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Sharma K, Sharma KK, Mahindra A, Sehra N, Bagra N, Aaghaz S, Parmar R, Rathod GK, Jain R. Design, synthesis, and applications of ring-functionalized histidines in peptide-based medicinal chemistry and drug discovery. Med Res Rev 2023. [PMID: 36710510 DOI: 10.1002/med.21936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 12/12/2022] [Accepted: 01/06/2023] [Indexed: 01/31/2023]
Abstract
Modified and synthetic α-amino acids are known to show diverse applications. Histidine, which possesses numerous applications when subjected to synthetic modifications, is one such amino acid. The utility of modified histidines varies widely from remarkable biological activities to catalysis, and from nanotechnology to polymer chemistry. This renders histidine residue an important place in scientific research. Histidine is a well-studied scaffold and constitutes the active site of various enzymes catalyzing important reactions in the biological systems. A rational modification in histidine structure with a distinctly developed protocol extensively changes its physical and chemical properties. The utilization of modified histidines in search of potent, target selective and proteostable scaffolds is vital in the development of bioactive peptides with enhanced drug-likeliness. This review is a compilation and analysis of reported side-chain ring modifications at histidine followed by applications of ring-modified histidines in the synthesis of various categories of bioactive peptides and peptidomimetics.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Amit Mahindra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Naina Sehra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Nitin Bagra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Shams Aaghaz
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Rajesh Parmar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Gajanan K Rathod
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Nagar, Punjab, India
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2
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Nguyen A, Gemmecker G, Softley CA, Movsisyan LD, Pfaffeneder T, Heine A, Reuter K, Diederich F, Sattler M, Klebe G. 19F-NMR Unveils the Ligand-Induced Conformation of a Catalytically Inactive Twisted Homodimer of tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:1745-1755. [PMID: 35763700 DOI: 10.1021/acschembio.2c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding the structural arrangements of protein oligomers can support the design of ligands that interfere with their function in order to develop new therapeutic concepts for disease treatment. Recent crystallographic studies have elucidated a novel twisted and functionally inactive form of the homodimeric enzyme tRNA-guanine transglycosylase (TGT), a putative target in the fight against shigellosis. Active-site ligands have been identified that stimulate the rearrangement of one monomeric subunit by 130° against the other one to form an inactive twisted homodimer state. To assess whether the crystallographic observations also reflect the conformation in solution and rule out effects from crystal packing, we performed 19F-NMR spectroscopy with the introduction of 5-fluorotryptophans at four sites in TGT. The inhibitor-induced conformation of TGT in solution was assessed based on 19F-NMR chemical shift perturbations. We investigated the effect of C(4) substituted lin-benzoguanine ligands and identified a correlation between dynamic protein rearrangements and ligand-binding features in the corresponding crystal structures. These involve the destabilization of a helix next to the active site and the integrity of a flexible loop-helix motif. Ligands that either completely lack an attached C(4) substituent or use it to stabilize the geometry of the functionally competent dimer state do not indicate the presence of the twisted dimer form in the NMR spectra. The perturbation of crucial structural motifs in the inhibitors correlates with an increasing formation of the inactive twisted dimer state, suggesting these ligands are able to shift a conformational equilibrium from active C2-symmetric to inactive twisted dimer conformations. These findings suggest a novel concept for the design of drug candidates for further development.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Gerd Gemmecker
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Charlotte A Softley
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Levon D Movsisyan
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Toni Pfaffeneder
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
| | - François Diederich
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, Zürich CH-8093, Switzerland
| | - Michael Sattler
- Biomolecular NMR, Bavarian NMR Center, Technical University of Munich, Lichtenbergstraße 4, Garching D-85747, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, Marburg D-35032, Germany
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3
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Hartman MCT. Non-canonical Amino Acid Substrates of E. coli Aminoacyl-tRNA Synthetases. Chembiochem 2022; 23:e202100299. [PMID: 34416067 PMCID: PMC9651912 DOI: 10.1002/cbic.202100299] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/03/2021] [Indexed: 01/07/2023]
Abstract
In this comprehensive review, I focus on the twenty E. coli aminoacyl-tRNA synthetases and their ability to charge non-canonical amino acids (ncAAs) onto tRNAs. The promiscuity of these enzymes has been harnessed for diverse applications including understanding and engineering of protein function, creation of organisms with an expanded genetic code, and the synthesis of diverse peptide libraries for drug discovery. The review catalogues the structures of all known ncAA substrates for each of the 20 E. coli aminoacyl-tRNA synthetases, including ncAA substrates for engineered versions of these enzymes. Drawing from the structures in the list, I highlight trends and novel opportunities for further exploitation of these ncAAs in the engineering of protein function, synthetic biology, and in drug discovery.
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Affiliation(s)
- Matthew C T Hartman
- Department of Chemistry and Massey Cancer Center, Virginia Commonwealth University, 1001 W Main St., Richmond, VA 23220, USA
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4
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Nieto-Domínguez M, Nikel PI. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. Chembiochem 2020; 21:2551-2571. [PMID: 32274875 DOI: 10.1002/cbic.202000091] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Indexed: 12/19/2022]
Abstract
The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
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5
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Crnković A, Vargas-Rodriguez O, Söll D. Plasticity and Constraints of tRNA Aminoacylation Define Directed Evolution of Aminoacyl-tRNA Synthetases. Int J Mol Sci 2019; 20:ijms20092294. [PMID: 31075874 PMCID: PMC6540133 DOI: 10.3390/ijms20092294] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023] Open
Abstract
Genetic incorporation of noncanonical amino acids (ncAAs) has become a powerful tool to enhance existing functions or introduce new ones into proteins through expanded chemistry. This technology relies on the process of nonsense suppression, which is made possible by directing aminoacyl-tRNA synthetases (aaRSs) to attach an ncAA onto a cognate suppressor tRNA. However, different mechanisms govern aaRS specificity toward its natural amino acid (AA) substrate and hinder the engineering of aaRSs for applications beyond the incorporation of a single l-α-AA. Directed evolution of aaRSs therefore faces two interlinked challenges: the removal of the affinity for cognate AA and improvement of ncAA acylation. Here we review aspects of AA recognition that directly influence the feasibility and success of aaRS engineering toward d- and β-AAs incorporation into proteins in vivo. Emerging directed evolution methods are described and evaluated on the basis of aaRS active site plasticity and its inherent constraints.
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Affiliation(s)
- Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.
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6
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Ring CM, Iqbal ES, Hacker DE, Hartman MCT, Cropp TA. Genetic incorporation of 4-fluorohistidine into peptides enables selective affinity purification. Org Biomol Chem 2018; 15:4536-4539. [PMID: 28517015 DOI: 10.1039/c7ob00844a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the lowered pKa of 4-fluorohistidine relative to histidine, peptides and proteins containing this amino acid are potentially endowed with novel properties. We report here the optimized synthesis of 4-fluorohistidine and show that it can efficiently replace histidine in in vitro translation reactions. Moreover, peptides containing 6×-fluorohistidine tags are able to be selectively captured and eluted from nickel resin in the presence of his-tagged protein mixtures.
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Affiliation(s)
- Christine M Ring
- Virginia Commonwealth University, Department of Chemistry, 1001 West Main Street, Richmond, Virginia 23284-2006, USA.
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7
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Bychek RM, Levterov VV, Sadkova IV, Tolmachev AA, Mykhailiuk PK. Synthesis of Functionalized Difluorocyclopropanes: Unique Building Blocks for Drug Discovery. Chemistry 2018; 24:12291-12297. [DOI: 10.1002/chem.201705708] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 01/16/2023]
Affiliation(s)
| | | | | | - Andrey A. Tolmachev
- Enamine Ltd.; Chervonotkatska 78 Kyiv 02094 Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 Kyiv 01601 Ukraine
| | - Pavel K. Mykhailiuk
- Enamine Ltd.; Chervonotkatska 78 Kyiv 02094 Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 Kyiv 01601 Ukraine
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8
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Dahanayake JN, Kasireddy C, Ellis JM, Hildebrandt D, Hull OA, Karnes JP, Morlan D, Mitchell-Koch KR. Evaluating electronic structure methods for accurate calculation of 19 F chemical shifts in fluorinated amino acids. J Comput Chem 2017; 38:2605-2617. [PMID: 28833293 DOI: 10.1002/jcc.24919] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/16/2017] [Accepted: 08/03/2017] [Indexed: 01/17/2023]
Abstract
The ability of electronic structure methods (11 density functionals, HF, and MP2 calculations; two basis sets and two solvation models) to accurately calculate the 19 F chemical shifts of 31 structures of fluorinated amino acids and analogues with known experimental 19 F NMR spectra has been evaluated. For this task, BHandHLYP, ωB97X, and Hartree-Fock with scaling factors (provided within) are most accurate. Additionally, the accuracy of methods to calculate relative changes in fluorine shielding across 23 sets of structural variants, such as zwitterionic amino acids versus side chains only, was also determined. This latter criterion may be a better indicator of reliable methods for the ultimate goal of assigning and interpreting chemical shifts of fluorinated amino acids in proteins. It was found that MP2 and M062X calculations most accurately assess changes in shielding among analogues. These results serve as a guide for computational developments to calculate 19 F chemical shifts in biomolecular environments. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Chandana Kasireddy
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Jonathan M Ellis
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Derek Hildebrandt
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Olivia A Hull
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Joseph P Karnes
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Dylan Morlan
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, Kansas, 67260-0051
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9
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Kasireddy C, Ellis JM, Bann JG, Mitchell-Koch KR. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties. Sci Rep 2017; 7:42651. [PMID: 28198426 PMCID: PMC5309746 DOI: 10.1038/srep42651] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine.
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Affiliation(s)
- Chandana Kasireddy
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, CV4 7AL, United States
| | - Jonathan M Ellis
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, CV4 7AL, United States
| | - James G Bann
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, CV4 7AL, United States
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, CV4 7AL, United States
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10
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Arntson KE, Pomerantz WCK. Protein-Observed Fluorine NMR: A Bioorthogonal Approach for Small Molecule Discovery. J Med Chem 2015; 59:5158-71. [PMID: 26599421 DOI: 10.1021/acs.jmedchem.5b01447] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The (19)F isotope is 100% naturally abundant and is the second most sensitive and stable NMR-active nucleus. Unlike the ubiquitous hydrogen atom, fluorine is nearly absent in biological systems, making it a unique bioorthogonal atom for probing molecular interactions in biology. Over 73 fluorinated proteins have been studied by (19)F NMR since the seminal studies of Hull and Sykes in 1974. With advances in cryoprobe production and fluorinated amino acid incorporation strategies, protein-based (19)F NMR offers opportunities to the medicinal chemist for characterizing and ultimately discovering new small molecule protein ligands. This review will highlight new advances using (19)F NMR for characterizing small molecule interactions with both small and large proteins as well as detailing NMR resonance assignment challenges and amino acid incorporation approaches.
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Affiliation(s)
- Keith E Arntson
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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11
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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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12
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Fraser SA, Easton CJ. Biosynthetic Incorporation of Fluorinated Amino Acids into Peptides and Proteins. Aust J Chem 2015. [DOI: 10.1071/ch14356] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Native and engineered protein biosynthetic machinery processes a wide range of fluorinated α-amino acids for incorporation into peptides and proteins, either as substitutes for structurally similar amino acids normally found in proteins, or as additional ones. In the former case, replacement occurs wherever the normal amino acid is encoded, while the latter method is site-specific. The fluorinated peptides have a diverse variety of interesting properties. The biochemical synthetic methods are straightforward, to the point that they should routinely be assessed as alternatives to traditional solid- and solution-phase peptide synthesis.
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13
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Marsh ENG, Suzuki Y. Using (19)F NMR to probe biological interactions of proteins and peptides. ACS Chem Biol 2014; 9:1242-50. [PMID: 24762032 DOI: 10.1021/cb500111u] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorine is a valuable probe for investigating the interactions of biological molecules because of its favorable NMR characteristics, its small size, and its near total absence from biology. Advances in biosynthetic methods allow fluorine to be introduced into peptides and proteins with high precision, and the increasing sensitivity of NMR spectrometers has facilitated the use of (19)F NMR to obtain molecular-level insights into a wide range of often-complex biological interactions. Here, we summarize the advantages of solution-state (19)F NMR for studying the interactions of peptides and proteins with other biological molecules, review methods for the production of fluorine-labeled materials, and describe some representative recent examples in which (19)F NMR has been used to study conformational changes in peptides and proteins and their interactions with other biological molecules.
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Affiliation(s)
- E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yuta Suzuki
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Arularasan P, Chakkaravarthi G, Mohan R. catena-Poly[[bis-(nitrato-κ(2) O,O')barium]-bis-(μ-l-histidine-κ(3) O,O':O]. Acta Crystallogr Sect E Struct Rep Online 2013; 69:m597. [PMID: 24454031 PMCID: PMC3884255 DOI: 10.1107/s1600536813027402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 10/06/2013] [Indexed: 11/18/2022]
Abstract
In the polymeric title compound, [Ba(NO3)2(C6H9N3O2)2]n, the BaII atom is located on a crystallographic twofold axis and is coordinated by ten O atoms. Six are derived from two zwitterionic l-histidine molecules that simultaneously chelate one BaII atom and bridge to another. The remaining four O atoms are derived from two chelating nitrates. The molecules assemble to form a chain along [010]. In the crystal, chains are linked via N—H⋯O and N—H⋯N hydrogen bonds, generating a three-dimensional network.
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Affiliation(s)
- P Arularasan
- Department of Physics, Presidency College, Chennai 600 005, India
| | - G Chakkaravarthi
- Department of Physics, CPCL Polytechnic College, Chennai 600 068, India
| | - R Mohan
- Department of Physics, Presidency College, Chennai 600 005, India
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15
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Incorporation of labile trans-4,5-difluoromethanoproline into a peptide as a stable label for 19F NMR structure analysis. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.03.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Kumari S, Swaminathan A, Chatterjee S, Senapati P, Boopathi R, Kundu TK. Chromatin organization, epigenetics and differentiation: an evolutionary perspective. Subcell Biochem 2013; 61:3-35. [PMID: 23150244 DOI: 10.1007/978-94-007-4525-4_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genome packaging is a universal phenomenon from prokaryotes to higher mammals. Genomic constituents and forces have however, travelled a long evolutionary route. Both DNA and protein elements constitute the genome and also aid in its dynamicity. With the evolution of organisms, these have experienced several structural and functional changes. These evolutionary changes were made to meet the challenging scenario of evolving organisms. This review discusses in detail the evolutionary perspective and functionality gain in the phenomena of genome organization and epigenetics.
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Affiliation(s)
- Sujata Kumari
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur Post, Bangalore, 560064, India
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17
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Hu L, Joshi SB, Andra KK, Thakkar SV, Volkin DB, Bann JG, Middaugh CR. Comparison of the structural stability and dynamic properties of recombinant anthrax protective antigen and its 2-fluorohistidine-labeled analogue. J Pharm Sci 2012; 101:4118-28. [PMID: 22911632 DOI: 10.1002/jps.23294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/19/2012] [Accepted: 07/31/2012] [Indexed: 01/15/2023]
Abstract
Protective antigen (PA) is the primary protein antigenic component of both the currently used anthrax vaccine and related recombinant vaccines under development. An analogue of recombinant PA (2-FHis rPA) has been recently shown to block the key steps of pore formation in the process of inducing cytotoxicity in cells, and thus can potentially be used as an antitoxin or a vaccine. This rPA analogue was produced by fermentation to incorporate the unnatural amino acid 2-fluorohistidine (2-FHis). In this study, the effects of 2-FHis labeling on rPA antigen's conformational stability and dynamic properties were investigated by various biophysical techniques. Temperature/pH stability profiles of rPA and 2-FHis rPA were analyzed by the empirical phase diagram (EPD) approach, and physical stability differences between them were identified. Results showed that rPA and 2-FHis rPA had similar stability at pH 7-8. With decreasing solution pH, however, 2-FHis rPA was found to be more stable. Dynamic sensitive measurements of the two proteins at pH 5 found that 2-FHis rPA was more dynamic and/or differentially hydrated under acidic pH conditions. The biophysical characterization and stability data provide information useful for the potential development of 2-FHis rPA as a more stable rPA vaccine candidate.
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Affiliation(s)
- Lei Hu
- Macromolecule and Vaccine Stabilization Center, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66047, USA
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18
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Kitevski-LeBlanc JL, Prosser RS. Current applications of 19F NMR to studies of protein structure and dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2012; 62:1-33. [PMID: 22364614 DOI: 10.1016/j.pnmrs.2011.06.003] [Citation(s) in RCA: 206] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 07/01/2011] [Indexed: 05/20/2023]
Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd., North Mississauga, Ontario, Canada
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19
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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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20
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Andra KK, Bullinger JC, Bann JG, Eichhorn DM. 2-Fluoro-l-histidine. Acta Crystallogr Sect E Struct Rep Online 2010; 66:o2713. [PMID: 21588926 PMCID: PMC3009228 DOI: 10.1107/s1600536810038663] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 09/27/2010] [Indexed: 11/29/2022]
Abstract
The title compound, C6H8FN3O2, an analog of histidine, shows a reduced side-chain pKa (ca 1). The title structure exhibits a shortening of the bond between the proximal ring N atom and the F-substituted ring C atom, indicating an increase in π-bond character due to an inductive effect of fluorine.
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Affiliation(s)
- Kiran K Andra
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, KS 67260-0051, USA
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21
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Wimalasena DS, Janowiak BE, Lovell S, Miyagi M, Sun J, Zhou H, Hajduch J, Pooput C, Kirk KL, Battaile KP, Bann JG. Evidence that histidine protonation of receptor-bound anthrax protective antigen is a trigger for pore formation. Biochemistry 2010; 49:6973-83. [PMID: 20672855 PMCID: PMC2924283 DOI: 10.1021/bi100647z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protective antigen (PA) component of the anthrax toxin forms pores within the low pH environment of host endosomes through mechanisms that are poorly understood. It has been proposed that pore formation is dependent on histidine protonation. In previous work, we biosynthetically incorporated 2-fluorohistidine (2-FHis), an isosteric analogue of histidine with a significantly reduced pK(a) ( approximately 1), into PA and showed that the pH-dependent conversion from the soluble prepore to a pore was unchanged. However, we also observed that 2-FHisPA was nonfunctional in the ability to mediate cytotoxicity of CHO-K1 cells by LF(N)-DTA and was defective in translocation through planar lipid bilayers. Here, we show that the defect in cytotoxicity is due to both a defect in translocation and, when bound to the host cellular receptor, an inability to undergo low pH-induced pore formation. Combining X-ray crystallography with hydrogen-deuterium (H-D) exchange mass spectrometry, our studies lead to a model in which hydrogen bonds to the histidine ring are strengthened by receptor binding. The combination of both fluorination and receptor binding is sufficient to block low pH-induced pore formation.
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Affiliation(s)
| | - Blythe E. Janowiak
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Scott Lovell
- Del Shankel Structural Biology Center, The University of Kansas, Lawrence, Kansas 66047
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Department of Pharmacology, Department of Ophthalmology and Visual Sciences, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4988
| | - Jianjun Sun
- Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Haiying Zhou
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Jan Hajduch
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, USA
| | - Chaya Pooput
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, USA
| | - Kenneth L. Kirk
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, USA
| | - Kevin P. Battaile
- IMCA-CAT, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Bldg 435A, Argonne, IL 60439, USA
| | - James G. Bann
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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Budisa N, Wenger W, Wiltschi B. Residue-specific global fluorination of Candida antarctica lipase B in Pichia pastoris. MOLECULAR BIOSYSTEMS 2010; 6:1630-9. [PMID: 20431819 DOI: 10.1039/c002256j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report the in vivo fluorination of the tryptophan, tyrosine, and phenylalanine residues in a glycosylation-deficient mutant of Candida antarctica lipase B, CalB N74D, expressed in the methylotrophic yeast Pichia pastoris and subsequently segregated into the growth medium. To achieve this, a P. pastoris strain auxotrophic for all three aromatic amino acids was supplemented with 5-fluoro-L-tryptophan, meta-fluoro-(DL)-tyrosine, or para-fluoro-L-phenylalanine during expression of CalB N74D. The residue-specific replacement of the canonical amino acids by their fluorinated analogs was confirmed by mass analysis. Although global fluorination induced moderate changes in the secondary structure of CalB N74D, the fluorous variant proteins were still active lipases. However, their catalytic activity was lower than that of the non-fluorinated parent protein while their resistance to proteolytic degradation by proteinase K remained unchanged. Importantly, we observed that the global fluorination prolonged the shelf life of the lipase activity, which is an especially useful feature for the storage of, e.g., therapeutic proteins. Our study represents the first step on the road to the production of biotechnologically and pharmacologically relevant fluorous proteins in P. pastoris.
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Affiliation(s)
- Nediljko Budisa
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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23
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Kitevski-LeBlanc JL, Evanics F, Prosser RS. Approaches for the measurement of solvent exposure in proteins by 19F NMR. JOURNAL OF BIOMOLECULAR NMR 2009; 45:255-264. [PMID: 19655092 DOI: 10.1007/s10858-009-9359-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 07/14/2009] [Indexed: 05/28/2023]
Abstract
Fluorine NMR is a useful tool to probe protein folding, conformation and local topology owing to the sensitivity of the chemical shift to the local electrostatic environment. As an example we make use of (19)F NMR and 3-fluorotyrosine to evaluate the conformation and topology of the tyrosine residues (Tyr-99 and Tyr-138) within the EF-hand motif of the C-terminal domain of calmodulin (CaM) in both the calcium-loaded and calcium-free states. We critically compare approaches to assess topology and solvent exposure via solvent isotope shifts, (19)F spin-lattice relaxation rates, (1)H-(19)F nuclear Overhauser effects, and paramagnetic shifts and relaxation rates from dissolved oxygen. Both the solvent isotope shifts and paramagnetic shifts from dissolved oxygen sensitively reflect solvent exposed surface areas.
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Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd, North Mississauga, ON, L5L 1C6, Canada
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Abstract
We report a new synthesis of enantiomerically pure (S)-4-fluorohisitidine based on diastereoselective alkylation of MOM-protected 4-fluoro-5-bromomethyl imidazole using the Schöllkopf bis-lactim amino acid synthesis. Improvements in procedures for preparation of key intermediates are also described. (S)-4-Fluorohisitidine prepared by this new method was identical in all respects to material prepared by previous procedures.
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Affiliation(s)
- Jan Hajduch
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892
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25
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Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo. Proc Natl Acad Sci U S A 2009; 106:15285-90. [PMID: 19706454 DOI: 10.1073/pnas.0905735106] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Incorporation of noncanonical amino acids into cellular proteins often requires engineering new aminoacyl-tRNA synthetase activity into the cell. A screening strategy that relies on cell-surface display of reactive amino acid side-chains was used to identify a diverse set of methionyl-tRNA synthetase (MetRS) mutants that allow efficient incorporation of the methionine (Met) analog azidonorleucine (Anl). We demonstrate that the extent of cell-surface labeling in vivo is a good indicator of the rate of Anl activation by the MetRS variant harbored by the cell. By screening at low Anl concentrations in Met-supplemented media, MetRS variants with improved activities toward Anl and better discrimination against Met were identified.
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Rajapaksha M, Eichler JF, Hajduch J, Anderson DE, Kirk KL, Bann JG. Monitoring anthrax toxin receptor dissociation from the protective antigen by NMR. Protein Sci 2009; 18:17-23. [PMID: 19177347 DOI: 10.1002/pro.26] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The binding of the Bacillus anthracis protective antigen (PA) to the host cell receptor is the first step toward the formation of the anthrax toxin, a tripartite set of proteins that include the enzymatic moieties edema factor (EF), and lethal factor (LF). PA is cleaved by a furin-like protease on the cell surface followed by the formation of a donut-shaped heptameric prepore. The prepore undergoes a major structural transition at acidic pH that results in the formation of a membrane spanning pore, an event which is dictated by interactions with the receptor and necessary for entry of EF and LF into the cell. We provide direct evidence using 1-dimensional (13)C-edited (1)H NMR that low pH induces dissociation of the Von-Willebrand factor A domain of the receptor capillary morphogenesis protein 2 (CMG2) from the prepore, but not the monomeric full length PA. Receptor dissociation is also observed using a carbon-13 labeled, 2-fluorohistidine labeled CMG2, consistent with studies showing that protonation of His-121 in CMG2 is not a mechanism for receptor release. Dissociation is likely caused by the structural transition upon formation of a pore from the prepore state rather than protonation of residues at the receptor PA or prepore interface.
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Dürr UHN, Grage SL, Witter R, Ulrich AS. Solid state 19F NMR parameters of fluorine-labeled amino acids. Part I: aromatic substituents. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 191:7-15. [PMID: 18155936 DOI: 10.1016/j.jmr.2007.11.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 10/30/2007] [Accepted: 11/21/2007] [Indexed: 05/25/2023]
Abstract
Structural parameters of peptides and proteins in biomembranes can be directly measured by solid state NMR of selectively labeled amino acids. The 19F nucleus is a promising label to overcome the low sensitivity of 2H, 13C or 15N, and to serve as a background-free reporter group in biological compounds. To make the advantages of solid state 19F NMR fully available for structural studies of polypeptides, we have systematically measured the chemical shift anisotropies and relaxation properties of the most relevant aromatic and aliphatic 19F-labeled amino acids. In this first part of two consecutive contributions, six different 19F-substituents on representative aromatic side chains were characterized as polycrystalline powders by static and MAS experiments. The data are also compared with results on the same amino acids incorporated in synthetic peptides. The spectra show a wide variety of lineshapes, from which the principal values of the CSA tensors were extracted. In addition, temperature-dependent T(1) and T(2) relaxation times were determined by 19F NMR in the solid state, and isotropic chemical shifts and scalar couplings were obtained in solution.
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Affiliation(s)
- Ulrich H N Dürr
- Max-Planck-Institute for Biophysical Chemistry, Department of NMR-Based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany
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Wimalasena DS, Cramer JC, Janowiak BE, Juris SJ, Melnyk RA, Anderson DE, Kirk KL, Collier RJ, Bann JG. Effect of 2-fluorohistidine labeling of the anthrax protective antigen on stability, pore formation, and translocation. Biochemistry 2007; 46:14928-36. [PMID: 18044973 DOI: 10.1021/bi701763z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The action of anthrax toxin relies in part upon the ability of the protective antigen (PA) moiety to form a heptameric pore in the endosomal membrane, providing a portal for entry of the enzymic moieties of the toxin into the cytosol. Pore formation is dependent on a conformational change in the heptameric prepore that occurs in the neutral to mildly acidic pH range, and it has been hypothesized that protonation of one or more histidine residues triggers this transition. To test this hypothesis, we used biosynthetic methods to incorporate the unnatural amino acid analogue 2-fluorohistidine (2-FHis) into PA. 2-FHis is isosteric with histidine but resists protonation at physiological pH values due to a dramatically reduced side-chain pKa ( approximately 1). We found that 2-FHis-labeled PA was biologically inactive, as judged by its inability to deliver a model intracellular effector, LFN-DTA, to the cytosol of CHO-K1 cells. However, whereas 2-FHis blocked a conformational transition in the full-length PA83 protein in the pH 5-6 range, the pH dependence of prepore-to-pore conversion of (PA63)7 was unchanged from the wild-type protein, implying that this conversion is not dependent on His protonation. Consistent with this result, the labeled, trypsin-activated PA was able to permeabilize liposomes to K+ and retained pore-forming activity in planar phospholipid bilayers. The pores in planar bilayers were incapable, however, of translocating a model ligand in response to a transmembrane pH gradient or elevated voltage. The results indicate that protonation of residues other than His, presumably Glu and/or Asp side chains, triggers pore formation in vitro, but His residues are nonetheless important for PA functioning in vivo.
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