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Ye S, Loll B, Berger AA, Mülow U, Alings C, Wahl MC, Koksch B. Fluorine teams up with water to restore inhibitor activity to mutant BPTI. Chem Sci 2015; 6:5246-5254. [PMID: 29449928 PMCID: PMC5669249 DOI: 10.1039/c4sc03227f] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 06/11/2015] [Indexed: 11/21/2022] Open
Abstract
Fluorinated derivatives of aminobutyric acid engage in unique interactions with structural waters within the BPTI/trypsin interface and restore inhibitor activity.
Introducing fluorine into molecules has a wide range of effects on their physicochemical properties, often desirable but in most cases unpredictable. The fluorine atom imparts the C–F bond with low polarizability and high polarity, and significantly affects the behavior of neighboring functional groups, in a covalent or noncovalent manner. Here, we report that fluorine, present in the form of a single fluoroalkyl amino acid side chain in the P1 position of the well-characterized serine-protease inhibitor BPTI, can fully restore inhibitor activity to a mutant that contains the corresponding hydrocarbon side chain at the same site. High resolution crystal structures were obtained for four BPTI variants in complex with bovine β-trypsin, revealing changes in the stoichiometry and dynamics of water molecules in the S1 subsite. These results demonstrate that the introduction of fluorine into a protein environment can result in “chemical complementation” that has a significantly favorable impact on protein–protein interactions.
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Affiliation(s)
- Shijie Ye
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Allison Ann Berger
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Ulrike Mülow
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
| | - Claudia Alings
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Markus Christian Wahl
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry, Structural Biochemistry , Takustr. 6 , Berlin, 14195 , Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy , Freie Universität Berlin , Institute of Chemistry and Biochemistry , Takustr. 3 , Berlin, 14195 , Germany . ; ; Tel: +49-30-83855344
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52
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Davies SG, Fletcher AM, Frost AB, Roberts PM, Thomson JE. Asymmetric Synthesis of Substituted anti-β-Fluorophenylalanines. Org Lett 2015; 17:2254-7. [DOI: 10.1021/acs.orglett.5b00880] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen G. Davies
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Ai M. Fletcher
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Aileen B. Frost
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Paul M. Roberts
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - James E. Thomson
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
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53
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Vukelić S, Ushakov DB, Gilmore K, Koksch B, Seeberger PH. Flow Synthesis of Fluorinated α-Amino Acids. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500300] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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54
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Appel R, Tacke S, Klingauf J, Besenius P. Tuning the pH-triggered self-assembly of dendritic peptide amphiphiles using fluorinated side chains. Org Biomol Chem 2015; 13:1030-9. [DOI: 10.1039/c4ob02185a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the synthesis of a series of anionic dendritic peptide amphiphiles of increasing hydrophobic character and describe their self-assembly into supramolecular nanorods using pH and ionic strength dependent state diagrams.
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Affiliation(s)
- Ralph Appel
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
| | - Sebastian Tacke
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Jürgen Klingauf
- Department of Cellular Biophysics
- Institute of Medical Physics and Biophysics
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
| | - Pol Besenius
- Organic Chemistry Institute
- Westfälische Wilhelms-Universität Münster
- 48149 Münster
- Germany
- Center for Nanotechnology (CeNTech)
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55
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Grage SL, Xu X, Schmitt M, Wadhwani P, Ulrich AS. (19)F-Labeling of Peptides Revealing Long-Range NMR Distances in Fluid Membranes. J Phys Chem Lett 2014; 5:4256-4259. [PMID: 26273971 DOI: 10.1021/jz502195t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
NMR distance measurements lie at the heart of structural biology. However, long-range distances could not yet be detected in liquid-crystalline biomembranes, because dipolar couplings are partially averaged by the intrinsic molecular mobility. Using conformationally constrained (19)F-labeled amino acids as reporter groups, we could more than double the accessible interatomic distance range by combining a highly sensitive solid-state multipulse (19)F-NMR scheme with a favorable sample geometry. Two rigid 4F-phenylglycine labels were placed into the helical antimicrobial peptide PGLa embedded in fluid oriented membrane samples. A modified Carr-Purcell-Meiboom-Gill sequence yielded an intramolecular distance of 6.6 Å for the labels spanning one helix turn, and 11.0 Å was obtained when the labels spanned two turns. This approach should now also allow the characterization of conformational changes in membrane-active peptides and of oligomeric assemblies in a biologically relevant lipid environment.
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Affiliation(s)
- Stephan L Grage
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Xiaojun Xu
- ‡Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Markus Schmitt
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Parvesh Wadhwani
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Anne S Ulrich
- †Institute of Biological Interfaces IBG-2, Karlsruhe Institute of Technology, P.O. Box 3640, 76021 Karlsruhe, Germany
- ‡Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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56
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Gerling UIM, Miettinen MS, Koksch B. Concluding the amyloid formation pathway of a coiled-coil-based peptide from the size of the critical nucleus. Chemphyschem 2014; 16:108-14. [PMID: 25257178 DOI: 10.1002/cphc.201402400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Indexed: 01/03/2023]
Abstract
The size of the critical nucleus acting as intermediate in the amyloid formation of a model peptide is calculated. The theoretical approach is based on experimentally determined amyloid formation rates and gives new insights into the amyloid formation pathway.
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Affiliation(s)
- Ulla I M Gerling
- Department of Chemistry and Biochemistry-Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin (Germany)
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57
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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: 140] [Impact Index Per Article: 14.0] [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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