1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Mir FM, Crisma M, Toniolo C, Lubell WD. Isolated α-turn and incipient γ-helix. Chem Sci 2019; 10:6908-6914. [PMID: 31391913 PMCID: PMC6640192 DOI: 10.1039/c9sc01683j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/07/2019] [Indexed: 12/17/2022] Open
Abstract
The unique abilities of homo-oligo-adamantyl peptides to adopt α- and γ-turn conformations are demonstrated by X-ray diffraction, and NMR and FT-IR absorption spectroscopies. Assembled by an Ugi multiple component reaction strategy, N α-formyl-adamantyl tripeptide iso-propyl and tert-butyl amides are respectively found to adopt an isolated α-turn and an incipient γ-helix conformation by X-ray diffraction crystallography. The shortest example of a single α-turn with ideal geometry is observed in the crystalline state. In solution both peptides predominantly assume γ-helical structures.
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Affiliation(s)
- Fatemeh M Mir
- Département de Chimie , Université de Montréal , C. P. 6128, Succursale Centre-Ville , Montréal , Québec , Canada H3C 3J7 .
| | - Marco Crisma
- Department of Chemistry , University of Padova and Institute of Biomolecular Chemistry , Padova Unit , CNR , 35131 Padova , Italy
| | - Claudio Toniolo
- Department of Chemistry , University of Padova and Institute of Biomolecular Chemistry , Padova Unit , CNR , 35131 Padova , Italy
| | - William D Lubell
- Département de Chimie , Université de Montréal , C. P. 6128, Succursale Centre-Ville , Montréal , Québec , Canada H3C 3J7 .
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3
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Mir FM, Crisma M, Toniolo C, Lubell WD. Influence of the C‐terminal substituent on the crystal‐state conformation of Adm peptides. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fatemeh M. Mir
- Département de ChimieUniversité de Montréal Montréal Québec Canada
| | - Marco Crisma
- Institute of Biomolecular ChemistryPadova Unit Padova Italy
| | - Claudio Toniolo
- Institute of Biomolecular ChemistryPadova Unit Padova Italy
- Department of ChemistryUniversity of Padova Padova Italy
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4
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Drouillat B, Peggion C, Biondi B, Wright K, Couty F, Crisma M, Formaggio F, Toniolo C. Heterochiral Ala/(
αMe)Aze
sequential oligopeptides:
S
ynthesis and conformational study. J Pept Sci 2019; 25:e3165. [DOI: 10.1002/psc.3165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Bruno Drouillat
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | | | - Barbara Biondi
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Karen Wright
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - François Couty
- Institut Lavoisier de Versailles, UMR CNRS 8180University of Versailles St‐Quentin en Yvelines Versailles 78035 France
| | - Marco Crisma
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Fernando Formaggio
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
| | - Claudio Toniolo
- Department of ChemistryUniversity of Padova Padova 35131 Italy
- Institute of Biomolecular Chemistry Padova Unit, CNR Padova 35131 Italy
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5
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Drouillat B, Peggion C, Biondi B, Wright K, Couty F, Crisma M, Formaggio F, Toniolo C. A novel peptide conformation: the γ-bend ribbon. Org Biomol Chem 2018; 16:7947-7958. [PMID: 30318540 DOI: 10.1039/c8ob02279h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unlike the extensively investigated relationship between the peptide β-bend ribbon and its prototypical 310-helix conformation, the corresponding relationship between the narrower γ-bend ribbon and its regular γ-helix counterpart still remains to be studied, as the latter 3D-structures have not yet been experimentally authenticated. In this paper, we describe the results of the first characterization, both in the crystal state and in solution, of the γ-bend ribbon conformation using X-ray diffraction and FT-IR absorption, electronic CD and 2D-NMR spectroscopies applied to an appropriate set of synthetic, homo-chiral, sequential dipeptide oligomers based on (S)-Ala and the known γ-bend inducer, Cα-tetrasubstituted, N-alkylated α-amino acid residue (S)-Cα-methyl-azetidine-carboxylic acid.
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Affiliation(s)
- Bruno Drouillat
- Institut Lavoisier de Versailles, UMR CNRS 8180, University of Versailles St-Quentin en Yvelines, 78035 Versailles, France.
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6
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Tomsett M, Maffucci I, Le Bailly BAF, Byrne L, Bijvoets SM, Lizio MG, Raftery J, Butts CP, Webb SJ, Contini A, Clayden J. A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal. Chem Sci 2017; 8:3007-3018. [PMID: 28451368 PMCID: PMC5380885 DOI: 10.1039/c6sc05474a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/24/2017] [Indexed: 11/21/2022] Open
Abstract
Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.
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Affiliation(s)
- Michael Tomsett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Bryden A F Le Bailly
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Stefan M Bijvoets
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - M Giovanna Lizio
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK
| | - Craig P Butts
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK.,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini" , Università degli Studi di Milano , Via Venezian , 21 20133 Milano , Italy
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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7
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Haspel N, Zheng J, Aleman C, Zanuy D, Nussinov R. A Protocol for the Design of Protein and Peptide Nanostructure Self-Assemblies Exploiting Synthetic Amino Acids. Methods Mol Biol 2017; 1529:323-352. [PMID: 27914060 PMCID: PMC7900906 DOI: 10.1007/978-1-4939-6637-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource. Structural databases contain large libraries of protein molecules and their building blocks with a range of sizes, shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these building blocks can greatly expand the available chemical space and enhance the desired properties. Herein, we summarize a protocol for designing nanostructures consisting of self-assembling building blocks, based on our recent works. We focus on the principles of nanostructure design with naturally occurring proteins and synthetic amino acids, as well as hybrid materials made of amyloids and synthetic polymers.
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Affiliation(s)
- Nurit Haspel
- Department of Computer Science, The University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA.
| | - Jie Zheng
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Carlos Aleman
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, E-08028, Barcelona, Spain
| | - David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028, Barcelona, Spain
| | - Ruth Nussinov
- Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Inst. of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
- Cancer and Inflammation Program, National Cancer Institute, Frederick, MD, 21702, USA
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8
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Mazzier D, Grassi L, Moretto A, Alemán C, Formaggio F, Toniolo C, Crisma M. En route towards the peptideγ-helix: X-ray diffraction analyses and conformational energy calculations of Adm-rich short peptides. J Pept Sci 2016; 23:346-362. [DOI: 10.1002/psc.2957] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Daniela Mazzier
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Luigi Grassi
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Alessandro Moretto
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Carlos Alemán
- Departament d'Enginyeria Quimica, ETSEIB; Universitat Politècnica de Catalunya; 08028 Barcelona Spain
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
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9
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Čakić Semenčić M, Kodrin I, Barišić L, Nuskol M, Meden A. Synthesis and Conformational Study of Monosubstituted Aminoferrocene‐Based Peptides Bearing Homo‐ and Heterochiral Pro‐Ala Sequences. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mojca Čakić Semenčić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Ivan Kodrin
- Department of ChemistryFaculty of ScienceUniversity of ZagrebHorvatovac 102A10000ZagrebCroatia
| | - Lidija Barišić
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Marko Nuskol
- Faculty of Food Technology and BiotechnologyUniversity of ZagrebPierottijeva 610000ZagrebCroatia
| | - Anton Meden
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVecna pot 1131000LjubljanaSlovenia
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10
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Konda M, Bhowmik S, Mobin SM, Biswas S, Das AK. Modulating Hydrogen Bonded Self-assembled Patterns and Morphological Features by a Change in Side Chain of Third Amino Acid of Synthetic γ- Amino Acid Based Tripeptides. ChemistrySelect 2016. [DOI: 10.1002/slct.201600557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maruthi Konda
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Soumitra Bhowmik
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Shaikh M. Mobin
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Sagar Biswas
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
| | - Apurba K. Das
- Department of Chemistry; Indian Institute of Technology Indore; Khandwa Road Indore 453552 India
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11
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Crisma M, Toniolo C. Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids. Biopolymers 2016; 104:46-64. [PMID: 25363510 DOI: 10.1002/bip.22581] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/14/2014] [Accepted: 10/24/2014] [Indexed: 01/09/2023]
Abstract
The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131, Padova, Italy
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12
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Peggion C, Moretto A, Formaggio F, Crisma M, Toniolo C. Multiple, consecutive, fully-extended 2.0₅-helix peptide conformation. Biopolymers 2016; 100:621-36. [PMID: 23893391 DOI: 10.1002/bip.22267] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 02/01/2023]
Abstract
The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131, Padova, Italy
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13
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Ingole TS, Vijayadas KN, Chaitanya KN, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. Disruption of Native β-Turns: Consequence of Folding Competition between Native and Orthanilic Acid Proline-BasedPseudoβ-Turn. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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14
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Konda M, Kauffmann B, Rasale DB, Das AK. Structural and morphological diversity of self-assembled synthetic γ-amino acid containing peptides. Org Biomol Chem 2016; 14:4089-102. [DOI: 10.1039/c6ob00380j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the synthesis of constrained amino acid building block gabapentin (Gpn) based hybrid peptides and their structural and morphological diversity in different conditions.
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Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
| | - Brice Kauffmann
- Université de Bordeaux
- UMS3033
- Institut Européen de Chimie et Biologie (IECB)
- 33600 Pessac
- France
| | | | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
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15
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Crisma M, De Zotti M, Moretto A, Peggion C, Drouillat B, Wright K, Couty F, Toniolo C, Formaggio F. Single and multiple peptide γ-turns: literature survey and recent progress. NEW J CHEM 2015. [DOI: 10.1039/c4nj01564a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Published data on peptide isolated and repetitive γ-turns are reviewed. Advancements in our laboratories on these 3D-structures are also presented.
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Affiliation(s)
- Marco Crisma
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | - Marta De Zotti
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
| | | | | | - Bruno Drouillat
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Karen Wright
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - François Couty
- ILV
- UMR CNRS 8180
- University of Versailles
- 78035 Versailles
- France
| | - Claudio Toniolo
- ICB
- Padova Unit
- CNR
- Department of Chemistry
- University of Padova
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16
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Murase SK, Haspel N, del Valle LJ, Perpète EA, Michaux C, Nussinov R, Puiggalí J, Alemán C. Molecular characterization of l-phenylalanine terminated poly(l-lactide) conjugates. RSC Adv 2014. [DOI: 10.1039/c4ra01534g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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17
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Dutt Konar A. Conformational studies of γ-turn in pseudopeptides containing α-amino acid and conformationally constrained meta amino benzoic acid/meta nitro aniline. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2012.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Vangala M, Dhokale SA, Gawade RL, Pattuparambil RR, Puranik VG, Dhavale DD. Sugar furanoid trans-vicinal diacid as a γ-turn inducer: synthesis and conformational study. Org Biomol Chem 2013; 11:6874-8. [DOI: 10.1039/c3ob41462k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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19
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20
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Zanuy D, Hamley IW, Alemán C. Modeling the Tetraphenylalanine-PEG Hybrid Amphiphile: From DFT Calculations on the Peptide to Molecular Dynamics Simulations on the Conjugate. J Phys Chem B 2011; 115:8937-46. [DOI: 10.1021/jp2031187] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ian W. Hamley
- School of Chemistry, Food Science and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, United Kingdom
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C′, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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21
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Jiménez AI, Vaquero V, Cabezas C, López JC, Cativiela C, Alonso JL. The Singular Gas-Phase Structure of 1-Aminocyclopropanecarboxylic Acid (Ac3c). J Am Chem Soc 2011; 133:10621-8. [DOI: 10.1021/ja2033603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana I. Jiménez
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - Vanesa Vaquero
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cabezas
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Juan C. López
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
| | - Carlos Cativiela
- Departamento de Química
Orgánica, ISQCH, Universidad de Zaragoza−CSIC, 50009 Zaragoza, Spain
| | - José L. Alonso
- Grupo de Espectroscopía
Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia
y Bioespectroscopia, Parque Científico Uva, Universidad de Valladolid, 45005 Valladolid, Spain
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22
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Structural Chemistry of Peptides Containing Backbone Expanded Amino Acid Residues: Conformational Features of β, γ, and Hybrid Peptides. Chem Rev 2010; 111:657-87. [DOI: 10.1021/cr100100x] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Prema. G. Vasudev
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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23
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Kang YK, Park HS. Conformational preferences and cis-trans isomerization of L-3,4-dehydroproline residue. Biopolymers 2009; 92:387-98. [PMID: 19373924 DOI: 10.1002/bip.21203] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conformational study of N-acetyl-N'-methylamide of L-3,4-dehydroproline (Ac-Dhp-NHMe, the Dhp dipeptide) is carried out using hybrid density functional methods with the self-consistent reaction field method in the gas phase and in solution (chloroform and water). The incorporation of a double bond between C(beta) and C(gamma) into the prolyl ring results in the puckering, backbone population, and barriers to prolyl cis-trans isomerization different from those of the Pro dipeptide. For local minima of the Dhp dipeptide in the gas phase and in water, the C(beta)-C(gamma) bonds become shorter by approximately 0.2 A and the bond angles C(alpha)-C(beta)-C(gamma) and C(beta)-C(gamma)-C(delta) are widened by approximately 8 degrees than those of the Pro dipeptide, and the puckering amplitude is computed to be 0.01-0.07 A, indicating that the 3,4-dehydroprolyl ring is quite less puckered. However, polyproline-like conformations become preferred and the relative stability of the conformation tC with a C(7) intramolecular hydrogen bond decreases as the solvent polarity increases, as found for the Pro dipeptide. The barriers to cis-trans isomerization of the Ac-Dhp peptide bond increase with the increase of solvent polarity and the isomerization is likely to proceed through the clockwise rotation in water, as found for the prolyl peptide bond. The hydrogen bond between the prolyl nitrogen and the following amide N-H group seems to contribute in stabilizing the transition state structures.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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24
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design. Acc Chem Res 2009; 42:1628-39. [PMID: 19572698 DOI: 10.1021/ar9001153] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nature has used the all-alpha-polypeptide backbone of proteins to create a remarkable diversity of folded structures. Sequential patterns of 20 distinct amino acids, which differ only in their side chains, determine the shape and form of proteins. Our understanding of these specific secondary structures is over half a century old and is based primarily on the fundamental elements: the Pauling alpha-helix and beta-sheet. Researchers can also generate structural diversity through the synthesis of polypeptide chains containing homologated (omega) amino acid residues, which contain a variable number of backbone atoms. However, incorporating amino acids with more atoms within the backbone introduces additional torsional freedom into the structure, which can complicate the structural analysis. Fortunately, gabapentin (Gpn), a readily available bulk drug, is an achiral beta,beta-disubstituted gamma amino acid residue that contains a cyclohexyl ring at the C(beta) carbon atom, which dramatically limits the range of torsion angles that can be obtained about the flanking C-C bonds. Limiting conformational flexibility also has the desirable effect of increasing peptide crystallinity, which permits unambiguous structural characterization by X-ray diffraction methods. This Account describes studies carried out in our laboratory that establish Gpn as a valuable residue in the design of specifically folded hybrid peptide structures. The insertion of additional atoms into polypeptide backbones facilitates the formation of intramolecular hydrogen bonds whose directionality is opposite to that observed in canonical alpha-peptide helices. If hybrid structures mimic proteins and biologically active peptides, the proteolytic stability conferred by unusual backbones can be a major advantage in the area of medicinal chemistry. We have demonstrated a variety of internally hydrogen-bonded structures in the solid state for Gpn-containing peptides, including the characterization of the C(7) and C(9) hydrogen bonds, which can lead to ribbons in homo-oligomeric sequences. In hybrid alphagamma sequences, distinct C(12) hydrogen-bonded turn structures support formation of peptide helices and hairpins in longer sequences. Some peptides that include the Gpn residue have hydrogen-bond directionality that matches alpha-peptide helices, while others have the opposite directionality. We expect that expansion of the polypeptide backbone will lead to new classes of foldamer structures, which are thus far unknown to the world of alpha-polypeptides. The diversity of internally hydrogen-bonded structures observed in hybrid sequences containing Gpn shows promise for the rational design of novel peptide structures incorporating hybrid backbones.
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Affiliation(s)
- Prema G. Vasudev
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
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25
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Alemán C, Jiménez AI, Cativiela C, Nussinov R, Casanovas J. Conformational preferences of 1-amino-2-phenylcyclohexanecarboxylic acid, a phenylalanine cyclohexane analogue. J Org Chem 2009; 74:7834-43. [PMID: 19772338 PMCID: PMC2771318 DOI: 10.1021/jo901594e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the restricted phenylalanine analogue generated by including the alpha and beta carbon atoms into a cyclohexane ring (1-amino-2-phenylcyclohexanecarboxylic acid, c(6)Phe) have been determined using quantum mechanical calculations. Specifically, the conformational profile of the N-acetyl-N'-methylamide derivative of the c(6)Phe stereoisomers exhibiting either a cis or a trans relative orientation between the amino and phenyl substituents has been analyzed in different environments (gas phase, chloroform, and aqueous solutions). Calculations were performed using B3LYP, MP2, and HF methods combined with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and a self-consistent reaction-field (SCRF) method was applied to analyze the influence of the solvent. The amino acids investigated can be viewed as constrained phenylalanine analogues with a rigidly oriented aromatic side chain that may interact with the peptide backbone not only sterically but also electronically through the aromatic pi orbitals. Their conformational propensities have been found to be strongly influenced by the specific orientation of the aromatic substituent in each stereoisomer and the conformation adopted by the cyclohexane ring, as well as by the environment.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, 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
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II n 69, Lleida E-25001, Spain
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26
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Baeza JL, Gerona-Navarro G, Thompson K, Pérez de Vega MJ, Infantes L, García-López MT, González-Muñiz R, Martín-Martínez M. Further Evidence for 2-Alkyl-2-carboxyazetidines as γ-Turn Inducers. J Org Chem 2009; 74:8203-11. [DOI: 10.1021/jo901712x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- José Luis Baeza
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Kevin Thompson
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Lourdes Infantes
- Instituto de Química Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
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27
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Zanuy D, Ballano G, Jiménez AI, Casanovas J, Haspel N, Cativiela C, Curcó D, Nussinov R, Alemán C. Protein segments with conformationally restricted amino acids can control supramolecular organization at the nanoscale. J Chem Inf Model 2009; 49:1623-9. [PMID: 19548653 DOI: 10.1021/ci9001487] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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28
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Vener MV, Egorova AN, Fomin DP, Tsirel’son VG. A quantum-topological analysis of noncovalent interactions in secondary polyalanine structures. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2009. [DOI: 10.1134/s1990793109040046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Grauer A, Späth A, Ma D, König B. Metal-catalyzed derivatization of C(alpha)-tetrasubstituted amino acids and their use in the synthesis of cyclic peptides. Chem Asian J 2009; 4:1134-40. [PMID: 19472262 DOI: 10.1002/asia.200900033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
C(alpha)-tetrasubstituted amino acids are important building blocks in the design and preparation of novel peptidomimetics. We report on the functionalization of the C(alpha)-tetrasubstituted THF amino acid rac-5 by copper(I) catalyzed N-arylation reactions. The aryl bromide substituent of rac-5 is replaced by a variety of aliphatic and aromatic amines. Intramolecular N-arylation yielded only small amounts of a cyclic tripeptide 2, whereas cyclic tripeptide ethers 4 and 50 were obtained in an enantiomerically pure form from a palladium(0)-catalyzed intramolecular O-arylation.
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Affiliation(s)
- Andreas Grauer
- Institut für Organische Chemie, Universität Regensburg, 93040 Regensburg, Germany
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30
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Grauer AA, Cabrele C, Zabel M, König B. Stable right- and left-handed peptide helices containing C(alpha)-tetrasubstituted alpha-amino acids. J Org Chem 2009; 74:3718-26. [PMID: 19354242 DOI: 10.1021/jo900222g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Short peptidomimetics with stable secondary structures in solution are of interest for applications in chemistry, biology, and medicine. One way to rigidify the backbone of a peptide is the use of cyclic C(alpha)-tetrasubstituted alpha-amino acids (TAAs) like compound 14. The structures resulting from the incorporation of this unnatural amino acid into peptides were investigated. In total, 13 different peptides with a length of up to eight residues and alternating sequences of TAA 14 and (S)- or (R)-valine were synthesized. Their structures were characterized by X-ray diffraction analysis and NMR and CD measurements showing that the all-S-backbone-configured peptides 5 and 6 (SS)(2-3) form right-handed 3(10)-helices, while the all-R-configured peptides 11-13 (RR)(2-4) form left-handed 3(10)-helices in the solid state and solution.
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Affiliation(s)
- Andreas A Grauer
- Institute for Organic Chemistry, University of Regensburg, D-93040 Regensburg, Germany
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31
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LaPointe SM, Farrag S, Bohórquez HJ, Boyd RJ. QTAIM Study of an α-Helix Hydrogen Bond Network. J Phys Chem B 2009; 113:10957-64. [DOI: 10.1021/jp903635h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shenna M. LaPointe
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Sarah Farrag
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Hugo J. Bohórquez
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Russell J. Boyd
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
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32
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Revilla-López G, Torras J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Side-chain to backbone interactions dictate the conformational preferences of a cyclopentane arginine analogue. J Org Chem 2009; 74:2403-12. [PMID: 19236034 PMCID: PMC2682113 DOI: 10.1021/jo802704h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The intrinsic conformational preferences of the nonproteinogenic amino acids constructed by incorporating the arginine side chain in the beta position of 1-aminocyclopentane-1-carboxylic acid (either in a cis or a trans orientation relative to the amino group) have been investigated by using computational methods. These compounds may be considered as constrained analogues of arginine (denoted as c(5)Arg) in which the orientation of the side chain is fixed by the cyclopentane moiety. Specifically, the N-acetyl-N'-methylamide derivatives of cis- and trans-c(5)Arg have been examined in the gas phase and in solution by using B3LYP/6-311+G(d,p) calculations and Molecular Dynamics simulations. Results indicate that the conformational space available to these compounds is highly restricted, their conformational preferences being dictated by the ability of the guanidinium group in the side chain to establish hydrogen bond interactions with the backbone. A comparison with the behavior previously described for the analogous phenylalanine derivatives is presented.
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Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, 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, Diagonal 647, Barcelona E-08028, Spain
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33
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Cativiela C, Ordóñez M. Recent Progress on the Stereoselective Synthesis of Cyclic Quaternary alpha-Amino Acids. TETRAHEDRON, ASYMMETRY 2009; 20:1-63. [PMID: 20300486 PMCID: PMC2839256 DOI: 10.1016/j.tetasy.2009.01.002] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The most recent papers describing the stereoselective synthesis of cyclic quaternary alpha-amino acids are collected in this review. The diverse synthetic approaches are classified according to the size of the ring and taking into account the bond that is formed to complete the quaternary skeleton.
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Affiliation(s)
- Carlos Cativiela
- Departamento de Química Orgánica, ICMA, Universidad de Zaragoza-CSIC, 50009 Zaragoza (Spain)
| | - Mario Ordóñez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, 62209 Cuernavaca, Morelos (México)
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34
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Ballano G, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids. J Phys Chem B 2008; 112:13101-15. [PMID: 18811190 DOI: 10.1021/jp8032116] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.
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Affiliation(s)
- Gema Ballano
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza-CSIC, Zaragoza, Spain
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35
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Alfonso I, Bolte M, Bru M, Burguete M, Luis S. Designed Folding of Pseudopeptides: The Transformation of a Configurationally Driven Preorganization into a Stereoselective Multicomponent Macrocyclization Reaction. Chemistry 2008; 14:8879-8891. [DOI: 10.1002/chem.200800726] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Tsai CJ, Zheng J, Zanuy D, Haspel N, Wolfson H, Alemán C, Nussinov R. Principles of nanostructure design with protein building blocks. Proteins 2007; 68:1-12. [PMID: 17407160 DOI: 10.1002/prot.21413] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Currently there is increasing interest in nanostructures and their design. Nanostructure design involves the ability to predictably manipulate the properties of the self-assembly of autonomous units. Autonomous units have preferred conformational states. The units can be synthetic material science-based or derived from functional biological macromolecules. Autonomous biological building blocks with available structures provide an extremely rich and useful resource for design. For proteins, the structural databases contain large libraries of protein molecules and their building blocks with a range of shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these can expand the available chemical space and enhance the desired properties. Here we focus on the principles of nanostructure design with protein building blocks.
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Affiliation(s)
- Chung-Jung Tsai
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21702, USA
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37
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Casanovas J, Jiménez AI, Cativiela C, Nussinov R, Alemán C. 1-amino-2-phenylcyclopentane-1-carboxylic acid: a conformationally restricted phenylalanine analogue. J Org Chem 2007; 73:644-51. [PMID: 18081347 DOI: 10.1021/jo702107s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DFT calculations at the B3LYP/6-311G(d,p) level have been used to investigate the intrinsic conformational preferences of 1-amino-2-phenylcyclopentane-1-carboxylic acid (c5Phe), a constrained analogue of phenylalanine in which the alpha and beta carbons are included in a cyclopentane ring. Specifically, the N-acetyl-N'-methylamide derivatives of the cis and trans stereoisomers, where cis and trans refer to the relative position between the amino group and the phenyl ring, have been calculated. Solvent effects have been examined using a self-consistent reaction field (SCRF) method. Results indicate that the conformational space of the cis stereoisomer is much more restricted than that of the trans derivative both in the gas phase and in solution.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II No. 69, Lleida E-25001, Spain.
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38
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Maity P, König B. Enantio- and diastereoselective syntheses of cyclic Cα-tetrasubstituted α-amino acids and their use to induce stable conformations in short peptides. Biopolymers 2007; 90:8-27. [DOI: 10.1002/bip.20902] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Chatterjee S, Roy RS, Balaram P. Expanding the polypeptide backbone: hydrogen-bonded conformations in hybrid polypeptides containing the higher homologues of alpha-amino acids. J R Soc Interface 2007; 4:587-606. [PMID: 17251160 PMCID: PMC2373382 DOI: 10.1098/rsif.2006.0203] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2006] [Accepted: 12/01/2006] [Indexed: 11/12/2022] Open
Abstract
Half a century has passed since the hydrogen-bonded secondary structures of polypeptides and proteins were first recognized. An extraordinary wealth of conformational information is now available on peptides and proteins, which are formed of alpha-amino acid residues. More recently, the discovery of well-folded structures in oligopeptides containing beta-amino acids has focused a great deal of current interest on the conformational properties of peptides constructed from higher homologues (omega) of alpha-amino acids. This review examines the nature of intramolecularly hydrogen-bonded conformations of hybrid peptides formed by amino acid residues, with a varying number of backbone atoms. The beta-turn, a ubiquitous structural feature formed by two residue (alphaalpha) segments in proteins and peptides, is stabilized by a 10-atom (C10) intramolecular 4-->1 hydrogen bond. Hybrid turns may be classified by comparison with their alphaalpha counterparts. The available crystallographic information on hydrogen-bonded hybrid turns is surveyed in this review. Several recent examples demonstrate that individual omega-amino acid residues and hybrid dipeptide segments may be incorporated into the regular structures of alpha-peptides. Examples of both peptide helices and hairpins are presented. The present review explores the relationships between folded conformations in hybrid sequences and their counterparts in all alpha-residue sequences. The use of stereochemically constrained omega-residues promises to expand the range of peptide design strategies to include omega-amino acids. This approach is exemplified by well-folded structures like the C12 (alphagamma) and C14 (gammagamma) helices formed in short peptides containing multiply substituted gamma-residues. The achiral gamma-residue gabapentin is a readily accessible building block in the design of peptides containing gamma-amino acids. The construction of globular polypeptide structures using diverse hybrid sequences appears to be a realistic possibility.
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Affiliation(s)
| | | | - P Balaram
- Molecular Biophysics Unit, Indian Institute of ScienceBangalore 560012, India
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40
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Casanovas J, Jiménez AI, Cativiela C, Pérez JJ, Aleman C. Conformational analysis of a cyclopropane analogue of phenylalanine with two geminal phenyl substituents. J Phys Chem B 2007; 110:5762-6. [PMID: 16539522 DOI: 10.1021/jp0542569] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical methods have been used to investigate the intrinsic conformational preferences of 1-amino-2,2-diphenylcyclopropanecarboxylic acid (c(3)Dip), a cyclopropane analogue of phenylalanine bearing two phenyl substituents on the same beta-carbon. Geometries, energies, and frequencies were calculated on the N-acetyl-N'-methylamide derivative at the HF and B3LYP levels using the 6-31G(d), 6-311G(d), and 6-31+G(d,p) basis sets. Four minimum energy conformations were characterized: axial C(7), equatorial C(7), right-handed helix, and polyproline II. Analysis of the whole results, which are fully consistent with available experimental data, indicates that c(3)Dip tends to promote gamma-turn conformations.
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Affiliation(s)
- Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/Jaume II N 69, 25001 Lleida, Spain.
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41
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Vener M, Egorova A, Fomin D, Tsirelson V. QTAIM study of the closed-shell interactions in peptide secondary structures: A cluster treatment of oligo- and polyalanines. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.04.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Crisma M, De Borggraeve WM, Peggion C, Formaggio F, Royo S, Jiménez AI, Cativiela C, Toniolo C. Preferred 3D-structure of peptides rich in a severely conformationally restricted cyclopropane analogue of phenylalanine. Chemistry 2007; 12:251-60. [PMID: 16281320 DOI: 10.1002/chem.200500865] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Terminally blocked, homo-peptide amides of (R,R)-1-amino-2,3-diphenylcyclopropane-1-carboxylic acid (c3diPhe), a chiral member of the family of Calpha-tetrasubstituted alpha-amino acids, from the dimer to the tetramer, and diastereomeric co-oligopeptides of (R,R)- or (S,S)-c3diPhe with (S)-alanine residues to the trimer level were prepared in solution and fully characterized. The synthetic effort was extended to terminally protected co-oligopeptide esters to the hexamer, where c3diPhe residues are combined with achiral alpha-aminoisobutyric acid residues. The preferred conformations of the peptides were assessed in solution by FT-IR absorption, NMR, and CD techniques, and for seven oligomers in the crystal state (by X-ray diffraction) as well. This study clearly indicates that c3diPhe, a sterically demanding cyclopropane analogue of phenylalanine, tends to fold peptides into beta-turn and 3(10)-helix conformations. However, when c3diPhe is in combination with other chiral residues, the conformation preferred by the resulting peptides is also dictated by the chiral sequence of the amino acid building blocks. The (S,S)-enantiomer of this alpha-amino acid, unusually lacking asymmetry in the main chain, strongly favors the left-handedness of the turn/helical peptides formed.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova via Marzolo 1, 35131 Padova, Italy
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Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Alemán C. Use of constrained synthetic amino acids in beta-helix proteins for conformational control. J Phys Chem B 2007; 111:3236-42. [PMID: 17388467 DOI: 10.1021/jp065025k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A highly constrained amino acid has been introduced in the turn region of a beta-helix to increase the conformational stability of the native fold for nanotechnological purposes. The influence of this specific amino acid replacement in the final organization of beta-helix motifs has been evaluated by combining ab initio first-principles calculations on model systems and molecular dynamics simulations of entire peptide segments. The former methodology, which has been applied to a sequence containing three amino acids, has been used to develop adjusted templates. Calculations indicated that 1-amino-2,2-diphenylcyclopropanecarboxylic acid, a constrained cyclopropane analogue of phenylalanine, exhibits a strong tendency to form and promote folded conformations. On the other hand, molecular dynamics simulations are employed to probe the ability of such a synthetic amino acid to enhance the conformational stability of the beta-helix motif, which is the first requirement for further protein nanoengineering. A highly regular segment from a naturally occurring beta-helix protein was selected as a potential nanoconstruct module. Simulations of wild type and mutated segments revealed that the ability of the phenylalanine analogue to nucleate turn conformations enhances the conformational stability of the beta-helix motif in isolated peptide segments.
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Affiliation(s)
- David Zanuy
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
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Edwards AA, Sanjayan GJ, Hachisu S, Tranter GE, Fleet GW. A novel series of oligomers from 4-aminomethyl-tetrahydrofuran-2-carboxylates with 2,4-cis and 2,4-trans stereochemistry. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.05.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Relevant parameters and stereochemical consequences of helices [alpha-helix, 3(10)-helix, beta-bend ribbon spiral, gamma-helix, 2.0(5)-helix, poly(Pro)(n) type-I and -II helices, and collagen triple helix] of peptides based on alpha-amino acids for use as templates in various branches of chemistry are briefly discussed.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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Alemán C, Zanuy D, Jiménez AI, Cativiela C, Haspel N, Zheng J, Casanovas J, Wolfson H, Nussinov R. Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids. Phys Biol 2006; 3:S54-62. [PMID: 16582465 DOI: 10.1088/1478-3975/3/1/s06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Physically building complex multi-molecular structures from naturally occurring biological macromolecules has aroused a great deal of interest. Here we focus on nanostructures composed of re-engineered, natural 'foldamer' building blocks. Our aim is to provide some of the underlying concepts and schemes for crafting structures utilizing such conformationally relatively stable molecular components. We describe how, via chemical biology strategies, it is further possible to chemically manipulate the foldamer building blocks toward specific shape-driven structures, which in turn could be used toward potential-designed functions. We outline the criteria in choosing candidate foldamers from the vast biological repertoire, and how to enhance their stability through selected targeted replacements by non-proteinogenic conformationally constrained amino acids. These approaches combine bioinformatics, high performance computations and mathematics with synthetic organic chemistry. The resulting artificially engineered self-organizing molecular scale structures take advantage of nature's nanobiology toolkit and at the same time improve on it, since their new targeted function differs from that optimized by evolution. The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines.
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Affiliation(s)
- Carlos Alemán
- Departament d'Enginyeria Química, ETS d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, Barcelona E-08028, Spain.
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Vasudev PG, Shamala N, Ananda K, Balaram P. C9 Helices and Ribbons in γ-Peptides: Crystal Structures of Gabapentin Oligomers. Angew Chem Int Ed Engl 2005; 44:4972-5. [PMID: 16003813 DOI: 10.1002/anie.200501055] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Prema G Vasudev
- Department of Physics, Indian Institute of Science, Bangalore 560 012, India
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Vasudev PG, Shamala N, Ananda K, Balaram P. C9 Helices and Ribbons in γ-Peptides: Crystal Structures of Gabapentin Oligomers. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200501055] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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