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  • 2000-2004
  • 1990-1994  (1,759)
  • 1965-1969
  • 1920-1924
  • 1820-1829
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  • 201
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1002-1021 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthesis of (3S,4R,3′S,4′R)- and (3S,4S,3′S,4′S)-Crustaxanthins and Further Compounds with 3,4-Dihydroxy β-End-groupsStarting from 3, the enantiomerically pure title compounds were synthesized in eight steps. Spectra and HPLC systems are presented that allow a distinction between these isomers.
    Additional Material: 6 Ill.
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  • 202
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A simple synthesis of 5-deoxy-L-[5-2H1]arabinose was performed to obtain L-[3′-2H1]biopterin. The reduced form of this model substance is needed to investigate the pathway of 7-substituted pterins in patients with primapterinuria.
    Additional Material: 3 Tab.
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  • 203
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1139-1147 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a new principle for the purification of oligodeoxynucleotides using a purification handle which leads to a covalent linkage of the desired DNA sequence to a solid matrix. Truncated sequences are removed by washing steps. The release of the pure target sequence is performed in such a way that it is obtained directly in its 5′-phosphorylated form which represents a further advantage. In addition, the system can be used for 5′-thiol modifications of synthetic DNA.
    Additional Material: 2 Tab.
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  • 204
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Total Synthesis of Naturally Occurring α-Tocopherol. Asymmetric Alkylation and Asymmetric Epoxidation as Means to Introduce (R)-Configuration at C(2) of the Chroman MoietyBased on the reductive, stereospecific ring closure of (2R,4′R,8′R)-α-Tocophcrylquinone′ or corresponding analogues with a short, functionalized side chain (B, Scheme 1) to 1 resp. the chroman system of 1 (C), two different approaches for the introduction of the required tertiary methyl-substituted alcohol structure in the side chain of the aromatic precursors (A, Scheme 1) were developed. The first approach uses asymmetric alkylation in three different versions featuring (a) diastereoselective steering with chiral auxiliaries I-IV (Scheme 2) attached as esters to a-keto acids, (b) intermediate transfer of chirality in an ester enolate (from 18, Scheme 4) derived from an optically active α-hydroxy acid, (c) enantioselective alkylation of phytenal (20) and subsequent ring closure with chirality transfer (Schemes 5-7). The second approach is based on the asymmetric epoxidation of β-metallylalcohol (Sharpless epoxidation), the corresponding epoxyalcohol being converted in situ to the (S)-or (R)-chlorodiol (S)-and (R)-29, respectively, for isolation (Schemes 8 and 9). Nucleophilic epoxide opening with a (3R 7R)-3,7,11-trimethyldodecyl (C15**) and an ArCH2 unit in appropriate sequence is used to assemble the C-framework of the target molecule via corresponding epoxide intermediates from either chlorodiol. Combined with the use of the methoxymethyl-ether function for protection of the hydroquinone system, the epoxide approach provides a short route to 1 (Scheme 10).
    Additional Material: 2 Tab.
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  • 205
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990) 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 206
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The metastable ions of Fe+ complexes of aldimines R1N=CHR2 exhibit a unique behaviour in that sequential loss of olefin/H2 follows two distinct pathways: one corresponds to the familiar pattern of double remote functionalization, involving either alkyl chain R1 and R2. In addition, based on labeling studies, evidence is presented demonstrating that the consecutive elimination of C2H4/H2 from the Fe+ complex of C6H13N=CHC3H7 involves exclusively the C6H13 part of the substrate. These and other Fe+-mediated C—H/C—C bond activations of aldimines are controlled by chain-length effects, reflecting the preferential formation of metallacyclic intermediates of particular ring sizes.
    Additional Material: 1 Tab.
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  • 207
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Compound (Z)-8a has been found to display interesting antiinflammatory activity. In order to prepare derivatives with a wide variety of substituents in the aromatic part of the molecule, a new synthesis of the key intermediates 9a-g was developed starting from thiophene-3-carboxylic acid (11) and substituted benzyl bromides. The conversion of 9a-g to 10a-g follows a known procedure. Ketones 10a-g, on reaction with alkyl (dialkoxy-phosphoryl)acetate, followed by isomer separation and alkaline ester hydrolysis, yielded the desired derivatives (Z)-8a-g and (E)-8a-g. The biologically most interesting compound (Z)-8a is currently undergoing clinical trials.
    Additional Material: 1 Tab.
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  • 208
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1215-1218 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The infrared quasi-resonance stepwise-multiphoton-dissociation spectra of the molecular ions of 1-bromo-propene, 2-bromopropene, 3-bromopropene, and bromocyclopropane have been obtained at selected wavelengths between 9. 2 and 10. 7 μm in a Fourier -transform mass spectrometer. The resulting spectra and the photo fragmentation kinetics suggest that these molecular ions retain their identity upon ionization, and can, thus, provide fingerprint spectral identifications for the ions.
    Additional Material: 2 Ill.
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  • 209
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1306-1313 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The absorption spectra, luminescence spectra, excited-state lifetimes, and electrochemical behavior of the cyclometalated [Rh(ppz)2bpy]+, [Rh(3-Cl-ppz)2(bpy)]+, [Rh(4-NO2-ppz)2(bpy)]+, [Rh(ppz)2(biq)]+ and [Rh(4-NO2-ppz)2(biq)]+ complexes (ppz-, 3-Cl-ppz-, and 4-NO2-ppz- are the ortho-C-deprotonated forms of 1-phenylpyrazole, l-(3-chlorophenyl)pyrazole and l-(4-nitrophenyl)pyrazole, respectively) have been investigated. The results obtained have been compared with those concerning the free protonated ligands and some previously studied mixed-ligand cyclometalated Rh(III) complexes. Luminescence originates from the lowest ligand-centered (LC) excited state, which involves the diimine ligands in all cases except for [Rh(4-NO2-ppz)2(bpy)]+, where it involves the ortho-metalating ligand. s. In the absorption spectra, LC and metal-to-ligand charge-transfer (MLCT) bands, involving the diimine and/or the ortho-metalating ligands, have been assigned, and correlations between spectroscopic and electrochemical data are discussed.
    Additional Material: 4 Ill.
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  • 210
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1359-1372 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The phosphonic acids 3 and 4 were prepared to compare their inhibitory activity on Vibrio cholerae sialidase with the one of the corresponding N-acetyl-2-deoxyneuraminic acids 5 and 6. Thus, hydrogenation and benzylation of methyl N-acetyl-2,3-didehydro-2-deoxyneuraminate (1MeNeu2en5Ac; 7) gave a mixture of the fully O-benzylated benzyl and methyl esters 9 and 10, the partially O-benzylated benzyl and methyl esters 11 and 12, and the fully O-and N-benzylated benzyl and methyl esters 13 and 14 (Scheme 1). Transesterification of 9 to 10 and hydrolysis of 10 gave the acid 15. Oxidative decarboxylation of 15 with Pb(OAc)4 gave a 1:9 mixture of the α-and β-D-glycero-D-galacto-acetates 16 and 17. Phosphonoylation of 17 with P(OMe)3 and Me3SiOTf gave a 1.3:1 mixture of the phosphonates 18 and 19, which were deprotected to give the (4-acetamido-2,4-dideoxy-D-glycero-α-and β-D-galacto-octopyranosyl)phosphonic acids 3 and 4, respectively. The acid 6 was obtained by epimerization of the tert-butyl ester 23 with lithium N-cyclohexylisoproylamide and deprotection. The phosphonic acids 3 (Ki 5.5 10-5 M) and 4 (Ki 2.3.10-4 M) are stronger inhibitors of Vibrio cholerae sialidase than the anomeric N-acetyl-2-deoxyneuraminic acids 5(Ki 2.3 10-3 M) and 6. Both 3 and 4 inhibit the Vibrio cholerae sialidase, while only the carboxylic acid 5, possessing an equatorial COOH group is an inhibitor.
    Additional Material: 5 Tab.
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  • 211
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Zero-current counter-transport studies as well as electrodialytic transport experiments on solvent polymeric membranes doped with ionophores for anions have been carried out and were compared with potentiometric measurements on the same membranes. A theoretical description of the observed phenomena corroborates that lipophilic complexes of Co(III) (e. g. aquacyano[heptakis(2-phenylethyl)]Co(III) cobyrinate perchlorate) and Mn(III) (e. g. lipophilic Mn(III)porphyrin complexes) act as positively charged carriers for anions, whereas a lipophilic Ru(II)porphyrin complex has to be described as an electrically neutral carrier for anions.
    Additional Material: 10 Ill.
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  • 212
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In four series of strictly related organocobalt complexes, derived from cobaloximes by replacement of the O…H…O with O…-BF2…O and/or (CH2)3 groups, the trends of 59Co-NMR shielding and electrochemical data are discussed. A largely parallel behaviour of the plots of E1/2(I) values for the first Co(III)/Co(II) electron transfer vs. the 59Co chemical shifts reflects the similar sensitivity of the two parameters to a change in electron affinity of the central metal ion due to a variation of the organic group R. E1/2(II) values for the second Co(II)/CO(I) electron transfer are less sensitive to the change of R, but the trend of the plot vs. δ(59Co) is still parallel in the four series. Consistent deviations from a roughly linear dependence of E1/2(I) on pKa of the hydrocarbon acid corresponding to R, on Taft constant s̰* and on 59Co shielding are noticed for the isopropyl derivatives and attributed to a steric effect. This was confirmed in a series of R—Co(DMG)pyridine complexes in which 59Co shielding decreases steadily with increasing steric parameter Es (Taft) of the alkyl group. There is experimental evidence from X-ray data that δ(59Co) decreases with an increase of the Co—C bond length, illustrating steric hindrance in alkyl coordination to be responsible for the decreased shielding of the 59Co nucleus. The relative displacements of the graphic displays for the different series reflect the effect of changes in electron affinity of the redox center, due to the equatorial ligand, which, in turn, is caused by variations in the electron-withdrawing power due to the introduction of the BF2 group and by the change from -2 to -1 valence of the (CH2)3-capped ligands.
    Additional Material: 8 Ill.
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  • 213
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthesis of New Heptafulvenes; X-Ray Analysis of ‘8,8-(1′,4′-Dioxotetramethylene)heptafulvene’ (2-(Cyclohepta-2,4,6-trien-1-ylidene)cyclopentane-1,3-dione)Experimental procedures for the synthesis of heptafulvene (3a), 8,8-tetramethylene heptafulvene (3c) and ‘8,8-(1′,4′-dioxotetramethylene) heptafulvene’ (2-(cyclohepta-2,4,6-trien-1-ylidene)-cyclopentane-1,3-dion; 3d) are described. The most important sequences include a low-temperature reaction of tropylium salts with lithium or Grignard carbenoids (Scheme 1) to give 3a and 3b as well as hydride abstraction from substituted cycloheptatrienes followed by deprotonation to give 3c and 3d. Limitations of these sequences are discussed. Two other heptafulvenes 3h and 3i are available by silylation of heptafulvenolates according to well-known procedures. NMR-Spectroscopic evidence as well as an X-ray analysis of 3d are presented. Compound 3d is a relatively polar heptafulvene with a planarised seven-membered ring as well as a partly delocalized π system.
    Additional Material: 2 Ill.
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  • 214
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1734-1741 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: On irradiation in the presence of Fe(CO)5, the allenic amides and imides showed a similar course of complexation to that of esters and lactones, respectively, e.g. the amides of type 10 led to diiron complexes of type 11 (Scheme 3), whereas the imide 12 yielded a mixture of a dinuclear and two mononuclear complexes (13-15, Scheme 4). The racemic ester 6 also gave mononuclear (7a, 7b, and 9) and dinuclear complexes (8a and 8b; Scheme 2). In case of the allenic acid 4, only complexation of type 5 was observed (Scheme 1).
    Additional Material: 1 Ill.
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  • 215
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The bimorphinans 6 and 7 have been prepared from 14-O-methylnaloxone (2) and 14-O-methylnaltrexone (3), respectively. The known compounds 2 and 3 were synthesized by a different route than the route described. Bimorphinan 7 possessed a similar χ receptor affinity to norbinaltorphimine (1) but had a reduced selectivity due to marked increases in μ and δ receptor affinity. Bimorphinan 6 was both a less selective and less potent χ antagonist than 1.
    Additional Material: 1 Tab.
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  • 216
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The complex [Ru(η5-C7H11)2H]BF4 (C7H11 = 2,4-dimethylpenta-2,4-dienyl) is highly reactive towards two- and six-electron ligands. e.g. giving with CO complex [RuCO(η4-C7H12)(η5-C7H11)]BF4. The 2,4-dimethylpenta-1,3-diene ligand (C7H12) of the latter complex is readily displaced giving, e.g. with excess cyclohexa-1,3-diene (C6H8) complex [RuCO(η4-C6H8)(η5-C7H11)]BF4. These reactions provide a convenient entry into monopentadienylruthenium chemistry.
    Additional Material: 1 Ill.
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  • 217
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 1980-1985 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Novel Synthesis of (-)-(R)-Cembrene A, Synthesis of (+)-(R)-Cembrenene and (+)-(S)-CembreneA novel synthesis of (-)-(R)-cembrene A ((-)-3) was developed using the Sharpless epoxidation for the introduction of the chiral center. Furthermore, the synthesis of (+)-(R)-cembrenene ((+)-4) showed that this cembranoid must have the (R)-configuration and not, as previously reported, the (S)-configuration. Selective hydrogenation of (+)-4 afforded (+)-(S)-cenibrene ((+)-5).
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  • 218
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Treatment of [η6-(bicyclo[4.2.0]octa-1,3-5 triene)]tricarbonylchromium(0) (2) with BuLi or lithium 2,2,6,6-tetramethylpiperidinide (TMPLi) gives rise to a highly regioselective deprotonation at C(2). Subsequent reaction with electrophiles (6 examples) gives [η6-(2-R-bicyclo[4.2.0]octa-1,3,5-triene)]tricarbonylchromiurn complexes 3 and 5-9 in moderate (R=I, 50%; R=CHO, 67%) to good (R=Me, D, SiMe3, CO2Me, 〉 80%) yield (Scheme 1). Analogous reactions with tricarbonyl (η6-indane)chromium (10) give mixtures of complexes substituted at C(4) and C(5) (Scheme 2). In 10, deprotonation β to the ring junction is strongly favoured with the bulky base TMPLi. Double lithiation/electrophile additions to 2 give access to [η6-(2-R′-5-R″-bicyclo[4.2.0]octa-1,3,5-triene)]tri-carbonylchromium complexes (e.g. 13 (R′=R″=Me3Si) and 14 (R′=Me3Si, R″=CHO)) as single products. The Cr(CO)3 group can be easily removed by oxidation (I2, Ce(IV), O2/light; 2 examples each) to give the free arenes. Base-catalyzed (CsF, DMF/D2O) deuterodesilylation of 13 yields the [(2,5-2H2)bicyclo[4.2.0]octa-1,3,5-triene]chromium complex 15, and treatment of 2,5-bis(trimethylsilyl) compound 16 with CF3COOD gives the 2,4-dideuterated 17. Compound 16 is also accessible more directly via reductive silylation/oxidation of bicyclo[4.2.0]octa-1,3,5-triene (1). Stereoselective base-catalyzed (t-BuOK.) H/D exchange of the benzylic H-atoms. opposite to the Cr(CO)3 moiety in 2 takes place rapidly in (D6)DMSO, but benzylic functionalization via this route remains elusive.
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  • 219
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1H- and 13C-chemical shifts of the dianion of dibenzo[a,c]naphthacene (1) have unambiguously been assigned by 2D-NMR spectroscopy. They indicate a remarkable charge distribution, as most of the negative charge is localized on the ‘anthracenic’ moiety, while the ‘phenanthrenic’ moiety is almost neutral. Association of 12- with alkali-metal counterions has only a minor effect on the chemical shifts. The charge partitioning in 12-, which is reproduced by ωβ calculations in the frame of the Hückel model, must, thus, be considered as an intrinsic property of the 4nπ-electron system of 12-. It is rationalized in terms of differing energy contents of the constituent anthracenic and phenanthrenic moieties. ESR and ENDOR studies of the radical anion 1\documentclass{article}\pagestyle{empty}\begin{document}$ 1^{\scriptstyle {{\relbar}\kern-4pt {.} }} $\end{document} and the radical cation 1\documentclass{article}\pagestyle{empty}\begin{document}$ 1^{+ \atop \dot{}} $\end{document} show that the π-charge distribution in 12- is reflected by the π-spin distributions in the two radical ions of the alternant hydrocarbon 1.
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  • 220
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Eu3+ complexes of the tripode and tetrapode ligands 1 and 2, respectively, containing 2,2′-bipyridine coordinating units have been prepared. The UV absorption and luminescence spectra, lifetimes, and quantum yields have been measured under a variety of experimental conditions. The contributions of different paths to the decay of the luminescent excited state are evaluated, and the structures of the complexes are discussed on the basis of spectroscopic and photophysical data.
    Additional Material: 2 Ill.
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  • 221
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In addition to the known C11H16 hydrocarbons multifidene (4), aucantene (2), and ectocarpene (5), the marine brown alga Cutleria multifida produces trace amounts of the C9H12 hydrocarbon 7-melhylcycloocta-1,3,5-triene (8) and its valence tautomer 7-methylbicyclo[4.2.0]octa-2,4-diene, A second novel C9H12 hydrocarbon is 6-vinyicyclo-hepta-1,4-diene (9), a lower homologue of ectocarpene (5). Among the C11H16 hydrocarbons, 7-((1E/Z)-prop-l-enyl)cycloocta-1,4-diene (10/11) is found for the first time. The structure of all new products is confirmed by synthesis and spectroscopic data. The biosynthesis of the new hydrocarbons 8-11 is obviously linked to the pathways which lead to the major products giffordene (7), (6S)-ectocarpene ((6S)-5), and (4R,5R)-aucantene ((4R,5R)-2). Consecutive reactions of certain thermolabile primary products proceed via electrocyclic ring closure, 3,3-sigmatropic rearrangement, or a 1,7-sigmatropic H-shift.
    Additional Material: 2 Ill.
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  • 222
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Reaction Behavior of 4H,8H-Benzo[1,2-c:4,5-c′]diisoxazole-4,8-dionos towards Reducing AgentsBy reduction of the 3,7-diamino-substituted heterocycles 1c-d and 6a-d, the quinoid 2,5-diamino-3,6-dioxo-cyclohexa- 1,4-diene- 1,4-dicarboxamides 2c-h and 7a-d are synthesized. The diaminodicarboxamides 2 can be recyclised by use of Pb(AcO)4. The dialkylamino-substituted derivatives 1c-h react with NaBH4 under conservation of the heterocyclic system to the tetrahydro-benzo[1,2-c:4,5-c′] diisoxazoldiones of type 5. The NMR-spectroscopic behavior of 2 and 7 is discussed.
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  • 223
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The study of specifically labeled alkoxides generated in the gas phase by deprotonation of epimeric norbernols demonstrates, beyond any doubt, that ‘solvated’ hydride ions are formed as intermediates in the course of enolate formation. Kinetic isotope effects and exo/endo-face selectivities for the dehydrogenation are discussed.
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  • 224
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    Electronic Resource
    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 2199-2208 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Does [6+4] Cycloaddition between Pentafulvene and Cyclopentadiene Take Place?Reaction of a 1:1 mixture of cyclopentadiene (CPD) and pentafulvene (1a) at 20° gives a complex mixture. The low-molecular-weight part mainly consists of pure and mixed dimers (ca. 73 %) besides corresponding trimers (ca. 20%) and some corresponding oligomers according to GC/MS investigations (Fig. 1). The 3 predominant ‘mixed dimers’ between CPD and 1a have been separated, and structures 4-6 (Scheme 3) are assigned according to 400- and 600-MHz 1H-NMR investigations. These results show that HOMO(CPD)-LUMO(fulvene) interactions are important in pentafulvene cycloadditions. Dimer 6 results from [6+4] cycloaddition followed by [1,5]-H shifts.
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  • 225
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 2242-2250 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The synthesis of diester 3, a synthon for the C(19)-to-C(27) segment of rifamycin S (1), is described, starting from the meso-diester 4 (Schemes 2 and 3). Inversion of the configuration at the later C(23) and two aldol condensations with the lithium enolate 18 of 2,6-dimethylphenyl propionate each producing two new chiral centres of threo-configuration, led to the desired diester 3. The absolute configuration of the new chiral centres was proven by a single X-ray analysis of intermediate 19 (Fig.) and by converting diester 3 into meso-diester 25.
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  • 226
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    New York, NY : Wiley-Blackwell
    Helvetica Chimica Acta 73 (1990), S. 2157-2164 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Microbial metabolism of the diterpene sclareol (1) was studied. Screening studies have shown a number of microorganisms capable of metabolizing 1. Preparative-scale fermentation with Septomyxa affinis ATCC 6737 has resulted in the production of three fungal metabolites that have been characterized by 2D-NMR techniques and chemical reactions. These metabolites have been identified as 8α,13β-dihydroxylabd-14-en-3-one (2), labd-14-ene-3β.8α,13β-triol (4), and labd-14-ene-2α,8α,13β-triol (6).
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  • 227
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    Helvetica Chimica Acta 73 (1990), S. 2165-2170 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Natural irones found in the essential oil of Iris rhizomes often are mixtures of enantiomers. The separation of all optical isomers of the irones by GLC on modified cyclodextrins and the determination of their composition within different Iris oils is described. The significance for the biosynthesis of the cycloiridals, C31-triterpenoids, which serve as precursors of the irones, is discussed.
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  • 228
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    Helvetica Chimica Acta 73 (1990), S. 2218-2224 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The ion/molecule reactions of the molecular ion, the C3H5+ ion, and the C3H3+ ion obtained from 3-chloropropene. 1-bromopropene, 2-bromopropene, 3-bromopropene, bromocyclopropane. and 3-iodopropene have been studied with their neutral precursor in a Fourier-transform mass spectrometer (FT/ICR). The molecular ions react to yield primarily C6H9+ except for the ion derived from 1-bromopropene that is unreactive. The kinetics of the 3-bromopropene molecular ion reveals that 18% of these ions must possess a different structure which is unreactive. The fact that C3H5+ ions obtained from 2-bromopropene are the only ones to undergo proton transfer is taken as evidence that only this parent compound gives rise to 2-propenyl cations by low-energy electron impact. The C3H3+ ions generated in these systems are shown to be roughly an equal mixture of propargylium ions that react to yield C6H7+ and unreactive cyclopropenium ions.
    Additional Material: 1 Ill.
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  • 229
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A New 1,3-Oxathiolane Synthesis: Spirocyclic 1,3-Oxathiolanes from the Lewis-Acid-Catalyzed Reaction of 1,3-Thiazole-5(4H)-thiones and OxiranesThe BF3·Et2O-catalyzed reaction of 2,4,4-trisubstituted 1,3-thiazole-5(4H)-thiones 13 with alkyl- and phenyl-substituted oxiranes 7 in CH2Cl2 at room temperature leads, in very good yields, to 1-oxa-4,6-dithia-8-azaspiro[4.4]non-7-enes 14 and 15.
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  • 230
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    Helvetica Chimica Acta 73 (1990), S. 25-47 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Several homo- and heteronuclear two-dimensional NMR techniques were used to assign all H- and C-resonances of the two conformers A and B of [7-(N-methyl-L-leucine)]didemnin B. Didemnine is a biologically highly active cytostaticum and immunosuppressivum. The assignment of the aliphatic C-atoms were done by the inverse H,C-COSY with TOCSY transfer which connects complete proton spin systems and represents them on C-atoms. The structure of both conformers (A and B) in (D6)DMSO solution was derived from homo- and heteronuclear couplings (J), temperature dependencies of NH protons, and NOE effects. Distances determined from the latter were used for refinements by restrained MD calculations using the GROMOS program. The solution structure of [Me-L-Leu7]didemnin B (A and B) was compared to that of didemnin B. The backbone structure of the macrocyclic ring and of the linear side-chain moiety are very similar in conformer A and didemnin B, though the Ist1-Hip2 region of the ring is slightly ex tended in conformer A. This may be caused by the influence of the Me-L-Leu7 residue in A and may be responsible for its reduced biological activity in comparison to didemnin B. The more weakly populated conformer B exhibits a βVI turn in the linear side-chain moiety.
    Additional Material: 15 Ill.
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  • 231
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    Helvetica Chimica Acta 73 (1990), S. 48-62 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Synthesis of Plectranthons, Diterpenoid Phenanthrene-1,4-dionesThe following phenanthrene-1,4-diones have been synthesized by using the photocyclization of the corresponding highly substituted stilbenes as the key step: 3-hydroxy-5,7,8-trimethyl-2-(prop-2-enyl)phenanthrene-1,4-dione (1), (RS)-, (R)-, and (S)-2-[3-hydroxy-5,7,8-trimethyl-1,4-dioxophenanthren-2-yl]-1-methylethyl acetate (2, 31, and 32, resp.), 3-hydroxy-7,8-dimethyl-2-(prop-2-enyl)phenanthrene-1,4-dione (3), 3-hydroxy-7,8,10-tri-methyl-2-(prop-2-enyl)phenanthrene-1,4-dione (4), 5,7,8-trimethyl-2-(prop-2-enyl)phenanthrene-1,4-dione (17), and 3-hydroxy-2-methylphenanthrene-1,4-dione (42). The quinones 1 and 3 proved to be identical with the recently isolated plectranthons A and C. Compounds 2, 31, and 32 exhibited the same UV/VIS, IR, 1H-NMR and mass spectra as natural plectranthon B, but had different melting points. This might be due either to crystal modifications or to diastereoisomerism caused by the helical structure of the phenanthrene-1,4-dione skeleton. The spectral data of synthetic 4 were not compatible with those of natural plectranthon D for which structure 4 had been proposed based mainly on 1H-NMR arguments concerning the chemical shifts of H—C(9) and H—C(10) in 1-3. Extensive 1H-NMR investigations have now revealed that the currently stated assignments of the H—C(9)/ H—C(10) AB system have to be reversed for highly substituted phenanthrene-1,4-diones: in the model compounds 2-methylphenanthrene-1,4-dione (41) and 2, H—C(10) resonates al lower field as expected (peri-position), whereas in the highly substituted congeners 1, 2, 3, 31, and 32, H—C(9) is shifted paramagnetically, a fact which had lead to the erroneous assignment of structure 4 for natural plectranthon D.
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  • 232
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    Helvetica Chimica Acta 73 (1990), S. 63-68 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: According to a general concept for the total synthesis of pseurotin A (1), a secondary metabolite of Pseudeurotium ovalis STOLK, 5-[(1S,2S,Z)-1,2-dihydroxyhex-3-enyl]-2,2,4-trimethylfuran-3(2H)-one (17) was prepared. It is a model substance for the substituted furan-3(2H)-one moiety of 1. The aldol condensation of the aldehyde 26, derived from D-glucose, and the enolate of ketone 29 served as key reaction.
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  • 233
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    Helvetica Chimica Acta 73 (1990), S. 69-80 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The isothiazole 1 is not only a dipolarophile but also a reactive and versatile dienophile: especially with oxy-substituted ‘donor’ 1,3-butadienes, it readily combines in Diels-Alder fashion; the regiospecificity of the addition is governed by the carbonyl group of the dienophile, whereas the sulfo group can be ignored for the purpose of predicting regioselectivity. upon dehydrobromination of the [4 + 2] adducts with DBN, the cycloaromatization process is completed, generating saccharin-like compounds. Besides the parent substance saccharin (14b), several hydroxylated derivatives have been synthesized by this new method; two of them, i.e. 16b and 18c, are of potential interest as non-nutritive sweetening agents (Scheme 3). In an alternative version of this principle, the isothiazole 22 is reacted with the renowned oxazole 21, affording, after acid-promoted rearrangement, pyrido-annelated isothiazoles 25 (Scheme 4). Since both processes generate saccharin-related structures, they may serve in syntheses of oxicams and analogs of ipsapirone. To demonstrate the viability of the approach, one representative of each series, i.e. 26a and 29, has been converted to an oxicam (7b and 31c, resp.; Scheme 5).
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  • 234
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    Helvetica Chimica Acta 73 (1990), S. 81-85 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Charge-Transfer Complexes of Tetrazinodiheteroarenes with Acceptor CompoundsThe formation of charge-transfer complexes and radical-ion pairs of donor compounds 1-6 with acceptor compounds 7-12 has been investigated by means of VIS/NIR-spectroscopic methods. The equilibrium constants KCT up to 1100M-1 for the donor/acceptor couple dipyrido[1,2-b:1,2′-e][1,2,4,5]tetrazine (2)/ethylenetetracarbonitrile (11) and spectra of the CT complexes have been determined in 1,2-dichloroethane solution at 25°. Results are discussed in relation to known CT-complex properties and to voltammetric redox-potentials E1/2.
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  • 235
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    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: 1,3,5-Trideoxy-1,3,5-tris(dimethylamino)-cis-inositol (TDCI) and 1,3,5-trideoxy-1,3,5-tris(trimethylammonio)-cis-inositol (TTCI) were prepared by methylation of 1,3,5-triamino-1,3,5-trideoxy-cis-inositol (TACI). The ability of TDCI to form both intermolecular and intramolecular H-bonds, as demonstrated by X-ray diffraction, is probably responsible for the good solubility of TDCI in almost every common solvent. TTCI was found to be a polyol of unusual high acidity (pK1 = 8.14 ± 0.02, pK2 = 13.0 ± 0.2). This phenomenon could be explained by electrostatic interactions between the charged substituents of the cyclohexane residue.
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  • 236
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Nα[(tert-Butoxy)carbonyl]-2-diazo-L-histidine methyl ester 1 was synthesized starting from the corresponding L-histidine derivative. The physico-chemical properties of this new photoactivatable amino-acid derivative were established. The synthetic precursor of 1, 2-amino-L-histidine derivative 3, was best isolated and characterized as 2-amino-Nα-[(tert-butoxy)carbonyl]-Nτ-tosyl-L-histidine methyl ester (4). Selective deprotections of 4 (Nα-Boc, Nα-Tos, COOMe) were achieved, thus allowing the use of the corresponding products in peptide synthesis. The optically active dipeptides 8 and 9 were synthesized by coupling 2-amino-Nτ-tosyl-L-histidine methyl ester (5) with N-[(tert-butoxy)carbonyl]-L-alanine and Nα-[(tert-butoxy)carbonyl]-Nτ-tosyl-L-histidine (6) with L-alanine methyl ester, respectively. The question of selective diazotization of a 2-aminohistidine residue in a synthetic peptide was studied using competitive diazotizations between 2-amino-1H-imidazole and several amino-acid derivatives susceptible to undergo nitrosylation. The results show that synthetic photoactivatable peptides incorporating a 2-diazohistidine residue might become useful photoaffinity probes.
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  • 237
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    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The lithium and europium(III) cryptates of a macrobicyclic ligand 1 incorporating the 3,3′-biisoquinoline 2,2′-dioxide 2 have been prepared. The Eu(III) complex [Eu(2)2]Cl3 has also been obtained. These Eu(III) complexes present characteristic 1H-NMR spectra containing markedly shifted resonances. They are strongly luminescent; the emission spectra, quantum yields, and lifetimes have been determined.
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  • 238
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    Helvetica Chimica Acta 73 (1990), S. 1986-1990 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Starting from 5-methyl-oxycodone (6), 5-methylnaloxone (4), and 5-methylnaltrexone (5) have been prepared in several steps. Both 4 and 5 behaved as partial agonists in the AcOH writhing agonism and antagonism test in mice.
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  • 239
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    Helvetica Chimica Acta 73 (1990) 
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
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  • 240
    ISSN: 0018-019X
    Keywords: Chemistry ; Organic Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Deuterium-induced isotope effects on 6Li chemical shifts, transmitted over two bonds, 2Δ(6Li)(2H/1H), have been measured for the first time for methyllithium and the system methyllithium/lithium iodide. The observed shifts are to low field and range from 15 to 20 ppb per CD3 group. The multiplicity and intensity distribution of the 6Li signals resulting for mixtures of CH3- and CD3-containing samples in the limit of slow inter- as well as intra-aggregate exchange yield information about the size of the various clusters present in diethylether solution. It is expected that these isotope shifts can facilitate structural investigations of organolithium compounds. In some cases, the results of such measurements are expected to be less ambiguous then the conclusions based on multiplets that arise from scalar 13C,6Li spin-spin coupling.
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  • 241
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 242
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 16-31 
    ISSN: 0887-3585
    Keywords: BPTI ; dithiothreitol ; DTT-sensitive mutants ; protein folding ; random mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A genetic screening procedure has been developed to identify mutant forms of bovine pancreatic trypsin inhibitor (BPTI) that can fold to an active conformation but are inactivated more rapidly than the wild type protein. Small cultures of Escherichia coli containing plasmids with mutagenized BPTI genes were grown in microtiter plates, lysed, and treated with dithiothreitol (DTT). Under these conditions, unfolding and inactivation of wild-type protein has a half-time of about 10 hours. Variants of BPTI that are inactivated within 1 hour were identified by adding trypsin and a chromogenic substrate. Approximately 11,000 mutagenized clones were screened in this way and 75 clones that produce proteins that can fold but are inactivated by DTT were isolated. The genes coding for 68 “DTT-sensitive” mutant proteins were sequenced, and 25 different single amino acid substitutions at 15 of the 58 residues of the protein were identified. Most of the altered residues are largely buried in the core of the naive wild-type structure and are highly conserved among proteins homologous to BPTI. These results indicate that a large fraction of the sequence of the protein contributes to the kinetic stability of the active conformation, but it also appears that substitutions can be tolerated a most sites without completely preventing folding Because this genetics, further studies of the isolated mutants are expected to provide information about the roles of the altered residues in folding and unfolding.
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  • 243
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 244
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 74-92 
    ISSN: 0887-3585
    Keywords: thermostability ; bacterial lactate dehydrogenase ; allosteric regulations ; crystallography ; molecular replacement ; coenzyme binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structures have been determined of Bacillus stearothermophilus “apo” and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-biosphosphate. The “apo” lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 Å resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 Å resolution data, in a restrained least-squares refnement in which the molecula rsymmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the “apo” enzyme.Further refinement proceeded with the isomorphous holo-enzyume from Bacillus Stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 Å and 1.7° r.m.s. deviation from idealized bond length and angles, respectively.Two sulfate ions per subunit were included in the final model of the “apo” -from-one at the substrate binding site and one close to the molecular P -axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the “apo” model.This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with incotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose, 1,6-bisphosphate were also analyzed.
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  • 245
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 185-197 
    ISSN: 0887-3585
    Keywords: restriction enzyme ; DNA-protein interactions ; DNA recognition ; enzyme-substrate interaction ; active site ; site-directed mutagenesis ; protein structure-function ; DNA double-strand breaks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme-DNA complex, EcoRI also serves as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase β-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 234-248 
    ISSN: 0887-3585
    Keywords: computer modelling ; Ca2+-binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of troponin are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecules. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).
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  • 247
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 249-256 
    ISSN: 0887-3585
    Keywords: β-barrels ; β-strand ; scaffold design ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 8-old parallel α/β-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the β-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-standard β-barrel. To facilitate the de novo design of such structures, a collection of modelling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the φ, ψ requirements to design symmetric eight standard β barrels with optimal hydrogen bonding between adjacent β-strands. It is observed that: (a) the β-sheet structure can be closed without introducing irregular stagger between β-strands and (b) the region of φ, ψ dihedral angle space compatible with the formation of regular symmetric eight standard β-barrels coincides with the φ, ψ region corresponding to average β-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on β-strand geometry.
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  • 248
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 280-290 
    ISSN: 0887-3585
    Keywords: proteases ; protein turnover ; post-translational processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system has been developed or the expression in E. coli of 12 of the 14 expressed mouse submandibular gland kallikreins as cassettes subcloned directly from cDNA. Using the epidermal growth factor binding protein (mGK-9) and the γ-subunit of nerve growth factor (nGK)-3, as test cases, mature processed forms, obtained as functionally active proteins, as well as various precursor forms, were isolated. The expression system described allows rapid isolation of kallikrein protein from corresponding cDNA with yields of approximately 1.0 mg of purified protein from 10 g of initial cell paste. This expression system will facilitate structure/function studies of the mouse glandular kallikrein gene family and help elucidate the regions of the mature proteins responsible for the diverse catalytic behavior and growth factors interactions observed in this family of proteins.
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  • 249
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 203-212 
    ISSN: 0887-3585
    Keywords: hydrogen bonding diagram ; motifs ; helical wheel ; helical net ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program is described which generates hydrogen bonding diagrams of protein structures and optionally helical wheels and helical nets. The program can also be used simply to calculate the connectivities of β-strands and to automatically extract simple structural motifs such as hairpins or Greek keys. The program greatly reduces the effort required to produce these diagrams and offers considerable flexibility in the information which can be represented. The usefulness of the program is illustrated by several examples including comparing homologous families, correlating protein structure with attributes of individual residues, and extracting all examples of the ψ-loop motif from the Brookhaven Data Bank.
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  • 250
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 251-257 
    ISSN: 0887-3585
    Keywords: peroxidase ; active site ; structure conservation ; hydrophobic cluster analysis ; sequence comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
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  • 251
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 257-264 
    ISSN: 0887-3585
    Keywords: protein families ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.
    Additional Material: 6 Ill.
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  • 252
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 291-295 
    ISSN: 0887-3585
    Keywords: full screen editor ; consensus calculation ; secondary structure ; automatic alignment ; alignment merging ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
    Additional Material: 3 Ill.
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  • 253
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 317-334 
    ISSN: 0887-3585
    Keywords: protein structure ; computer modeling ; structure prediction ; sequence homology ; structure homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
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  • 254
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 366-377 
    ISSN: 0887-3585
    Keywords: computer modeling ; protein ; structure ; α-carbons ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β-helix), where the coordinates are available only for the α-carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.
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  • 255
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 378-402 
    ISSN: 0887-3585
    Keywords: conformational distance ; conformational comparison ; generalized bond matrix representation ; structure space ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x-ray structures. The resulting data are analyzed (on the four-Cα length scale) to determine both the large-scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all-sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four-Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame-work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
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  • 256
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 173-178 
    ISSN: 0887-3585
    Keywords: mitochondria ; amino acid composition ; hydrophobicity ; composition space ; membrane protein ; transmembrane region ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.
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  • 257
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 213-225 
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy calculations ; δ-hemolysin ; melittin ; crystal packing ; raft ; bilayer ; membrane insertion ; channel formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular modeling and energy calculations have been used to study how δ-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ-hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ-hemolysin with six or eight monomers per channel.
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  • 258
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 280-286 
    ISSN: 0887-3585
    Keywords: circular dichroism ; secondary structure ; insulin ; insulin analogs ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2-zinc human insulin, zinc-free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2-zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β-strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10-15% increase in antiparallel β-structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2-zinc, zinc-free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two-state processes.
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  • 259
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 334-340 
    ISSN: 0887-3585
    Keywords: protein structure ; structural comparison ; α-β barrels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By exhaustive structural comparisons, we have found that about one-third of the α-helix-turn-β-strand polypeptides in α-β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α-helix and the β-strand is somewhat constrained, and second, the β-strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α-helix. The geometry of the turn does not seem to be a major determinant of the α-β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn-for instance, when the turns between the α-helix and the β-strands are very long. It also occurs much less frequently in flat-sheet α-β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α-β barrels are constructed.
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  • 260
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 341-351 
    ISSN: 0887-3585
    Keywords: conserved sequence ; diagnostic peptide ; superfamily classificaiton ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
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  • 261
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 352-364 
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure comparison ; molecular replacement ; precision ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 Å resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 Å resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.
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  • 262
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 1-15 
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
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  • 263
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 52-61 
    ISSN: 0887-3585
    Keywords: molecular dynamics ; protein simulations ; dihydrofolate reductase ; trimethoprim ; drug binding ; solvation ; binding free energies ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structural and thermodynamic interactions for the binding of trimethoprim and related congeners to the binary complex of diphydrofolate reductase (from chicken) and NADPH are explored using free energy simulation methods. Good agreement between structures from experimental X-ray refinement and molecular dynamics simulations is found for the complexes. Agreement with thermodyanmic measurements is found as well. Our thermodynamic calculations suggest that entropic contributions and desolvation thermodynamics can play a crucial role in overall bindings, and that extreme care must be taken in the use of simple model building to rationalize or predict protein-drug binding.
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  • 264
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 172-184 
    ISSN: 0887-3585
    Keywords: aspartic proteases ; retroviral proteases ; sequence homology ; related structures ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The model of human immuno-deficiency virus (HIV-1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV-1 protease. The overall difference between the model and crystal structure was 1.4 Å root mean square (rms) deviation for 86 superimposed Cα atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.11 Å runs deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 Å rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and thereof could be used to design inhibitors, The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non-viral aspartic proteases.
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  • 265
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    Keywords: phosphorylation ; tyrosine ; cis-peptide ; exocytosis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Seven proteins each contain 8 to 52 tandem repeats of a unique class of oligopeptide. The consensus peptide for each is rhodopsin Tyr Pro Pro Gln Glysynapto-physin Tyr Gly Pro Gln Glysynexin Tyr Pro Pro Pro Pro Glygliadin Tyr Pro Pro Pro Gln ProRNA polymerase II Tyr Ser Pro Thr Ser Pro Serhordein Phe Pro Gln Gln Pro Gln Gln Progluten Tyr Pro Thr Ser Pro Gln Gn Gly TyrAlthough there is obvious variations of sequence and of length, the penta-to nonapeptides share an initial Tyr(or Phe) and have high Pro contents and abundant Gly, Gln, and Ser. We have evaluated helical models that both recognize the uniqueness of these sequence repeats and accommodate variations on the basic theme.We have developed a group of related heical model for these proteins with about three oligopeptide repeats per turn of 10-20 Å. These models share several common features: Most of the φ dihedral angels are -54°, to accommodate Pro at all positions expect the first (Tyr). Except for the β-turns, most ψ dihedral angles are near +140° as found in polyproline. Each oligopeptide has at least one β-turn; several have two. Some contains a cis-Tyr, Pro peptide bond; a few have a cis-bond plus one β-turn. Tyr side chains vary from totally exposed to buried within the helices and could mode to accommodate either external hydrophobic interactions or phosphorylation. The several related structures seem to be readily interconverted without major change in the overall helical parameters, and therein may lie the key to their functions.
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  • 266
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 156-171 
    ISSN: 0887-3585
    Keywords: β-lactamase ; penicillinase ; penicillin-binding protein ; penicillin antibiotics ; X-ray diffraction ; protein structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two crystal (A and B) of the 29,500 Da Class A β-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 Å resolution, the starting model for which was a 3.5 Å structure obtained from A-form crystals. The β-lactamase has an α + β structure with 11 helices and 5 β-strands seen also in a peinicilin target DD-peptidase of Streptomyces R61.1 Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 Å resolution. The R factor is 0.208 for the 27,330 data greater than 3 (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conversed Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of β-lactam substrates is facilitated by interactions with Lys-234, Tyhr-235, and Ala-237 in a conserved β-strand peptide, which is antiparallel to the β-lactam's acylamido linkage; an exposed cavity near Asn-170 exits for acylamido Substituent. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth β-strand. A very similar binding site architecture is seen in the DD-peptidase.
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  • 267
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 198-204 
    ISSN: 0887-3585
    Keywords: protein stability ; protein design ; strain ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: An attempt has been made to identify residues in T4 phage lyoszyme that may have strained conformations and, by appropriate site-directed replacements, to reduce this strain and thus increase the thermostability of the protein. Valine 131, within α-helix 126-134, was identified as a potential candidate. Its side-chain rotational as a potential candidate. Its side-chain rotation angle, χ1, differs by approximately 18° from the low-energy trans configuration. In addition, it is largely solvent exposed, yet is held in a rigid conformation. The mutant protein with Val 131 replaced by alanine temperature 0.9°C higher than that of wildtype lyoszyme at pH 2.8. As a control, The mutant Val 131 → Thr was also constructed and its melting temperature was found to be marginally lower than wild type. Higher-resolution crystal structure determination of the mutant lysozymes show that their structure are virtually identical with that of wild-type lyoszyme, except for the Val → Ala or Val → Thr replacement. Analysis of the different structures suggests that the design of the Val→Ala substitution was, in principle, successful, although the apparent gain in stability caused by reduction in strain is modest and is somewhat offset by the loss of hydrophobic interactions and by entrophic effects. The results also help to provide a structural retionalization that alanine has a higher helix propensity than valine or theronine.
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  • 268
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 265-279 
    ISSN: 0887-3585
    Keywords: potential of means force ; motions of helices ; correlated fluctuations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
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  • 269
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 299-305 
    ISSN: 0887-3585
    Keywords: protein stability ; guanidine hydrochloride denaturation ; conformational changes ; polypeptide backbone ; alanine insertion ; glycine insertion ; circular dichroism spectra ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Single alanine and glycine insertions were introduced at 20 randomly selected positions in staphylococcal nuclease. The resulting changes in catalytic activity and in stability to guanidine hydrochloride denaturation indicate that the native state structure is frequently able to accommodate the extra residue without great difficulty, even insertions within secondary structural elements such as alpha helices and beta sheets. On average, an inserted residue reduces the free energy of denaturation (ΔGH2O) by an amount roughly comparable to an alanine or glycine substitution for one of the residues flanking the site of insertion. Several positions outside of the enzyme active site were found where insertions, but not substitutions, lead to structural changes that modify catalytic activity and the circular dichroism spectrum. Amino acid insertions represent a virtually unexplored class of genetic mutation that may prove complementary to amino acid substitutions for engineering proteins with altered functional and structural properties.
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  • 270
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 358-365 
    ISSN: 0887-3585
    Keywords: synthetic myoglobins ; X-ray crystallography ; protein engineering ; heme proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystal have been grown of myoglobin produced in Escherichia coli from a synthetic gene, and the structure has been solved to 1.9 Å resolution. The space group of the crystals is P6, which is different from previously solved myoglobin crystal forms. The synthetic myoglobin is essentially identical to myoglobin isolated from sperm whale tissue, except for the retention of the initiator methionine at the N-terminus and the substitution of asparagine for aspartic acid at position 122. Superposition of the coordinates of native and synthetic sperm whale myoglobins reveals only minor changes in the positions of main chain atoms and roeientation of some surface side chains. Crystals of variant of the “synthetic” myoglobin have also been grown for structural analysis of the role of key amino acid residues in ligand and specificity.
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  • 271
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    Proteins: Structure, Function, and Genetics 8 (1990), S. i 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 272
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 14-22 
    ISSN: 0887-3585
    Keywords: computation ; conformational energy ; interactions in proteins ; protein folding ; twisted β-sheets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The preferred structural pattern of antiparallel β-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of β-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel β-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted β-barrel is favored energetically, in agreement with anti-parallel β-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of β-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel β-barrels of globular proteins. The computations indicate that a structure with Val…Gly pairs can be accommodated in a β-barrel with no distortion.
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  • 273
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    Proteins: Structure, Function, and Genetics 8 (1990) 
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    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 274
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 133-155 
    ISSN: 0887-3585
    Keywords: evolution ; alignment ; globins ; phycocyanin ; helix interfaces ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Globins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3-10 C helix and the unusual “crossed-ridge” packing pattern at the B/E helix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phycocyanins.
    Additional Material: 12 Ill.
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  • 275
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51 
    ISSN: 0887-3585
    Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
    Additional Material: 3 Ill.
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  • 276
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 99-111 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 7 Ill.
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  • 277
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 205-214 
    ISSN: 0887-3585
    Keywords: protein secondary structures ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 8 Ill.
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  • 278
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
    Additional Material: 6 Ill.
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  • 279
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 30-43 
    ISSN: 0887-3585
    Keywords: molecular mechanics ; solvation energy ; trypsin ; energy minimization ; side chains ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A “knowledge-based” method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchangin the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
    Additional Material: 13 Ill.
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  • 280
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 386-397 
    ISSN: 0887-3585
    Keywords: LGIC superfamily ; proto-binding site ; cys-loop motif ; docking model ; anionic site ; specificity residue ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A generalized model is presented of agonist binding to ligand-gated ion channels (LGICs). Broad similarity in the structure of agonists suggests that the binding sites of LGICs may have evolved from a protobinding site. Aligned sequence data identified as a candidate for such a site a highly conserved 15 residue stretch of primary structure in the N-terminal extracellular region of all known LGIC subunits. We modeled this subregion, termed the cys-loop, as a rigid, amphiphilic β-hairpin and propose that it may form a major determinant of a conserved structural binding cleft.In the model of the binding complex (1) an invariant aspartate residue at position 11 of the cys-loop is the anionic site interacting with the positively charged amine group of agonists, (2) a local dipole within the π-electron system of agonists is favorably oriented in the electrostatic field of the invariant aspartate, (3) the ε ring-proton of a conserved aromatic residue at the turn of the cys-loop interacts orthogonally with the agonist α-electron density at its electronegative center, and (4) selective recognition is partly a result of the type of amino acid residue at position 6 of the cys-loop. Additionally, the formation of a hydrogen bond between the electronegative atom of the π-electron system of agonist and a complementary group in the receptor may be important in the high-affinity binding of agonists.
    Additional Material: 5 Ill.
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  • 281
    ISSN: 0887-3585
    Keywords: gonadotropin-releasing hormone ; molecular dynamics ; nuclear magnetic resonance ; antagonist design ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[Δ3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-βAla], led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.
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  • 282
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 195-202 
    ISSN: 0887-3585
    Keywords: simulated annealing ; computer-aided drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
    Additional Material: 2 Ill.
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  • 283
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 226-236 
    ISSN: 0887-3585
    Keywords: protein structure ; ionic pores ; neural membranes ; protein design ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Channel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage-sensitive sodium channel and the nicotinic cholinergic receptor. We report low-energy arrangements of α-helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion-conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3-5 amphipathic α-helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar-neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area ∼ 16 Å2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of α-helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area ∼ 46 Å2). Thus, bundles of amphipathic α-helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.
    Additional Material: 8 Ill.
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  • 284
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    Proteins: Structure, Function, and Genetics 8 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 285
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 377-385 
    ISSN: 0887-3585
    Keywords: structure deteremination ; two-dimensional NMR ; molecular mechanics ; molecular dynamics ; conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observation, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHNα coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance contraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics apporach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
    Additional Material: 5 Ill.
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  • 286
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 93-98 
    ISSN: 0887-3585
    Keywords: protein conformation ; CONGEN ; immunoglobulin ; hydrogen bond ; digoxin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The mouse hybridoma cell line 40-150 scretes antibodies with high affinity towards the cardiac glycosides digoxin and digitoxin. A spontaneous mutant, 40-150 A2.4, produces and antibody which carries a single residue mutation, Ser → Arg, in its heavy chain (H94) and has an altered specificity. A second order mutant 40-150 A2.4 P.10, produces two antibody molecules, one the same as 40-150 A2.4, the other lacking two residues at the N-terminus of its H chain, and having a specificity profile approaching that of 40-150 antibody. 1 The N-terminus and the position H94 are distant from the antigen-binding site of the antibody; thus, the structural basic of the specificity changes was not immediately clear. Approximate structures of the 40-150 antibody and its mutants were constructed in the computer, based on atomic coordinates of the homologous mouse antibody McPC 603. Using the program OCNGEN, the torsional space of the polypeptide backbone and side chains around position H94 was uniformly sampled, and the lowest energy conformations were analyzed in detail. The results indicate that when Arg-H94 is substituted for Ser. Agr-H94 can hydrogen bond to side chains of Asp-H101, Arg-L46, and Asp-L55. The results in a change in the surface of the combining site which may account for the affinity changes. Deletion of the two N-terminal residues increases solvent accessibility of Arg-H94. The solvation may cause a hydrogen bond between Arg-H94 and Asp-H101 to be lost, restoring the structure to one similar to that of 40-150.
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  • 287
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 296-297 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Tab.
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  • 288
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    Proteins: Structure, Function, and Genetics 7 (1990) 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
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  • 289
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 44-61 
    ISSN: 0887-3585
    Keywords: RBP ; RBP family ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R-factor of 18.1% with 2Å resolution data. The protein topology results in an anti-parallel β-barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.
    Additional Material: 15 Ill.
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  • 290
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 82-101 
    ISSN: 0887-3585
    Keywords: chymosin ; acid proteinase ; rennin ; X-ray structure ; structure comparison ; catalytic site ; crystal packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of recombinant bovine chymosin (EC 3.4.23.4; renin), which was cloned and expressed in Escherichia coli, has been determined using X-ray data extending to 2.3 Å resolution. The crystals of the enzyme used in this study belong to the space group I222 with unit cell dimensions a = 72.7 Å, b = 80.3 Å, and c = 114.8 Å. The structure was solved by the molecular replacement method and was refined by a restrained least-squares procedure. The crystallographic R factor is 0.165 and the deviation of bond distances from ideality is 0.020 Å. The resulting model includes all 323 amino acid residues, as well as 297 water molecules. The enzyme has an irregular shape with approximate maximum dimensions of 40 × 50 × 65 Å. The secondary structure consists primarily of parallel and antiparallel β-strands with a few short α-helices. The enzyme can be subdivided into N- and C- terminal domains which are separated by a deep cleft containing the active aspartate residues Asp-34 and Asp-216. The amino acid residues and waters at the active site form an extensive hydrogen-bonded network which maintains the pseudo 2-fold symmetry of the entire structure. A comparison of recombinant chymosin with other acid proteinases reveals the high degree of structural similarity with other members of this family of proteins as well as the subtle differences which make chymosin unique. In particular, Tyr-77 of the flap region of chymosin does not hydrogen bond to Trp-42 but protrudes out in the P1 pocket forming hydrophobic interactions with Phe-119 and Leu-32. This may have important implications concerning the mechanism of substrate binding and substrate specificity.
    Additional Material: 11 Ill.
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  • 291
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 164-172 
    ISSN: 0887-3585
    Keywords: protein secondary structure ; sodium channel ; CD spectra analysis program ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three scorpion toxins have been analyzed by circular dichroism in water and in 2,2,2-trifluoroethanol (TFE) solutions. These toxins were chosen because they are representative of three kinds of pharmacological activities: (1) toxin AaH IT2, an antiinsect toxin purified from the venom of Androctonus australis Hector, which is able to bind to insect nervous system preparation, (2) toxin Css II, from the venom of Centruroides suffusus suffusus, which is a β-type antimammal toxin capable of binding to mammal nervous system preparation, and (3) the toxin Ts VII from the venom of Tityus serrulatus, which is able to bind to both types of nervous systems. In order to minimize bias, CD data were analyzed by a predictive algorithm to assess secondary structure content. Among the three molecules, Ts VII presented the most unordered secondary structure in water, but it gained in ordered forms when solubilized in TFE. These results indicated that the Ts VII backbone is the most flexible, which might result in a more pronounced tendency for this toxin molecule to undergo conformational changes. This is consistent with the fact that it competes with both antiinsect and β-type antimammal toxins for the binding to the sodium channel.
    Additional Material: 6 Ill.
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  • 292
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 306-316 
    ISSN: 0887-3585
    Keywords: neutral mutations ; random mutagenesis ; protein structure ; protein folding ; protein families ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method of targeted random mutagenesis has been used in investigate the informational content of 25 residue positions in two α-helical regions of the N-terminal domain of λ repressor. Examination of the functionally allowed sequences indicates that there is a wide range in tolerance to amino acid substitution at these position. At position that are buried in the structure, there are severe limitations on the number and type of residues allowed. At most surface positions, many different residues and residue types are tolerated. However, at several surface positions there is a string preference for hydrophilic amino acids, and at one surface position proline is absolutely conserved. The results reveal the high level of degeneracy in the information that specifies a particular protein fold.
    Additional Material: 4 Ill.
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  • 293
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    Proteins: Structure, Function, and Genetics 7 (1990), S. 343-357 
    ISSN: 0887-3585
    Keywords: engineered disulfide groups ; X-ray structure ; hydrophobic cavities ; water structure, altered ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of four genetically engineered disulfide variants of subtilisin have been analyzed to determine the energetic and structural constraints involved in inserting disulfide bonds into proteins. Each of the engineered disulfides exhibited atypical sets of dihedral angles compared with known structures of natural disulfide bridges in proteins and affected its local structural environment to a different extent. The disulfides located in buried regions, Cys26-Cys232 and Cys29-Cys87 and Cys22-Cys87, which are located on the surface of the molecule. An analysis of the concerted changes in secondary structure units such as α-helices and β-sheets indicated systematic long-range effects. The observed changes in the mutants were largely distributed asymmetrically around the inserted disulfides, reflecting different degrees of inherent flexibility of neighboring secondary structure types. The disulfide substitution in each variant molecule created some invaginations or cavities, causing a reorganization of the surrounding water structure. These changes are described, as well as the changes in side chain positions of groups that border the cavities.
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  • 294
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 1-5 
    ISSN: 0887-3585
    Keywords: accessible area ; crystalline environment ; hydrophobic interaction ; linear correlation ; monomeric proteins ; dimeric proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The accessible surface areas of 58 monomeric and dimeric proteins, when measured in the crystalline environment, are found to be simply related to molecular weight. The loss of accessible surface when the proteins go from a free to their crystalline environment is well defined, implying that the hydrophobic interaction, which has been found to contribute to protein folding and stability in living systems, also contributes to protein crystal stability.
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  • 295
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 23-29 
    ISSN: 0887-3585
    Keywords: urea induced unfolding ; increased stability ; site-directed mutagenesis ; calbindin D9k ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: To investigate the contribution to protein stability of electrostatic interactions between charged surface residues, we have studied the effect of substituting three negatively charged solvent exposed residues with their side-chain amide analogs in bovine calbindin D9k - a small (Mr 8,500) globular protein of the calmodulin superfamily. The free energy of urea-induced unfolding for the wildtype and seven mutant proteins has been measured. The mutant proteins have increased stability towards unfolding relative to the wildtype. The experimental results correlate reasonably well with theoretically calculated relative free energies of unfolding and show that electrostatic interactions between charges on the surface of a protein can have significant effects on protein stability.
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  • 296
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 103-117 
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 3 Ill.
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  • 297
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 118-132 
    ISSN: 0887-3585
    Keywords: molecular modeling ; α1-purothionin ; x-ray structure determination ; molecular replacement ; comparison of crystal structure and predicted models ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: α1-Purothionin (α1-P), a wheatgerm protein and lytic toxin, has a secondary and tertiary structure similar to that of crambin as revealed by CD and NMR studies. α1-P crystallizes in the tetragonal space group I422 with unit cell dimensions: a = b = 53.59 and c = 69.79 Å. X-ray diffraction data have been measured to 2.5 Å Bragg spacing. The crystal structure has been determined by molecular replacement methods, using an energy-minimized α1-P model structure derived from crambin (Whitlow and Teeter: Journal of Biomolecular Structure and Dynamics 2:831-848, 1985, Journal of the American Chemical Society 108:7163-7172, 1986). The energy-minimized model gives a slightly cleaner rotation solution and better refinement against the x-ray data than do the crambin or unminimized α1-P structures. The final crystallographic residual with the data in the 10-2.5 Å resolution range is 0.216. The refined α1-P structure has a backbone rms difference of 0.74 Å from crambin and 0.55 Å from the energy-minimized α1-P model. A low resolution NMR model of α1-P calculated from metric matrix distance geometry and restrained molecular dynamics differs from crambin's backbone by 2.3 Å rms deviation (Clore et al.: EMBO Journal 5:2729-2735, 1986). Backbone dihedral angles for our predicted model differ from the refined α1-P structure in only one region (at a turn where there is a deletion relative to crambin). The NMR model had differences in four regions.
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  • 298
    ISSN: 0887-3585
    Keywords: lectins ; crystal structure ; lectin specificity ; mannose ; glucose ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of the methyl-α-D-mannopyranoside-LOL I complex has been solved by the molecular replacement method using the refined saccharide-free LOL I coordinates as starting model. The methyl-α-D-mannopyranoside-LOL I complex was refined by simulated annealing using the program X-PLOR. The final R-factor value is 0.182 [Fo 〉 1σ(Fo)]. The isostructural methyl-α-D-glucopyranoside-LOL I complex was refined by X-Ray coupled energy minimization using the methyl-α-D-mannopyranoside-LOL I structure as a starting model to an R factor of 0.179 (all data). In both crystal forms, each dimer binds two molecules of sugar in pockets found near the calcium ions. The two saccharide moieties, which are in the C1 chair conformation, establish the same hydrogen bond pattern with the lectin. However, the van der Walls contacts are different between the O2, C2, C6, and O6 atoms of the two molecules and the backbone atoms of residues 208-211. Mannose, due to its axial C2 conformation, encloses the backbone atoms of the protein in a clamplike way. Van der Waals energy calculations suggest that this better complementarity of the mannoside molecule with the lectin could explain its higher affinity for isolectin I.
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  • 299
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    Proteins: Structure, Function, and Genetics 8 (1990), S. 62-81 
    ISSN: 0887-3585
    Keywords: pepsin ; aspartic proteinases ; subdomains ; structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A revised three-dimensional crystal structure of ethanol-inhibited porcine pepsin refined to an R-factor of 0.171 at 2.3 Å resolution is presented and compared to the refined structures of the fungal aspartic proteinases: penicillopepsin, rhizopuspepsin, and endothiapepsin. Pepsin is composed of two nearly equal N and C domains related by an intra dyad. The overall polypeptide fold and active site structures are homologous for pepsin and the fungal enzymes. The weak inhibition of pepsin by ethanol can be explained by the presence of one or more ethanol molecules, in the vicinity of the active site carboxylates, which slightly alter the hydrogen-bonding network and which may compete with substrate binding in the active site. Structural superposition analysis showed that the N domains aligned better than the C-domains for pepsin and the fungal aspartic proteinases: 107-140 Cα pairs aligned to 0.72-0.85 Å rms for the N domains; 64-95 Cα pairs aligned to 0.78-1.03 Å rms for the C domains. The major structural difference between pepsin and the fungal enzymes concerns a newly described subdomain whose conformation varies markedly among these enzyme structures. The subdomain in pepsin comprises nearly 100 residues and is composed of two contiguous segments within the C domain (residues 192-212 and 223-299). The subdomain is connected, or “hinged,” to a mixed β-sheet that forms one of the structurally invariant, active site ψ-loops. Relative subdomain displacements as large as a 21.0° rotation and a 5.9 Å translation were observed among the different enzymes. There is some suggestion in pepsin that the subdomain may be flexible and perhaps plays a structural role in mediating substrate binding, determining the substrate specificity, or in the activation of the zymogen.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
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  • 300
    Electronic Resource
    Electronic Resource
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 156-163 
    ISSN: 0887-3585
    Keywords: transcription activation ; secondary structure ; machine learning ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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