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Perczel A, Farkas Ö, Csizmadia IG. Peptide Models. 18. Hydroxymethyl Side-Chain Induced Backbone Conformational Shifts of l-Serine Amide. All ab Initio Conformers of For-l-Ser-NH2. J Am Chem Soc 1996. [DOI: 10.1021/ja960464q] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- András Perczel
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Ödön Farkas
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Imre G. Csizmadia
- Contribution from the Institute of Organic Chemistry, Eötvös University, 112 Budapest P.O.B. 32, H-1117, Hungary, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, Department of Chemistry, Wayne State University, Detroit, Michigan 48202, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 1A1, Canada
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Abstract
In 1968 C. Venkatachalam (Biopolymers, Vol. 6, pp. 1425-1436) predicted the ideal forms of beta-turns (type I, type II, etc.) based entirely on theoretical calculations. Subsequently, over a thousand x-ray structures of different globular proteins have been analyzed, with results suggesting that the most important form among the hairpin conformers is the type I beta-turn. For the latter type of hairpin conformation, the original computations had predicted phi i+I = -60 degrees, psi i+1 = -30 degrees, phi i+2 = -90 degrees, and psi i +2 = 0 degrees as backbone torsion angle values, and these have been used from that time as reference values for the identification of the type I beta-turn. However, it has never been clarified whether these "ideal" backbone torsion angle values exist in real structures, or whether these torsion angles are only "theoretical values." Using the most recent release of the Protein Data Bank (1994), a survey has been made to assign amino acid pairs that approach the ideal form of the type I beta-turn. The analysis resulted in four sequences where the deviation from ideal values for any main-chain torsion angles was less than 2 degrees. In order to determine whether such a backbone fold is possible only in proteins owing to fortuitous cooperation of different folding effects, or whether it occurs even in short peptides, various attempts have been made to design the optimal amino acid sequence. Such a peptide model compound adopting precisely the predicted torsion angle values [phi i+1 = -60 degrees, psi i +1 = -30 degrees, phi i +2 = -90 degrees, and psi i+2 = 0 degrees] could provide valuable information. The solid state conformation of cyclo[(delta)Ava-Gly-Pro-Thr(OtBu)-Gly] reported herein, incorporating the -Pro-Thr- subunit, yields values suggesting that the "ideal" type I beta-turn is even possible for a peptide where there are no major environmental effects present.
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Affiliation(s)
- A Perczel
- Institute of Organic Chemistry, Eötvös University, Budapest, Hungary
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Abstract
The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.
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Affiliation(s)
- M Marraud
- LCPM, CNRS-URA 494, ENSIC-INPL, Nancy, France
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Benedetti E, Pedone EM, Kawahata NH, Goodman M. Conformational studies of retro-inverso peptides: the crystal and molecular structure of the hydantoin from H-Ala-g-Ala-mGly-OBzl. Biopolymers 1995; 36:659-67. [PMID: 7578956 DOI: 10.1002/bip.360360511] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of the hydantoin 1-[(S)-1'-aminoethylmalonyl benzyl ester]-(S)-4-methylimidazolidin-2,5-dione (1) derived from the peptide H-Ala-gAla-mGly-OBzl, having the retro-inverso modification of the Ala-Gly bond, has been determined by x-ray diffraction analysis. The crystals are orthorhombic, space group P2(1)2(1)2(1) with a = 6.539, b = 14.721, c = 17.101 A, z = 4. The structure was solved by direct methods and refined with anisotropic thermal factors to a final R value of 0.067 for the 947 observed reflections. Reversal of the Ala-Gly amide bond perturbs the folding tendency of the backbone shown by the parent peptide t-BuCO-Ala-Gly-NHiPr. The gem-diamino residue, gAla, and the malonyl moieties are found in the helical and the extended conformations, respectively. Intramolecular hydrogen bonding is not observed. The molecules in the crystal are held together by the formation of two intermolecular hydrogen bonds of the N-H ... O=C type with N ... O distances of 2.86 and 3.17 A, respectively.
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Affiliation(s)
- E Benedetti
- CNR Department of Chemistry, University of Naples, Federico II, Italy
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Schäfer L, Bin Drees IS, Frey RF, Van Alsenoy C, Ewbank JD. Molecular orbital constrained gas electron diffraction study of N-acetyl N′-methyl alanine amide. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/0166-1280(94)04049-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Perczel A, Lengyel I, Mantsch HH, Fasman GD. Analysis of hydrogen bonds in peptides, based on the hydration affinity of amides. J Mol Struct 1993. [DOI: 10.1016/0022-2860(93)80166-s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Marraud M, Dupont V, Grand V, Zerkout S, Lecoq A, Boussard G, Vidal J, Collet A, Aubry A. Modifications of the amide bond and conformational constraints in pseudopeptide analogues. Biopolymers 1993. [DOI: 10.1002/bip.360330715] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Gomez EJ, Vitoux B, Marraud M, Sakarellos C, el Masdouri L, Aubry A. Conformational perturbations in retro-analogs of the tBuCO-Ala-Gly-NHiPr dipeptide. Crystal structure of the retro-dipeptide with a reversed Ala-Gly amide bond. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1989; 34:480-6. [PMID: 2635694 DOI: 10.1111/j.1399-3011.1989.tb01397.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The three retro-analogs of the tBuCO-Ala-Gly-NHiPr dipeptide, in which each amide bond had been successively reversed, were studied in solution by 1H-n.m.r. and i.r. spectroscopy with reference to the conformational properties of their parent dipeptide. Reversal of the Ala-Gly amide bond proved to perturb the folding tendency of the backbone less than the inversion of either of the terminal amide bonds. The crystal structure of the retro-peptide containing a reversed Ala-Gly amide bond was also solved by X-ray diffraction and constitutes the first available data for this retro-peptide series. In contrast to the beta II-folded structure of the parent dipeptide, the retro-peptide molecule adopts an open conformation in the crystal.
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Affiliation(s)
- E J Gomez
- UA-CNRS-494, ENSIC-INPL, Nancy, France
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Aubry A, Marraud M. Pseudopeptides and beta folding: x-ray structures compared with structures in solution. Biopolymers 1989; 28:109-22. [PMID: 2720098 DOI: 10.1002/bip.360280113] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO-X-Y-NHR' model dipeptides in the depsi, N-methylated, reduced, retro, alpha, beta-dehydro, beta-amino acid, and hydrazino series, in the solid state by x-ray diffraction, and in solution by ir and 1H-nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences.
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