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  • 1
    Electronic Resource
    Electronic Resource
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biochemistry 68 (1999), S. 779-819 
    ISSN: 0066-4154
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Chemistry and Pharmacology , Biology
    Notes: Abstract De novo protein design has recently emerged as an attractive approach for studying the structure and function of proteins. This approach critically tests our understanding of the principles of protein folding; only in de novo design must one truly confront the issue of how to specify a protein's fold and function. If we truly understand proteins, it should be possible to design receptors, enzymes, and ion channels from scratch. Further, as this understanding evolves and is further refined, it should be possible to design proteins and biomimetic polymers with properties unprecedented in nature.
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  • 2
    ISSN: 1432-1327
    Keywords: Key words Hemoprotein models ; Iron-porphyrin peptides ; Epr ; Resonance raman ; Styrene catalytic epoxidation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract  The coordination state of Fe(III)- and Fe(II)-mimochrome I, a covalent peptide-deuteroheme sandwich involving two nonapeptides bearing a histidine residue in a central position, was studied by UV-visible, EPR, and resonance Raman spectroscopy. The ferric and ferrous states of this new iron species mainly exist, at pH 7, in a low-spin hexacoordinate form with two axial histidine ligands coming from the peptide chains. A minor amount of high-spin form for the ferric state is also present at pH 7. However, it is mainly high-spin at pH 2 or in DMSO. Fe(II)-mimochrome I binds CO with an affinity comparable to that of myoglobin and hemoglobin. Fe(III)-mimochrome I reacts with alkylhydroxylamine and arylhydrazines, leading to the corresponding Fe(II)-nitrosoalkyl and Fe(III)-σ-aryl complexes, respectively. These reactions were greatly dependent on the solvent used and on the pH, and were much slower than the corresponding reactions performed by deuterohemin in the presence of excess imidazole. All these results indicate that the reactivity of iron-mimochrome I is controlled by the binding of the peptide chains to the iron. The reactivity shown by this complex at neutral pH is intermediate between that observed for iron porphyrins in the presence of excess imidazole and that of hemoproteins characterized by a strong bis-histidine axial coordination, such as cytochrome b 5. Fe(III)-mimochrome I is able to catalyze styrene epoxidation by using a [Fe(III)-mimochrome I]/[H2O2]/[stryrene] ratio of 1 : 10 : 2000 in phosphate buffer solution (pH 7.2) containing 2% CTAB both under strictly anaerobic conditions and in the presence of oxygen, at 0  °C.
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  • 3
    ISSN: 0947-6539
    Keywords: helical structures ; heme proteins ; iron ; peptides ; synthesis design ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In this paper we describe the design, synthesis, and spectroscopic characterization of a covalent helix-heme-helix sandwich named FeIII mimochrome I. It contains deuterohemin bound through both propionyl groups to two identical N-and C-terminal protected nonapeptides as α-helical scaffolds. Each peptide moiety bears a His residue in the central position, which acts as axial ligand to the metal ion. The newly developed synthetic strategy is based on a combination of solution and solid-phase methodologies. It represents a powerful method for obtaining a large variety of analogues containing two symmetric or unsymmetric peptide chains covalently bound to the deuteroporphyrin ring. UV/Visible spectroscopic characterization in buffered 2,2,2-trifluoroethanol/water solution proves low-spin bis(his-tidine) iron(III) coordination; circular dichroism (CD) measurements show an α-helical conformation for the peptide moieties. Thus, all the data are in agreement with the designed hypothetical model regarding both the iron(III) coordination and the peptide chain structural organization.
    Additional Material: 9 Ill.
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  • 4
    ISSN: 0947-6539
    Keywords: cobalt ; helical structures ; heme proteins ; NMR spectroscopy ; por-phyrinoids ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: FeIII mimochrome I is the prototype of a new class of hemoprotein models characterized by a covalent helix-heme-helix sandwich. It contains deuterohemin bound through two propionyl groups to two identical N- and C-terminal protected α-helical nonapeptides, each of which bears a His residue (a potential axial lig-and of the iron ion) in the central position. In order to understand better the three-dimensional structure of FeIII mimochrome I and its correlation with spectral properties, we have characterized the fully diamagnetic parent compound CoIII mimochrome I by UV/visible, CD, and NMR spectroscopy, coupled with conformational energy calculations. CoIII mimochrome I is a highly water-soluble compound present in solution as two isomers, which slowly interconvert only at very low pH values. These isomers were isolated and separately characterized. Their UV/visible spectral properties are very similar, while their CD spectral properties differ markedly in both the far UV and Soret regions. The isomers were identified by 1H NMR spectroscopy as diastereomers of the δ and δ type. This is the first example of an accurate three-dimensional structure determination in solution of a hemoprotein mimetic that allows a straightforward correlation between structure and spectral properties.
    Additional Material: 13 Ill.
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  • 5
    ISSN: 1075-2617
    Keywords: Cα,α-disubstituted amino acids ; crystal structure ; molecular dynamics ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The crystal structures of three fully protected tripeptides containing the Dφg residue (Cα,α-diphenylglycine) in the central position are reported, namely Z-Gly-Dφg-Gly-OMe (a), Z-Gly-Dφg-Aib-OMe (b) and Z-Aib-Dφg-Aib-OMe (c). The molecular conformations are quite unusual because the Dφg residue adopts a folded conformation in the 310-helical region when the following residue adopts a folded conformation of opposite handedness (peptidesbandc). In contrast, the Dφg residue adopts the more frequently observed fully extended conformation when the following residue adopts a semi-extended conformation (peptidea). These findings are in agreement with the theoretical calculations on Ac-Dφg-Aib-NHCH3 and Ac-Aib-Dφg-NHCH3 also reported in this work. © 1998 European Peptide Society and John Wiley & Sons, Ltd.
    Additional Material: 9 Ill.
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  • 6
    ISSN: 1434-193X
    Keywords: Receptor selectivity ; Agonist activity ; Distance geometry ; Conformation ; Chemistry ; General Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: To identify the peptide conformation that is preferentially recognized by the receptor, we have synthetized by solid-phase method a series of deltorphin I analogs with increasing selectivity for δ- and μ-opioid receptor. Structure-selectivity relationship of these peptides were evaluated on the basis of receptor-binding properties and conformational features, computed by two-dimensional NMR spectra and distance-geometry techniques. These compounds in solution are present with a large number of conformers with no defined secondary structural elements. The analysis of the average properties of these compounds indicate the presence of some distinct conformational preferences that can be related to the observed opioid receptor selectivities. Selectivity for the δ- and μ-opioid receptors can be ascribed to the spatial arrangement of the aromatic moieties. In addition, substitutions in position 2 and 4 are important for the correct arrangement and must be taken into account in the design of δ-opioid receptor-selective ligands.
    Additional Material: 6 Ill.
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  • 7
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Irregular protein secondary structures are believed to be important structural domains involved in molecular recognition processes between proteins, in interactions between peptide substrates and receptors, and in protein folding. In these respects tight turns are being studied in detail. They also represent template structures for the design of new molecules such as drugs, pesticides, or antigens. Isolated α-turns, not participating in α-helical structures, have received little attention due to the overwhelming presence of other types of tight turns in peptide and protein structures. The growing number of protein X-ray structures allowed us to undertake a systematic search into the Protein Data Bank of this uncharacterized protein secondary structure. A classification of isolated α-turns into different types, based on conformational similarity, is reported here. A preliminary analysis on the occurrence of some particular amino acids in certain positions of the turned structure is also presented. © 1996 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 8
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the present paper we describe the solution nmr structural analysis and restrained molecular dynamic simulation of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-β-Ala-β-Ala). The conformational analysis carried out in CD3CN and dimethylsulfoxide (DMSO) solutions by nmr spectroscopy was based on interproton distances derived from rotating frame nuclear Overhauser effect spectroscopy spectra and homonuclear coupling constants. A restrained molecular dynamic simulation in vacuo was also performed to build refined molecular models. The molecule is present in both solvent systems as two slowly interconverting conformers, characterized by a cis-trans isomerism around the β-Ala5-Pro1 peptide bond. In CD3CN solution, the conformer with a cis peptide bond is quite similar to that observed in the solid state, while the conformer containing all trans peptide bonds is characterized by an intramolecular hydrogen bond stabilizing a C10- and a C13-ring structure. In DMSO solution, the trans isomer is partly similar to that observed in CD3CN solution while the cis isomer is different from that observed in the solid state. The effect of the solvent in stabilizing different conformations was also investigated in DMSO-CD3CN solvent mixtures. © 1996 John Wiley & Sons, Inc.
    Additional Material: 9 Ill.
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  • 9
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the present paper we describe the synthesis, purification, and single crystal x-ray analysis of the cyclic pentapeptide cyclo-(Pro-Phe-Phe-β-Ala-β-Ala). This compound crystallizes in the orthorhombic space group P212121 from methanol and adopts in the solid state an unusual conformation characterized by a cis β-Ala5-Pro1 peptide bond and by an intramolecular hydrogen bond stabilizing a C11- and a C12-ring structure. The C11, structure contains the Phe3 and the β-Ala4 at the corner position of the turn; it is the first observation of a type II β-turn enlargement due to the insertion of an extra methylene group of the β-alanine residue. The rest of the molecule participates in a newly characterized C12-ring structure, which incorporates a β-Ala residue at position i of the turn. © 1996 John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
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  • 10
    ISSN: 0006-3525
    Keywords: molecular scaffolds ; β-turn ; tachykinin antagonist ; x-ray ; nmr ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We recently reported the rational design, synthesis, and structural characterization of the most potent and selective peptide-based neurokinin A antagonist thus far described: cyclo(Met1-Asp2-Trp3-Phe4-Dap5-Leu6)cyclo(2β-5β). Its bicyclic structure is characterized by a type I and a type II two β-turn around Trp3-Phe4 and Leu6-Met1, respectively. In order to understand whether the two different β-turned structures are determined by the bicyclic structure or by the amino acid type at the corner positions, we have synthesized the pseudosymmetrical analogue cyclo(Phe1-Asp2-Trp3-Phe4-Dap5-Trp6)cyclo(2β-5β). The structural characterization in the crystal state and in solution, here reported, gives an experimental evidence that the backbone of the bicyclic structure is a rigid scaffold that can be used to build both a type I and type II β-turn independently from the amino acid composition. © 1997 John Wiley & Sons, Inc. Biopoly 40: 505-518, 1996
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