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Castro TG, Melle-Franco M, Sousa CEA, Cavaco-Paulo A, Marcos JC. Non-Canonical Amino Acids as Building Blocks for Peptidomimetics: Structure, Function, and Applications. Biomolecules 2023; 13:981. [PMID: 37371561 DOI: 10.3390/biom13060981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
This review provides a fresh overview of non-canonical amino acids and their applications in the design of peptidomimetics. Non-canonical amino acids appear widely distributed in nature and are known to enhance the stability of specific secondary structures and/or biological function. Contrary to the ubiquitous DNA-encoded amino acids, the structure and function of these residues are not fully understood. Here, results from experimental and molecular modelling approaches are gathered to classify several classes of non-canonical amino acids according to their ability to induce specific secondary structures yielding different biological functions and improved stability. Regarding side-chain modifications, symmetrical and asymmetrical α,α-dialkyl glycines, Cα to Cα cyclized amino acids, proline analogues, β-substituted amino acids, and α,β-dehydro amino acids are some of the non-canonical representatives addressed. Backbone modifications were also examined, especially those that result in retro-inverso peptidomimetics and depsipeptides. All this knowledge has an important application in the field of peptidomimetics, which is in continuous progress and promises to deliver new biologically active molecules and new materials in the near future.
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Affiliation(s)
- Tarsila G Castro
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - Manuel Melle-Franco
- CICECO-Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Cristina E A Sousa
- BioMark Sensor Research-School of Engineering of the Polytechnic Institute of Porto, 4249-015 Porto, Portugal
| | - Artur Cavaco-Paulo
- CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- LABBELS-Associate Laboratory, Braga/Guimarães, Portugal
| | - João C Marcos
- Centre of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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2
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Jewgiński MP, Makowski M, Pawełczak M, Goldeman W, Trojanowska-Laskowska A, Kafarski P, Latajka R. Synthesis of Hybrid Tripeptide Peptidomimetics Containing Dehydroamino Acid and Aminophosphonic Acid in the Chain and Evaluation of Their Activity toward Cathepsin C. Chem Biodivers 2022; 19:e202101019. [PMID: 35343636 DOI: 10.1002/cbdv.202101019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/25/2022] [Indexed: 11/09/2022]
Abstract
Synthesis of a new group of hybrid phosphonodehydropeptides composed of glycyl-(Z)-dehydrophenylalanine and structurally variable aminophosphonates alongside with investigations of their activity towards cathepsin C are presented. Obtained results suggest that the introduction of (Z)-dehydrophenylalanine residue into the short phosphonopeptide chain does induce the ordered conformation. Investigated peptides appeared to act as weak or moderate inhibitors of cathepsin C.
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Affiliation(s)
- Michał Paweł Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Maciej Makowski
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | | | - Waldemar Goldeman
- Department of Organic and Medical Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wroclaw, Poland
| | | | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wroclaw, Poland.,Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspianskiego 27, 50-370, Wroclaw, Poland
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3
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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4
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Joaquin D, Lee MA, Kastner DW, Singh J, Morrill ST, Damstedt G, Castle SL. Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3 10-Helical Peptides. J Org Chem 2019; 85:1601-1613. [PMID: 31730750 DOI: 10.1021/acs.joc.9b02747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comparative study of the impact of small, medium-sized, and bulky α,β-dehydroamino acids (ΔAAs) on the structure and stability of Balaram's incipient 310-helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a-c that maintained the 310-helical shape of 1. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a-c that preferred a β-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a-c and 3a-c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and more accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.
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Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Michael A Lee
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - David W Kastner
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Jatinder Singh
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Shardon T Morrill
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Gracie Damstedt
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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5
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Tomar K, Soni S, Bhadauriya P, Parihar R, Ganesh S, Nair NN, Ramanathan G. Mercuric Ion Sensing by an Overlapping β-turn Containing Peptide. ChemistrySelect 2017. [DOI: 10.1002/slct.201701058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kalpana Tomar
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Satyendra Soni
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Pratibha Bhadauriya
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Rashmi Parihar
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Subramaniam Ganesh
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Nisanth N. Nair
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Gurunath Ramanathan
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
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6
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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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7
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Greco A, Tani S, De Marco R, Gentilucci L. Synthesis and Analysis of the Conformational Preferences of 5-Aminomethyloxazolidine-2,4-dione Scaffolds: First Examples of β2- and β2, 2-Homo-Freidinger Lactam Analogues. Chemistry 2014; 20:13390-404. [PMID: 25182659 DOI: 10.1002/chem.201402519] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 07/07/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Arianna Greco
- Dept. of Chemistry "G. Ciamician", University of Bologna via Selmi 2, 40126, Bologna (Italy), Fax: (+39) 0512099456
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8
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Jewgiński M, Krzciuk-Gula J, Makowski M, Latajka R, Kafarski P. Conformation of dehydropentapeptides containing four achiral amino acid residues - controlling the role of L-valine. Beilstein J Org Chem 2014; 10:660-6. [PMID: 24778717 PMCID: PMC3999861 DOI: 10.3762/bjoc.10.58] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/05/2014] [Indexed: 12/01/2022] Open
Abstract
Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.
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Affiliation(s)
- Michał Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Krzciuk-Gula
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Makowski
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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9
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Yadav S, Mahato M, Pathak R, Jha D, Kumar B, Deka SR, Gautam HK, Sharma AK. Multifunctional self-assembled cationic peptide nanostructures efficiently carry plasmid DNA in vitro and exhibit antimicrobial activity with minimal toxicity. J Mater Chem B 2014; 2:4848-4861. [DOI: 10.1039/c4tb00657g] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An amphiphilic peptide–aminoglycoside (Pep–Neo) conjugate has been synthesized, self-assembled into nanostructures and evaluated for its multifunctional properties.
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Affiliation(s)
- Santosh Yadav
- Nucleic Acids Research Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110007, India
| | - Manohar Mahato
- Nucleic Acids Research Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110007, India
| | - Rajiv Pathak
- Microbial Biotechnology Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110020, India
| | - Diksha Jha
- Microbial Biotechnology Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110020, India
| | - Bipul Kumar
- Microbial Biotechnology Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110020, India
| | - Smriti Rekha Deka
- Nucleic Acids Research Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110007, India
| | - Hemant Kumar Gautam
- Microbial Biotechnology Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110020, India
| | - Ashwani Kumar Sharma
- Nucleic Acids Research Laboratory
- CSIR-Institute of Genomics and Integrative Biology
- Delhi – 110007, India
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10
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Zhao X, Xie M, Liu X, Zhang Y, Xiao X, Lin L, Feng X. ChiralN,N′-Dioxide-Yttrium Triflate Complexes-Catalyzed Asymmetric Aldol Cyclization of α-Keto Esters with α-Isothiocyanato Imide. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300593] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Jaremko M, Jaremko L, Mazur A, Makowski M, Lisowski M. Enhanced β-turn conformational stability of tripeptides containing ΔPhe in cis over trans configuration. Amino Acids 2013; 45:865-75. [PMID: 23812673 DOI: 10.1007/s00726-013-1534-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/07/2013] [Indexed: 11/28/2022]
Abstract
Conformations of three pairs of dehydropeptides with the opposite configuration of the ΔPhe residue, Boc-Gly-Δ(Z/E)Phe-Phe-p-NA (Z- p -NA and E- p -NA), Boc-Gly-Δ(Z/E)Phe-Phe-OMe (Z-OMe and E-OMe), and Boc-Gly-Δ(Z/E)Phe-Phe-OH (Z-OH and E-OH) were compared on the basis of CD and NMR studies in MeOH, TFE, and DMSO. The CD results were used as the additional input data for the NMR-based calculations of the detailed solution conformations of the peptides. It was found that Z- p -NA, E- p -NA, Z-OMe, and Z-OH adopt the β-turn conformations and E-OMe and E-OH are unordered. There are two overlapping type III β-turns in Z- p -NA, type II' β-turn in E- p -NA, and type II β-turn in Z-OMe and Z-OH. The results obtained indicate that in the case of methyl esters and peptides with a free carboxyl group, Δ(Z)Phe is a much stronger inducer of ordered conformations than Δ(E)Phe. It was also found that temperature coefficients of the amide protons are not reliable indicators of intramolecular hydrogen bonds donors in small peptides.
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Affiliation(s)
- Mariusz Jaremko
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany,
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12
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Dutta MG, Mathur P, Chauhan VS. De novo design, synthesis and solution conformational study of two didehydroundecapeptides: effect of nature and number of amino acids interspersed between Phe residues. J Pept Sci 2011; 17:783-90. [DOI: 10.1002/psc.1402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 07/04/2011] [Accepted: 07/07/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Madhvi Gupta Dutta
- Malaria Lab; International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi; 110067; India
| | - Puniti Mathur
- Amity Institute of Biotechnology; Amity University; Sector 125; Noida; Uttar Pradesh; India
| | - Virander S Chauhan
- Malaria Lab; International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi; 110067; India
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13
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Gupta M, Chauhan VS. De novo design of α,β-didehydrophenylalanine containing peptides: from models to applications. Biopolymers 2011; 95:161-73. [PMID: 21053260 DOI: 10.1002/bip.21561] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The de novo design of peptides and proteins has emerged as an approach for investigating protein structure and function. The success relies heavily on the ability to design relatively short peptides that can adopt stable secondary structures. To this end, substitution with α,β-dehydroamino acids, especially α,β-didehydrophenylalanine (ΔPhe or ΔF) has blossomed in manifold directions, providing a rich diversity of well-defined structural motifs. Introduction of α,β-didehydrophenylalanine induces β-bends in small and 3(10)-helices in longer peptide sequences. Most favorable conformation of ΔF residues are (φ,ψ) ∼(60°, 30°), (-60°, -30°), (-60°, 150°), and (60°, -150°). These features have been exploited in designing helix-turn-helix, helical bundle arrangements, and glycine zipper type super secondary structural motifs. The unusual capability of α,β-didehydrophenylalanine ring to form a variety of multicentered interactions (N-H…O, C-H…O, C-H…π, and N-H…π) suggests its possible exploitation for future de novo design of supramolecular structures. This work has now been extended to the de novo design of peptides with antibiotic, antifibrillization activity, etc. More recently, self-assembling properties of small dehydropeptides have been explored. This review focuses primarily on the structural and functional behavior of α,β-didehydrophenylalanine containing peptides.
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Affiliation(s)
- Madhvi Gupta
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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14
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Lisowski M, Jaremko Ł, Jaremko M, Mazur A, Latajka R, Makowski M. Effect of the ΔPhe residue configuration on a didehydropeptides conformation: A combined CD and NMR study. Biopolymers 2010; 93:1055-64. [DOI: 10.1002/bip.21522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Demizu Y, Yamagata N, Sato Y, Doi M, Tanaka M, Okuda H, Kurihara M. Controlling the helical screw sense of peptides with C
-terminal L-valine. J Pept Sci 2010; 16:153-8. [DOI: 10.1002/psc.1213] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Tokyo 158-8501, Japan.
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Abstract
During molecular recognition of proteins in biological systems, helices, reverse turns, and beta-sheets are dominant motifs. Often there are therapeutic reasons for blocking such recognition sites, and significant progress has been made by medicinal chemists in the design and synthesis of semirigid molecular scaffolds on which to display amino acid side chains. The basic premise is that preorganization of the competing ligand enhances the binding affinity and potential selectivity of the inhibitor. In this chapter, current progress in these efforts is reviewed.
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17
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Latajka R, Jewginski M, Makowski M, Krezel A. Conformational studies of hexapeptides containing two dehydroamino acid residues in positions 3 and 5 in peptide chain. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Latajka R, Jewginski M, Makowski M, Pawełczak M, Huber T, Sewald N, Kafarski P. Pentapeptides containing two dehydrophenylalanine residues--synthesis, structural studies and evaluation of their activity towards cathepsin C. J Pept Sci 2008; 14:1084-95. [PMID: 18523964 DOI: 10.1002/psc.1045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Synthesis, structural and biological studies of pentapeptides containing two DeltaPhe residues (Z and E isomers) in position 2 and 4 in peptide chain were performed. All the investigated peptides adopted bent conformation and majority of them could exist as two different conformers in solution. Only pentapeptides, containing free N-termini appeared to act as weak inhibitors of cathepsin C with the slow-binding, competitive mechanism of inhibition, free acids being bound slightly better than their methyl esters. Results of molecular modeling suggested significant difference between peptides, depending of the type of amino acid residue in position 5 in peptide chain. Dehydropeptides containing Gly residue in this position may act as competitive slow-reacting substrates and therefore exhibit inhibitory-like properties.
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Affiliation(s)
- R Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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19
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Ousaka N, Inai Y. Transfer of Noncovalent Chiral Information along an Optically Inactive Helical Peptide Chain: Allosteric Control of Asymmetry of the C-Terminal Site by External Molecule that Binds to the N-Terminal Site. J Org Chem 2008; 74:1429-39. [DOI: 10.1021/jo801686m] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Naoki Ousaka
- Department of Environmental Technology and Urban Planning and Department of Frontier Materials, Shikumi College, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yoshihito Inai
- Department of Environmental Technology and Urban Planning and Department of Frontier Materials, Shikumi College, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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20
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Panda JJ, Mishra A, Basu A, Chauhan VS. Stimuli responsive self-assembled hydrogel of a low molecular weight free dipeptide with potential for tunable drug delivery. Biomacromolecules 2008; 9:2244-50. [PMID: 18624454 DOI: 10.1021/bm800404z] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bottom-up fabrication by molecular self-assembly is now widely recognized as a potent method for generating interesting and functional nano- and mesoscale structures. Hydrogels from biocompatible molecules are an interesting class of mesoscale assemblies with potential biomedical applications. The self-assembly of a proteolysis resistant aromatic dipeptide containing a conformational constraining residue (DeltaPhe) into a stable hydrogel has been studied in this work. The reported dipeptide has free -N and -C termini. The hydrogel was self-supportive, was fractaline in nature, and possessed high mechanical strength. It was responsive to environmental conditions like pH, temperature, and ionic strength. The gel matrix could encapsulate and release bioactive molecules in a sustained manner. The described hydrogel showed no observable cytotoxicity to the HeLa and L929 cell lines in culture.
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Affiliation(s)
- Jiban J Panda
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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21
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Lisowski M, Latajka R, Picur B, Lis T, Bryndal I, Rospenk M, Makowski M, Kafarski P. Combined effect of the ΔPhe or ΔAla residue and thep-nitroanilide group on a didehydropeptides conformation. Biopolymers 2008; 89:220-34. [DOI: 10.1002/bip.20897] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Latajka R, Jewginski M, Makowski M, Krezel A, Paluch S. Conformational studies of hexapeptides containing two dehydroamino acid residues in positions 2 and 5 in peptide chain. Biopolymers 2008; 89:691-9. [DOI: 10.1002/bip.20994] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Mathur P, Jagannathan NR, Chauhan VS. Alpha,beta-dehydrophenylalanine containing cecropin-melittin hybrid peptides: conformation and activity. J Pept Sci 2007; 13:253-62. [PMID: 17394119 DOI: 10.1002/psc.841] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synthesis and conformational studies of a cecropin-melittin hybrid pentadecapeptide CA(1-7)MEL(2-9), and its three alpha, beta-dehydrophenylalanine (DeltaPhe) containing analogs in water-TFE mixtures are described. DeltaPhe is placed at strategic positions in order to preserve the amphipathicity of the molecule. The wild type CAMEL0 and its three analogs, containing one, two and three DeltaPhe residues namely CAMELDeltaPhe1, CAMELDeltaPhe2 and CAMELDeltaPhe3 respectively were synthesized in solid phase and their conformation determined by CD and NMR. CAMELDeltaPhe2 and CAMELDeltaPhe3 peptides exhibit the presence of 3(10)-helix and beta-turns in the former and only turns in the latter. CAMELDeltaPhe1 peptide was found to have a largely extended conformation. Antibacterial and hemolytic activities of the peptides were also evaluated. CAMELDeltaPhe2 peptide is maximally potent against both Staphylococcus aureus ATCC 259230 and Escherichia coli ATCC 11303. CAMELDeltaPhe1 with a single DeltaPhe at the center shows minimal hemolysis.
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Affiliation(s)
- Puniti Mathur
- Department of N. M. R, All India Institute of Medical Sciences, New Delhi, India
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Inai Y, Ousaka N, Ookouchi Y. Chiral interaction in peptide molecules: Effects of chiral peptide species on helix-sense induction in an N-terminal-free achiral peptide. Biopolymers 2006; 82:471-81. [PMID: 16506166 DOI: 10.1002/bip.20491] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Noncovalent chiral domino effect (NCDE) has been proposed as terminal-specific interaction upon a 3(10)-helical peptide chain, of which the helix sense is manipulated by an external chiral stimulus (mainly amino acid derivatives) operating on the N-terminus (Inai, Y., et al. J Am Chem Soc 2000, 122, 11731-11732; ibid., 2002, 124, 2466-2473; ibid., 2003, 125, 8151-8162). We have investigated here a helix-sense induction in an optically inactive N-terminal-free nonapeptide (1) through the screening of several peptide species that differ in chiral sequence, chain length, and C-terminal group. Helix-sense induction in peptide 1 depends largely on both the C-terminal chirality and carboxyl group in the external peptide, in which N-carbonyl-blocked amino acids, "monopeptide acids," should be the minimum requirement for effective induction. N-Protected mono- to tetrapeptides of L-Leu residue commonly induce a right-handed helix. NMR study and theoretical computation reveal that the N-terminal segment of peptide 1 binds the N-protected dipeptide molecule through multipoint coordination to induce a right-handed helix preferentially. The present findings not only will improve our understanding of the chiral roles in peptide or protein helical termini, but also might demonstrate potential applications to chirality-responsive materials based on peptide helical fragments.
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Affiliation(s)
- Yoshihito Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan.
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25
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Komori H, Inai Y. Electronic CD Study of a Helical Peptide Incorporating Z-Dehydrophenylalanine Residues: Conformation Dependence of the Simulated CD Spectra. J Phys Chem A 2006; 110:9099-107. [PMID: 16854021 DOI: 10.1021/jp056501u] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electronic circular dichroism (CD) spectra as well as transitions from ground to excited states were predicted for a helical nonapeptide based on alternative sequence--[Z-alpha,beta-dehydrophenylalanine (Delta(Z)Phe)-X]--through semiempirical molecular orbital computation combined with time-dependent (TD) method. The simulation was performed for its various conformers that differ in helix type, helix sense, and Delta(Z)Phe side-chain orientation. These conformational variations have been shown to depend largely on its CD spectra. Comparison between simulated and observed CD profiles reveals that peptide 1 in solution favors a right-handed 3(10)-helix that adopts phenyl (Delta(Z)Phe) planes basically in a vertical orientation with respect to the helix axis. These predictions were essentially supported from CD simulation of a shorter helical analogue at ab inito or density functional TD levels. The theoretical CD-conformation relationship should provide us useful guideline for determination of helix sense in the dehydropeptide, and for estimation of its conformations statistically averaged in solution.
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Affiliation(s)
- Hisatoshi Komori
- Department of Environmental Technology and Urban Planning, Shikumi College, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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26
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Latajka R, Makowski M, Jewgiński M, Pawełczak M, Koroniak H, Kafarski P. Peptide p-nitrophenylanilides containing (E)-dehydrophenylalanine—synthesis, structural studies and evaluation of their activity towards cathepsin C. NEW J CHEM 2006. [DOI: 10.1039/b601634k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Ousaka N, Inai Y, Okabe T. Chiral interaction in Gly-capped N-terminal motif of 310-helix and domino-type induction in helix sense. Biopolymers 2006; 83:337-51. [PMID: 16767770 DOI: 10.1002/bip.20557] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chiral interaction of helical peptide with chiral molecule, and concomitant induction in its helix sense have been demonstrated in optically inactive nonapeptide (1) possessing Gly at its N-terminus: H-Gly-(Delta(Z)Phe-Aib)(4)-OCH(3) (1: Delta(Z)Phe = Z-dehydrophenylalanine; Aib = alpha-aminoisobutyric acid). Spectroscopic measurements [mainly nuclear magnetic resonance (NMR) and circular diochroism (CD)] as well as theoretical simulation have been carried out for that purpose. Peptide 1 in the 3(10)-helix tends to adopt preferentially a right-handed screw sense by chiral Boc-L-amino acid (Boc: t-butoxycarbonyl). Induction in the helix sense through the noncovalent chiral domino effect should be derived primarily from the complex supported by the three-point coordination on the N-terminal sequence. Thus the 3(10)-helical terminus consisting of only alpha-amino acid residues enables chiral recognition of the Boc-amino acid molecule, leading to modulation of the original chain asymmetry. Dynamics in the helix-sense induction also have been discussed on the basis of a low-temperature NMR study. Furthermore, the inversion of induced helix sense has been achieved through solvent effects.
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Affiliation(s)
- Naoki Ousaka
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan
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Gupta M, Ramakumar S, Chauhan VS. Helix packing motif common to the crystal structures of two undecapeptides containing dehydrophenylalanine residues: Implications for the de novo design of helical bundle super secondary structural modules. Biopolymers 2005; 80:617-27. [PMID: 16193455 DOI: 10.1002/bip.20279] [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: 11/12/2022]
Abstract
De novo designed peptide based super secondary structures are expected to provide scaffolds for the incorporation of functional sites as in proteins. Self-association of peptide helices of similar screw sense, mediated by weak interactions, has been probed by the crystal structure determination of two closely related peptides: Ac-Gly1-Ala2-Delta Phe3-Leu4-Val5-DeltaPhe6-Leu7-Val8-DeltaPhe9-Ala10-Gly11-NH2 (I) and Ac-Gly1-Ala2-DeltaPhe3-Leu4-Ala5-DeltaPhe6-Leu7-Ala8-DeltaPhe9-Ala10-Gly11-NH2 (II). The crystal structures determined to atomic resolution and refined to R factors 8.12 and 4.01%, respectively, reveal right-handed 3(10)-helical conformations for both peptides. CD has also revealed the preferential formation of right-handed 3(10)-helical conformations for both molecules. Our aim was to critically analyze the packing of the helices in the solid state with a view to elicit clues for the design of super secondary structural motifs such as two, three, and four helical bundles based on helix-helix interactions. An important finding is that a packing motif could be identified common to both the structures, in which a given peptide helix is surrounded by six other helices reminiscent of transmembrane seven helical bundles. The outer helices are oriented either parallel or antiparallel to the central helix. The helices interact laterally through a combination of N--H...O, C--H...O, and C--H...pi hydrogen bonds. Layers of interacting leucine residues are seen in both peptide crystal structures. The packing of the peptide helices in the solid state appears to provide valuable leads for the design of super secondary structural modules such as two, three, or four helix bundles by connecting adjacent antiparallel helices through suitable linkers such as tetraglycine segments.
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Mathur P, Ramakumar S, Chauhan VS. Peptide design using alpha,beta-dehydro amino acids: from beta-turns to helical hairpins. Biopolymers 2004; 76:150-61. [PMID: 15054895 DOI: 10.1002/bip.10571] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Incorporation of alpha,beta-dehydrophenylalanine (DeltaPhe) residue in peptides induces folded conformations: beta-turns in short peptides and 3(10)-helices in larger ones. A few exceptions-namely, alpha-helix or flat beta-bend ribbon structures-have also been reported in a few cases. The most favorable conformation of DeltaPhe residues are (phi,psi) approximately (-60 degrees, -30 degrees ), (-60 degrees, 150 degrees ), (80 degrees, 0 degrees ) or their enantiomers. DeltaPhe is an achiral and planar residue. These features have been exploited in designing DeltaPhe zippers and helix-turn-helix motifs. DeltaPhe can be incorporated in both right and left-handed helices. In fact, consecutive occurrence of three or more DeltaPhe amino acids induce left-handed screw sense in peptides containing L-amino acids. Weak interactions involving the DeltaPhe residue play an important role in molecular association. The C--H.O==C hydrogen bond between the DeltaPhe side-chain and backbone carboxyl moiety, pi-pi stacking interactions between DeltaPhe side chains belonging to enantiomeric helices have shown to stabilize folding. The unusual capability of a DeltaPhe ring to form the hub of multicentered interactions namely, a donor in aromatic C--H.pi and C--H.O==C and an acceptor in a CH(3).pi interaction suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures.
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Affiliation(s)
- Puniti Mathur
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India
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Ramakumar S, Ramagopal UA, Inai Y, Goel S, Sahal D, Chauhan VS. De Novo Design and Characterization of a Helical Hairpin Eicosapeptide. Structure 2004; 12:389-96. [PMID: 15016355 DOI: 10.1016/j.str.2004.02.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Revised: 11/07/2003] [Accepted: 11/19/2003] [Indexed: 12/01/2022]
Abstract
De novo design of supersecondary structures is expected to provide useful molecular frameworks for the incorporation of functional sites as in proteins. A 21 residue long, dehydrophenylalanine-containing peptide has been de novo designed and its crystal structure determined. The apolar peptide folds into a helical hairpin supersecondary structure with two right-handed helices, connected by a tetraglycine linker. The helices of the hairpin interact with each other through a combination of C-H.O and N-H.O hydrogen bonds. The folding of the apolar peptide has been realized without the help of either metal ions or disulphide bonds. A remarkable feature of the peptide is the unanticipated occurrence of an anion binding motif in the linker region, strikingly similar in conformation and function to the "nest" motif seen in several proteins. The observation supports the view for the possible emergence of rudimentary functions over short sequence stretches in the early peptides under prebiotic conditions.
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Inai Y, Ousaka N, Okabe T. Mechanism for the noncovalent chiral domino effect: new paradigm for the chiral role of the N-terminal segment in a 3(10)-helix. J Am Chem Soc 2003; 125:8151-62. [PMID: 12837085 DOI: 10.1021/ja035040s] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, novel chiral interactions on 3(10)-helical peptides, of which the helicity is controlled by external chiral stimulus operating on the N-terminus, were proposed as a "noncovalent chiral domino effect (NCDE)" (Inai, Y.; et al. J. Am. Chem. Soc. 2000, 122, 11731. Inai, Y.; et al. J. Am. Chem. Soc. 2002, 124, 2466). The present study clarifies the mechanism for generating the NCDE. For this purpose, achiral nonapeptide (1), H-beta-Ala-(Delta(Z)Phe-Aib)(4)-OMe [Delta(Z)Phe = (Z)-didehydrophenylalanine, Aib = alpha-aminoisobutyric acid], was synthesized. Peptide 1 alone adopts a 3(10)-helical conformation in chloroform. On the basis of the induced CD signals of peptide 1 with chiral additives, chiral acid enabling the predominant formation of a one-handed helix was shown to need at least both carboxyl and urethane groups; that is, Boc-l-amino acid (Boc = tert-butoxycarbonyl) strongly induces a right-handed helix. NMR studies (NH resonance variations, low-temperature measurement, and NOESY) were performed for a CDCl(3) solution of peptide 1 and chiral additive, supporting the view that the N-terminal H-beta-Ala-Delta(Z)Phe-Aib, including the two free amide NH's, captures effectively a Boc-amino acid molecule through three-point interactions. The H-beta-Ala's amino group binds to the carboxyl group to form a salt bridge, while the Aib(3) NH is hydrogen-bonded to either oxygen of the carboxylate group. Subsequently, the free Delta(Z)Phe(2) NH forms a hydrogen bond to the urethane carbonyl oxygen. A semiempirical molecular orbital computation explicitly demonstrated that the dynamic looping complexation is energetically permitted and that the N-terminal segment of a right-handed 3(10)-helix binds more favorably to a Boc-l-amino acid than to the corresponding d-species. In conclusion, the N-terminal segment of a 3(10)-helix, ubiquitous in natural proteins and peptides, possesses the potency of chiral recognition in the backbone itself, furthermore enabling the conversion of the terminally acquired chiral sign and power into a dynamic control of the original helicity and helical stability.
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Affiliation(s)
- Yoshihito Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.
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32
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Padyana AK, Ramakumar S, Mathur P, Jagannathan NR, Chauhan VS. Role of a two-residue spacer in an alpha,beta-Didehydrophenylalanine containing hexapeptide: crystal and solution structure of Boc-val-deltaPhe-Leu-Ala-deltaPhe-Ala-OMe. J Pept Sci 2003; 9:54-63. [PMID: 12587883 DOI: 10.1002/psc.432] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The peptide Boc-Val1-deltaPhe2-Leu3-Ala4-deltaPhe5-Ala6-OMe has been examined for the structural consequence of placing a two-residue segment between the deltaPhe residues. The peptide is stabilized by four consecutive beta-turns. The overall conformation of the molecule is a right-handed 3(10)-helix, with average (phi, psi) values (-67.7 degrees, -22.7 degrees), unwound at the C-terminus. The 1H NMR results also suggest that the peptide maintains its 3(10)-helical structure in solution as observed in the crystal state. The crystal structure is stabilized through head-to-tail hydrogen bonds and a repertoire of aromatic interactions laterally directed between adjacent helices, which are antiparallel to each other. The aromatic ring of deltaPhe5 forms the hub of multicentred interactions, namely as a donor in aromatic C-H...pi and aromatic C-H...O=C interactions and as an acceptor in a CH3...pi interaction. The present structure uniquely illustrates the unusual capability of a deltaPhe ring to host such concerted interactions and suggests its exploitation in introducing long-range interactions in the folding of supersecondary structures.
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Affiliation(s)
- Anil K Padyana
- Department of Physics, Indian Institute of Science, Bangalore 560012, India
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33
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Inai Y, Komori H, Takasu A, Hirabayashi T. Noncovalent chiral domino effect on one-handed helix of nonapeptide containing a midpoint L-residue. Biomacromolecules 2003; 4:122-8. [PMID: 12523856 DOI: 10.1021/bm0256303] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We here clarify whether noncovalent chiral domino effect characterized by the terminal interaction of a helical peptide with a chiral small molecule can alter the helical stability of N-deprotected peptides containing an L-residue covalently incorporated into the inner position. Two nonapeptides consisting of the midpoint L-leucine (1) or L-phenylalanine (2) and the achiral helix-forming residues were employed. NMR and IR spectroscopy and energy calculation indicated that both peptides adopt a 3(10)-helical conformation in chloroform. They strongly preferred a right-handed screw sense because of the presence of the midpoint L-residue. These original right-handed screw senses were retained on addition of chiral Boc-amino acid, but their helical stabilities clearly depended on its added chirality. Here, Boc-L-amino acid stabilizes the original right-handed helix, whereas the corresponding Boc-D-amino acid tends to less stabilize or destabilize it. This tendency was not observed for the corresponding N-Boc-protected peptides 1 and 2, strongly suggesting that the N-terminal amino group is required for controlling the stabilization of the original right-handed helix. Therefore, noncovalent chiral domino effect in peptides 1 and 2 can contribute even to the helical stability of a chiral peptide prevailing one-handed helix strongly through the midpoint L-residue. In addition, the N-terminal moiety of a 3(10)-helical peptide was found to generate chiral discrimination in complexation process with racemic additives.
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Affiliation(s)
- Yoshihito Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan.
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Ramagopal UA, Ramakumar S, Mathur P, Joshi R, Chauhan VS. Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions. Protein Eng Des Sel 2002; 15:331-5. [PMID: 11983934 DOI: 10.1093/protein/15.4.331] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A decapeptide Boc-L-Ala-(Delta Delta Phe)(4)-L-Ala-(Delta Delta Phe)3-Gly-OMe (Peptide I) was synthesized to study the preferred screw sense of consecutive alpha,beta-dehydrophenylalanine (Delta Delta Phe) residues. Crystallographic and CD studies suggest that, despite the presence of two L-Ala residues in the sequence, the decapeptide does not have a preferred screw sense. The peptide crystallizes with two conformers per asymmetric unit, one of them a slightly distorted right-handed 3(10)-helix (X) and the other a left-handed 3(10)-helix (Y) with X and Y being antiparallel to each other. An unanticipated and interesting observation is that in the solid state, the two shape-complement molecules self-assemble and interact with an extensive network of C-H...O hydrogen bonds and pi-pi interactions, directed laterally to the helix axis with amazing regularity. Here, we present an atomic resolution picture of the weak interaction mediated mutual recognition of two secondary structural elements and its possible implication in understanding the specific folding of the hydrophobic core of globular proteins and exploitation in future work on de novo design.
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Affiliation(s)
- Udupi A Ramagopal
- Department of Physics and Bioinformatics Center, Indian Institute of Science, Bangalore-560012, India
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35
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Inai Y, Kurokawa Y, Kojima N. Screw sense preference of non-polarL-amino acid residues second from the N-terminal position. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b206664e] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Inai Y, Hirabayashi T. A helical arrangement of beta-substituents of dehydropeptides: synthesis and conformational study of sequential nona- and dodecapeptides possessing (Z)-beta-(1-naphthyl)dehydroalanine residues. Biopolymers 2001; 59:356-69. [PMID: 11514939 DOI: 10.1002/1097-0282(20011015)59:5<356::aid-bip1033>3.0.co;2-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Sequential nona- and dodecapeptides possessing three and four (Z)-beta -(1-naphthyl)dehydroalanine (Delta(Z)Nap) residues, Boc-(L-Ala-Delta(Z)Nap-L-Leu)(n)-OCH(3) (n = 3 and 4; Boc = t-butoxycarbonyl), were synthesized to design a rigid 3(10)-helical backbone for a regular arrangement of functional groups using dehydropeptides. Their solution conformations were investigated by NMR and CD analyses, and theoretical energy calculations. Both peptides were found to adopt a 3(10)-helical conformation in CDCl(3) from their nuclear Overhauser effect spectroscopy (NOESY) spectra, which showed intense cross peaks for N(i)H-N(i+1)H proton pairs, but no cross peaks for C(alpha)(i)H-N(i+4)H pairs. The predominance of a 3(10)-helix was also supported by solvent accessibility of NH resonances. CD spectra of both peptides in tetrahydrofuran showed strong exciton couplets at around 228 nm assignable to naphthyl side chains, which are regularly arranged along a right-handed helical backbone. Chain-length effects on conformational preference in sequential peptide -(Ala-Delta(Z)Nap-Leu)(n)- were discussed based on spectroscopic analysis, energy minimization, and molecular dynamics simulations. Consequently, the repeating number n > or = 3 forms predominantly a right-handed 3(10)-helical conformation. The energy calculation also revealed that the midpoint naphthyl groups of peptide n = 4 are highly restricted to one stable orientation. In conclusion, beta-substituted alpha,beta-dehydroalanine is expected to be a unique tool for designing a rigid molecular frame of 3(10)-helix along which beta-functional groups are regularly arranged in a specific manner.
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Affiliation(s)
- Y Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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37
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The effect of a terminal chiral residue on the helicity of a peptide chain. Int J Pept Res Ther 2001. [DOI: 10.1007/bf02443577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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38
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Inai Y, Kurashima S, Hirabayashi T, Yokota K. Synthesis of delta(E)Phe-containing tripeptide via photoisomerization and its conformation in solution. Biopolymers 2000; 53:484-96. [PMID: 10775064 DOI: 10.1002/(sici)1097-0282(200005)53:6<484::aid-bip5>3.0.co;2-a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A new synthetic route to (E)-beta-phenyl-alpha,beta-dehydroalanine (delta(E)Phe)-containing peptide was presented via photochemical isomerization of the corresponding (Z)-beta-phenyl-alpha,beta-dehydroalanine (delta(Z)Phe)-containing peptide. By applying this method to Boc-Ala-delta(Z)Phe-Val-OMe (Z-I: Boc, t-butoxycarbonyl; OMe, methoxy), Boc-Ala-delta(E)Phe-Val-OMe (E-I) was obtained. The identification of peptide E-I was evidenced by 1H-nmr, 13C-nmr, and uv absorption spectroscopy, elemental analysis, and hydrogenation. The conformation of peptide E-I in CDCl3 was investigated by 1H-nmr spectroscopy (solvent dependence of NH chemical shift and difference nuclear Overhauser effect). Interestingly, peptide E-I differed from peptide Z-I in the hydrogen-bonding mode. Namely, for peptide Z-I, only Val NH participates in intramolecular hydrogen bonding, which leads to a type II beta-turn conformation supported by hydrogen bonding between CO(Boc) and NH(Val). On the other hand, for peptide E-I, two NHs, delta(E)Phe NH and Val NH, participate in intramolecular hydrogen bonding. In both peptides, a remarkable NOE (approximately 11-13%) was observed for Ala C(alpha) H-deltaPhe NH pair. Based on the nmr data and conformational energy calculation, it should be concluded that peptide E-I takes two consecutive gamma-turn conformations supported by hydrogen bonding between CO(Boc) and NH(delta(E)Phe), and between CO(Ala) and NH(Val) as its plausible conformation.
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Affiliation(s)
- Y Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Japan
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39
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Inai Y, Kurokawa Y, Hirabayashi T. Solvent Dependence on the Preference of Helical Screw Sense: Effect of l-Leu Residue Second from N-Terminal on Screw Sense in Achiral Peptide. Macromolecules 1999. [DOI: 10.1021/ma9901442] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yoshihito Inai
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Kurokawa
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Tadamichi Hirabayashi
- Department of Environmental Technology and Urban Planning, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
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Inai Y, Ashitaka S, Hirabayashi T. A Study of Chain-Length Effect on Helical Screw Sense in Peptides Having an N-Terminal L-Leu Residue. Polym J 1999. [DOI: 10.1295/polymj.31.246] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Inai Y, Kurokawa Y, Ida A, Hirabayashi T. Effects of N-Terminal L-Amino Acid Residues on Helical Screw Sense in Achiral Peptides. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.55] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [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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Ramagopal UA, Ramakumar S, Joshi RM, Chauhan VS. Crystal structure of Boc-LAla-deltaPhe-deltaPhe-deltaPhe-deltaPhe-NHMe: a left-handed helical peptide. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1998; 52:208-15. [PMID: 9774234 DOI: 10.1111/j.1399-3011.1998.tb01478.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Alpha,beta-dehydrophenylalanine residues constrain the peptide backbone to beta-bend conformation. A pentapeptide containing four consecutive (deltaPhe) residues has been synthesised and crystallised. The peptide Boc-LAla-deltaPhe-deltaPhe-deltaPhe-deltaPhe+ ++-NHMe (C45H46N6O7, MW = 782.86) was crystallised from an acetonitrile/methanol mixture. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1) with a = 19.455(6), b = 20.912(9), c = 11.455(4) A and Z = 4. The X-ray (MoKalpha, lambda = 0.7107 A) intensity data were collected using the Rigaku-AFC7 diffractrometer. The crystal structure was determined by direct methods and refined using the least-squares technique, R = 8.41% for 1827 reflections with absolute value of Fo > 4sigma(absolute value of Fo). The molecule contains the largest stretch of consecutive dehydrophenylalanine residues whose crystal structure has been determined so far. The peptide adopts left-handed 3(10)-helical conformation despite the presence of LAla at the N-terminus. The mean phi, psi values, averaged across the last four residues are 56.8 degrees and 17.5 degrees, respectively. There are four 4-->1 intramolecular hydrogen bonds, characteristic of the 310-helix. In the crystal each molecule interacts with four crystallographically symmetric molecules with one hydrogen bond each.
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Affiliation(s)
- U A Ramagopal
- Department of Physics, Indian Institute of Science, Bangalore
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Inai Y, Sakakura Y, Hirabayashi T. Design of Novel Helical Backbone. Conformational Energy Calculation and Synthesis of Sequential Polypeptide Containing Z-Dehydrophenylalanine and Proline Residues. Polym J 1997. [DOI: 10.1295/polymj.29.649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Jain RM, Rajashankar KR, Ramakumar S, Chauhan VS. First Observation of Left-Handed Helical Conformation in a Dehydro Peptide Containing Two l-Val Residues. Crystal and Solution Structure of Boc-l-Val-ΔPhe-ΔPhe-ΔPhe-l-Val-OMe,. J Am Chem Soc 1997. [DOI: 10.1021/ja961460o] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- R. M. Jain
- Contribution from the International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India, and Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - K. R. Rajashankar
- Contribution from the International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India, and Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - S. Ramakumar
- Contribution from the International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India, and Department of Physics, Indian Institute of Science, Bangalore-560012, India
| | - V. S. Chauhan
- Contribution from the International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India, and Department of Physics, Indian Institute of Science, Bangalore-560012, India
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