denaturation of adsorbed proteins (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 168-176 
    Details
    ISSN: 0887-3585
    Schlagwort(e): denaturation kinetics ; irreversible conformational changes ; metastable states ; folding temperature ; lattice model ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Denaturation of model proteinlike molecules at the liquid-solid interface is simulated over a wide temperature range by employing the lattice Monte Carlo technique. Initially, the molecule containing 27 monomers of two types (A and B) is assumed to be adsorbed in the native folded state (a 3 × 3 × 3 cube) so that one of its sides is in contact with the surface. The details of the denaturation kinetics are found to be slightly dependent on the choice of the side, but the main qualitative conclusions hold for all the sides. In particular, the kinetics obey approximately the conventional first-order law at T 〉 Tc (Tc is the collapse temperature for solution). With decreasing temperature, below Tc but above Tf (Tf is the folding temperature for solution), deviations appear from the first-order kinetics. For the most interesting temperatures, that is, below Tf, the denaturation kinetics are shown to be qualitatively different from the conventional ones. In particular, the denaturation process occurs via several intermediate steps due to trapping in metastable states. Mathematically, this means that (i) the transition to the denatured state of a given molecule is nonexponential, and (ii) the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of values of this rate constant (different values of kr correspond to the transitions to the altered state via different metastable states). Proteins 30:168-176, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
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  • 64
    Digitale Medien
    Digitale Medien
    Monte Carlo simulation of the kinetics of protein adsorption (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 177-182 
    Details
    ISSN: 0887-3585
    Schlagwort(e): adsorption ; irreversible conformational changes ; denaturation rate constant ; kinetic control ; diffusion control ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Adsorption of proteins occurs via diffusion toward the interface, actual adsorption, and subsequent irreversible conformational changes resulting in denaturation of the native protein structure. The conventional kinetic models describing these steps are based on the assumption that the denaturation transitions obey the first-order law with a single value of the denaturation rate constant kr. Meanwhile, recent Monte Carlo simulations indicate that, in general, the denaturation process cannot be described by a single rate constant kr. One should rather introduce a distribution of this rate constant (physically, different values of kr correspond to the transitions to the altered state via different metastable states). We have calculated the kinetics of irreversible adsorption of proteins with and without distribution of the denaturation rate constant kr in the limits when protein diffusion in the solution is, respectively, rapid or slow. In both cases, the adsorption kinetics with distribution of kr are found to be close to those with a single-valued rate constant kr provided that the average value of kr in the former case is equal to kr for the latter case. This conclusion holds even for wide distributions of kr. The consequences of this finding for the fitting of global experimental kinetics on the basis of phenomenological equations are briefly discussed. Proteins 30:177-182, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 65
    Digitale Medien
    Digitale Medien
    Structural diversity of sequentially identical subsequences of proteins: Identical octapeptides can have different conformations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 228-231 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; local vs. non-local interactions ; secondary structure prediction ; fragment matching algorithms ; PDB ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: One of the most important questions in the protein folding problem is whether secondary structures are formed entirely by local interactions. One way to answer this question is to compare identical subsequences of proteins to see if they have identical structures. Such an exercise would also reveal a lower limit on the number of amino acids needed to form unique secondary structures. In this context, we have searched the April 1996 release of the Protein Data Bank for sequentially identical subsequences of proteins and compared their structures. We find that identical octamers can have different conformations. In addition, there are several examples of identical heptamers with different conformations, and the number of identical hexamers with different conformations has increased since the previous PDB releases. These observations imply that secondary structure can be formed entirely by non-local interactions and that an identical match of up to eight amino acids may not imply structural similarity. In addition to the larger context of the protein folding problem, these observations have implications for protein structure prediction methods. Proteins 30:228-231, 1998. © 1998 Wiley-Liss, Inc.
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  • 66
    Digitale Medien
    Digitale Medien
    Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 249-263 
    Details
    ISSN: 0887-3585
    Schlagwort(e): antibody-antigen complex ; snake toxin ; protein docking ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The antibody Mα2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin α, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin α:Mα2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy,1 was docked to models of the variable fragment of the antibody combining site2 by using a method based on surface complementarity and maximization of buried surface area3,4 while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3. Proteins 30:249-263, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 67
    Digitale Medien
    Digitale Medien
    Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 287-294 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein structure prediction ; side chain contact prediction ; lattice protein models ; CREB-binding protein ; KIX domain ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 Å. This is to be compared with the estimate of 12.9 Å that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). Proteins 30:287-294, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 68
    Digitale Medien
    Digitale Medien
    Mass spectrometric identification and microcharacterization of proteins from electrophoretic gels: Strategies and applications (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 74-89 
    Details
    ISSN: 0887-3585
    Schlagwort(e): mass spectrometry ; matrix-assisted laser desorption/ionization ; electrospray ; database searching ; gel electrophoresis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The entire genomic DNA sequences of a number of prokaryotic and eukaryotic species are now available and many more, including the human genome, will be completed in the near future. The state-of-life of a cell at any given time, however, is defined by its protein composition, i.e., its proteome. Gel electrophoresis, mass spectrometry, and bioinformatics will be important tools for protein and proteome analysis in the post-genome era. Protein identification from electrophoretic gels by mass spectrometric peptide mapping or peptide sequencing combined with sequence database searching is established and has been applied to numerous biological systems. We describe current strategies and selected applications in molecular and cell biology. The next challenges are detailed structure/function analyses, which include studying the molecular composition of multiprotein complexes and characterization of secondary modifications of proteins. The advantages and limitations of a number of mass spectrometry-based strategies designed for microcharacterization of low amounts of protein from electrophoretic gels are discussed and illustrated by examples. Proteins Suppl. 2:74-89, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 69
    Digitale Medien
    Digitale Medien
    A fusion protein between serum amyloid A and staphylococcal nuclease - synthesis, purification, and structural studies (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 381-387 
    Details
    ISSN: 0887-3585
    Schlagwort(e): serum amyloid A ; fluorescence ; circular dichroism ; acute phase ; denaturation ; nuclease ; amyloidosis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating α-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA - the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA. Proteins 30:381-387, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
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  • 70
    Digitale Medien
    Digitale Medien
    The PDP: Past, present, and future (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 30 (1998), S. 1-1 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 71
    Digitale Medien
    Digitale Medien
    Direct observation of an altered quaternary-structure transition in a mutant aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 383-390 
    Details
    ISSN: 0887-3585
    Schlagwort(e): time-resolved small-angle X-ray scattering ; allosterism ; domain closure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Time-resolved small-angle X-ray scattering (TR-SAXS) was used to monitor the structural changes that occur upon the binding of the natural substrates to a mutant version of the allosteric enzyme aspartate transcarbamoylase from Escherichia coli, in which the creation of a critical link stabilizing the R state of the enzyme is hindered. Previously, SAXS experiments at equilibrium showed that the structures of the unligated mutant enzyme and the mutant enzyme saturated with a bisubstrate analog are indistinguishable from the T and R state structures, respectively, of the wild-type enzyme (Tauc et al., Protein Sci. 3:1998-2004, 1994). However, as opposed to the wild-type enzyme, the combination of one substrate, carbamoyl phosphate, and succinate, an analog of aspartate, did not convert the mutant enzyme into the R state. By using TR-SAXS we have been able to study the transient steady-state during catalysis using the natural substrates rather than the nonreactive substrate analogs. The steady-state in the presence of saturating amount of substrates is a mixture of 60% T and 40% R structures, which is further converted entirely to R in the additional presence of ATP. These results provide a structural explanation for the reduced cooperativity observed with the mutant enzyme as well as for the stimulation by ATP at saturating concentrations of substrates. They also illustrate the crucial role played by domain motions and quaternary-structure changes for both the homotropic and heterotropic aspects of allostery. Proteins 31:383-390, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 72
    Digitale Medien
    Digitale Medien
    Structural investigation of C4b-binding protein by molecular modeling: Localization of putative binding sites (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 391-405 
    Details
    ISSN: 0887-3585
    Schlagwort(e): complement control protein ; protein modeling ; blood coagulation ; C4b-binding protein ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: C4b-binding protein (C4BP) contributes to the regulation of the classical pathway of the complement system and plays an important role in blood coagulation. The main human C4BP isoform is composed of one β-chain and seven α-chains essentially built from three and eight complement control protein (CCP) modules, respectively, followed by a nonrepeat carboxy-terminal region involved in polymerization of the chains. C4BP is known to interact with heparin, C4b, complement factor I, serum amyloid P component, streptococcal Arp and Sir proteins, and factor VIII/VIIIa via its α-chains and with protein S through its β-chain. The principal aim of the present study was to localize regions of C4BP involved in the interaction with C4b, Arp, and heparin. For this purpose, a computer model of the 8 CCP modules of C4BP α-chain was constructed, taking into account data from previous electron microscopy (EM) studies. This structure was investigated in the context of known and/or new experimental data. Analysis of the α-chain model, together with monoclonal antibody studies and heparin binding experiments, suggests that a patch of positively charged residues, at the interface between the first and second CCP modules, plays an important role in the interaction between C4BP and C4b/Arp/Sir/heparin. Putative binding sites, secondary-structure prediction for the central core, and an overall reevaluation of the size of the C4BP molecule are also presented. An understanding of these intermolecular interactions should contribute to the rational design of potential therapeutic agents aiming at interfering specifically some of these protein-protein interactions. Proteins 31:391-405, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
    Materialart: Digitale Medien
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  • 73
    Digitale Medien
    Digitale Medien
    Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 406-416 
    Details
    ISSN: 0887-3585
    Schlagwort(e): electrostatics ; Brownian dynamics ; triose phosphate isomerase ; diffusion-control ; similarity index ; rate enhancement ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Triose phosphate isomerase (TIM) is a diffusion-controlled enzyme whose rate is limited by the diffusional encounter of the negatively charged substrate glyceraldehyde 3-phosphate (GAP) with the homodimeric enzyme's active sites. Translational and orientational steering of GAP toward the active sites by the electrostatic field of chicken muscle TIM has been observed in previous Brownian dynamics (BD) simulations. Here we report simulations of the association of GAP with TIMs from four species with net charges at pH 7 varying from -12e to +12e. Computed second-order rate constants are in good agreement with experimental data. The BD simulations and computation of average Boltzmann factors of substrate-protein interaction energies show that the protein electrostatic potential enhances the rates for all the enzymes. There is much less variation in the computed rates than might be expected on the basis of the net charges. Comparison of the electrostatic potentials by means of similarity indices shows that this is due to conservation of the local electrostatic potentials around the active sites which are the primary determinants of electrostatic steering of the substrate. Proteins 31:406-416, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 3 Ill.
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  • 74
    Digitale Medien
    Digitale Medien
    Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 434-444 
    Details
    ISSN: 0887-3585
    Schlagwort(e): hinge ; structural change ; xylose ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hingefind program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a ‘hinge-bending’ motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII. Proteins 31:434-444, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
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  • 75
    Digitale Medien
    Digitale Medien
    Interaction of human SRY protein with DNA: A molecular dynamics study (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 417-433 
    Details
    ISSN: 0887-3585
    Schlagwort(e): molecular dynamics ; sex-determining region Y (SRY) protein ; high mobility group (HMG) box ; DNA-binding proteins ; DNA bending ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Molecular dynamics simulations have been conducted to study the interaction of human sex-determining region Y (hSRY) protein with DNA. For this purpose, simulations of the hSRY high mobility group (HMG) domain (hSRY-HMG) with and without its DNA target site, a DNA octamer, and the DNA octamer alone have been carried out, employing the NMR solution structure of hSRY-HMG-DNA complex as a starting model. Analyses of the simulation results demonstrated that the interaction between hSRY and DNA was hydrophobic, just a few hydrogen bonds and only one water molecule as hydrogen-bonding bridge were observed at the protein-DNA interface. These two hydrophobic cores in the hSRY-HMG domain were the physical basis of hSRY-HMG-DNA specific interaction. They not only maintained the stability of the complex, but also primarily caused the DNA deformation. The salt bridges formed between the positive-charged residues of hSRY and phosphate groups of DNA made the phosphate electroneutral, which was advantageous for the deformation of DNA and the formation of a stable complex. We predicted the structure of hSRY-HMG domain in the free state and found that both hSRY and DNA changed their conformations to achieve greater complementarity of geometries and properties during the binding process; that is, the protein increased the angle between its long and short arms to accommodate the DNA, and the DNA became bent severely to adapt to the protein, although the conformational change of DNA was more severe than that of the hSRY-HMG domain. The sequence specificity and the role of residue Met9 are also discussed. Proteins 31:417-433, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 12 Ill.
    Materialart: Digitale Medien
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  • 76
    Digitale Medien
    Digitale Medien
    Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 453-459 
    Details
    ISSN: 0887-3585
    Schlagwort(e): quantum mechanical calculations ; substrate-enzyme interactions ; mutants ; functional role of amino acids ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The enzyme herpes simplex virus type 1 thymidine kinase (HSV1 TK) salvages thymidine into the DNA metabolism of the virus. In the active site, the thymine ring of the nucleoside binds in a pocket, formed by two residues, Tyr-172 and Met-128, in a sandwich-type orientation. To investigate the nature of the thymine-enzyme pocket interactions, we have carried out density functional theory calculations with gradient-corrected exchange-correlation functionals of models of the thymine-HSV1 TK adduct. Our calculations indicate that the role of Met-128 in the substrate fixation is purely steric and hydrophobic, while the substrate-Tyr-172 interaction is essentially electrostatic in nature. These findings are completely consistent with the available catalytic properties of mutants on the 128 position. Proteins 31:453-459, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 77
    Digitale Medien
    Digitale Medien
    Electrostatics, allostery, and activity of the yeast chorismate mutase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 445-452 
    Details
    ISSN: 0887-3585
    Schlagwort(e): chorismate mutase ; activity ; allosteric ; electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The predicted active site of chorismate mutase of baker's yeast Saccharomyces cerevisiae has been studied by continuum electrostatics, molecular surface/volume calculations, and molecular modeling. Our study shows that despite being subject to an allosteric transition, the enzyme's active-site pocket neither decreased in volume nor deformed significantly in shape between the active R state and the inactive T state. We find that the polar atmosphere in the pocket is responsible for the enzyme's affinity. A single amino acid, Glu23, can adequately account for the atmospheric variation. This residue swings into the active-site pocket from the R state to the T state. In the R state, Glu23 on helix H2 doubly pairs with Arg204 and Lys208 of H11, which is packed against H2. In the T state, a slide occurs between H11 and H2 such that Glu23 can no longer interact with Lys208 and competes with Asp24 for interacting with Arg204. Consequently, Glu23 is found in the T state to couple with Arg157, an active-site residue critical to substrate binding. The tandem sliding of H11 in both monomers profoundly changes the interactions in the dimer interface. The loop between H11 and H12 demonstrates the largest conformational change. Hence, we establish a connection between the allosteric transition and the activity of the enzyme. The conformational change in the transition is suggested to propagate into the active-site pocket via a series of polar interactions that result in polarity reversal in the active-site pocket, which regulates the enzyme's activity. Proteins 31:445-452, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 78
    Digitale Medien
    Digitale Medien
    Evidence of new cadmium binding sites in recombinant horse L-chain ferritin by anomalous Fourier difference map calculation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 31 (1998), S. 477-485 
    Details
    ISSN: 0887-3585
    Schlagwort(e): X-ray structure ; L-chain apoferritin ; metal binding sites ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We refined the structure of the tetragonal form of recombinant horse L-chain apoferritin to 2.0 Å and we compared it with that of the cubic form previously refined to the same resolution. The major differences between the two structures concern the cadmium ions bound to the residues E130 at the threefold axes of the molecule. Taking advantage of the significant anomalous signal (f′′ = 3.6 e-) of cadmium at 1.375 Å, the wavelength used here, we performed anomalous Fourier difference maps with the refined model phases. These maps reveal the positions of anomalous scatterers at different locations in the structure. Among these, some are found near residues that were known previously to bind metal ions, C48, E57, C126, D127, E130, and H132. But new cadmium binding sites are evidenced near residues E53, E56, E57, E60, and H114, which were suggested to be involved in the iron loading process. The quality of the anomalous Fourier difference map increases significantly with noncrystallographic symmetry map averaging. Such maps reveal density peaks that fit the positions of Met and Cys sulfur atoms, which are weak anomalous scatterers (f′′ = 0.44 e-). Proteins 31:477-485, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 7 Ill.
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  • 79
    Digitale Medien
    Digitale Medien
    The biology workbench - A seamless database and analysis environment for the biologist (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 1-2 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: No abstract.
    Materialart: Digitale Medien
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  • 80
    Digitale Medien
    Digitale Medien
    Calculation of HyHel10-lysozyme binding free energy changes: Effect of ten point mutations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 39-48 
    Details
    ISSN: 0887-3585
    Schlagwort(e): antibody ; antigen ; electrostatics ; binding ; finite difference ; Poisson-Boltzmann ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The change in free energy of binding of hen egg white lysozyme (HEL) to the antibody HyHel-10 arising from ten point mutations in HEL (D101K, D101G, K96M, K97D, K97G, K97G, R21E, R21K, W62Y, and W63Y) was calculated using a combination of the finite difference Poisson-Boltzmann method for the electrostatic contribution, a solvent accessible surface area term for the non-polar contribution, and rotamer counting for the sidechain entropy contribution. Comparison of experimental and calculated results indicate that because of pKa shifts in some of the mutated residues, primarily those involving Aspartate or Glutamate, proton uptake or release occurs in binding. When this effect was incorporated into the binding free energy calculations, the agreement with experiment improved significantly, and resulted in a mean error of about 1.9 kcal/mole. Thus these calculations predict that there should be a significant pH dependence to the change in binding caused by these mutations. The other major contributions to binding energy changes comes from solvation and charge charge interactions, which tend to oppose each other. Smaller contributions come from nonpolar interactions and sidechain entropy changes. The structures of the HyHel-10-HEL complexes with mutant HEL were obtained by modeling, and the effect of the modeled structure on the calculations was also examined. “Knowledge based” modeling and automatic generation of models using molecular mechanics produced comparable results. Proteins 33:39-48, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
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  • 81
    Digitale Medien
    Digitale Medien
    Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase KAtomic coordinates have been deposited with the Protein Data Bank, Brookhaven National Laboratory. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 30-38 
    Details
    ISSN: 0887-3585
    Schlagwort(e): lactoferrin ; proteinase K ; complex, hydrolysis ; structure ; inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Lactoferrin is an iron binding glycoprotein with a molecular weight of 80 kDa. The molecule is divided into two lobes representing the N-terminal and C-terminal halves of the polypeptide chain, each containing an iron binding site. The serine proteinases such as trypsin, chymotrypsin, and pepsin hydrolyze lactoferrin into two unequal halves while proteinase K divides this protein into two equal halves. In the first step of hydrolysis by proteinase K, the C- and N-lobes, each having a molecular weight of approximately 40 kDa, are generated. In the next step, the lobes are further hydrolyzed into small molecular weight peptides. The proteinase K isolated from the hydrolyzed product does not show enzymatic activity suggesting that the enzyme is inhibited. Furthermore, the hydrolysis experiments on N-lobe and C-lobe showed that the inhibitory fragment came from the C-lobe. The purified lactoferrin fragment was found to be a decapeptide with an amino acid sequence of H2N-Val-Ala-Gln-Gly-Ala-Ala-Gly-Leu-Ala-COOH. The complex formed between proteinase K and lactoferrin fragment was crystallized by microdialysis. The crystals belonged to the monoclinic space group P21with cell dimensions a = 44.4 Å, b = 38.6 Å, c = 79.2 Å, β = 105.8o and Z = 2. The crystal structure has been determined at 2.4 Å resolution. It has been refined to an R factor of 0.163 for 9044 reflections. The Lf-fragment forms several intermolecular interactions with proteinase K. The Ser-224 Oγ and His-57 Nε2 move away to a distance of 3.68 Å in the complex. In the crystal structure, Gln-3I (I indicates inhibitor i.e., lactoferrin fragment) is involved in a direct intermolecular interaction with a symmetry related proteinase K molecule through a strong hydrogen bond with Asp-254. The mode of intermolecular interactions in the complex conformational features of the enzyme and placement of the fragment with respect to the enzyme resemble with the molecular complex of proteinase K with its natural inhibitor PKI3 from wheat. Proteins 33:30-38, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 82
    Digitale Medien
    Digitale Medien
    Dictionary of recurrent domains in protein structures (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 88-96 
    Details
    ISSN: 0887-3585
    Schlagwort(e): fold classification ; substructures ; Dali ; protein families ; structural similarity ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The rapid growth in the number of experimentally determined three-dimensional protein structures has sharpened the need for comprehensive and up-to-date surveys of known structures. Classic work on protein structure classification has made it clear that a structural survey is best carried out at the level of domains, i.e., substructures that recur in evolution as functional units in different protein contexts. We present a method for automated domain identification from protein structure atomic coordinates based on quantitative measures of compactness and, as the new element, recurrence. Compactness criteria are used to recursively divide a protein into a series of successively smaller and smaller substructures. Recurrence criteria are used to select an optimal size level of these substructures, so that many of the chosen substructures are common to different proteins at a high level of statistical significance. The joint application of these criteria automatically yields consistent domain definitions between remote homologs, a result difficult to achieve using compactness criteria alone. The method is applied to a representative set of 1,137 sequence-unique protein families covering 6,500 known structures. Clustering of the resulting set of domains (substructures) yields 594 distinct fold classes (types of substructures). The Dali Domain Dictionary (http://www.embl-ebi.ac.uk/dali) not only provides a global structural classification, but also a comprehensive description of families of protein sequences grouped around representative proteins of known structure. The classification will be continuously updated and can serve as a basis for improving our understanding of protein evolution and function and for evolving optimal strategies to complete the map of all natural protein structures. Proteins 33:88-96, 1998. © 1998 Wiley-Liss, Inc.
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  • 83
    Digitale Medien
    Digitale Medien
    Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 97-106 
    Details
    ISSN: 0887-3585
    Schlagwort(e): antigenic peptides ; class I MHC molecules ; HLA-A2 complexes ; hydrogen bonds ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The crystal structures of class I major histocompatibility complex (MHC) molecules complexed with antigenic peptides revealed a network of hydrogen bonds between the charged amino- and carboxyl-termini of the peptides and conserved MHC residues at both ends of the peptide binding site. These interactions were shown to contribute substantially to the stability of class I MHC/peptide complexes by thermal denaturation studies using synthetic peptides in which either the amino- or carboxyl-terminal group is substituted by a methyl group. Here we report crystal structures of HLA-A*0201 complexed with these terminally modified synthetic peptides showing that they adopt the same bound conformation as antigenic peptides. A number of variations in peptide conformation were observed for the terminally modified peptides, including in one case, a large conformational difference in four central peptide residues that is apparently caused by the lattice contact. This is reminiscent of the way binding a T-cell receptor changed the conformation of central residues of an MHC-bound peptide. The structures determined identify which conserved hydrogen bonds are eliminated in terminally substituted peptides and suggest an increased energetic importance of the interactions at the peptide termini for MHC-peptide stability. Proteins 33:97-106, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 84
    Digitale Medien
    Digitale Medien
    AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 26-42 
    Details
    ISSN: 0887-3585
    Schlagwort(e): intermolecular restraints ; solid-state NMR ; symmetric multimer ; branch and bound ; amyloid ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The determination of structures of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found and the transformations to produce the packing interfaces must be described. A substantial difficulty results from ambiguities in assigning intermolecular distance measurements (from nuclear magnetic resonance, for example) to particular intermolecular interfaces in the structure. Here we present a rapid and efficient method to solve the packing and the assignment problems simultaneously given rigid monomer structures and (potentially ambiguous) intermolecular distance measurements. A promising application of this algorithm is to couple it with a monomer searching protocol such that each monomer structure consistent with intramolecular constraints can be subsequently input to the current algorithm to check whether it is consistent with (potentially ambiguous) intermolecular constraints. The algorithm AmbiPack uses a hierarchical division of the search space and the branch-and-bound algorithm to eliminate infeasible regions of the space. Local search methods are then focused on the remaining space. The algorithm generally runs faster as more constraints are included because more regions of the search space can be eliminated. This is not the case for other methods, for which additional constraints increase the complexity of the search space. The algorithm presented is guaranteed to find all solutions to a predetermined resolution. This resolution can be chosen arbitrarily to produce outputs at various level of detail. Illustrative applications are presented for the P22 tailspike protein (a trimer) and portions of β-amyloid (an ordered aggregate). Proteins 32:26-42, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 17 Ill.
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  • 85
    Digitale Medien
    Digitale Medien
    Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 204-217 
    Details
    ISSN: 0887-3585
    Schlagwort(e): rotamer libraries ; energy minimization ; self consistent mean-field theory ; torsion space ; modeling ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The ab initio folding problem can be divided into two sequential tasks of approximately equal computational complexity: the generation of native-like backbone folds and the positioning of side chains upon these backbones. The prediction of side-chain conformation in this context is challenging, because at best only the near-native global fold of the protein is known. To test the effect of displacements in the protein backbones on side-chain prediction for folds generated ab initio, sets of near-native backbones (≤ 4 Å Cα RMS error) for four small proteins were generated by two methods. The steric environment surrounding each residue was probed by placing the side chains in the native conformation on each of these decoys, followed by torsion-space optimization to remove steric clashes on a rigid backbone. We observe that on average 40% of the χ1 angles were displaced by 40° or more, effectively setting the limits in accuracy for side-chain modeling under these conditions. Three different algorithms were subsequently used for prediction of side-chain conformation. The average prediction accuracy for the three methods was remarkably similar: 49% to 51% of the χ1 angles were predicted correctly overall (33% to 36% of the χ1+2 angles). Interestingly, when the inter-side-chain interactions were disregarded, the mean accuracy increased. A consensus approach is described, in which side-chain conformations are defined based on the most frequently predicted χ angles for a given method upon each set of near-native backbones. We find that consensus modeling, which de facto includes backbone flexibility, improves side-chain prediction: χ1 accuracy improved to 51-54% (36-42% of χ1+2). Implications of a consensus method for ab initio protein structure prediction are discussed. Proteins 33:204-217, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 86
    Digitale Medien
    Digitale Medien
    Molecular dynamics simulations of human carbonic anhydrase II: Insight into experimental results and the role of solvation (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 119-134 
    Details
    ISSN: 0887-3585
    Schlagwort(e): molecular modeling ; proton transfer ; enzyme catalysis ; mutations ; molecular mechanics ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In this paper, the carbonic anhydrase II (CA II) enzyme active site is modeled using ab initio calculations and molecular dynamics simulations to examine a number of important issues for the enzyme function. It is found that the Zn2+ ion is dominantly tetrahedrally coordinated, which agrees with X-ray crystallographic studies. However, a transient five-fold coordination with an extra water molecule is also found. Studies of His64 conformations upon a change in the protonation states of the Zn-bound water and the His64 residue also confirm the results of an X-ray study which suggest that the His64 conformation is quite flexible. However, the degree of water solvation is found to affect this behavior. Water bridge formation between the Zn-bound water and the His64 residue was found to involve a free energy barrier of 2-3 kcal/mol and an average lifetime of several picoseconds, which supports the concept of a proton transfer mechanism through such a bridge. Mutations of various residues around the active site provide further insight into the corresponding experimental results and, in fact, suggest an important role for the solvent water molecules in the CA II catalytic mechanism. Proteins 33:119-134, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 9 Ill.
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  • 87
    Digitale Medien
    Digitale Medien
    Sequence and structure conservation in a protein core (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 358-366 
    Details
    ISSN: 0887-3585
    Schlagwort(e): homologous proteins ; superfamilies ; sequence conservation ; protein structure ; protein evolution ; sequence-structure relationships ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In order to study structural aspects of sequence conservation in families of homologous proteins, we have analyzed structurally aligned sequences of 585 proteins grouped into 128 homologous families. The conservation of a residue in a family is defined as the average residue similarity in a given position of aligned sequences. The residue similarities were expressed in the form of log-odd substitution tables that take into account the environments of amino acids in three-dimensional structures. The protein core is defined as those residues that have less then 7% solvent accessibility. The density of a protein core is described in terms of atom packing, which is investigated as a criterion for residue substitution and conservation. Although there is no significant correlation between sequence conservation and average atom packing around nonpolar residues such as leucine, valine and isoleucine, a significant correlation is observed for polar residues in the protein core. This may be explained by the hydrogen bonds in which polar residues are involved; the better their protection from water access the more stable should be the structure in that position. Proteins 33:358-366, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 88
    Digitale Medien
    Digitale Medien
    Extraction of geometrically similar substructures: Least-squares and Chebyshev fitting and the difference distance matrix (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 320-328 
    Details
    ISSN: 0887-3585
    Schlagwort(e): structural similarity ; optimal superposition ; common substructure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: In analysis, comparison and classification of conformations of proteins, a common computational task involves extractions of similar substructures. Structural comparisons are usually based on either of two measures of similarity: the root-mean-square (r.m.s.) deviation upon optimal superposition, or the maximal element of the difference distance matrix. The analysis presented here clarifies the relationships between different measures of structural similarity, and can provide a basis for developing algorithms and software to extract all maximal common well-fitting substructures from proteins.Given atomic coordinates of two proteins, many methods have been described for extracting some substantial (if not provably maximal) common substructure with low r.m.s. deviation. This is a relatively easy task compared with the problem addressed here, i.e., that of finding all common substructures with r.m.s. deviation less than a prespecified threshold. The combinatorial problems associated with similar subset extraction are more tractable if expressed in terms of the maximal element of the difference distance matrix than in terms of the r.m.s. deviation. However, it has been difficult to correlate these alternative measures of structural similarity. The purpose of this article is to make this connection.We first introduce a third measure of structural similarity: the maximum distance between corresponding pairs of points after superposition to minimize this value. This corresponds to fitting in the Chebyshev norm. Properties of Chebyshev superposition are derived.We describe relationships between the r.m.s. and minimax (Chebyshev) deviations upon optimal superposition, and between the Chebyshev deviation and the maximal element of the difference distance matrix. Combining these produces a relationship between the r.m.s. deviation upon optimal superposition and the maximal element of the difference distance matrix. Based on these results, we can apply algorithms and software for finding subsets of the difference distance matrix for which all elements are less than a specified bound, either to select only subsets for which the r.m.s.deviation is less than or equal to a specified threshold, or to select subsets that include all subsets for which the r.m.s. deviation is less than or equal to a threshold. Proteins 33:320-328, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 1 Ill.
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  • 89
    Digitale Medien
    Digitale Medien
    Flexible docking using tabu search and an empirical estimate of binding affinity (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 367-382 
    Details
    ISSN: 0887-3585
    Schlagwort(e): ligand-protein docking ; molecular recognition ; tabu search ; empirical scoring function ; binding affinity prediction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367-382, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 10 Ill.
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  • 90
    Digitale Medien
    Digitale Medien
    Folding-unfolding energy change of a simple sphere model protein and an energy landscape of the folding process (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 408-416 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein folding ; potential energy curve ; two state model ; semi-empirical calculation ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have calculated the free energy of a spherical model of a protein or part of a protein generated in the way of protein folding. Two spherical models are examined; one is a homogeneous model consisting of only one residue type - hydrophobic. The other is a heterogeneous model consisting of two residue types - strong hydrophobic and weak hydrophobic. Both models show a folding transition state, and the latter model reproduces the trend of the experimental folded-unfolded energy change. The heterogeneous model suggests that in the folding process of a protein of more than 70 residues, a specific region of the protein folds first to form a stable region, then the other residues follow the folding process. The energy landscape of folding of a small protein is approximately a funnel model, whereas a flatter energy landscape is suggested for larger proteins of more than 55-70 residues. Proteins 33:408-416, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 91
    Digitale Medien
    Digitale Medien
    Structural model for family 32 of glycosyl-hydrolase enzymes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 383-395 
    Details
    ISSN: 0887-3585
    Schlagwort(e): glycosidases ; protein structure prediction ; correlated mutations ; sequence space ; phylogenic relationships ; threading ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A structural model is presented for family 32 of the glycosyl-hydrolase enzymes based on the beta-propeller fold. The model is derived from the common prediction of two different threading methods, TOPITS and THREADER. In addition, we used a correlated mutation analysis and prediction of active-site residues to corroborate the proposed model. Physical techniques (circular dichroism and differential scanning calorimetry) confirmed two aspects of the prediction, the proposed all-beta fold and the multi-domain structure. The most reliable three-dimensional model was obtained using the structure of neuraminidase (1nscA) as template. The analysis of the position of the active site residues in this model is compatible with the catalytic mechanism proposed by Reddy and Maley (J. Biol. Chem. 271:13953-13958, 1996), which includes three conserved residues, Asp, Glu, and Cys. Based on this analysis, we propose the participation of one more conserved residue (Asp 162) in the catalytic mechanism. The model will facilitate further studies of the physical and biochemical characteristics of family 32 of the glycosyl-hydrolases. Proteins 33:383-395, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 11 Ill.
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  • 92
    Digitale Medien
    Digitale Medien
    Molecular dynamics simulations of epidermal growth factor and transforming growth factor-α structures in water (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 396-407 
    Details
    ISSN: 0887-3585
    Schlagwort(e): AMBER ; epidermal growth factor ; transforming growth factor-alpha ; conformation ; receptor binding ; domain movement ; weakly polar interaction ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: AMBER v. 4.1 force field in 1.5 ns NPT molecular dynamics simulations of murine epidermal growth factor (mEGF), human epidermal growth factor (hEGF), and human transforming growth factor-α (hTGF-α) structures with explicit TIP3P solvation were used to investigate differences in backbone stability, changes in secondary structure, interdomain flexibility, and weakly polar interactions. Backbone root mean square deviations of sections of each peptide show that the most stable regions in mEGF and hEGF are the A-, B-, and C-loops, whereas the most stable regions in hTGF-α are the A- and B-loops. The secondary structure in the B-loops of mEGF and hEGF differ significantly from the nuclear magnetic resonance (NMR) structures of mEGF and hEGF. The position and type of turns in the B-loop of mEGF and hEGF increase the interstrand distance of the antiparallel β-sheets thereby disrupting their structure. The interdomain flexibility of simulated hTGF-α structure is greater than in either mEGF or hEGF. The φ, ψ dihedrals of hTGF-α occupy two distinct populations of phase space corresponding to either a C7eq or an α-helical conformation. This change in dihedral angle is stabilized by Phe15 with Arg42 and Phe17 with Arg42 N-π weakly polar interactions that are present only in hTGF-α but not in mEGF or hEGF. Proteins 33:396-407, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
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  • 93
    Digitale Medien
    Digitale Medien
    Analysis of domain motions by approximate normal mode calculations (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 417-429 
    Details
    ISSN: 0887-3585
    Schlagwort(e): protein energy surface ; crambin ; lysozyme ; ATCase ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: The identification of dynamical domains in proteins and the description of the low-frequency domain motions are one of the important applications of numerical simulation techniques. The application of these techniques to large proteins requires a substantial computational effort and therefore cannot be performed routinely, if at all. This article shows how physically motivated approximations permit the calculation of low-frequency normal modes in a few minutes on standard desktop computers. The technique is based on the observation that the low-frequency modes, which describe domain motions, are independent of force field details and can be obtained with simplified mechanical models. These models also provide a useful measure for rigidity in proteins, allowing the identification of quasi-rigid domains. The methods are validated by application to three well-studied proteins, crambin, lysozyme, and ATCase. In addition to being useful techniques for studying domain motions, the success of the approximations provides new insight into the relevance of normal mode calculations and the nature of the potential energy surface of proteins. Proteins 33:417-429, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 6 Ill.
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  • 94
    Digitale Medien
    Digitale Medien
    Helix-helix packing angle preferences for finite helix axes (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 457-459 
    Details
    ISSN: 0887-3585
    Schlagwort(e): Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Recently, James Bowie addressed the question of how to normalize correctly the distribution of observed helix-helix packing angles in proteins (Bowie, Nature Struct. Biol. 4:915-917, 1997). A hitherto unrealized yet significant bias toward crossed packing angles was revealed. However, the derived random reference distribution of packing angles requires that helices have to be assumed as infinite in length. Here, we complement Bowie's analysis by consideration of the more realistic case where helices are of finite length. As a result, the statistical bias toward near perpendicular packings appears to be even stronger. Proteins 33:457-459, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 2 Ill.
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  • 95
    Digitale Medien
    Digitale Medien
    A homology model for the human theta-class glutathione transferase T1-1 (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 444-454 
    Details
    ISSN: 0887-3585
    Schlagwort(e): hGSTT1-1 ; homology modeling ; menaphthyl sulfate ; dichloromethane ; dehalogenase ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A manual threading approach is used to model the human glutathione transferase T1-1 based on the coordinates of the related Theta class enzyme T2-2. The low level of sequence identity (about 20%), found in the C-terminal extension in conjunction with a relative deletion of about five residues makes this a challenging modeling problem. The C-terminal extension contributes to the active site of the molecule and is thus of particular interest for understanding the molecular mechanism of the enzyme. Manual docking of known substrates and non-substrates has implicated potential candidates for the T1-1 catalytic residues involved in the dehalogenation and epoxide-ring opening activities. These include the conserved Theta class residues Arg 107, Trp 115, and the conserved GSTT1 subclass residue His 176. Also, the residue at position 234 is implicated in the modulation of T1-1 activity with different substrates between species. Proteins 33:444-454, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 4 Ill.
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  • 96
    Digitale Medien
    Digitale Medien
    Intersubunit hydrogen bond acts as a global molecular switch in Escherichia coli aspartate transcarbamoylase (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 430-443 
    Details
    ISSN: 0887-3585
    Schlagwort(e): pyrimidine biosynthesis ; protein crystallography ; allostery ; long-range interactions ; site-directed mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Tyr 165 in the catalytic subunit of Escherichia coli aspartate transcarbamoylase (ATCase, EC 2.1.3.2) forms an intersubunit hydrogen bond in the T state with Glu 239 in the 240s loop of a second catalytic subunit, which is broken in the T to R transition. Substitution of Tyr 165 by Phe lowers substrate affinity by approximately an order of magnitude and alters the pH profile for enzyme function. We have determined the crystal structure of Y165F at 2.4 Å resolution by molecular replacement, using a wild-type T state structure as the probe, and refined it to an R value of 25.2%. The Y165F mutation induces a global conformational change that is in the opposite direction to the T to R transition and therefore results in an extreme T state. The two catalytic trimers move closer by ∼0.14 Å and rotate by ∼0.2°, in the opposite direction to the T→R rotation; the two domains of each catalytic chain rotate by ∼2.1°, also in the opposite direction to the T→R transition; and the 240s loop adopts a new conformation. Residues 229 to 236 shift by ∼2.4 Å so that the active site is more open. Residues 237 to 244 rotate by ∼24.1°, altering interactions within the 240s loop and at the C1-C4 and C1-R4 interfaces. Arg 167, a key residue in domain closure and interactions with L-Asp, swings out from the active site to interact with Tyr 197. This crystal structure is consistent with the functional properties of Y165F, expands our knowledge of the conformational repertoire of ATCase, and indicates that the canonical T state does not represent an extreme. Proteins 33:430-443, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 8 Ill.
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  • 97
    Digitale Medien
    Digitale Medien
    A hierarchical method for generating low-energy conformers of a protein-ligand complex (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 475-495 
    Details
    ISSN: 0887-3585
    Schlagwort(e): docking ; landscape ; dynamics ; dielectric ; affinity ; binding ; methotrexate ; thermolysin ; dihydrofolate reductase ; HIV protease ; generalized Born ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: A novel dynamical protocol for finding the low-energy conformations of a protein-ligand complex is described. The energy functions examined consist of an empirical force field with four different dielectric screening models; the generalized Born/surface area model also is examined. Application of the method to three complexes of known crystal structure provides insights into the energy functions used for selecting low-energy docked conformations and into the structure of the binding-energy surface. Evidence is presented that the local energy minima of a ligand in a binding site are arranged in a hierarchical fashion. This observation motivates the construction of a hierarchical docking algorithm that substantially enriches the population of ligand conformations close to the crystal conformation. The algorithm is also adapted to permit docking into a flexible binding site and preliminary tests of this method are presented. Proteins 33:475-495, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 24 Ill.
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  • 98
    Digitale Medien
    Digitale Medien
    Energy landscape of a native protein: Jumping-among-minima model (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 496-517 
    Details
    ISSN: 0887-3585
    Schlagwort(e): energy landscape ; hierarchical conformational substates ; molecular dynamics ; normal mode analysis ; principal component analysis ; jumping-among-minima model ; human lysozyme ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation. Proteins 33:496-517, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 13 Ill.
    Materialart: Digitale Medien
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  • 99
    Digitale Medien
    Digitale Medien
    Patterns of protein-fold usage in eight microbial genomes: A comprehensive structural census (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 518-534 
    Details
    ISSN: 0887-3585
    Schlagwort(e): structure databank ; superfold ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: Eight microbial genomes are compared in terms of protein structure. Specifically, yeast, H. influenzae, M. genitalium, M. jannaschii, Synechocystis, M. pneumoniae, H. pylori, and E. coli are compared in terms of patterns of fold usage - whether a given fold occurs in a particular organism. Of the ∼340 soluble protein folds currently in the structure databank (PDB), 240 occur in at least one of the eight genomes, and 30 are shared amongst all eight. The shared folds are depleted in all-helical structure and enriched in mixed helix-sheet structure compared to the folds in the PDB. The top-10 most common of the shared 30 are enriched in superfolds, uniting many non-homologous sequence families, and are especially similar in overall architecture - eight having helices packed onto a central sheet. They are also very different from the common folds in the PBD, highlighting databank biases. Folds can be ranked in terms of expression as well as genome duplication. In yeast the top-10 most highly expressed folds are considerably different from the most highly duplicated folds. A tree can be constructed grouping genomes in terms of their shared folds. This has a remarkably similar topology to more conventional classifications, based on very different measures of relatedness. Finally, folds of membrane proteins can be analyzed through transmembrane-helix (TM) prediction. All the genomes appear to have similar usage patterns for these folds, with the occurrence of a particular fold falling off rapidly with increasing numbers of TM-elements, according to a “Zipf-like” law. This implies there are no marked preferences for proteins with particular numbers of TM-helices (e.g. 7-TM) in microbial genomes. Further information pertinent to this analysis is available at http://bioinfo.mbb.yale.edu/genome. Proteins 33:518-534, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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  • 100
    Digitale Medien
    Digitale Medien
    The slow step of folding of Staphylococcus aureus PC1 β-lactamase involves the collapse of a surface loop rate limited by the Trans to Cis isomerization of a non-proline peptide bond (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 33 (1998), S. 550-557 
    Details
    ISSN: 0887-3585
    Schlagwort(e): mutagenesis ; c.d. spectroscopy ; unfolding ; Ω-loop ; molten-globule ; Chemistry ; Biochemistry and Biotechnology
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Medizin
    Notizen: We wished to test the hypothesis that the non proline cis to trans isomerization of the peptide bond at position 167 in the S. aureus β-lactamase PC1 exerts a significant controlling effect on the folding pathway of this enzyme. The previous data presented in support of this hypothesis could not rule out the effect of factors unrelated to non-proline cis/trans isomerization. We have used the plasmid pET9d to direct soluble overproduction of the S. aureus β-lactamase PC1 and a site-directed mutant (Ile 167 to Pro) in Escherichia coli. Following purification the proteins were subjected to a comparative analysis of the kinetics of unfolding and refolding using the techniques of near- and far-UV circular dichroism spectroscopy and fluorescence spectroscopy in conjunction with “double-jump” experiments. Results show that the fully-unfolded I167P mutant enzyme retains 20% of molecules in a fast-refolding form and that slower-refolding molecules fold faster than the recombinant wild-type enzyme. The final stage of folding involves folding of the Ω-loop into a conformation essential for enzymatic activity. In support of the original hypothesis, the folding of this Ω-loop is rate limited by the isomerization of the Glu 166-Ile 167 peptide bond. Proteins 33:550-557, 1998. © 1998 Wiley-Liss, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
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