1
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Heath SL, Horne WS, Lengyel GA. Effects of chirality and side chain length in C α,α-dialkylated residues on β-hairpin peptide folded structure and stability. Org Biomol Chem 2023; 21:6320-6324. [PMID: 37503895 PMCID: PMC10445279 DOI: 10.1039/d3ob00963g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Strategic incorporation of achiral Cα,α-dialkylated amino acids with bulky substituents into peptides can be used to promote extended strand conformations and inhibit protein-protein interactions associated with amyloid formation. In this work, we evaluate the thermodynamic impact of chiral Cα,α monomers on folding preferences in such systems through introduction of a series of Cα-methylated and Cα-ethylated residues into a β-hairpin host sequence. Depending on stereochemical configuration of the artificial monomer and potential for additional hydrophobic packing, a Cα-ethyl-Cα-propyl glycine residue can provide similar or enhanced folded stability relative to an achiral Cα,α-diethyl analogue.
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Affiliation(s)
- Shelby L Heath
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - George A Lengyel
- Department of Chemistry, Slippery Rock University, Slippery Rock, PA 16057, USA.
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2
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The amphibian antimicrobial peptide uperin 3.5 is a cross-α/cross-β chameleon functional amyloid. Proc Natl Acad Sci U S A 2021; 118:2014442118. [PMID: 33431675 DOI: 10.1073/pnas.2014442118] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial activity is being increasingly linked to amyloid fibril formation, suggesting physiological roles for some human amyloids, which have historically been viewed as strictly pathological agents. This work reports on formation of functional cross-α amyloid fibrils of the amphibian antimicrobial peptide uperin 3.5 at atomic resolution, an architecture initially discovered in the bacterial PSMα3 cytotoxin. The fibrils of uperin 3.5 and PSMα3 comprised antiparallel and parallel helical sheets, respectively, recapitulating properties of β-sheets. Uperin 3.5 demonstrated chameleon properties of a secondary structure switch, forming mostly cross-β fibrils in the absence of lipids. Uperin 3.5 helical fibril formation was largely induced by, and formed on, bacterial cells or membrane mimetics, and led to membrane damage and cell death. These findings suggest a regulation mechanism, which includes storage of inactive peptides as well as environmentally induced activation of uperin 3.5, via chameleon cross-α/β amyloid fibrils.
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3
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Marafon G, Menegazzo I, De Zotti M, Crisma M, Toniolo C, Moretto A. Tuning morphological architectures generated through living supramolecular assembly of a helical foldamer end-capped with two complementary nucleobases. SOFT MATTER 2017; 13:4231-4240. [PMID: 28509927 DOI: 10.1039/c7sm00764g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Two appropriately functionalized nucleobases, thymine and adenine, have been covalently linked at the N- and C-termini, respectively, of two α-aminoisobutyric acid-rich helical peptide foldamers, aiming at driving self-assembly through complementary recognition. A crystal-state analysis (by X-ray diffraction) on the shorter, achiral foldamer 1 unambiguously shows that adeninethymine base pairing, through Watson-Crick intermolecular H-bonding, does take place between either end of each peptide molecule. In the crystals, π-stacking between base pairs is also observed. Evidence for time-dependent foldameroldamer associations for the longer, chiral foldamer 2 in solution is provided by circular dichroism measurements. The self-assembly of foldamer 2, through living supramolecular polymerization, eventually leads to the formation of twisted fibers. Such a supramolecular organization can be affected by addition of either pristine adenine or thymine, that acts as a "terminator" by selectively matching a pairing nucleobase at one end of the foldamer. The co-assembly of foldamer 2 with a porphyrin-derivatized thymine, under appropriate experimental conditions, leads to the formation of vesicles which, in turn, can be converted to the fiber morphology by changing the environmental polarity. Conversely, dendrimeric, star polymer-like microstructures are generated when the supramolecular assembly of foldamer 2 is seeded by adenine-capped gold nanoparticles.
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Affiliation(s)
- Giulia Marafon
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.
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4
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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5
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Longo E, Moretto A, Formaggio F, Toniolo C. The critical main-chain length for helix formation in water: determined in a peptide series with alternating Aib and Ala residues exclusively and detected with ECD spectroscopy. Chirality 2012; 23:756-60. [PMID: 22135805 DOI: 10.1002/chir.20986] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Critical main-chain length for peptide helix formation in the crystal (solid) state and in organic solvents has been already reported. In this short communication, we describe our results aiming at assessing the aforementioned parameter in water solution. To this goal, we synthesized step-by-step by solution procedures a complete series of N-terminally acetylated, C-terminally methoxylated oligopeptides, characterized only by alternating Aib and Ala residues, from the dimer to the nonamer level. All these compounds were investigated by electronic circular dichroism in the far-UV region in water solution as a function of chemical structure, namely presence/absence of an ester moiety or a negative charge at the C-terminus, and temperature. We find that the critical main-chain lengths for 3(10)- and α-helices, although still formed to a limited extent, in aqueous solution are six and eight residues, respectively.
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Affiliation(s)
- Edoardo Longo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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6
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De Zotti M, Biondi B, Crisma M, Hjørringgaard CU, Berg A, Brückner H, Toniolo C. Isovaline in naturally occurring peptides: A nondestructive methodology for configurational assignment. Biopolymers 2011; 98:36-49. [DOI: 10.1002/bip.21679] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2011] [Revised: 05/03/2011] [Accepted: 05/10/2011] [Indexed: 11/08/2022]
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7
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Yang D, Chang XW, Zhang DW, Jiang ZF, Song KS, Zhang YH, Zhu NY, Weng LH, Chen MQ. Chiral alpha-aminoxy acid/achiral cyclopropane alpha-aminoxy acid unit as a building block for constructing the alpha N-O helix. J Org Chem 2010; 75:4796-805. [PMID: 20568786 DOI: 10.1021/jo100810m] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The monomer 1 derived from achiral 1-(aminoxy)cyclopropanecarboxylic acid (OAcc) and oligopeptides 2-9 consisting of a chiral alpha-aminoxy acid and an achiral alpha-aminoxy acid such as OAcc were synthesized and their structures characterized. The eight-membered-ring intramolecular hydrogen bond, namely the alpha N-O turn, was formed between adjacent residues independent of their chirality. However, the helix formation was sequence-dependent. Dipeptide 2 bearing chiral alpha-aminoxy acid (d-OAA) at the N-terminus and achiral OAcc at the C-terminus preferentially adopted a right-handed 1.8(8) helical structure, but dipeptide 3 (OAcc-d-OAA) did not. Theoretical calculation results, in good agreement with experimental ones, revealed that the biased handedness of alpha N-O turn found in OAcc residue depends on its preceding chiral residue. It was then found that the helical conformation was destroyed in the case of oligopeptides 6 and 7 [OAA-(OAcc)(n), n = 2, 3]. The crystal structure of tripeptide 8 ((i)PrCO-d-OVal-OAcc-d-OVal-NH(i)Bu) further disclosed the helical structure formed by three consecutive homochiral alpha N-O turns. This study has uncovered achiral aminoxy acid residues such as the OAcc unit as a useful building block to be incorporated into chiral aminoxy peptides to mimic chiral helix structure.
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Affiliation(s)
- Dan Yang
- Department of Chemistry, Fudan University, Shanghai 200433, China.
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8
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Castiglioni E, Biscarini P, Abbate S. Experimental aspects of solid state circular dichroism. Chirality 2010; 21 Suppl 1:E28-36. [PMID: 19722271 DOI: 10.1002/chir.20770] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The interest of circular dichroism in the solid state is stimulated by several needs, such as the desire to get solvent free spectra, the insolubility of the sample or the intrinsic process in which the sample itself is prepared or manipulated. We approach the argument on the basis of the sampling technique, since each different case calls for specific care in getting proper results.
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9
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Pescitelli G, Kurtán T, Flörke U, Krohn K. Absolute structural elucidation of natural products--a focus on quantum-mechanical calculations of solid-state CD spectra. Chirality 2010; 21 Suppl 1:E181-201. [PMID: 19902530 DOI: 10.1002/chir.20795] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this review article we examine state-of-the-art techniques for the structural elucidation of organic compounds isolated from natural sources. In particular, we focus on the determination of absolute configuration (AC), perhaps the most challenging but inevitable step in the whole process, especially when newly isolated compounds are screened for biological activity. Among the many methods employed for AC assignment that we review, special attention is paid to electronic circular dichroism (CD) and to the modern tools available for quantum-mechanics CD predictions, including TDDFT. In this context, we stress that conformational flexibility often poses a limit to practical CD calculations of solution CD spectra. Many crystalline natural products suitable for X-ray analysis do not contain heavy atoms for a confidential AC assignment by resonant scattering. However, their CD spectra can be recorded in the solid state, for example with the KCl pellet technique, and analyzed possibly by nonempirical means to provide stereochemical information. In particular, solid-state CD spectra can be compared with those calculated with TDDFT or other high-level methods, using the X-ray geometry as input. The solid-state CD/TDDFT approach, described in detail, represents a quick and reliable tool for AC assignment of natural products.
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Affiliation(s)
- Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Pisa, Italy.
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10
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Flores-Ortega A, Jiménez AI, Cativiela C, Nussinov R, Alemán C, Casanovas J. Conformational preferences of alpha-substituted proline analogues. J Org Chem 2008; 73:3418-27. [PMID: 18351745 PMCID: PMC2679371 DOI: 10.1021/jo702710x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the alpha hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N'-methylamide derivatives of L-proline, L-alpha-methylproline, and L-alpha-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated by using a Self-Consistent Reaction Field model. As expected, tetrasubstitution at the alpha carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at C (alpha) may play a significant role in modulating the conformational preferences of proline.
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Affiliation(s)
- Alejandra Flores-Ortega
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal n° 647, 08028 Barcelona, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n° 69, 25001 Lleida, Spain
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11
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Andreetto E, Peggion C, Crisma M, Toniolo C. Handedness control of peptide helices by amino acid side-chain chirality: Ile/aIle peptides. Biopolymers 2006; 84:490-501. [PMID: 16680718 DOI: 10.1002/bip.20534] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A set of four hexapeptide sequences, each characterized by four strongly helicogenic Aib residues and all combinations of two isomeric Ile/aIle residues at positions 2 and 5, was synthesized by solution methods and fully characterized. A detailed solution (by FT-IR absorption, NMR, and CD techniques) and solid/crystalline state (by X-ray diffraction) conformational investigation allowed us to validate our assumption that all four peptides are folded in well-developed 3(10)-helical structures. However, the most relevant conformational conclusion extracted from the present 3D-analysis is that the handedness of the 3(10)-helical structures formed does not seem to be sensitive to the configurational change at the beta-carbon atom of the constituent Ile versus the diastereomeric aIle residues (in other words, the dominant control on this important structural parameter appears to be exerted by the chirality of the amino acid alpha-carbon atom). These results complement published findings on the diverging relative stabilities of the intermolecularly H-bonded beta-sheet structures generated by Ile versus aIle homo-oligopeptides.
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Affiliation(s)
- Erika Andreetto
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padua, 35131 Padua, Italy
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12
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Kawai M, Nagai U, Inai Y, Yamamura H, Akasaka R, Takagi S, Miwa Y, Taga T. CD spectral study of Dnp derivatives of amino acids and peptides for their configurational and conformational analysis. Biopolymers 2005; 80:186-98. [PMID: 15657880 DOI: 10.1002/bip.20198] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rules relating the stereochemistry of N-Dnp (Dnp: 2,4-dinitrophenyl) derivatives of alpha-amino acids and peptides and the sign of the Cotton effects at the longest wavelength band (ca. 400 nm) are surveyed. Some new data and insights concerning the CD spectra of Dnp-alpha-amino acids are included: i.e., the spectra of Dnp derivatives as the composite of the corresponding o-nitrophenyl and p-nitrophenyl derivatives; the crystal structure of Dnp-I-phenylalanine and its solid-state CD spectra; the CD spectra of Dnp-alpha-amino acids containing sulfur atom on their side chains; and the theoretical approach to the CD spectra using molecular orbital method-based calculation. Conformational analyses of cyclic and linear peptides by the CD spectra of their Dnp derivatives are also discussed.
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Affiliation(s)
- Masao Kawai
- Graduate School of Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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13
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Formaggio F, Peggion C, Crisma M, Kaptein B, Broxterman QB, Mazaleyrat JP, Wakselman M, Toniolo C. Recent contributions of electronic circular dichroism to the investigation of oligopeptide conformations. Chirality 2004; 16:388-97. [PMID: 15190584 DOI: 10.1002/chir.20051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Recent applications in our laboratories of electronic circular dichroism to the study of peptide secondary structures and their changes under external stimuli are briefly reviewed. More specifically, this article deals with: 1). characterization of a novel peptide conformation; 2). origin of amino acid homo-chirality on Earth; 3). bend and helical peptides as spacers; and 4). transfer and propagation of chirality in peptides.
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Affiliation(s)
- Fernando Formaggio
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, Padova, Italy.
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14
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Oku H, Ohyama T, Hiroki A, Yamada K, Fukuyama K, Kawaguchi H, Katakai R. Addition of a peptide fragment on an ?-helical depsipeptide induces ?/310-conjugated helix: Synthesis, crystal structure, and CD spectra of Boc-Leu-Leu-Ala-(Leu-Leu-Lac)3-Leu-Leu-OEt. Biopolymers 2004; 75:242-54. [PMID: 15316916 DOI: 10.1002/bip.20117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The depsipeptide Boc(1)-Leu(2)-Leu(3)-Ala(4)-Leu(5)-Leu(6)-Lac(7)-Leu(8)-Leu(9)-Lac(10)-Leu(11)-Leu(12)-Lac(13)-Leu(14)-Leu(15)-OEt(16) (1) (Boc = tert-butyloxycarbonyl, Lac = L-lactic acid residue) has been synthesized from the peptide Boc-Leu-Leu-Ala-OEt (2) and a depsipeptide, Boc-(Leu-Leu-Lac)(3)-Leu-Leu-OEt (3). Single crystals of 1 were successfully obtained and the structure has been solved by direct methods (such as Sir2002 and Shake-and-Bake). Interestingly, 1 adopts an alpha/3(10)-conjugated helix containing a kink at the junction of peptide and depsipeptide segments, Leu3-Lac7. This is significantly different from the conformation of 3, which has a straight alpha-helical structure with standard phi and psi angles. Microcrystalline CD spectra were also studied to compare structural properties of 1 and 3. The differences between alpha/3(10)- and alpha-helices appear in these CD spectra.
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Affiliation(s)
- Hiroyuki Oku
- Department of Chemistry, Gunma University, Kiryu, Gunma 376-8515, Japan
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15
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Toniolo C, Crisma M, Formaggio F, Peggion C. Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution). Biopolymers 2002; 60:396-419. [PMID: 12209474 DOI: 10.1002/1097-0282(2001)60:6<396::aid-bip10184>3.0.co;2-7] [Citation(s) in RCA: 580] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.
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Affiliation(s)
- C Toniolo
- Department of Organic Chemistry, University of Padova, Institute of Biomolecular Chemistry, CNR, 35131 Padova, Italy.
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16
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Crisma M, Bisson W, Formaggio F, Broxterman QB, Toniolo C. Factors governing 3(10)-helix vs alpha-helix formation in peptides: percentage of C(alpha)-tetrasubstituted alpha-amino acid residues and sequence dependence. Biopolymers 2002; 64:236-45. [PMID: 12115131 DOI: 10.1002/bip.10178] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As an additional step toward the dissection of the factors responsible for the onset of 3(10)-helix vs alpha-helix in peptides, in this paper we describe the results of a three-dimensional (3D) structural analysis by x-ray diffraction of the N(alpha)-acylated heptapeptide alkylamide mBrBz-L-Iva-L-(alphaMe)Val-L-Abu-L-(alphaMe)Val-L-(alphaMe)Phe-L-(alphaMe)Val-L-Iva-NHMe characterized by a single (L-Abu3) C(alpha)-trisubstituted and six C(alpha)-tetrasubstituted alpha-amino acids. We find that in the crystal state this peptide is folded in a mixed helical structure with short elements of 3(10)-helix at either terminus and a central region of alpha-helix. This finding, taken together with the published NMR and x-ray diffraction data on the all C(alpha)-methylated parent sequence and its L-Val2 analog (also the latter heptapeptide has a single C(alpha)-trisubstituted alpha-amino acid) strongly supports the view that one C(alpha)-trisubstituted alpha-amino acid inserted near the N-terminus of an N(alpha)-acylated heptapeptide alkylamide sequence may be enough to switch a regular 3(10)-helix into an essentially alpha-helical conformation. As a corollary of this work, the x-ray diffraction structure of the N(alpha)-protected, C-terminal tetrapeptide alkylamide Z-L-(alphaMe)Val-L-(alphaMe)Phe-L-(alphaMe)Val-L-Iva-NHMe, also reported here, is clearly indicative of the preference of this fully C(alpha)-methylated, short peptide for the 3(10)-helix. As the same terminally blocked sequence is mixed 3(10)/alpha-helical in the L-Abu3 heptapeptide amide but regular 3(10)-helical in the tetrapeptide amide and in the parent heptapeptide amide, these results point to an evident plasticity even of a fully C(alpha)-methylated short peptide.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Organic Chemistry, University of Padova, 35131 Padova, Italy
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Sagan S, Lequin O, Frank F, Convert O, Ayoub M, Lavielle S, Chassaing G. Calpha methylation in molecular recognition. Application to substance P and the two neurokinin-1 receptor binding sites. ACTA ACUST UNITED AC 2001; 268:2997-3005. [PMID: 11358518 DOI: 10.1046/j.1432-1327.2001.02192.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two binding sites NK-1M (major, more abundant) and NK-1m (minor) are associated with the neurokinin-1 receptor. For the first time with a bioactive peptide, the Calpha methylation constraint, shown to be a helix stabiliser in model peptides, was systematically used to probe the molecular requirements of NK-1M and NK-1m binding sites and the previously postulated bioactive helical conformation of substance P (SP). Seven Calpha methylated analogues of the undecapeptide SP (from position 5-11) have been assayed for their affinities and their potencies to stimulate second messenger production. The consequences of Calpha methylation on the structure of SP have been analysed by circular dichroism and nuclear magnetic resonance combined with restrained molecular dynamics. The decreased potencies of six out of these seven Calpha methylated SP analogues do not allow the identification of any clear-cut differences in the structural requirements between the two binding sites. Strikingly, the most active analogue, [alphaMeMet5]SP, leads to variable subnanomolar affinity and potency when interacting with the NK-1m binding site. The conformational analyses show that the structural consequences associated with Calpha methylation of SP are sequence dependent. Moreover, a single Calpha methylation is not sufficient by itself to drastically stabilize a helical structure even pre-existing in solution, except when Gly9 is substituted by an alpha-aminoisobutyric acid. Furthermore, Calpha methylation of residues 5 and 6 of SP in the middle of the postulated helix does not stabilize, but decreases (to different extents) the stability of the helical structure previously observed in the 4-8 domain of other potent SP analogues.
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Affiliation(s)
- S Sagan
- Laboratoire de Chimie Organique Biologique and Laboratoire de Chimie Structurale Organique et Biologique, Université Pierre et Marie Curie, Paris, France.
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18
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Minguet M, Amabilino DB, Wurst K, Veciana J. Chirality of α-Nitronyl Nitroxide Radicals in the Solid State. J SOLID STATE CHEM 2001. [DOI: 10.1006/jssc.2001.9175] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Hu HY, Li Q, Cheng HC, Du HN. beta-sheet structure formation of proteins in solid state as revealed by circular dichroism spectroscopy. Biopolymers 2001; 62:15-21. [PMID: 11135188 DOI: 10.1002/1097-0282(2001)62:1<15::aid-bip30>3.0.co;2-j] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cross beta-sheet structure formation and abnormal aggregation of proteins are thought to be pathological characteristics of some neurodegenerative disorders. To investigate the novel structural transformation and aggregation, the solid-state secondary structures of some proteins and peptides associated in thin films were determined by circular dichroism spectroscopy. Insulin, lysozyme, DsbA protein, luciferase, and ovalbumin peptide fall into one group; they show no or slight structural rearrangement from solution to the solid state. Another group, including bovine serum albumin, ovalbumin, alpha-synuclein, and plasminogen activator inhibitor-1 (PAIRC) peptide, undergo structural transformation with an increase of beta-sheet structure in the solid state. The beta-sheet formation of PAIRC peptide may reflect the structural transformation of the serpin reactive center that is relevant to the inhibitor activity. The beta-sheet structure of alpha-synuclein in the solid state may correspond to the amyloid-like aggregates, which are implicated in the pathogenesis of some neurodegenerative diseases.
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Affiliation(s)
- H Y Hu
- Shanghai Institute of Biochemistry, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.
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Inai Y, Oshikawa T, Yamashita M, Hirabayashi T, Kurokawa Y. Conformational Preference ofβ-Aryldehydroalanine. Solid-State Conformation of Tripeptide Possessing a (Z)-β-(1-Pyrenyl)dehydroalanine Residue in the Second Position. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2001. [DOI: 10.1246/bcsj.74.959] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Inai Y, Sakakura Y, Hirabayashi T. FT-IR and CD Measurement of Z-Dehydrophenylalanine-Containing Peptides in the Solid State and in Solution. Polym J 1998. [DOI: 10.1295/polymj.30.828] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Yoder G, Polese A, Silva RAGD, Formaggio F, Crisma M, Broxterman QB, Kamphuis J, Toniolo C, Keiderling TA. Conformational Characterization of Terminally Blocked l-(αMe)Val Homopeptides Using Vibrational and Electronic Circular Dichroism. 310-Helical Stabilization by Peptide−Peptide Interaction. J Am Chem Soc 1997. [DOI: 10.1021/ja971392l] [Citation(s) in RCA: 127] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gorm Yoder
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Alessandra Polese
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - R. A. G. D. Silva
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Fernando Formaggio
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Marco Crisma
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Quirinus B. Broxterman
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Johan Kamphuis
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Claudio Toniolo
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
| | - Timothy A. Keiderling
- Contribution from the Department of Chemistry, University of Illinois at Chicago, M/C 111, Chicago, Illinois 60607-7061, Department of Organic Chemistry, Biopolymer Research Center, CNR, University of Padova, 35131 Padova, Italy, Organic Chemistry and Biotechnology Section, DSM Research, P.O. Box 18, 6160 MD Geleen, The Netherlands, and DSM Fine Chemicals, 6401 JH Heerlen, The Netherlands
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Jaun B, Tanaka M, Seiler P, Kühnle FNM, Braun C, Seebach D. Studies on the Conformation of Boc-Protected (S)-(+)-Isovaline Homopeptide Methyl Esters in the Solid State and in Solution. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970811] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Polese A, Formaggio F, Crisma M, Valle G, Toniolo C, Bonora GM, Broxterman QB, Kamphuis J. Peptide Helices as Rigid Molecular Rulers: A Conformational Study of Isotactic Homopeptides from α-Methyl-α-isopropylglycine, [L-(αMe)Val]n. Chemistry 1996. [DOI: 10.1002/chem.19960020911] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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