51
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Kaldas SJ, O'Keefe KTV, Mendoza-Sanchez R, Yudin AK. Amphoteric Borylketenimines: Versatile Intermediates in the Synthesis of Borylated Heterocycles. Chemistry 2017; 23:9711-9715. [DOI: 10.1002/chem.201702008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Sherif J. Kaldas
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Kowan T. V. O'Keefe
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
| | - Andrei K. Yudin
- Davenport Research Laboratories; Department of Chemistry; University of Toronto; 80 St. George St. Toronto ON M5S 3H6 Canada
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52
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Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc 2016; 4:042004. [PMID: 28192292 PMCID: PMC5308470 DOI: 10.1088/2050-6120/4/4/042004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.
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53
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Abstract
![]()
Pd-catalyzed
cross-coupling reactions that form C–N bonds
have become useful methods to synthesize anilines and aniline derivatives,
an important class of compounds throughout chemical research. A key
factor in the widespread adoption of these methods has been the continued
development of reliable and versatile catalysts that function under
operationally simple, user-friendly conditions. This review provides
an overview of Pd-catalyzed N-arylation reactions found in both basic
and applied chemical research from 2008 to the present. Selected examples
of C–N cross-coupling reactions between nine classes of nitrogen-based
coupling partners and (pseudo)aryl halides are described for the synthesis
of heterocycles, medicinally relevant compounds, natural products,
organic materials, and catalysts.
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Affiliation(s)
- Paula Ruiz-Castillo
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Stephen L Buchwald
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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54
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Xiao H, Schultz PG. At the Interface of Chemical and Biological Synthesis: An Expanded Genetic Code. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023945. [PMID: 27413101 DOI: 10.1101/cshperspect.a023945] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ability to site-specifically incorporate noncanonical amino acids (ncAAs) with novel structures into proteins in living cells affords a powerful tool to investigate and manipulate protein structure and function. More than 200 ncAAs with diverse biological, chemical, and physical properties have been genetically encoded in response to nonsense or frameshift codons in both prokaryotic and eukaryotic organisms with high fidelity and efficiency. In this review, recent advances in the technology and its application to problems in protein biochemistry, cellular biology, and medicine are highlighted.
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Affiliation(s)
- Han Xiao
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037 California Institute for Biomedical Research, La Jolla, California 92037
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55
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Huynh Nhat KP, Watanabe T, Yoshikoshi K, Hohsaka T. Antibody-based fluorescent and fluorescent ratiometric indicators for detection of phosphotyrosine. J Biosci Bioeng 2016; 122:146-54. [DOI: 10.1016/j.jbiosc.2016.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
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56
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Chowdhury SR, Chauhan PS, Dedkova LM, Bai X, Chen S, Talukder P, Hecht SM. Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes. Biochemistry 2016; 55:2427-40. [PMID: 27050631 DOI: 10.1021/acs.biochem.6b00102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Described herein are the synthesis and photophysical characterization of a library of aryl-substituted oxazole- and thiazole-based dipeptidomimetic analogues, and their incorporation into position 66 of green fluorescent protein (GFP) in lieu of the natural fluorophore. These fluorescent analogues resemble the fluorophore formed naturally by GFP. As anticipated, the photophysical properties of the analogues varied as a function of the substituents at the para position of the phenyl ring. The fluorescence emission wavelength maxima of compounds in the library varied from ∼365 nm (near-UV region) to ∼490 nm (visible region). The compounds also exhibited a large range of quantum yields (0.01-0.92). The analogues were used to activate a suppressor tRNACUA and were incorporated into position 66 of GFP using an in vitro protein biosynthesizing system that employed engineered ribosomes selected for their ability to incorporate dipeptides. Four analogues with interesting photophysical properties and reasonable suppression yields were chosen, and the fluorescent proteins (FPs) containing these fluorophores were prepared on a larger scale for more detailed study. When the FPs were compared with the respective aminoacyl-tRNAs and the actual dipeptide analogues, the FPs exhibited significantly enhanced fluorescence intensities at the same concentrations. Part of this was shown to be due to the presence of the fluorophores as an intrinsic element of the protein backbone. There were also characteristic shifts in the emission maxima, indicating the environmental sensitivity of these probes. Acridon-2-ylalanine and oxazole 1a were incorporated into positions 39 and 66 of GFP, respectively, and were shown to form an efficient Förster resonance energy transfer (FRET) pair, demonstrating that the analogues can be used as FRET probes.
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Affiliation(s)
- Sandipan Roy Chowdhury
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Pradeep S Chauhan
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Xiaoguang Bai
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Poulami Talukder
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics, and School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287, United States
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57
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Haney CM, Wissner RF, Warner JB, Wang YJ, Ferrie JJ, J Covell D, Karpowicz RJ, Lee VMY, Petersson EJ. Comparison of strategies for non-perturbing labeling of α-synuclein to study amyloidogenesis. Org Biomol Chem 2016; 14:1584-92. [PMID: 26695131 PMCID: PMC4733880 DOI: 10.1039/c5ob02329g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of the amyloidogenic Parkinson's disease protein α-synuclein (αS) has proven difficult due to its structural plasticity. Here, we present a number of complementary methods to site-specifically introduce fluorescent probes to examine αS fibril formation and cellular uptake. By using various combinations of conventional Cys modification, amber codon suppression, transferase mediated N-terminal modification, and native chemical ligation, several variants of singly- and doubly-labeled αS were produced. We validated the nonperturbative nature of the label by a combination of in vitro aggregation kinetics measurements and imaging of the resulting fibrils. The labeled αS can then be used to monitor conformational changes during fibril formation or cellular uptake of αS fibrils in models of disease propagation.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Rebecca F Wissner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John B Warner
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
| | - Dustin J Covell
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Richard J Karpowicz
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - Virginia M-Y Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania, 3600 Spruce Street, Philadelphia, PA 19104, USA
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, 213 South 34th Street, Philadelphia, PA 19104, USA.
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58
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Wang YJ, Szantai-Kis DM, Petersson EJ. Semi-synthesis of thioamide containing proteins. Org Biomol Chem 2016; 13:5074-81. [PMID: 25811732 DOI: 10.1039/c5ob00224a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Our laboratory has shown that the thioamide, a single atom O-to-S substitution, can be a versatile fluorescence quenching probe that is minimally-perturbing when placed at many locations in a protein sequence. In order to make these and other thioamide experiments applicable to full-sized proteins, we have developed methods for incorporating thioamides by generating thiopeptide fragments through solid phase synthesis and ligating them to protein fragments expressed in E. coli. To install donor fluorophores, we have adapted unnatural amino acid mutagenesis methods, including the generation of new tRNA synthetases for the incorporation of small, intrinsically fluorescent amino acids. We have used a combination of these two methods, as well as chemoenzymatic protein modification, to efficiently install sidechain and backbone modifications to generate proteins labeled with fluorophore/thioamide pairs.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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59
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Rauch BJ, Porter JJ, Mehl RA, Perona JJ. Improved Incorporation of Noncanonical Amino Acids by an Engineered tRNA(Tyr) Suppressor. Biochemistry 2016; 55:618-28. [PMID: 26694948 DOI: 10.1021/acs.biochem.5b01185] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The Methanocaldcoccus jannaschii tyrosyl-tRNA synthetase (TyrRS):tRNA(Tyr) cognate pair has been used to incorporate a large number of noncanonical amino acids (ncAAs) into recombinant proteins in Escherichia coli. However, the structural elements of the suppressor tRNA(Tyr) used in these experiments have not been examined for optimal performance. Here, we evaluate the steady-state kinetic parameters of wild-type M. jannaschii TyrRS and an evolved 3-nitrotyrosyl-tRNA synthetase (nitroTyrRS) toward several engineered tRNA(Tyr) suppressors, and we correlate aminoacylation properties with the efficiency and fidelity of superfolder green fluorescent protein (sfGFP) synthesis in vivo. Optimal ncAA-sfGFP synthesis correlates with improved aminoacylation kinetics for a tRNA(Tyr) amber suppressor with two substitutions in the anticodon loop (G34C/G37A), while four additional mutations in the D and variable loops, present in the tRNA(Tyr) used in all directed evolution experiments to date, are deleterious to function both in vivo and in vitro. These findings extend to three of four other evolved TyrRS enzymes that incorporate distinct ncAAs. Suppressor tRNAs elicit decreases in amino acid Km values for both TyrRS and nitroTyrRS, suggesting that direct anticodon recognition by TyrRS need not be an impediment to superior performance of this orthogonal system and offering insight into novel approaches for directed evolution. The G34C/G37A tRNA(Tyr) may enhance future incorporation of many ncAAs by engineered TyrRS enzymes.
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Affiliation(s)
- Benjamin J Rauch
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Joseph J Porter
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University , 2011 Agriculture and Life Sciences Building, Corvallis, Oregon 97331, United States
| | - John J Perona
- Department of Chemistry, Portland State University , P.O. Box 751, Portland, Oregon 97207, United States.,Department of Biochemistry & Molecular Biology, Oregon Health & Sciences University , 3181 Southwest Sam Jackson Park Road, Portland, Oregon 97239, United States
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60
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Harkiss AH, Sutherland A. Recent advances in the synthesis and application of fluorescent α-amino acids. Org Biomol Chem 2016; 14:8911-8921. [DOI: 10.1039/c6ob01715k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The design and synthesis of new fluorescent α-amino acids as well as their application in imaging of biological systems has been reviewed.
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Affiliation(s)
- Alexander H. Harkiss
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow G12 8QQ
| | - Andrew Sutherland
- WestCHEM
- School of Chemistry
- The Joseph Black Building
- University of Glasgow
- Glasgow G12 8QQ
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61
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Ko W, Kim S, Lee S, Jo K, Lee HS. Genetically encoded FRET sensors using a fluorescent unnatural amino acid as a FRET donor. RSC Adv 2016. [DOI: 10.1039/c6ra17375f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
FRET sensors based on fluorescent proteins have been powerful tools for probing protein–protein interactions and structural changes within proteins.
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Affiliation(s)
- Wooseok Ko
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Sanggil Kim
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Seonghyun Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Kyubong Jo
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry
- Sogang University
- Seoul 121-742
- Republic of Korea
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62
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Talukder P, Chen S, Roy B, Yakovchuk P, Spiering MM, Alam MP, Madathil MM, Bhattacharya C, Benkovic SJ, Hecht SM. Cyanotryptophans as Novel Fluorescent Probes for Studying Protein Conformational Changes and DNA–Protein Interaction. Biochemistry 2015; 54:7457-69. [DOI: 10.1021/acs.biochem.5b01085] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Poulami Talukder
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Basab Roy
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Petro Yakovchuk
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Michelle M. Spiering
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mohammad P. Alam
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Manikandadas M. Madathil
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Chandrabali Bhattacharya
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Stephen J. Benkovic
- Department
of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sidney M. Hecht
- Center
for BioEnergetics, Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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63
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Siraj N, El-Zahab B, Hamdan S, Karam TE, Haber LH, Li M, Fakayode SO, Das S, Valle B, Strongin RM, Patonay G, Sintim HO, Baker GA, Powe A, Lowry M, Karolin JO, Geddes CD, Warner IM. Fluorescence, Phosphorescence, and Chemiluminescence. Anal Chem 2015; 88:170-202. [PMID: 26575092 DOI: 10.1021/acs.analchem.5b04109] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Noureen Siraj
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Bilal El-Zahab
- Department of Mechanical and Materials Engineering, Florida International University , Miami, Florida 33174, United States
| | - Suzana Hamdan
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Tony E Karam
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Louis H Haber
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Min Li
- Process Development Center, Albemarle Corporation , Baton Rouge, Louisiana 70805, United States
| | - Sayo O Fakayode
- Department of Chemistry, Winston-Salem State University , Winston-Salem, North Carolina 27110, United States
| | - Susmita Das
- Department of Civil Engineering, Adamas Institute of Technology , Barasat, Kolkata 700126, West Bengal India
| | - Bertha Valle
- Department of Chemistry, Texas Southern University , Houston, Texas 77004, United States
| | - Robert M Strongin
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Gabor Patonay
- Department of Chemistry, Georgia State University , Atlanta, Georgia 30302-4098, United States
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
| | - Gary A Baker
- Department of Chemistry, University of Missouri Columbia , Columbia, Missouri 65211-7600, United States
| | - Aleeta Powe
- Department of Chemistry, University of Louisville , Louisville, Kentucky 40208, United States
| | - Mark Lowry
- Department of Chemistry, Portland State University , Portland, Oregon 97207, United States
| | - Jan O Karolin
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Chris D Geddes
- Institute of Fluorescence, University of Maryland Baltimore County , Baltimore, Maryland 21202, United States
| | - Isiah M Warner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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64
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Multiply labeling proteins for studies of folding and stability. Curr Opin Chem Biol 2015; 28:123-30. [PMID: 26253346 DOI: 10.1016/j.cbpa.2015.07.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/09/2015] [Accepted: 07/16/2015] [Indexed: 11/22/2022]
Abstract
Fluorescence spectroscopy is a powerful method for monitoring protein folding in real-time with high resolution and sensitivity, but requires the site-specific introduction of labels into the protein. The ability to genetically incorporate unnatural amino acids (Uaas) allows for the efficient synthesis of fluorescently labeled proteins with minimally perturbing fluorophores. Here, we describe recent uses of labeled proteins in dynamic structure determination experiments and advances in unnatural amino acid incorporation for dual site-specific fluorescent labeling. The advent of increasingly sophisticated bioorthogonal chemistry reactions and the diversity of Uaas available for incorporation will greatly enable protein folding and stability studies.
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65
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Fluorescent CD4 probe for potential HIV-1 gp120 protein detection. Bioorg Med Chem Lett 2015; 25:1182-5. [DOI: 10.1016/j.bmcl.2015.01.071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 02/02/2023]
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66
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Batjargal S, Walters CR, Petersson EJ. Inteins as traceless purification tags for unnatural amino acid proteins. J Am Chem Soc 2015; 137:1734-7. [PMID: 25625321 DOI: 10.1021/ja5103019] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The expression of proteins containing unnatural amino acids through suppression of a stop codon can be limited by truncation due to competition with release factors. When the site of incorporation is near the C-terminus, it may not be feasible to separate the full-length unnatural amino acid protein from the truncated form. We report a simple, traceless procedure that allows one to isolate the desired protein using a C-terminal intein fusion.
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Affiliation(s)
- Solongo Batjargal
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
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67
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A general method to improve fluorophores for live-cell and single-molecule microscopy. Nat Methods 2015; 12:244-50, 3 p following 250. [PMID: 25599551 PMCID: PMC4344395 DOI: 10.1038/nmeth.3256] [Citation(s) in RCA: 969] [Impact Index Per Article: 107.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 12/08/2014] [Indexed: 12/23/2022]
Abstract
Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here, we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.
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68
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FRET-based analysis of protein-nucleic acid interactions by genetically incorporating a fluorescent amino acid. Amino Acids 2014; 47:729-34. [PMID: 25540052 DOI: 10.1007/s00726-014-1900-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
Protein-nucleic acid interaction is an important process in many biological phenomena. In this study, a fluorescence resonance energy transfer (FRET)-based protein-DNA binding assay has been developed, in which a fluorescent amino acid is genetically incorporated into a DNA-binding protein. A coumarin-containing amino acid was incorporated into a DNA-binding protein, and the mutant protein specifically produced a FRET signal upon binding to its cognate DNA labeled with a fluorophore. The protein-DNA binding affinity was then measured under equilibrium conditions. This method is advantageous for studying protein-nucleic acid interactions, because it is performed under equilibrium conditions, technically easy, and applicable to any nucleic acid-binding protein.
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69
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Talukder P, Chen S, Liu CT, Baldwin EA, Benkovic SJ, Hecht SM. Tryptophan-based fluorophores for studying protein conformational changes. Bioorg Med Chem 2014; 22:5924-34. [PMID: 25284250 PMCID: PMC4254292 DOI: 10.1016/j.bmc.2014.09.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/03/2014] [Accepted: 09/08/2014] [Indexed: 11/19/2022]
Abstract
With the continuing interest in deciphering the interplay between protein function and conformational changes, small fluorescence probes will be especially useful for tracking changes in the crowded protein interior space. Presently, we describe the potential utility of six unnatural amino acid fluorescence donors structurally related to tryptophan and show how they can be efficiently incorporated into a protein as fluorescence probes. We also examine the various photophysical properties of the new Trp analogues, which are significantly redshifted in their fluorescence spectra relative to tryptophan. In general, the Trp analogues were well tolerated when inserted into Escherichia coli DHFR, and did not perturb enzyme activity, although substitution for Trp22 did result in a diminution in DHFR activity. Further, it was demonstrated that D and E at position 37 formed efficient FRET pairs with acridon-2-ylalanine (Acd) at position 17. The same was also true for a DHFR construct containing E at position 79 and Acd at position 17. Together, these findings demonstrate that these tryptophan analogues can be introduced into DHFR with minimal disruption of function, and that they can be employed for the selective study of targeted conformational changes in proteins, even in the presence of unmodified tryptophans.
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Affiliation(s)
- Poulami Talukder
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - C Tony Liu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Edwin A Baldwin
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
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Padmanarayana M, Hams N, Speight LC, Petersson EJ, Mehl RA, Johnson CP. Characterization of the lipid binding properties of Otoferlin reveals specific interactions between PI(4,5)P2 and the C2C and C2F domains. Biochemistry 2014; 53:5023-33. [PMID: 24999532 PMCID: PMC4144714 DOI: 10.1021/bi5004469] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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Otoferlin
is a transmembrane protein consisting of six C2 domains,
proposed to act as a calcium sensor for exocytosis. Although otoferlin
is believed to bind calcium and lipids, the lipid specificity and
identity of the calcium binding domains are controversial. Further,
it is currently unclear whether the calcium binding affinity of otoferlin
quantitatively matches the maximal intracellular presynaptic calcium
concentrations of ∼30–50 μM known to elicit exocytosis.
To characterize the calcium and lipid binding properties of otoferlin,
we used isothermal titration calorimetry (ITC), liposome sedimentation
assays, and fluorescence spectroscopy. Analysis of ITC data indicates
that with the exception of the C2A domain, the C2 domains of otoferlin
bind multiple calcium ions with moderate (Kd = 25–95 μM) and low affinities (Kd = 400–700 μM) in solution. However, in the presence
of liposomes, the calcium sensitivity of the domains increased by
up to 10-fold. It was also determined that calcium enhanced liposome
binding for domains C2B–C2E, whereas the C2F domain bound liposomes
in a calcium-independent manner. Mutations that abrogate calcium binding
in C2F do not disrupt liposome binding, supporting the conclusion
that the interaction of the C2F domain with phosphatidylserine is
calcium-independent. Further, domains C2C and C2F, not domains C2A,
C2B, C2D, and C2E, bound phosphatidylinositol 4,5-bisphosphate 1,2-dioleoyl-sn-glycero-3-phospho(1′-myoinositol-4′,5′-bisphosphate) [PI(4,5)P2], which preferentially
steered them toward liposomes harboring PI(4,5)P2. Remarkably, lysine
mutations L478A and L480A in C2C selectively weaken the PI(4,5)P2
interaction while leaving phosphatidylserine binding unaffected. Finally,
shifts in the emission spectra of an environmentally sensitive fluorescent
unnatural amino acid indicate that the calcium binding loops of the
C2F domain directly interact with the lipid bilayer of negatively
charged liposomes in a calcium-independent manner. On the basis of
these results, we propose that the C2F and C2C domains of otoferlin
preferentially bind PI(4,5)P2 and that PI(4,5)P2 may serve to target
otoferlin to the presynapse in a calcium-independent manner. This
positioning would facilitate fast calcium-dependent exocytosis at
the hair cell synapse.
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Affiliation(s)
- Murugesh Padmanarayana
- Department of Biochemistry and Biophysics, Oregon State University , Corvallis, Oregon 973331, United States
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71
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Cooley RB, Karplus PA, Mehl RA. Gleaning unexpected fruits from hard-won synthetases: probing principles of permissivity in non-canonical amino acid-tRNA synthetases. Chembiochem 2014; 15:1810-9. [PMID: 25044993 DOI: 10.1002/cbic.201402180] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Indexed: 11/09/2022]
Abstract
The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins is an important tool for understanding biological function. Traditionally, each new ncAA targeted for incorporation requires a resource-consuming process of generating new ncAA aminoacyl tRNA synthetase/tRNACUA pairs. However, the discovery that some tRNA synthetases are "permissive", in that they can incorporate multiple ncAAs, means that it is no longer always necessary to develop a new synthetase for each newly desired ncAA. Developing a better understanding of what factors make ncAA synthetases more permissive would increase the utility of this new approach. Here, we characterized two synthetases selected for the same ncAA that have markedly different "permissivity profiles." Remarkably, the more permissive synthetase incorporated an ncAA for which we had not been able to generate a synthetase through de novo selection methods. Crystal structures revealed that the two synthetases recognize their parent ncAA through a conserved core of interactions, with the more permissive synthetase displaying a greater degree of flexibility in its interaction geometries. We also observed that intraprotein interactions not directly involved in ncAA binding can play a crucial role in synthetase permissivity and suggest that optimization of such interactions might provide an avenue to engineering synthetases with enhanced permissivity.
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Affiliation(s)
- Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, 2011 Ag and Life Sciences Building, Corvallis, OR 97331 (USA)
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72
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Soares JA, Kiessling LL. A symposium in honor of Peter B. Dervan, the 2014 ACS Chemical Biology Lectureship Award Winner. ACS Chem Biol 2014; 9:1221-3. [PMID: 25120068 DOI: 10.1021/cb5003703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jitesh A Soares
- Department of Chemistry, University of Wisconsin, Madition , 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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73
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Schmidt MJ, Borbas J, Drescher M, Summerer D. A Genetically Encoded Spin Label for Electron Paramagnetic Resonance Distance Measurements. J Am Chem Soc 2014; 136:1238-41. [DOI: 10.1021/ja411535q] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Moritz J. Schmidt
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Julia Borbas
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Daniel Summerer
- Department of Chemistry,
Zukunftskolleg, and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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74
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Speight LC, Samanta M, Petersson EJ. Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck. Aust J Chem 2014. [DOI: 10.1071/ch13554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
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