1
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West NG, Bamford SE, Pigram PJ, Pan J, Qi DC, Mechler A. Controllable hierarchical self-assembly: systematic study forming metallosupramolecular frameworks on the basis of helical beta-oligoamides. MATERIALS HORIZONS 2023; 10:5584-5596. [PMID: 37815516 DOI: 10.1039/d3mh01327h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Self-assembly is a key guiding principle for the design of complex nanostructures. Substituted beta oligoamides offer versatile building blocks that can have inherent folding characteristics, offering geometrically defined functionalities that can specifically bind and assemble with predefined morphological characteristics. In this work hierarchical self-assembly is implemented based on metal coordinating helical beta-oligoamides crosslinked with transition metals selected for their favourable coordination geometries, Fe2+, Cu2+, Ni2+, Co2+, Zn2+, and two metalates, MoO42-, and WO42-. The oligoamide Ac-β3Aβ3Vβ3S-αHαHαH-β3Aβ3Vβ3A (3H) was designed to allow crosslinking via three distinct faces of the helical unit, with a possibility of forming three dimensional framework structures. Atomic force microscopy (AFM) confirmed the formation of specific morphologies that differ characteristically with each metal. X-Ray photoelectron spectroscopy (XPS) results reveal that the metal centres can be reduced in the final structures, confirming strong chemical interaction. Time of flight secondary ion mass spectrometry (ToF-SIMS) confirmed the spatial distribution of metals within the self-assembled networks, also revealing molecular fragments that confirm coordination to histidine and carboxyl moieties. The metalates MoO42- and WO42- were also able to induce the formation of specific superstructure morphologies. It was observed that assembly with either of nickel, copper, and molybdate form thin films, while cobalt, zinc, and tungstate produced specific three dimensional networks of oligoamides. Iron was found to form both a thin film and a complex hierarchical assembly with the 3H simultaneously. The design of the 3H substituted beta oligoamide to readily form metallosupramolecular frameworks was demonstrated with a range of metals and metalates with a degree of control over layer thicknesses as a function of the metal/metalate. The results validate and broaden the metallosupramolecular framework concept and establish a platform technology for the design of functional thin layer materials.
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Affiliation(s)
- Norton G West
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore.
| | - Sarah E Bamford
- Center for Materials and Surface Science, and Department of Mathematical and Physical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Paul J Pigram
- Center for Materials and Surface Science, and Department of Mathematical and Physical Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jisheng Pan
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore.
| | - Dong-Chen Qi
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Adam Mechler
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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2
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Shah SKH, Modi U, Patel K, James A, N S, De S, Vasita R, Prabhakaran P. Site-selective post-modification of short α/γ hybrid foldamers: a powerful approach for molecular diversification towards biomedical applications. Biomater Sci 2023; 11:6210-6222. [PMID: 37526301 DOI: 10.1039/d3bm00766a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification approach is successful in peptides, proteins, and polymers to modulate their functions. To the best of our knowledge, site-selective post-modification of a foldamer affording molecules with different pendant functional groups within a molecular scaffold has not yet been reported. We demonstrate for the first time that late-stage site-selective functionalization of short hybrid oligomers is an efficient approach to afford molecules with diverse functional groups. In this article, we report the design and synthesis of hybrid peptides with repeating units of leucine (Leu) and 5-amino salicylic acid (ASA), regioselective post-modification, conformational analyses (based on solution-state NMR, circular dichroism and computational studies) and morphological studies of the peptide nanostructures. As a proof-of-concept, we demonstrate the applications of differently modified peptides as drug delivery agents, imaging probes, and anticancer agents. The novel feature of the work is that the difference in reactivity of two phenolic OH groups in short biomimetic peptides was utilized to achieve site-selective post-modification. It is challenging to apply the same approach to short α-peptides having a poor folding tendency, and their post-functionalization may considerably affect their conformation.
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Affiliation(s)
| | - Unnati Modi
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Anjima James
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi 682022, India
| | - Sreerag N
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
| | - Susmita De
- Department of Chemistry, University of Calicut, Calicut 673635, India
| | - Rajesh Vasita
- School of Life Sciences, Central University of Gujarat, Gandhinagar 382030, India
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar 382030, India.
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3
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Yoo SH, Buratto J, Roy A, Morvan E, Pasco M, Pulka-Ziach K, Lombardo CM, Rosu F, Gabelica V, Mackereth CD, Collie GW, Guichard G. Adaptive Binding of Alkyl Glycosides by Nonpeptidic Helix Bundles in Water: Toward Artificial Glycolipid Binding Proteins. J Am Chem Soc 2022; 144:15988-15998. [PMID: 35998571 DOI: 10.1021/jacs.2c05234] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amphipathic water-soluble helices formed from synthetic peptides or foldamers are promising building blocks for the creation of self-assembled architectures with non-natural shapes and functions. While rationally designed artificial quaternary structures such as helix bundles have been shown to contain preformed cavities suitable for guest binding, there are no examples of adaptive binding of guest molecules by such assemblies in aqueous conditions. We have previously reported a foldamer 6-helix bundle that contains an internal nonpolar cavity able to bind primary alcohols as guest molecules. Here, we show that this 6-helix bundle can also interact with larger, more complex guests such as n-alkyl glycosides. X-ray diffraction analysis of co-crystals using a diverse set of guests together with solution and gas-phase studies reveals an adaptive binding mode whereby the apo form of the 6-helix bundle undergoes substantial conformational change to accommodate the hydrocarbon chain in a manner reminiscent of glycolipid transfer proteins in which the cavity forms upon lipid uptake. The dynamic nature of the self-assembling and molecular recognition processes reported here marks a step forward in the design of functional proteomimetic molecular assemblies.
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Affiliation(s)
- Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Jérémie Buratto
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Arup Roy
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Estelle Morvan
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France
| | - Morgane Pasco
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | | | - Caterina M Lombardo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, IECB, UAR3033, US001, F-33600 Pessac, France.,Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR5320, U1212, IECB, F-33600 Bordeaux, France
| | - Gavin W Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR5248, IECB, 2 rue Robert Escarpit, F-33600 Pessac, France
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4
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Li MC, Liu YJ, Hsu KC, Lin TH, Lin CW, Horng JC, Wang SK. Design and synthesis of fluorinated peptides for analysis of fluorous effects on the interconversion of polyproline helices. Bioorg Chem 2021; 119:105491. [PMID: 34838334 DOI: 10.1016/j.bioorg.2021.105491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 12/15/2022]
Abstract
The unique interaction between fluorine atoms has been exploited to alter protein structures and to develop synthetic and analytical applications. To expand such fluorous interaction for novel applications, polyproline peptides represent an excellent molecular nanoscaffold for controlling the presentation of perfluoroalkyl groups on their unique secondary structure. We develop approaches to synthesis fluorinated peptides to systematically investigate how the number, location and types of the fluorous groups on polyproline affect the conformation by monitoring the transition between the two major polyproline structures PPI and PPII. This work provides valuable information on how fluorous interaction affects the peptide structure and also benefits the design of functional fluorous molecules.
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Affiliation(s)
- Meng-Che Li
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Ying-Jie Liu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Kuang-Cheng Hsu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tse-Hsueh Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Wei Lin
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sheng-Kai Wang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan.
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5
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Fuller AA, Moreno JL, Nguyen MT. Using Fluorescence to Enable Innovative Functions of Foldamers. Isr J Chem 2021. [DOI: 10.1002/ijch.202000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry & Biochemistry Santa Clara University 500 El Camino Real Santa Clara CA 95053 USA
| | - Jose L. Moreno
- Department of Chemistry & Biochemistry Santa Clara University 500 El Camino Real Santa Clara CA 95053 USA
| | - Michelle T. Nguyen
- Department of Chemistry & Biochemistry Santa Clara University 500 El Camino Real Santa Clara CA 95053 USA
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6
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Sloand JN, Miller MA, Medina SH. Fluorinated peptide biomaterials. Pept Sci (Hoboken) 2021; 113:e24184. [PMID: 34541446 PMCID: PMC8448251 DOI: 10.1002/pep2.24184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.
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Affiliation(s)
- Janna N Sloand
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Michael A Miller
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Scott H Medina
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
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7
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Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
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Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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8
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Habila N, Kulkarni K, Lee TH, Al-Garawi ZS, Serpell LC, Aguilar MI, Del Borgo MP. Transition of Nano-Architectures Through Self-Assembly of Lipidated β 3-Tripeptide Foldamers. Front Chem 2020; 8:217. [PMID: 32296680 PMCID: PMC7136582 DOI: 10.3389/fchem.2020.00217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/09/2020] [Indexed: 12/18/2022] Open
Abstract
β3-peptides consisting exclusively of β3-amino acids adopt a variety of non-natural helical structures and can self-assemble into well-defined hierarchical structures by axial head-to-tail self-assembly resulting in fibrous materials of varying sizes and shapes. To allow control of fiber morphology, a lipid moiety was introduced within a tri-β3-peptide sequence at each of the three amino acid positions and the N-terminus to gain finer control over the lateral assembly of fibers. Depending on the position of the lipid, the self-assembled structures formed either twisted ribbon-like fibers or distinctive multilaminar nanobelts. The nanobelt structures were comprised of multiple layers of peptide fibrils as revealed by puncturing the surface of the nanobelts with an AFM probe. This stacking phenomenon was completely inhibited through changes in pH, indicating that the layer stacking was mediated by electrostatic interactions. Thus, the present study is the first to show controlled self-assembly of these fibrous structures, which is governed by the location of the acyl chain in combination with the 3-point H-bonding motif. Overall, the results demonstrate that the nanostructures formed by the β3-tripeptide foldamers can be tuned via sequential lipidation of N-acetyl β3-tripeptides which control the lateral interactions between peptide fibrils and provide defined structures with a greater homogeneous population.
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Affiliation(s)
- Nathan Habila
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Zahraa S Al-Garawi
- School of Life Sciences, University of Sussex, Brighton, United Kingdom.,Chemistry Department, Mustansiriyah University, Baghdad, Iraq
| | - Louise C Serpell
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Department of Pharmacology, Monash University, Clayton, VIC, Australia
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9
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Capaccio V, Sicignano M, Rodríguez RI, Della Sala G, Alemán J. Asymmetric Synthesis of α-Trifluoromethylthio-β-Amino Acids under Phase Transfer Catalysis. Org Lett 2019; 22:219-223. [DOI: 10.1021/acs.orglett.9b04195] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Vito Capaccio
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marina Sicignano
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Ricardo I. Rodríguez
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Giorgio Della Sala
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - José Alemán
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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10
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Ikeda A, Capellan A, Welch JT. The secondary structure of a heptapeptide containing trifluoromethyl-λ 6-tetrafluorosulfanyl substituted amino acids. Org Biomol Chem 2019; 17:8079-8082. [PMID: 31454017 DOI: 10.1039/c9ob01797f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Site specific introduction of the polar hydrophobic trifluoromethyl-λ6-tetrafluorosulfanyl (CF3SF4) group can effectively control the secondary structure of a heptapeptide, the minimum repeat unit of an α-helix. The structural influence of CF3SF4-containing amino acid on the heptapeptide was established using NMR methods.
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Affiliation(s)
- Akari Ikeda
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - Aimée Capellan
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
| | - John T Welch
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY 12222, USA.
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11
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Wang PSP, Schepartz A. β-Peptide bundles: Design. Build. Analyze. Biosynthesize. Chem Commun (Camb) 2016; 52:7420-32. [PMID: 27146019 DOI: 10.1039/c6cc01546h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.
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Affiliation(s)
- Pam S P Wang
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06511, USA.
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12
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Gopalan R, Del Borgo M, Mechler A, Perlmutter P, Aguilar MI. Geometrically Precise Building Blocks: the Self-Assembly of β-Peptides. ACTA ACUST UNITED AC 2015; 22:1417-1423. [DOI: 10.1016/j.chembiol.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/30/2015] [Accepted: 10/03/2015] [Indexed: 12/23/2022]
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13
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van Straaten KE, Kuttiyatveetil JRA, Sevrain CM, Villaume SA, Jiménez-Barbero J, Linclau B, Vincent SP, Sanders DAR. Structural basis of ligand binding to UDP-galactopyranose mutase from Mycobacterium tuberculosis using substrate and tetrafluorinated substrate analogues. J Am Chem Soc 2015; 137:1230-44. [PMID: 25562380 DOI: 10.1021/ja511204p] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
UDP-Galactopyranose mutase (UGM) is a flavin-containing enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf) and plays a key role in the biosynthesis of the mycobacterial cell wall galactofuran. A soluble, active form of UGM from Mycobacterium tuberculosis (MtUGM) was obtained from a dual His6-MBP-tagged MtUGM construct. We present the first complex structures of MtUGM with bound substrate UDP-Galp (both oxidized flavin and reduced flavin). In addition, we have determined the complex structures of MtUGM with inhibitors (UDP and the dideoxy-tetrafluorinated analogues of both UDP-Galp (UDP-F4-Galp) and UDP-Galf (UDP-F4-Galf)), which represent the first complex structures of UGM with an analogue in the furanose form, as well as the first structures of dideoxy-tetrafluorinated sugar analogues bound to a protein. These structures provide detailed insight into ligand recognition by MtUGM and show an overall binding mode similar to those reported for other prokaryotic UGMs. The binding of the ligand induces conformational changes in the enzyme, allowing ligand binding and active-site closure. In addition, the complex structure of MtUGM with UDP-F4-Galf reveals the first detailed insight into how the furanose moiety binds to UGM. In particular, this study confirmed that the furanoside adopts a high-energy conformation ((4)E) within the catalytic pocket. Moreover, these investigations provide structural insights into the enhanced binding of the dideoxy-tetrafluorinated sugars compared to unmodified analogues. These results will help in the design of carbohydrate mimetics and drug development, and show the enormous possibilities for the use of polyfluorination in the design of carbohydrate mimetics.
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Affiliation(s)
- Karin E van Straaten
- Department of Chemistry, University of Saskatchewan , 110 Science Place, Saskatoon S7N 5C9, Canada
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14
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Appel R, Tacke S, Klingauf J, Besenius P. Tuning the pH-triggered self-assembly of dendritic peptide amphiphiles using fluorinated side chains. Org Biomol Chem 2015; 13:1030-9. [DOI: 10.1039/c4ob02185a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the synthesis of a series of anionic dendritic peptide amphiphiles of increasing hydrophobic character and describe their self-assembly into supramolecular nanorods using pH and ionic strength dependent state diagrams.
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Affiliation(s)
- Ralph Appel
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
| | - Sebastian Tacke
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jürgen Klingauf
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Pol Besenius
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
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15
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Miller J, Melicher MS, Schepartz A. Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle. J Am Chem Soc 2014; 136:14726-9. [PMID: 25290247 PMCID: PMC4210112 DOI: 10.1021/ja508872q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Indexed: 01/19/2023]
Abstract
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.
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Affiliation(s)
- Jonathan
P. Miller
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Michael S. Melicher
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
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16
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Tressler C, Zondlo NJ. (2S,4R)- and (2S,4S)-perfluoro-tert-butyl 4-hydroxyproline: two conformationally distinct proline amino acids for sensitive application in 19F NMR. J Org Chem 2014; 79:5880-6. [PMID: 24870929 PMCID: PMC4076032 DOI: 10.1021/jo5008674] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Indexed: 01/19/2023]
Abstract
(2S,4R)- and (2S,4S)-perfluoro-tert-butyl 4-hydroxyproline were synthesized (as Fmoc-, Boc-, and free amino acids) in 2-5 steps. The key step of each synthesis was a Mitsunobu reaction with perfluoro-tert-butanol, which incorporated a perfluoro-tert-butyl group, with nine chemically equivalent fluorines. Both amino acids were incorporated in model α-helical and polyproline helix peptides. Each amino acid exhibited distinct conformational preferences, with (2S,4R)-perfluoro-tert-butyl 4-hydroxyproline promoting polyproline helix. Peptides containing these amino acids were sensitively detected by (19)F NMR, suggesting their use in probes and medicinal chemistry.
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Affiliation(s)
- Caitlin
M. Tressler
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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17
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Mándity IM, Monsignori A, Fülöp L, Forró E, Fülöp F. Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element. Chemistry 2014; 20:4591-7. [PMID: 24664416 DOI: 10.1002/chem.201304448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/09/2022]
Abstract
Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.
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Affiliation(s)
- István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720 Szeged (Hungary), Fax: (+36) 62-545705
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18
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Johansson JR, Hermansson E, Nordén B, Kann N, Beke-Somfai T. δ-Peptides from RuAAC-Derived 1,5-Disubstituted Triazole Units. European J Org Chem 2014. [DOI: 10.1002/ejoc.201400018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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19
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Gerling UIM, Salwiczek M, Cadicamo CD, Erdbrink H, Czekelius C, Grage SL, Wadhwani P, Ulrich AS, Behrends M, Haufe G, Koksch B. Fluorinated amino acids in amyloid formation: a symphony of size, hydrophobicity and α-helix propensity. Chem Sci 2014. [DOI: 10.1039/c3sc52932k] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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20
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Krishnamurthy VM, Kumar K. Fluorination in the design of membrane protein assemblies. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 1063:227-43. [PMID: 23975781 DOI: 10.1007/978-1-62703-583-5_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Protein design approaches based on the binary patterning of nonpolar and polar amino acids have been successful in generating native-like protein structures of amphiphilic α-helices or idealized amphiphilic β-strands in aqueous solution. Such patterning is not possible in the nonpolar environment of biological membranes, precluding the application of conventional approaches to the design of membrane proteins that assemble into discrete aggregates. This review surveys a promising, new strategy for membrane protein design that exploits the unique properties of fluorocarbons-in particular, their ability to phase separate from both water (due to their hydrophobicity) and hydrocarbons (due to their lipophobicity)-to generate membrane protein assemblies. The ability to design such discrete assemblies should enable the disruption of protein-protein interactions and provide templates for novel biomaterials and therapeutics.
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21
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Del Borgo MP, Mechler AI, Traore D, Forsyth C, Wilce JA, Wilce MCJ, Aguilar MI, Perlmutter P. Supramolecular Self-Assembly ofN-Acetyl-Capped β-Peptides Leads to Nano- to Macroscale Fiber Formation. Angew Chem Int Ed Engl 2013; 52:8266-70. [DOI: 10.1002/anie.201303175] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Indexed: 12/26/2022]
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22
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Del Borgo MP, Mechler AI, Traore D, Forsyth C, Wilce JA, Wilce MCJ, Aguilar MI, Perlmutter P. Supramolecular Self-Assembly ofN-Acetyl-Capped β-Peptides Leads to Nano- to Macroscale Fiber Formation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One 2013; 8:e63906. [PMID: 23717507 PMCID: PMC3661552 DOI: 10.1371/journal.pone.0063906] [Citation(s) in RCA: 261] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.
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Affiliation(s)
- Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shane Ó. Conchúir
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin Drew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Brian D. Weitzner
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Parin Sripakdeevong
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Benjamin Borgo
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - James J. Havranek
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tanja Kortemme
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Physics, Stanford University, Stanford, California, United States of America
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24
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Sonti R, Gopi HN, Muddegowda U, Ragothama S, Balaram P. A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide. Chemistry 2013; 19:5955-65. [DOI: 10.1002/chem.201204327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 01/25/2023]
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25
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Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle. Chem Sci 2013. [DOI: 10.1039/c2sc21117c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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26
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Bellucci MC, Terraneo G, Volonterio A. Multi-component synthesis of peptide–sugar conjugates. Org Biomol Chem 2013; 11:2421-44. [DOI: 10.1039/c3ob27176e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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March TL, Johnston MR, Duggan PJ, Gardiner J. Synthesis, Structure, and Biological Applications ofα-Fluorinatedβ-Amino Acids and Derivatives. Chem Biodivers 2012; 9:2410-41. [DOI: 10.1002/cbdv.201200307] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Indexed: 01/30/2023]
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28
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Clark GA, Baleja JD, Kumar K. Cross-strand interactions of fluorinated amino acids in β-hairpin constructs. J Am Chem Soc 2012; 134:17912-21. [PMID: 23078597 DOI: 10.1021/ja212080f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe herein the design, synthesis, and thermodynamic characterization of fluorinated β-hairpin constructs. Introduction of hexafluoroleucine (Hfl) did not perturb β-hairpin formation, as judged by (1)H NMR structures of four peptides determined to <1 Å backbone RMSDs, allowing direct comparison of thermodynamic stabilities of fluorinated peptides to their hydrocarbon counterparts. Judicious fluorination of peptides often results in increased thermal and chemical stability of the resultant folded structures. However, we found that when cross-strand residue partners were varied, the side-chain interaction energies followed the order Leu-Leu > Hfl-Leu > Hfl-Hfl. All peptides were more structured in 90% MeOH than in aqueous buffers. The peptides with Hfl-Leu or Hfl-Hfl cross-strand partners showed increased interaction energies in this solvent compared to those in water, in contrast to the insignificant effect on Leu-Leu. Our results inform the binding and assembly of peptides containing Hfl in the context of β-sheet structures and may be useful in interpreting binding of fluorinated ligands and peptides to biological targets.
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Affiliation(s)
- Ginevra A Clark
- Department of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, USA
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29
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Wang PSP, Craig CJ, Schepartz A. Relationship between side-chain branching and stoichiometry in β(3)-peptide bundles. Tetrahedron 2012; 68:4342-4345. [PMID: 22822272 DOI: 10.1016/j.tet.2012.03.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The stability and stoichiometry of β(3)-peptide bundles is influenced by side-chain identity. β(3)-peptides containing β(3)-homoleucine on one helical face assemble into octamers, whereas those containing β(3)-homovaline form tetramers. From a structural perspective, the side chains of β(3)-homoleucine and β(3)-homovaline differ in terms of both side-chain length and γ-carbon branching. To evaluate the extent to which these two parameters control β(3)-peptide bundle stoichiometry, we synthesized the β(3)-peptide Acid-3Y, which contains β(3)-homoisoleucine in place of β(3)-homoleucine or β(3)-homovaline. Acid-3Y assembles into a stable tetramer whose stability resembles that of the previously characterized Acid-VY tetramer. These results suggest that β(3)-peptide bundle stoichiometry is dominated by the presence or absence of γ-carbon branching on core side chains.
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Affiliation(s)
- Pam Shou-Ping Wang
- Department of Chemistry, Yale University, 275 Prospect St., New Haven, CT 06520-8107
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30
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31
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Priya G, Kotmale AS, Gawade RL, Mishra D, Pal S, Puranik VG, Rajamohanan PR, Sanjayan GJ. Helical folding in heterogeneous foldamers without inter-residual backbone hydrogen-bonding. Chem Commun (Camb) 2012; 48:8922-4. [DOI: 10.1039/c2cc33235c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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32
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33
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Nishimoto K, Okada Y, Kim S, Chiba K. Rate acceleration of Diels–Alder reactions utilizing a fluorous micellar system in water. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.02.087] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Pomerantz WC, Yuwono VM, Drake R, Hartgerink JD, Abbott NL, Gellman SH. Lyotropic Liquid Crystals Formed from ACHC-Rich β-Peptides. J Am Chem Soc 2011; 133:13604-13. [DOI: 10.1021/ja204874h] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- William C. Pomerantz
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Virany M. Yuwono
- Department of Chemistry and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Ryan Drake
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jeffrey D. Hartgerink
- Department of Chemistry and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin−Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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35
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Romero-Romero ML, Inglés-Prieto A, Ibarra-Molero B, Sanchez-Ruiz JM. Highly anomalous energetics of protein cold denaturation linked to folding-unfolding kinetics. PLoS One 2011; 6:e23050. [PMID: 21829584 PMCID: PMC3146537 DOI: 10.1371/journal.pone.0023050] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/05/2011] [Indexed: 11/29/2022] Open
Abstract
Despite several careful experimental analyses, it is not yet clear whether protein cold-denaturation is just a “mirror image” of heat denaturation or whether it shows unique structural and energetic features. Here we report that, for a well-characterized small protein, heat denaturation and cold denaturation show dramatically different experimental energetic patterns. Specifically, while heat denaturation is endothermic, the cold transition (studied in the folding direction) occurs with negligible heat effect, in a manner seemingly akin to a gradual, second-order-like transition. We show that this highly anomalous energetics is actually an apparent effect associated to a large folding/unfolding free energy barrier and that it ultimately reflects kinetic stability, a naturally-selected trait in many protein systems. Kinetics thus emerges as an important factor linked to differential features of cold denaturation. We speculate that kinetic stabilization against cold denaturation may play a role in cold adaptation of psychrophilic organisms. Furthermore, we suggest that folding-unfolding kinetics should be taken into account when analyzing in vitro cold-denaturation experiments, in particular those carried out in the absence of destabilizing conditions.
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Affiliation(s)
- M. Luisa Romero-Romero
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Alvaro Inglés-Prieto
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, Universidad de Granada, Granada, Spain
- * E-mail:
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36
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Ducho C. A Kaleidoscope of Contemporary Organic Chemistry: The 46th Bürgenstock Conference. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/anie.201103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Ducho C. Ein Kaleidoskop der zeitgenössischen organischen Chemie: die 46. Bürgenstock-Konferenz. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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Korendovych IV, Shandler SJ, Montalvo GL, DeGrado WF. Environment- and sequence-dependence of helical type in membrane-spanning peptides composed of β3-amino acids. Org Lett 2011; 13:3474-7. [PMID: 21651308 PMCID: PMC3124938 DOI: 10.1021/ol201218y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane (TM) β-peptides comprised of acyclic β(3)-amino acids demonstrate equilibrium between 12- and 14-helical structures in an environment- and sequence-dependent manner. Circular dichroism (CD) spectra of TM β(3)-peptides may be described as linear combinations of the 12- and 14-helical CD spectra. The apparent malleability of β(3)-substituted acyclic β-peptides has practical implications for foldamer design, as it suggests that both the 14-helix and 12-helix might be reasonable platforms for molecular recognition.
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Affiliation(s)
- Ivan V Korendovych
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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39
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Cametti M, Crousse B, Metrangolo P, Milani R, Resnati G. The fluorous effect in biomolecular applications. Chem Soc Rev 2011; 41:31-42. [PMID: 21691620 DOI: 10.1039/c1cs15084g] [Citation(s) in RCA: 319] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
From being a niche area only a few decades ago, fluorous chemistry has gained momentum and is, nowadays, a fervent area of research. It has brought forth, in fact, numerous applicative innovations that stretch among different fields: from catalysis to separation science, from supramolecular to materials and analytical chemistry. Recently, the unique features of perfluorinated compounds have reached the attention of the biochemists' audience. This tutorial review introduces the basic concepts of fluorous chemistry and illustrates its main biomolecular applications. Special attention has been given to fluorous microarrays and their combination with Mass-Spectroscopy (MS) techniques, to protein properties modification by the introduction of local fluorous domains, and to the most recent applications of (19)F-Magnetic Resonance Imaging ((19)F-MRI).
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Affiliation(s)
- Massimo Cametti
- NFMLab-DCMIC Giulio Natta, Politecnico di Milano, via Mancinelli 7, I-20131 Milan, Italy
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40
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Craig CJ, Goodman JL, Schepartz A. Enhancing β3 -peptide bundle stability by design. Chembiochem 2011; 12:1035-8. [PMID: 21455925 DOI: 10.1002/cbic.201000753] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/07/2022]
Abstract
We reported recently that certain β(3) -peptides self-assemble in aqueous solution into discrete bundles of unique structure and defined stoichiometry. The first β-peptide bundle reported was the octameric Zwit-1F, whose fold is characterized by a well-packed, leucine-rich core and a salt-bridge-rich surface. Close inspection of the Zwit-1F structure revealed four nonideal interhelical salt-bridge interactions whose heavy atom-heavy atom distances were longer than found in natural proteins of known structure. Here we demonstrate that the thermodynamic stability of a β-peptide bundle can be enhanced by optimizing the length of these four interhelical salt bridges. Combined with previous work on the role of internal packing residues, these results provide another critical step in the "bottom-up" formation of β-peptide assemblies with defined sizes, reproducible structures, and sophisticated function.
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Affiliation(s)
- Cody J Craig
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA.
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41
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Delsuc N, Massip S, Léger JM, Kauffmann B, Huc I. Relative helix-helix conformations in branched aromatic oligoamide foldamers. J Am Chem Soc 2011; 133:3165-72. [PMID: 21306159 DOI: 10.1021/ja110677a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The de novo design and synthesis of large and well-organized, tertiary-like, α-peptidic folded architectures is difficult because it relies on multiple cooperative interactions within and between secondary folded motifs of relatively weak intrinsic stability. The very stable helical structures of oligoamides of 8-amino-2-quinoline carboxylic acid offer a way to circumvent this difficulty thanks to their ability to fold into predictable and stable secondary motifs. Branched architectures comprised of two pairs of tetrameric (1), pentameric (2), or octameric (3) oligomers connected via an ethylene glycol spacer were designed and synthesized. The short spacer holds two helices in close proximity, thus enabling interactions between them. Degrees of freedom allowed in the system are well-defined: the relative P or M handedness of the two helices; the relative orientation of the helix axes; and the gauche or anti conformation of the ethylene spacer. Investigating the structures of 1-3 in the solid state and in solution allowed a detailed picture to be drawn of their conformational preferences and dynamics. The high variability of the solid state structures provides many snapshots of possible solution conformations. Helix-helix handedness communication was evidenced and shown to depend both on solvent and on a defined set of side chains at the helix-helix interface. Interdigitation of the side chains was found to restrict free rotation about the ethylene spacer. One solid state structure shows a high level of symmetry and provides a firm basis to further design specific side chain/side chain directional interactions.
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Affiliation(s)
- Nicolas Delsuc
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR5248 and UMS3033, 2 rue Robert Escarpit, 33607 Pessac, France
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42
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Wang J, Lin D, Zhou S, Ding X, Soloshonok VA, Liu H. Asymmetric synthesis of sterically and electronically demanding linear ω-trifluoromethyl containing amino acids via alkylation of chiral equivalents of nucleophilic glycine and alanine. J Org Chem 2010; 76:684-7. [PMID: 21182272 DOI: 10.1021/jo102031b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An operationally convenient, scalable asymmetric synthesis of linear, ω-trifluoromethyl-containing amino acids, which were not previously produced in their enantiomerically pure form, has been developed via alkylation of chiral equivalents of nucleophilic glycine and alanine. The simplicity of the experimental procedures and high stereochemical outcome (yields up to 90% and diastereoselectivity up to 99%) of the presented method render these fluorinated amino acids readily available for systematic medicinal chemistry studies and de novo peptide design.
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Affiliation(s)
- Jiang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu chong zhi Road, Shanghai 201203, People's Republic of China
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Mándity IM, Fülöp L, Vass E, Tóth GK, Martinek TA, Fülöp F. Building β-peptide H10/12 foldamer helices with six-membered cyclic side-chains: fine-tuning of folding and self-assembly. Org Lett 2010; 12:5584-7. [PMID: 21050013 DOI: 10.1021/ol102494m] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The ability of the β-peptidic H10/12 helix to tolerate side-chains containing six-membered alicyclic rings was studied. cis-2-Aminocyclohex-3-ene carboxylic acid (cis-ACHEC) residues afforded H10/12 helix formation with alternating backbone configuration. Conformational polymorphism was observed for the alternating cis-ACHC hexamer, where chemical exchange takes place between the major left-handed H10/12 helix and a minor folded conformation. The hydrophobically driven self-assembly was achieved for the cis-ACHC-containing helix which was observed as vesicles ~100 nm in diameter.
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Affiliation(s)
- István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720 Szeged, Eötvös u. 6, Hungary
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Bellucci MC, Volonterio A. Multicomponent Synthesis of Peptide-Sugar Conjugates Incorporating Hexafluorovaline. Adv Synth Catal 2010. [DOI: 10.1002/adsc.201000489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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