1
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Schene ME, Infield DT, Ahern CA. Expression and purification of fluorinated proteins from mammalian suspension culture. Methods Enzymol 2024; 696:341-354. [PMID: 38658087 DOI: 10.1016/bs.mie.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The site-specific encoding of noncanonical amino acids allows for the introduction of rationalized chemistry into a target protein. Of the methods that enable this technology, evolved tRNA and synthetase pairs offer the potential for expanded protein production and purification. Such an approach combines the versatility of solid-phase peptide synthesis with the scalable features of recombinant protein production. We describe the large scale production and purification of eukaryotic proteins bearing fluorinated phenylalanine in mammalian suspension cell preparations. Downstream applications of this approach include scalable recombinant protein preparation for ligand binding assays with small molecules and ligands, protein structure determination, and protein stability assays.
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Affiliation(s)
- Miranda E Schene
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA.
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2
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Zeng LY, Qu PZ, Tao M, Pu G, Jia J, Wang P, Shang M, Li X, He CY. Synthesis of Alkylated Polyfluorobenzenes through Decarboxylative Giese Addition of Aliphatic N-Hydroxyphthalimide Esters with Polyfluorostyrene. J Org Chem 2023; 88:14105-14114. [PMID: 37708081 DOI: 10.1021/acs.joc.3c01672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Polyfluoroaromatic compounds play crucial roles in medicinal and material science. However, the synthesis of alkylated polyfluoroarenes has been relatively underdeveloped. In this study, we devised a novel decarboxylative coupling reaction between aliphatic N-hydroxyphthalimide esters and polyfluorostyrene, leveraging the photochemical activity of electron donor-acceptor (EDA) complexes. This method offers simple reaction conditions, a broad substrate scope, and excellent functional group tolerance. Furthermore, we have demonstrated the practicality of this protocol through late-stage polyfluoroaryl modification of biologically active molecules using readily available carboxylic acids as starting materials, thus providing an important supplement to the current toolbox for accessing alkylated polyfluoroaryl motifs.
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Affiliation(s)
- Lin-Yuan Zeng
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Pei-Zhen Qu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Maoling Tao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Guoliang Pu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Jia Jia
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Pan Wang
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Maocai Shang
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
| | - Xuefei Li
- Central Research Institute, United-Imaging Healthcare Group Co., Ltd, Shanghai 201807, P.R. China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563003, P.R. China
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, School of Pharmacy, Zunyi Medical University, Zunyi 563003, P.R. China
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3
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Bathgate RAD, Praveen P, Sethi A, Furuya WI, Dhingra RR, Kocan M, Ou Q, Valkovic AL, Gil-Miravet I, Navarro-Sánchez M, Olucha-Bordonau FE, Gundlach AL, Rosengren KJ, Gooley PR, Dutschmann M, Hossain MA. Noncovalent Peptide Stapling Using Alpha-Methyl-l-Phenylalanine for α-Helical Peptidomimetics. J Am Chem Soc 2023; 145:20242-20247. [PMID: 37439676 DOI: 10.1021/jacs.3c02743] [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: 07/14/2023]
Abstract
Peptides and peptidomimetics are attractive drug candidates because of their high target specificity and low-toxicity profiles. Developing peptidomimetics using hydrocarbon (HC)-stapling or other stapling strategies has gained momentum because of their high stability and resistance to proteases; however, they have limitations. Here, we take advantage of the α-methyl group and an aromatic phenyl ring in a unique unnatural amino acid, α-methyl-l-phenylalanine (αF), and propose a novel, noncovalent stapling strategy to stabilize peptides. We utilized this strategy to create an α-helical B-chain mimetic of a complex insulin-like peptide, human relaxin-3 (H3 relaxin). Our comprehensive data set (in vitro, ex vivo, and in vivo) confirmed that the new high-yielding B-chain mimetic, H3B10-27(13/17αF), is remarkably stable in serum and fully mimics the biological function of H3 relaxin. H3B10-27(13/17αF) is an excellent scaffold for further development as a drug lead and an important tool to decipher the physiological functions of the neuropeptide G protein-coupled receptor, RXFP3.
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Affiliation(s)
- Ross A D Bathgate
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Praveen Praveen
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ashish Sethi
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
- Australian Nuclear Science Technology Organisation, The Australian Synchrotron, Clayton, VIC 3168, Australia
| | - Werner I Furuya
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Rishi R Dhingra
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Martina Kocan
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Qinghao Ou
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Adam L Valkovic
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Isis Gil-Miravet
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Mónica Navarro-Sánchez
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Francisco E Olucha-Bordonau
- Predepartmental Unit of Medicine, Faculty of Health Sciences, Universitat Jaume I, Avenida de Vicent Sos Baynat, s/n, 12071 Castelló de La Plana, Spain
| | - Andrew L Gundlach
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3052, Australia
- Bio21 Molecular Science and Biotechnology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mathias Dutschmann
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mohammed Akhter Hossain
- The Florey, The University of Melbourne, Parkville, VIC 3052, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
- School of Chemistry, The University of Melbourne, Parkville, VIC 3052, Australia
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4
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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5
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Lin Y, Yong S, Scholtz CR, Du C, Sun S, Steinkruger JD, Zhou X, Zhou C, Yang S. Exploration of surface chemistry effects on the biodistribution and pharmacokinetics of dual-ligand luminescent gold nanoparticles. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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6
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Neitz H, Bessi I, Kachler V, Michel M, Höbartner C. Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA. Angew Chem Int Ed Engl 2023; 62:e202214456. [PMID: 36344446 PMCID: PMC10107946 DOI: 10.1002/anie.202214456] [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] [Received: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Irene Bessi
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Valentin Kachler
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Manuela Michel
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
- Center for Nanosystems Chemistry (CNC)University of WürzburgTheodor-Boveri-Weg97074WürzburgGermany
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7
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Kanbayashi N, Kataoka Y, Okamura TA, Onitsuka K. Stability Enhancement of a π-Stacked Helical Structure Using Substituents of an Amino Acid Side Chain: Helix Formation via a Nucleation-Elongation Mechanism. J Am Chem Soc 2022; 144:6080-6090. [PMID: 35325538 DOI: 10.1021/jacs.2c01337] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular design involving the incorporation of an α-amino acid residue into the side chain or main chain of a polymer is often used to stabilize artificial molecular architectures through intramolecular hydrogen bonding. However, this molecular design strategy rarely considers the importance of interactions between substituents at the α-position of amino acid moieties, as found in nature. Herein, we report the synthesis of a novel series of π-stacked helical poly(quinolylene-2,3-methylene) with amino acid derivatives bearing different substituents at the α-position. We found that the thermal stability of π-stacked helical poly(quinolylene-2,3-methylene) is significantly improved by packing the substituents in the empty spaces between the side chains. In particular, when a bulky cyclohexyl alanine derivative was used as the side chain, the π-stacked helical structure maintained its stability even in dimethylsulfoxide, a hydrogen bond competitor. The stabilization of the π-stacked structure by the amino acid substituents resulted in a unique polymerization behavior involving nucleation-elongation steps. In the case of derivatives with leucine and cyclohexyl alanine, which form stable π-stacked helical structures, metastable structures with entangled main chains were formed in the initial polymerization stage. These structures subsequently underwent an irreversible structural change to achieve a thermodynamically stable helical π-stacked conformation as a nucleus for subsequent polymerization. Thereafter, the polymerization reaction proceeded with the elongation of the π-stacked helical structure. Differences in the stability of these systems indicated that the amino acid substituents on the side chains determine the most thermodynamically stable π-stacked helical structure.
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Affiliation(s)
- Naoya Kanbayashi
- Department of Macromolecular Science Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 Japan
| | - Yuki Kataoka
- Department of Macromolecular Science Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 Japan
| | - Taka-Aki Okamura
- Department of Macromolecular Science Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 Japan
| | - Kiyotaka Onitsuka
- Department of Macromolecular Science Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043 Japan
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8
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Gou FH, Ma MJ, Wang AJ, Zhao L, Wang H, Tong J, Wang Z, Wang Z, He CY. Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids. Org Lett 2022; 24:240-244. [PMID: 34958223 DOI: 10.1021/acs.orglett.1c03884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp3-Csp3 cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.
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Affiliation(s)
- Fei-Hu Gou
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ming-Jian Ma
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - An-Jun Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Liang Zhao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Haoyang Wang
- Laboratory of Mass Spectrometry Analysis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Tong
- School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Ze Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zhen Wang
- School of Pharmaceutical Science, University of South China, Hengyang 421001, China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
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9
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Lee GY, Hu E, Rheingold AL, Houk KN, Sletten EM. Arene-Perfluoroarene Interactions in Solution. J Org Chem 2021; 86:8425-8436. [PMID: 34077211 DOI: 10.1021/acs.joc.1c00921] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic study of arene-perfluoroarene interactions in solution is presented. Using a combination of NMR titration experiments, X-ray crystallography, and computational analysis, we analyze the effects of fluorination, substituents, ring size, and solvation on the arene-perfluoroarene interaction. We find that fluorination, extension of the π systems, and enhancement of solvent polarity greatly stabilize the stacking energy up to 3 orders of magnitude (Ka = <1 to 6000 M-1), with the highest Ka achieved for the interaction of water-soluble variants of perfluoronaphthalene and anthracene in buffered D2O (pD = 12). Combining computational and experimental results, we conclude that this impressive binding energy is a result of enthalpically favorable electrostatic and dispersion interactions as well as the entropically driven hydrophobic effect. The enhanced understanding of arene-perfluoroarene interactions in aqueous solution sets the stage for the implementation of this abiotic intermolecular interaction in biology and medicine.
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Affiliation(s)
- Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Elizabeth Hu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Arnold L Rheingold
- Department of Chemistry and Biochemistry, University of California, San Diego, California 92093, United States
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
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10
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Potenti S, Spada L, Fusè M, Mancini G, Gualandi A, Leonardi C, Cozzi PG, Puzzarini C, Barone V. 4-Fluoro-Threonine: From Diastereoselective Synthesis to pH-Dependent Conformational Equilibrium in Aqueous Solution. ACS OMEGA 2021; 6:13170-13181. [PMID: 34056467 PMCID: PMC8158790 DOI: 10.1021/acsomega.1c01007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
4-Fluoro-threonine, the only fluoro amino acid of natural origin discovered so far, is an interesting target for both synthetic and theoretical investigations. In this work, we lay the foundation for spectroscopic characterization of 4-fluoro-threonine. First, we report a diastereoselective synthetic route, which is suitable to produce synthetic material for experimental characterization. The addition of the commercially available ethyl isocyanoacetate to benzyloxyacetaldehyde led to the corresponding benzyloxy-oxazoline, which was hydrolyzed and transformed into ethyl (4S*,5S*)-5-hydroxymethyl-2-oxo-4-oxazolidinecarboxylate in a few steps. Fluorination with diethylamino sulfur trifluoride (DAST) afforded ethyl (4S*,5S*)-5-fluoromethyl-2-oxo-4-oxazolidinecarboxylate, which was deprotected to give the desired diastereomerically pure 4-fluoro-threonine, in 8-10% overall yield. With the synthetic material in our hands, acid-base titrations have been carried out to determine acid dissociation constants and the isoelectric point, which is the testing ground for the theoretical analysis. We have used machine learning coupled with quantum chemistry at the state-of-the-art to analyze the conformational space of 4-fluoro-threonine, with the aim of gaining insights from the comparison of computational and experimental results. Indeed, we have demonstrated that our approach, which couples a last-generation double-hybrid density functional including empirical dispersion contributions with a model combining explicit first-shell molecules and a polarizable continuum for describing solvent effects, provides results and trends in remarkable agreement with experiments. Finally, the conformational analysis applied to fluoro amino acids represents an interesting study for the effect of fluorine on the stability and population of conformers.
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Affiliation(s)
- Simone Potenti
- Laboratorio
SMART, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Lorenzo Spada
- Laboratorio
SMART, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Dipartimento
di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Marco Fusè
- Laboratorio
SMART, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giordano Mancini
- Laboratorio
SMART, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Istituto
Nazionale di Fisica Nucleare (INFN), Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Andrea Gualandi
- Dipartimento
di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Costanza Leonardi
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università
di Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Pier Giorgio Cozzi
- Dipartimento
di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Cristina Puzzarini
- Dipartimento
di Chimica “Giacomo Ciamician”, Alma Mater Studiorum—Università di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Vincenzo Barone
- Laboratorio
SMART, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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11
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Niedek D, Erb FR, Topp C, Seitz A, Wende RC, Eckhardt AK, Kind J, Herold D, Thiele CM, Schreiner PR. In Situ Switching of Site-Selectivity with Light in the Acetylation of Sugars with Azopeptide Catalysts. J Org Chem 2020; 85:1835-1846. [PMID: 31763833 DOI: 10.1021/acs.joc.9b01913] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present a novel concept for the in situ control of site-selectivity of catalytic acetylations of partially protected sugars using light as external stimulus and oligopeptide catalysts equipped with an azobenzene moiety. The isomerizable azobenzene-peptide backbone defines the size and shape of the catalytic pocket, while the π-methyl-l-histidine (Pmh) moiety transfers the electrophile. Photoisomerization of the E- to the Z-azobenzene catalyst (monitored via NMR) with an LED (λ = 365 nm) drastically changes the chemical environment around the catalytically active Pmh moiety, so that the light-induced change in the catalyst shape alters site-selectivity. As a proof of principle, we employed (4,6-O-benzylidene)methyl-α-d-pyranosides, which provide a change in regioselectivity from 2:1 (E) to 1:5 (Z) for the monoacetylated products at room temperature. The validity of this new catalyst-design concept is further demonstrated with the regioselective acetylation of the natural product quercetin. In situ irradiation NMR spectroscopy was used to quantify photostationary states under continuous irradiation with UV light.
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Affiliation(s)
- Dominik Niedek
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Frederik R Erb
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Christopher Topp
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Alexander Seitz
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Raffael C Wende
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - André K Eckhardt
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
| | - Jonas Kind
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Dominik Herold
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt , Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry , Justus Liebig University , Heinrich-Buff-Ring 17 , 35392 Giessen , Germany
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12
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Garcia AM, Lavendomme R, Kralj S, Kurbasic M, Bellotto O, Cringoli MC, Semeraro S, Bandiera A, De Zorzi R, Marchesan S. Self-Assembly of an Amino Acid Derivative into an Antimicrobial Hydrogel Biomaterial. Chemistry 2020; 26:1880-1886. [PMID: 31868256 DOI: 10.1002/chem.201905681] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Indexed: 02/06/2023]
Abstract
N-(4-Nitrobenzoyl)-Phe self-assembled into a transparent supramolecular hydrogel, which displayed high fibroblast and keratinocyte cell viability. The compound showed a mild antimicrobial activity against E. coli both as a hydrogel and in solution. Single-crystal XRD data revealed packing details, including protonation of the C-terminus due to an apparent pKa shift, as confirmed by pH titrations. MicroRaman analysis revealed almost identical features between the gel and crystal states, although more disorder in the former. The hydrogel is thermoreversible and disassembles within a range of temperatures that can be fine-tuned by experimental conditions, such as gelator concentration. At the minimum gelling concentration of 0.63 wt %, the hydrogel disassembles in a physiological temperature range of 39-42 °C, thus opening the way to its potential use as a biomaterial.
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Affiliation(s)
- Ana M Garcia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Roy Lavendomme
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Slavko Kralj
- Materials Synthesis Department, Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Marina Kurbasic
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Ottavia Bellotto
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Maria C Cringoli
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Sabrina Semeraro
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Antonella Bandiera
- Dipartimento di Scienze della Vita, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Rita De Zorzi
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
| | - Silvia Marchesan
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127, Trieste, Italy
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13
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Tyrikos-Ergas T, Fittolani G, Seeberger PH, Delbianco M. Structural Studies Using Unnatural Oligosaccharides: Toward Sugar Foldamers. Biomacromolecules 2019; 21:18-29. [DOI: 10.1021/acs.biomac.9b01090] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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14
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Thota CK, Berger AA, Harms B, Seidel M, Böttcher C, von Berlepsch H, Xie C, Süssmuth R, Roth C, Koksch B. Short self‐assembling cationic antimicrobial peptide mimetics based on a 3,5‐diaminobenzoic acid scaffold. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24130] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chaitanya K. Thota
- Department of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Allison A. Berger
- Department of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Björn Harms
- Department of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | - Maria Seidel
- Institute of ChemistryTechnische Universität Berlin Berlin Germany
| | - Christoph Böttcher
- Research Center for Electron MicroscopyFreie Universität Berlin Berlin Germany
| | - Hans von Berlepsch
- Research Center for Electron MicroscopyFreie Universität Berlin Berlin Germany
| | - Chaunxiong Xie
- Department of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
| | | | - Christian Roth
- Department of Biomolecular SystemsMax Planck Institute of Colloids and Interfaces Berlin Germany
| | - Beate Koksch
- Department of Chemistry and BiochemistryFreie Universität Berlin Berlin Germany
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15
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Real-time and in-situ monitoring of Abrin induced cell apoptosis by using SERS spectroscopy. Talanta 2019; 195:8-16. [DOI: 10.1016/j.talanta.2018.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 02/07/2023]
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16
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Hosseini AS, Pace CJ, Esposito AA, Gao J. Non-additive stabilization by halogenated amino acids reveals protein plasticity on a sub-angstrom scale. Protein Sci 2017; 26:2051-2058. [PMID: 28737009 PMCID: PMC5606540 DOI: 10.1002/pro.3242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 01/21/2023]
Abstract
It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity. In this contribution, we present a systematic study of three well-folded model protein systems, in which their structural stabilities are assessed in response to various hydrogen-to-halogen atom mutations. Halogenation allows for the perturbation of proteins on a sub-angstrom scale, offering unprecedented precision of protein engineering. The thermodynamic results from these model systems reveal that in certain cases, proteins can display modest steric tolerance to halogenation, yielding non-additive consequences to protein stability. The observed sub-angstrom sensitivity of protein stability highlights the delicate arrangement of a folded protein core structure. The stability data of various halogenated proteins presented herein should also provide guidelines for using halogenation as a strategy to improve the stability of protein therapeutics.
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Affiliation(s)
- Azade S. Hosseini
- Department of ChemistryMerkert Chemistry Center, Boston CollegeChestnut HillMassachusetts02467
- Present address:
Department of ChemistryMassachusetts Institute of Technology77 Massachusetts Avenue, CambridgeMassachusetts02139
| | - Christopher J. Pace
- Department of ChemistryMerkert Chemistry Center, Boston CollegeChestnut HillMassachusetts02467
| | - Adam A. Esposito
- Department of ChemistryMerkert Chemistry Center, Boston CollegeChestnut HillMassachusetts02467
| | - Jianmin Gao
- Department of ChemistryMerkert Chemistry Center, Boston CollegeChestnut HillMassachusetts02467
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17
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Fisher BF, Hong SH, Gellman SH. Helix Propensities of Amino Acid Residues via Thioester Exchange. J Am Chem Soc 2017; 139:13292-13295. [PMID: 28898059 PMCID: PMC5995559 DOI: 10.1021/jacs.7b07930] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We describe the use of thioester exchange equilibria to measure the propensities of amino acid residues to participate in helical secondary structure at room temperature in the absence of denaturants. Thermally or chemically induced unfolding has previously been employed to measure α-helix propensities among proteinogenic α-amino acid residues, and quantitative comparison with precedents indicates that the thioester exchange system is reliable for residues that lack side chain charge. This system allows the measurement of α-helix propensities for d-α-amino acid residues and propensities of residues with nonproteinogenic backbones, such as those derived from a β-amino acid, to participate in an α-helix-like secondary structure.
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Affiliation(s)
- Brian F. Fisher
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Seong Ho Hong
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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18
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Yan B, Ye L, Xu W, Liu L. Recent advances in racemic protein crystallography. Bioorg Med Chem 2017; 25:4953-4965. [DOI: 10.1016/j.bmc.2017.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
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19
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Rajbhandary A, Raymond DM, Nilsson BL. Self-Assembly, Hydrogelation, and Nanotube Formation by Cation-Modified Phenylalanine Derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5803-5813. [PMID: 28514156 DOI: 10.1021/acs.langmuir.7b00686] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorenylmethoxycarbonyl-protected phenylalanine (Fmoc-Phe) derivatives are a privileged class of molecule that spontaneously self-assemble into hydrogel fibril networks. Fmoc-Phe-derived hydrogels are typically formed by dilution of the hydrogelator from an organic cosolvent into water, by dissolution of the hydrogelator under basic aqueous conditions followed by adjustment of the pH with acid, or by other external triggering forces, including sonication and heating. These conditions complicate biological applications of these hydrogels. Herein, we report C-terminal cation-modified Fmoc-Phe derivatives that are positively charged across a broad range of pH values and that can self-assemble and form hydrogel networks spontaneously without the need to adjust pH or to use an organic cosolvent. In addition, these cationic Fmoc-Phe derivatives are found to self-assemble into novel sheet-based nanotube structures at higher concentrations. These nanotube structures are unique to C-terminal cationic Fmoc-Phe derivatives; the parent Fmoc-Phe carboxylic acids form only fibril or worm-like micelle structures. Nanotube formation by the cationic Fmoc-Phe molecules is dependent on positive charge at the C-terminus, since at basic pH where the positive charge is reduced only fibrils/worm-like micelles are formed and nanotube formation is suppressed. These studies provide an important example of Fmoc-Phe derivatives that can elicit hydrogelation without organic cosolvent or pH modification and also provide insight into how subtle modification of structure can perturb the self-assembly pathways of Fmoc-Phe derivatives.
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Affiliation(s)
- Annada Rajbhandary
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Danielle M Raymond
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester , Rochester, New York 14627-0216, United States
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20
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Li SS, Guan QY, Meng G, Chang XF, Wei JW, Wang P, Kang B, Xu JJ, Chen HY. Revealing chemical processes and kinetics of drug action within single living cells via plasmonic Raman probes. Sci Rep 2017; 7:2296. [PMID: 28536451 PMCID: PMC5442120 DOI: 10.1038/s41598-017-02510-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/12/2017] [Indexed: 01/18/2023] Open
Abstract
Better understanding the drug action within cells may extend our knowledge on drug action mechanisms and promote new drugs discovery. Herein, we studied the processes of drug induced chemical changes on proteins and nucleic acids in human breast adenocarcinoma (MCF-7) cells via time-resolved plasmonic-enhanced Raman spectroscopy (PERS) in combination with principal component analysis (PCA). Using three popular chemotherapy drugs (fluorouracil, cisplatin and camptothecin) as models, chemical changes during drug action process were clearly discriminated. Reaction kinetics related to protein denaturation, conformational modification, DNA damage and their associated biomolecular events were calculated. Through rate constants and reaction delay times, the different action modes of these drugs could be distinguished. These results may provide vital insights into understanding the chemical reactions associated with drug-cell interactions.
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Affiliation(s)
- Shan-Shan Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qi-Yuan Guan
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Gang Meng
- Jiangsu Key Laboratory of Molecular Medicine, Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Xiao-Feng Chang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - Ji-Wu Wei
- Jiangsu Key Laboratory of Molecular Medicine, Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Peng Wang
- National Laboratory of Solid State Microstructures, College of Engineering and Applied Sciences and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
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21
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Chen Y, Li T, Li J, Cheng S, Wang J, Verma C, Zhao Y, Wu C. Stabilization of peptides against proteolysis through disulfide-bridged conjugation with synthetic aromatics. Org Biomol Chem 2017; 15:1921-1929. [DOI: 10.1039/c6ob02786e] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We developed an efficient strategy for the stabilization of peptides against proteolysis, which involves noncovalent π–π interactions between aromatic amino acid residues in peptides and synthetic electron-deficient aromatics.
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Affiliation(s)
- Yaqi Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Tao Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Jianguo Li
- Singapore Eye Research Institute
- Singapore
- Bioinformatics Institute (A*STAR)
- Singapore
| | - Shiyan Cheng
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Jinghui Wang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Chandra Verma
- Bioinformatics Institute (A*STAR)
- Singapore
- National University of Singapore
- Department of Biological Sciences
- Singapore
| | - Yibing Zhao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Department of Chemistry
- College of Chemistry and Chemical Engineering
- Xiamen University
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22
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Kang B, Li SS, Guan QY, Chen AP, Zhang PK, Zhang LB, Wei JW, Xu JJ, Chen HY. Plasmon-enhanced Raman spectroscopic metrics for in situ quantitative and dynamic assays of cell apoptosis and necrosis. Chem Sci 2016; 8:1243-1250. [PMID: 28451266 PMCID: PMC5369531 DOI: 10.1039/c6sc02486f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/01/2016] [Indexed: 01/24/2023] Open
Abstract
Plasmon-enhanced Raman spectroscopic metrics were developed for in situ quantitative and dynamic assays of viable, apoptotic and necrotic cells.
Apoptosis and necrosis are distinct cell death processes related to many cellular pathways. In situ, quantitatively and dynamically monitoring such processes may provide vitally important information for cell studies. However, such a method still remains elusive, even though current immunochemical methodologies have developed extremely valuable tools. Herein, we demonstrate Raman spectroscopic metrics for validating and quantifying apoptotic and necrotic cells based on their distinct molecular vibrational fingerprints. It not only allows us to quantify apoptotic and necrotic cell populations in situ in adherent cell samples, but also to be capable of continuously monitoring the dynamical processes of apoptosis and necrosis at the same time in one sample. This method provides comparable results with the “gold standard” of flow cytometry, moreover, with several incomparable advantages. Our work offers a powerful new tool for cell apoptosis and necrosis assays and is expected to become a benchmark technology in biological and medical studies.
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Affiliation(s)
- Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Shan-Shan Li
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Qi-Yuan Guan
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Ai-Ping Chen
- Jiangsu Key Laboratory of Molecular Medicine , Medical School , The State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , 210093 , China
| | - Pan-Ke Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Li-Bin Zhang
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Ji-Wu Wei
- Jiangsu Key Laboratory of Molecular Medicine , Medical School , The State Key Laboratory of Pharmaceutical Biotechnology , Nanjing University , 210093 , China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science , Collaborative Innovation Center of Chemistry for Life Sciences , School of Chemistry and Chemical Engineering , Nanjing University , 210023 , China . ;
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23
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Brachvogel RC, von Delius M. The Dynamic Covalent Chemistry of Esters, Acetals and Orthoesters. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600388] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- René-Chris Brachvogel
- Institute of Organic Chemistry and Advanced Materials; University of Ulm; Albert-Einstein-Allee 11 89081 Ulm Germany
- Friedrich-Alexander University Erlangen-Nürnberg (FAU); Department of Chemistry and Pharmacy & Interdisciplinary Center of Molecular Materials (ICMM); Henkestr. 42 91054 Erlangen Germany
| | - Max von Delius
- Institute of Organic Chemistry and Advanced Materials; University of Ulm; Albert-Einstein-Allee 11 89081 Ulm Germany
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24
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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25
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Yu YB, Luo ZJ, Zhang X. Copper-Catalyzed Direct Propargylation of Polyfluoroarenes with Secondary Propargyl Phosphates. Org Lett 2016; 18:3302-5. [DOI: 10.1021/acs.orglett.6b01642] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan-Bo Yu
- Key Laboratory of Organofluorine
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Zhi-Ji Luo
- Key Laboratory of Organofluorine
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
| | - Xingang Zhang
- Key Laboratory of Organofluorine
Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Lu, Shanghai 200032, China
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26
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Hsu WL, Shih TC, Horng JC. Folding stability modulation of the villin headpiece helical subdomain by 4-fluorophenylalanine and 4-methylphenylalanine. Biopolymers 2016; 103:627-37. [PMID: 26017817 DOI: 10.1002/bip.22689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/25/2015] [Accepted: 05/25/2015] [Indexed: 11/10/2022]
Abstract
HP36, the helical subdomain of villin headpiece, contains a hydrophobic core composed of three phenylalanine residues (Phe47, Phe51, and Phe58). Hydrophobic effects and electrostatic interactions were shown to be the critical factors in stabilizing this core and the global structure. To assess the interactions among Phe47, Phe51, and Phe58 residues and investigate how they affect the folding stability, we implanted 4-fluorophenylalanine (Z) and 4-methylphenylalanine (X) into the hydrophobic core of HP36. We chemically synthesized HP36 and its seven variants including four single mutants whose Phe51 or Phe58 was replaced with Z or X, and three double mutants whose Phe51 and Phe58 were both substituted. Circular dichroism and nuclear magnetic resonance measurements show that the variants exhibit a native HP36 like fold, of which F51Z and three double mutants are more stable than the wild type. Molecular modeling provided detailed interaction energy within the phenylalanine residues, revealing that electrostatic interactions dominate the stability modulation upon the introduction of 4-fluorophenylalanine and 4-methylphenylalanine. Our results show that these two non-natural amino acids can successfully tune the interactions in a relatively compact hydrophobic core and the folding stability without inducing dramatic steric effects. Such an approach may be applied to other folded motifs or proteins.
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Affiliation(s)
- Wei-Lin Hsu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
| | - Ting-Chia Shih
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan, 30013, R.O.C
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27
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Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
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28
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Odar C, Winkler M, Wiltschi B. Fluoro amino acids: A rarity in nature, yet a prospect for protein engineering. Biotechnol J 2015; 10:427-46. [DOI: 10.1002/biot.201400587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
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29
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Matsuzaki K, Okuyama K, Tokunaga E, Shiro M, Shibata N. Sterically Demanding Unsymmetrical Diaryl-λ(3)-iodanes for Electrophilic Pentafluorophenylation and an Approach to α-Pentafluorophenyl Carbonyl Compounds with an All-Carbon Stereocenter. ChemistryOpen 2015; 3:233-7. [PMID: 25558441 PMCID: PMC4280821 DOI: 10.1002/open.201402045] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Indexed: 01/09/2023] Open
Abstract
A sterically demanding unsymmetrical pentafluorophenyl-triisopropylphenyl-λ(3)-iodane was developed as an effective reagent for the electrophilic pentafluorophenylation of various β-keto esters and a β-keto amide. 17 examples of α-pentafluorophenylated 1,3-dicarbonyl compounds 3 having a quaternary carbon center are provided. The resulting compounds were nicely transformed into chiral α-pentafluorophenyl ketones with an all-carbon stereogenic center in high yields and high enantioselectivities using asymmetric organocatalysis (up to 98 % ee) or asymmetric metal catalysis (up to 82 % ee).
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Affiliation(s)
- Kohei Matsuzaki
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Kenta Okuyama
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Etsuko Tokunaga
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
| | - Motoo Shiro
- Rigaku Corporation 3-9-12 Mastubara-cho, Akishima, Tokyo 196-8666 (Japan)
| | - Norio Shibata
- Department of Nanopharmaceutical Science & Department of Frontier Materials, Nagoya Institute of Technology Gokiso, Showa-ku, Nagoya 466-8555 (Japan) E-mail:
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30
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Maynard SJ, Almeida AM, Yoshimi Y, Gellman SH. New charge-bearing amino acid residues that promote β-sheet secondary structure. J Am Chem Soc 2014; 136:16683-8. [PMID: 25393077 PMCID: PMC4277779 DOI: 10.1021/ja510265e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Proteinogenic
amino acid residues that promote β-sheet secondary
structure are hydrophobic (e.g., Ile or Val) or only moderately polar
(e.g., Thr). The design of peptides intended to display β-sheet
secondary structure in water typically requires one set of residues
to ensure conformational stability and an orthogonal set, with charged
side chains, to ensure aqueous solubility and discourage self-association.
Here we describe new amino acids that manifest substantial β-sheet
propensity, by virtue of β-branching, and also bear an ionizable
group in the side chain.
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Affiliation(s)
- Stacy J Maynard
- Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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31
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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32
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Asano A, Yamada T, Doi M. Modulating the structure of phenylalanine-incorporated ascidiacyclamide through fluorination. J Pept Sci 2014; 20:794-802. [DOI: 10.1002/psc.2668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/14/2014] [Accepted: 06/03/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Akiko Asano
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
| | - Takeshi Yamada
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences; 4-20-1, Nasahara Takatsuki Osaka 569-1094 Japan
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33
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Kang B, Austin LA, El-Sayed MA. Observing real-time molecular event dynamics of apoptosis in living cancer cells using nuclear-targeted plasmonically enhanced Raman nanoprobes. ACS NANO 2014; 8:4883-92. [PMID: 24708404 DOI: 10.1021/nn500840x] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Apoptosis is a biological process that plays important roles in embryogenesis, aging, and various diseases. During the process of apoptosis, cells undergo a series of morphological and molecular events such as blebbing, cell shrinkage, proteolysis, and nuclear DNA fragmentation. Investigating these events on a molecular level is crucial for gaining a more complete understanding of the intricate mechanism of apoptosis; however, the simultaneous direct observation of morphological and molecular events in real-time on a single living cell scale still remains a challenge. Herein, we directly monitored morphological and molecular events during cellular apoptosis in real-time after the treatment of an apoptosis-inducing agent, by utilizing our previously described plasmonically enhanced Rayleigh/Raman spectroscopic technique. Spectroscopic analysis of the DNA/protein composition around the cell nucleus revealed the occurrence and dynamics of three apoptotic molecular events: protein denaturation, proteolysis, and DNA fragmentation. The molecular event dynamics were used to create a temporal profile of apoptotic events in single cells. It is found that the sequence of events occurring in the apoptotic process induced by hydrogen peroxide addition is protein denaturation through disulfide bond breakage as well as DNA fragmentation, followed in time by protein unraveling with hydrophobic amino acid exposure, and finally protein degradation. These results demonstrate the potential of using this time-dependent plasmonically enhanced vibrational imaging technique to study the detailed mechanism of other apoptosis molecular pathways induced by different agents (e.g., anticancer drugs). A note is given in the conclusion discussing the expected large difference between the SERS spectrum of biological molecules in solution and that observed in live cells which are enhanced by the plasmonic field of the aggregated nanoparticles.
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Affiliation(s)
- Bin Kang
- Laser Dynamics Laboratory, School of Chemistry and Biochemistry, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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34
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Avan I, Hall CD, Katritzky AR. Peptidomimetics via modifications of amino acids and peptide bonds. Chem Soc Rev 2014; 43:3575-94. [DOI: 10.1039/c3cs60384a] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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35
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Abstract
Highly fluorinated analogs of hydrophobic amino acids have proven to be generally effective in increasing the thermodynamic stability of proteins. These non-proteogenic amino acids can be incorporated into both α-helix and β-sheet structural motifs and generally enhance protein stability towards unfolding by heat and chemical denaturants, and retard their degradation by proteases. Recent detailed structural and thermodynamic studies have demonstrated that the increase in buried hydrophobic surface area that accompanies fluorination is primarily responsible for the stabilizing properties of fluorinated side chains. Fluorination appears to be a particularly useful strategy for increasing protein stability because fluorinated amino acids closely retain the shape of the side chain, and are thus minimally perturbing to protein structure and function. The first part of this chapter discusses some examples of highly fluorinated model proteins designed by our laboratory and protocols for their synthesis. In the second part, methods for determining their thermodynamic stability, along with conditions that have proven to be useful for crystallizing these proteins, are presented.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109, USA
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36
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Mortenson DE, Kreitler DF, Yun HG, Gellman SH, Forest KT. Evidence for small-molecule-mediated loop stabilization in the structure of the isolated Pin1 WW domain. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2506-12. [PMID: 24311591 PMCID: PMC3852655 DOI: 10.1107/s090744491302444x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 09/02/2013] [Indexed: 11/10/2022]
Abstract
The human Pin1 WW domain is a small autonomously folding protein that has been useful as a model system for biophysical studies of β-sheet folding. This domain has resisted previous attempts at crystallization for X-ray diffraction studies, perhaps because of intrinsic conformational flexibility that interferes with the formation of a crystal lattice. Here, the crystal structure of the human Pin1 WW domain has been obtained via racemic crystallization in the presence of small-molecule additives. Both enantiomers of a 36-residue variant of the Pin1 WW domain were synthesized chemically, and the L- and D-polypeptides were combined to afford diffracting crystals. The structural data revealed packing interactions of small carboxylic acids, either achiral citrate or a D,L mixture of malic acid, with a mobile loop region of the WW-domain fold. These interactions with solution additives may explain our success in crystallization of this protein racemate. Molecular-dynamics simulations starting from the structure of the Pin1 WW domain suggest that the crystal structure closely resembles the conformation of this domain in solution. The structural data presented here should provide a basis for further studies of this important model system.
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Affiliation(s)
- David E. Mortenson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dale F. Kreitler
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Hyun Gi Yun
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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37
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Pace CJ, Gao J. Exploring and exploiting polar-π interactions with fluorinated aromatic amino acids. Acc Chem Res 2013; 46:907-15. [PMID: 23095018 DOI: 10.1021/ar300086n] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorination has become an increasingly attractive strategy in protein engineering for both basic research and biomedical applications. Thus researchers would like to understand the consequences of fluorination to the structure, stability, and function of target proteins. Although a substantial amount of work has focused on understanding the properties of fluorinated aliphatic amino acids, much less is known about fluorinated aromatic residues. In addition, polar-π interactions, often referred to as aromatic interactions, may play a significant role in protein folding and protein-protein interactions. Fluorination of aromatic residues presents an ideal strategy for probing polar-π interactions in proteins. This Account summarizes the recent studies of the incorporation of fluorinated aromatic amino acids into proteins. Herein we discuss the effects of fluorinating aromatic residues and rationalize them in the context of polar-π interactions. The results strongly support the proposal that polar-π interactions are energetically significant to protein folding and function. For example, an edge-face interaction of a pair of phenylalanines contributes as much as -1 kcal/mol to protein stability, while cation-π interactions can be much stronger. Furthermore, this new knowledge provides guidelines for protein engineering with fluorination. Importantly, incorporating perfluorinated aromatic residues into proteins enables novel mechanisms of molecular recognition that do not exist in native proteins, such as arene-perfluoroarene stacking. Such novel mechanisms can be used for programming protein folding specificity and engineering peptide-based materials.
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Affiliation(s)
- Christopher J. Pace
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467, United States
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38
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Profit AA, Felsen V, Chinwong J, Mojica ERE, Desamero RZB. Evidence of π-stacking interactions in the self-assembly of hIAPP(22-29). Proteins 2013; 81:690-703. [PMID: 23229921 PMCID: PMC3594381 DOI: 10.1002/prot.24229] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/29/2012] [Accepted: 11/28/2012] [Indexed: 12/16/2022]
Abstract
The role aromatic amino acids play in the formation of amyloid is a subject of controversy. In an effort to clarify the contribution of aromaticity to the self-assembly of human islet amyloid polypeptide (hIAPP)22-29 , peptide analogs containing electron donating groups (EDGs) or electron withdrawing groups (EWGs) as substituents on the aromatic ring of Phe-23 at the para position have been synthesized and characterized using turbidity measurements in conjunction with Raman and fluorescence spectroscopy. Results indicate the incorporation of EDGs on the aromatic ring of Phe-23 virtually abolish the ability of hIAPP22-29 to form amyloid. Peptides containing EWGs were still capable of forming aggregates. These aggregates were found to be rich in β-sheet secondary structure. Transmission electron microscopy images of the aggregates confirm the presence of amyloid fibrils. The observed difference in amyloidogenic propensity between peptides containing EDGs and those with EWGs appears not to be based on differences in peptide hydrophobicity. Fluorescence and Raman spectroscopic investigations reveal that the environment surrounding the aromatic ring becomes more hydrophobic and ordered upon aggregation. Furthermore, Raman measurements of peptide analogs containing EWGs, conclusively demonstrate a distinct downshift in the CC ring mode (ca. 1600 cm(-1) ) upon aggregation that has previously been shown to be indicative of π-stacking. While previous work has demonstrated that π-stacking is not an absolute requirement for fibrillization, our findings indicate that Phe-23 also contributes to fibril formation through π-stacking interactions and that it is not only the hydrophobic nature of this residue that is relevant in the self-assembly of hIAPP22-29 . © Proteins 2013. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Adam A. Profit
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Valentina Felsen
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Justina Chinwong
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Elmer-Rico E. Mojica
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
| | - Ruel Z. B. Desamero
- York College, Institute for Macromolecular Assemblies and the Graduate Center of the City University of New York, Jamaica, New York, 11451
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39
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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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40
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Daeffler KNM, Lester HA, Dougherty DA. Functionally important aromatic-aromatic and sulfur-π interactions in the D2 dopamine receptor. J Am Chem Soc 2012; 134:14890-6. [PMID: 22897614 PMCID: PMC3461201 DOI: 10.1021/ja304560x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The recently published crystal structure of the D3 dopamine receptor shows a tightly packed region of aromatic residues on helices 5 and 6 in the space bridging the binding site and what is thought to be the origin of intracellular helical motion. This highly conserved region also makes contacts with residues on helix 3, and here we use double mutant cycle analysis and unnatural amino acid mutagenesis to probe the functional role of several residues in this region of the closely related D2 dopamine receptor. Of the eight mutant pairs examined, all show significant functional coupling (Ω > 2), with the largest coupling coefficients observed between residues on different helices, C3.36/W6.48, T3.37/S5.46, and F5.47/F6.52. Additionally, three aromatic residues examined, F5.47, Y5.48, and F5.51, show consistent trends upon progressive fluorination of the aromatic side chain. These trends are indicative of a functionally important electrostatic interaction with the face of the aromatic residue examined, which is likely attributed to aromatic-aromatic interactions between residues in this microdomain. We also propose that the previously determined fluorination trend at W6.48 is likely due to a sulfur-π interaction with the side chain of C3.36. We conclude that these residues form a tightly packed structural microdomain that connects helices 3, 5, and 6, thus forming a barrier that prevents dopamine from binding further toward the intracellular surface. Upon activation, these residues likely do not change their relative conformation, but rather act to translate agonist binding at the extracellular surface into the large intracellular movements that characterize receptor activation.
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Affiliation(s)
- Kristina N.-M. Daeffler
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Henry A. Lester
- Division of Biology, California Institute of Technology, Pasadena, California 91125, United States
| | - Dennis A. Dougherty
- Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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41
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Buer BC, Levin BJ, Marsh ENG. Influence of Fluorination on the Thermodynamics of Protein Folding. J Am Chem Soc 2012; 134:13027-34. [DOI: 10.1021/ja303521h] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin C. Buer
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - Benjamin J. Levin
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
| | - E. Neil G. Marsh
- Departments of †Chemistry and ‡Biological Chemistry, University of Michigan, Ann Arbor, Michigan
48109, United States
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42
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Chung MK, White PS, Lee SJ, Waters ML, Gagné MR. Self-Assembled Multi-Component Catenanes: Structural Insights into an Adaptable Class of Molecular Receptors and [2]-Catenanes. J Am Chem Soc 2012; 134:11415-29. [DOI: 10.1021/ja302345n] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mee-Kyung Chung
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Peter S. White
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Stephen J. Lee
- U.S. Army Research Office, P.O.
Box 12211, Research Triangle Park, North Carolina 27709, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
| | - Michel R. Gagné
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel
Hill, North Carolina 27599-3290, United States
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43
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Buer BC, Marsh ENG. Fluorine: a new element in protein design. Protein Sci 2012; 21:453-62. [PMID: 22274989 PMCID: PMC3375745 DOI: 10.1002/pro.2030] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 01/09/2012] [Indexed: 11/08/2022]
Abstract
Fluorocarbons are quintessentially man-made molecules, fluorine being all but absent from biology. Perfluorinated molecules exhibit novel physicochemical properties that include extreme chemical inertness, thermal stability, and an unusual propensity for phase segregation. The question we and others have sought to answer is to what extent can these properties be engineered into proteins? Here, we review recent studies in which proteins have been designed that incorporate highly fluorinated analogs of hydrophobic amino acids with the aim of creating proteins with novel chemical and biological properties. Fluorination seems to be a general and effective strategy to enhance the stability of proteins, both soluble and membrane bound, against chemical and thermal denaturation, although retaining structure and biological activity. Most studies have focused on small proteins that can be produced by peptide synthesis as synthesis of large proteins containing specifically fluorinated residues remains challenging. However, the development of various biosynthetic methods for introducing noncanonical amino acids into proteins promises to expand the utility of fluorinated amino acids in protein design.
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Affiliation(s)
- Benjamin C Buer
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
| | - E Neil G Marsh
- Department of Chemistry, University of MichiganAnn Arbor, Michigan 48109
- Department of Biological Chemistry, University of Michigan Medical SchoolAnn Arbor, Michigan 48109
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44
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Brown JW, Farelli JD, McKnight CJ. On the unyielding hydrophobic core of villin headpiece. Protein Sci 2012; 21:647-54. [PMID: 22467489 DOI: 10.1002/pro.2048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 11/06/2022]
Abstract
Villin headpiece (HP67) is a small, autonomously-folding domain that has become a model system for understanding the fundamental tenets governing protein folding. In this communication, we explore the role that Leu61 plays in the structure and stability of the construct. Deletion of Leu61 results in a completely unfolded protein that cannot be expressed in Escherichia coli. Omission of only the aliphatic leucine side chain (HP67 L61G) perturbed neither the backbone conformation nor the orientation of local hydrophobic side chains. As a result, a large, solvent-exposed hydrophobic pocket, a negative replica of the leucine side-chain, was created on the surface. The loss of the hydrophobic interface between leucine 61 and the hydrophobic pocket destabilized the construct by ~3.3 kcal/mol. Insertion of a single glycine residue immediately before Leu61 (HP67 L61[GL]) was also highly destabilizing and had the effect of altering the backbone conformation (α-helix to π-helix) in order to precisely preserve the wild-type position and conformation of all hydrophobic residues, including Leu61. In addition to demonstrating that the hydrophobic side-chain of Leu61 is critically important for the stability of villin headpiece, our results are consistent with the notion that the precise interactions present within the hydrophobic core, rather than the hydrogen bonds that define the secondary structure, specify a protein's fold.
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Affiliation(s)
- Jeffrey W Brown
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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45
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46
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Mortenson DE, Satyshur KA, Guzei IA, Forest KT, Gellman SH. Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations. J Am Chem Soc 2012; 134:2473-6. [PMID: 22280019 PMCID: PMC3351109 DOI: 10.1021/ja210045s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.
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Affiliation(s)
- David E. Mortenson
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
| | - Kenneth A. Satyshur
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 (USA)
| | - Ilia A. Guzei
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
| | - Katrina T. Forest
- Department of Bacteriology, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 (USA)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave. Madison, WI 53706 (USA)
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47
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Steinkruger JD, Bartlett GJ, Hadley EB, Fay L, Woolfson DN, Gellman SH. The d'--d--d' vertical triad is less discriminating than the a'--a--a' vertical triad in the antiparallel coiled-coil dimer motif. J Am Chem Soc 2012; 134:2626-33. [PMID: 22296518 DOI: 10.1021/ja208855x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Elucidating relationships between the amino-acid sequences of proteins and their three-dimensional structures, and uncovering non-covalent interactions that underlie polypeptide folding, are major goals in protein science. One approach toward these goals is to study interactions between selected residues, or among constellations of residues, in small folding motifs. The α-helical coiled coil has served as a platform for such studies because this folding unit is relatively simple in terms of both sequence and structure. Amino acid side chains at the helix-helix interface of a coiled coil participate in so-called "knobs-into-holes" (KIH) packing whereby a side chain (the knob) on one helix inserts into a space (the hole) generated by four side chains on a partner helix. The vast majority of sequence-stability studies on coiled-coil dimers have focused on lateral interactions within these KIH arrangements, for example, between an a position on one helix and an a' position of the partner in a parallel coiled-coil dimer, or between a--d' pairs in an antiparallel dimer. More recently, it has been shown that vertical triads (specifically, a'--a--a' triads) in antiparallel dimers exert a significant impact on pairing preferences. This observation provides impetus for analysis of other complex networks of side-chain interactions at the helix-helix interface. Here, we describe a combination of experimental and bioinformatics studies that show that d'--d--d' triads have much less impact on pairing preference than do a'--a--a' triads in a small, designed antiparallel coiled-coil dimer. However, the influence of the d'--d--d' triad depends on the lateral a'--d interaction. Taken together, these results strengthen the emerging understanding that simple pairwise interactions are not sufficient to describe side-chain interactions and overall stability in antiparallel coiled-coil dimers; higher-order interactions must be considered as well.
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Affiliation(s)
- Jay D Steinkruger
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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48
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Merkel L, Budisa N. Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes. Org Biomol Chem 2012; 10:7241-61. [DOI: 10.1039/c2ob06922a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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49
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Qin L, Sheridan C, Gao J. Synthesis of tetrafluorinated aromatic amino acids with distinct signatures in 19F NMR. Org Lett 2011; 14:528-31. [PMID: 22196053 DOI: 10.1021/ol203140n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorinated amino acids serve as powerful tools in protein chemistry. We synthesized a series of para-substituted tetrafluorophenylalanines via the regioselective S(NAr) chemistry of the commercially available pentafluorophenylalanine Boc-Z. These novel unnatural amino acids display distinct (19)F NMR signatures, making them powerful tools for analyzing protein-membrane interactions with NMR spectroscopy.
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Affiliation(s)
- Luoheng Qin
- Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467-3801, USA
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Salwiczek M, Nyakatura EK, Gerling UIM, Ye S, Koksch B. Fluorinated amino acids: compatibility with native protein structures and effects on protein-protein interactions. Chem Soc Rev 2011; 41:2135-71. [PMID: 22130572 DOI: 10.1039/c1cs15241f] [Citation(s) in RCA: 327] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fluorinated analogues of the canonical α-L-amino acids have gained widespread attention as building blocks that may endow peptides and proteins with advantageous biophysical, chemical and biological properties. This critical review covers the literature dealing with investigations of peptides and proteins containing fluorinated analogues of the canonical amino acids published over the course of the past decade including the late nineties. It focuses on side-chain fluorinated amino acids, the carbon backbone of which is identical to their natural analogues. Each class of amino acids--aliphatic, aromatic, charged and polar as well as proline--is presented in a separate section. General effects of fluorine on essential properties such as hydrophobicity, acidity/basicity and conformation of the specific side chains and the impact of these altered properties on stability, folding kinetics and activity of peptides and proteins are discussed (245 references).
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Affiliation(s)
- Mario Salwiczek
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany.
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