51
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Walters CR, Szantai-Kis DM, Zhang Y, Reinert ZE, Horne WS, Chenoweth DM, Petersson EJ. The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts. Chem Sci 2017; 8:2868-2877. [PMID: 28553525 PMCID: PMC5428018 DOI: 10.1039/c6sc05580j] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/24/2017] [Indexed: 12/17/2022] Open
Abstract
Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.
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Affiliation(s)
- Christopher R Walters
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - D Miklos Szantai-Kis
- Biochemistry and Molecular Biophysics Graduate Group , University of Pennsylvania , 3700 Hamilton Walk , Philadelphia , PA 19104 , USA
| | - Yitao Zhang
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - Zachary E Reinert
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA 15260 , USA
| | - W Seth Horne
- Department of Chemistry , University of Pittsburgh , 219 Parkman Avenue , Pittsburgh , PA 15260 , USA
| | - David M Chenoweth
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
| | - E James Petersson
- Department of Chemistry , University of Pennsylvania , 231 S. 34th Street , Philadelphia , PA 19104 , USA
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52
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Park HS, Kang YK. Effects of isosteric substitutions on the conformational preference and cis–trans isomerization of proline-containing peptides. NEW J CHEM 2017. [DOI: 10.1039/c7nj01403a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Isosteric substitutions of the peptide CO group by CS and CSe groups increased thetranspopulation and rotational barrier to the prolylcis–transisomerization of proline-containing peptides.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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53
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Mukherjee S, Chatterjee J. Suppressing the epimerization of endothioamide peptides during Fmoc/t-Bu-based solid phase peptide synthesis. J Pept Sci 2016; 22:664-672. [DOI: 10.1002/psc.2929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Somnath Mukherjee
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit; Indian Institute of Science; Bangalore 560012 India
- NMR Research Centre; Indian Institute of Science; Bangalore 560012 India
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54
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Pál D, Móczár I, Kormos A, Baranyai P, Huszthy P. Synthesis and enantiomeric recognition studies of optically active 5,5-dioxophenothiazine bis(urea) and bis(thiourea) derivatives. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.tetasy.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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55
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Lu W, Xiao P, Liu Z, Gu J, Zhang J, Huang Y, Huang Q, Chen T. Reaction-Driven Self-Assembled Micellar Nanoprobes for Ratiometric Fluorescence Detection of CS2 with High Selectivity and Sensitivity. ACS APPLIED MATERIALS & INTERFACES 2016; 8:20100-20109. [PMID: 27419849 DOI: 10.1021/acsami.6b06472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The detection of highly toxic CS2, which is known as a notorious occupational hazard in various industrial processes, is important from both environmental and public safety perspectives. We describe here a robust type of chemical-reaction-based supramolecular fluorescent nanoprobes for ratiometric determination of CS2 with high selectivity and sensitivity in water medium. The micellar nanoprobes self-assemble from amphiphilic pyrene-modified hyperbranched polyethylenimine (Py-HPEI) polymers with intense pyrene excimer emission. Selective sensing is based on a CS2-specific reaction with hydrophilic amino groups to produce hydrophobic dithiocarbamate moieties, which can strongly quench the pyrene excimer emission via a known photoinduced electron transfer (PET) mechanism. Therefore, the developed micellar nanoprobes are free of the H2S interference problem often encountered in the widely used colorimetric assays and proved to show high selectivity over many potentially competing chemical species. Importantly, the developed approach is capable of CS2 sensing even in complex tap and river water samples. In addition, in view of the modular design principle of these powerful micellar nanoprobes, the sensing strategy used here is expected to be applicable to the development of various sensory systems for other environmentally important guest species.
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Affiliation(s)
- Wei Lu
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Peng Xiao
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Zhenzhong Liu
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Jincui Gu
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Jiawei Zhang
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Youju Huang
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Qing Huang
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
| | - Tao Chen
- Key Laboratory of Marine Materials and Related Technologies, Ningbo Institute of Material Technology and Engineering, Chinese Academy of Science , Ningbo 315201, China
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56
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Wang YJ, Szantai-Kis DM, Petersson EJ. Chemoselective modifications for the traceless ligation of thioamide-containing peptides and proteins. Org Biomol Chem 2016; 14:6262-9. [PMID: 27264841 DOI: 10.1039/c6ob01020b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Thioamides are single-atom substitutions of canonical amide bonds, and have been proven to be versatile and minimally perturbing probes in protein folding studies. Previously, our group showed that thioamides can be incorporated into proteins by native chemical ligation (NCL) with Cys as a ligation handle. In this study, we report the expansion of this strategy into non-Cys ligation sites, utilizing radical initiated desulfurization to "erase" the side chain thiol after ligation. The reaction exhibited high chemoselectivity against thioamides, which can be further enhanced with thioacetamide as a sacrificial scavenger. As a proof-of-concept example, we demonstrated the incorporation of a thioamide probe into a 56 amino acid protein, the B1 domain of Protein G (GB1). Finally, we showed that the method can be extended to β-thiol amino acid analogs and selenocysteine.
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Affiliation(s)
- Yanxin J Wang
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104, USA.
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57
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Lai HP, Gao RC, Huang CL, Chen IC, Tan KT. Fluorescence switchable probes based on a molecular rotor for selective detection of proteins and small molecules. Chem Commun (Camb) 2016; 51:16197-200. [PMID: 26396997 DOI: 10.1039/c5cc06714f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this communication, we report a general strategy to create fluorescence switchable probes, where a small molecule ligand is conjugated to a fluorescent molecular rotor, for the selective detection of proteins through a non-enzymatic process. In the presence of target proteins, bond rotation of the molecular rotor is restricted, thereby triggering the emission of strong fluorescence.
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Affiliation(s)
- Hsiu-Ping Lai
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - Ruo-Cing Gao
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - Chi-Ling Huang
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China.
| | - I-Chia Chen
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China. and Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101 Sec. 2, Kuang Fu Rd, Hsinchu 30013, Taiwan, Republic of China
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58
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Phosphorylation regulates proteolytic efficiency of TEV protease detected by a 5(6)-carboxyfluorescein-pyrene based fluorescent sensor. Talanta 2016; 150:340-5. [DOI: 10.1016/j.talanta.2015.12.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/01/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022]
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59
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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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60
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Sun XF, Zhang ZX, Li W, Bai FQ, Wang J, Jia R, Kong CP, Zhang HX. DFT/TD-DFT calculations on the sensing mechanism of a dual response near-infrared fluorescent chemosensor for superoxide anion and hydrogen polysulfides: photoinduced electron transfer. RSC Adv 2016. [DOI: 10.1039/c6ra23724j] [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
Fluorescence quenching by the PET process in HCy-FN.
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Affiliation(s)
- Xiao-Fei Sun
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Zhi-Xiang Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Wei Li
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Fu-Quan Bai
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Jian Wang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Ran Jia
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Chui-Peng Kong
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
| | - Hong-Xing Zhang
- International Joint Research Laboratory of Nano-Micro Architecture Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- People's Republic of China
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61
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Liu H, Xu X, Peng H, Chang X, Fu X, Li Q, Yin S, Blanchard GJ, Fang Y. New solvatochromic probes: performance enhancement via regulation of excited state structures. Phys Chem Chem Phys 2016; 18:25210-25220. [DOI: 10.1039/c6cp04293g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Regulation of excited state structures resulted in new fluorophores with much enhanced solvatochromic properties.
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Affiliation(s)
- Huijing Liu
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Materials Science and Engineering
| | - Xiaojie Xu
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Chemistry and Chemical Engineering
| | - Haonan Peng
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Chemistry and Chemical Engineering
| | - Xingmao Chang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Materials Science and Engineering
| | - Xuwei Fu
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Chemistry and Chemical Engineering
| | - Qianshu Li
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
| | - Shiwei Yin
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Chemistry and Chemical Engineering
| | | | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education)
- Shaanxi Normal University
- Xi'an 710062
- P. R. China
- School of Chemistry and Chemical Engineering
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62
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Liu W, Chen C, Liu H. Dimethylamine as the key intermediate generated in situ from dimethylformamide (DMF) for the synthesis of thioamides. Beilstein J Org Chem 2015; 11:1721-6. [PMID: 26664591 PMCID: PMC4660898 DOI: 10.3762/bjoc.11.187] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022] Open
Abstract
An improved and efficient method for the synthesis of thioamides is presented. For this transformation, dimethylamine as the key intermediate is generated in situ from dimethylformamide (DMF). All the tested substrates produced the desired products with excellent isolated yields.
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Affiliation(s)
- Weibing Liu
- College of Chemical Engineering, Guangdong University of Petrochemical Technology, 2 Guandu Road, Maoming 525000, P. R. China, ; Tel: +86-668-2923956
| | - Cui Chen
- College of Chemical Engineering, Guangdong University of Petrochemical Technology, 2 Guandu Road, Maoming 525000, P. R. China, ; Tel: +86-668-2923956
| | - Hailing Liu
- College Analytical and Testing Centre, Beijing Normal University, No. 19, Xinjiekouwai St., Haidian District, Beijing 100875, P. R. China; Tel: +86-15010928428
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63
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Maini R, Dedkova LM, Paul R, Madathil MM, Chowdhury SR, Chen S, Hecht SM. Ribosome-Mediated Incorporation of Dipeptides and Dipeptide Analogues into Proteins in Vitro. J Am Chem Soc 2015; 137:11206-9. [PMID: 26301427 DOI: 10.1021/jacs.5b03135] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Plasmids containing 23S rRNA randomized at positions 2057-2063 and 2502-2507 were introduced into Escherichia coli, affording a library of clones which produced modified ribosomes in addition to the pre-existing wild-type ribosomes. These clones were screened with a derivative of puromycin, a natural product which acts as an analogue of the 3'-end of aminoacyl-tRNA and terminates protein synthesis by accepting the growing polypeptide chain, thereby killing bacterial cells. The puromycin derivative in this study contained the dipeptide p-methoxyphenylalanylglycine, implying the ability of the modified ribosomes in clones sensitive to this puromycin analogue to recognize dipeptides. Several clones inhibited by the puromycin derivative were used to make S-30 preparations, and some of these were shown to support the incorporation of dipeptides into proteins. The four incorporated species included two dipeptides (Gly-Phe (2) and Phe-Gly (3)), as well as a thiolated dipeptide analogue (4) and a fluorescent oxazole (5) having amine and carboxyl groups approximately the same distance apart as in a normal dipeptide. A protein containing both thiolated dipeptide 4 and a 7-methoxycoumarin fluorophore was found to undergo fluorescence quenching. Introduction of the oxazole fluorophore 5 into dihydrofolate reductase or green fluorescent protein resulted in quite strong enhancement of its fluorescence emission, and the basis for this enhancement was studied. The aggregate results demonstrate the feasibility of incorporating dipeptides as a single ribosomal event, and illustrate the lack of recognition of the central peptide bond in the dipeptide, potentially enabling the incorporation of a broad variety of structural analogues.
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Affiliation(s)
- Rumit Maini
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Larisa M Dedkova
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Rakesh Paul
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Manikandadas M Madathil
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Sandipan Roy Chowdhury
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Shengxi Chen
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, United States
| | - Sidney M Hecht
- Center for BioEnergetics, Biodesign Institute, and Department of Chemistry & Biochemistry, Arizona State University , Tempe, Arizona 85287, 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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Xu B, Wang YP, Yao ZJ, Jin GX. Metal-induced B-H bond activation: reactions between half-sandwich Ir and Rh complexes with carboranylthioamide. Dalton Trans 2015; 44:1530-3. [PMID: 25492590 DOI: 10.1039/c4dt03624g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Novel half-sandwich metal (Ir, Rh) complexes constructed from carboranylthioamide ligands containing an unexpected metal-boron bond were synthesized and characterized. The strong base n-butyllithium is demonstrated to be necessary in the reaction process.
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Affiliation(s)
- Bin Xu
- Shanghai Key Laboratory for Molecular Catalysis and Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, P. R. China.
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66
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Pospíšil P, Luxem KE, Ener M, Sýkora J, Kocábová J, Gray HB, Vlček A, Hof M. Fluorescence quenching of (dimethylamino)naphthalene dyes Badan and Prodan by tryptophan in cytochromes P450 and micelles. J Phys Chem B 2014; 118:10085-91. [PMID: 25079965 PMCID: PMC4148165 DOI: 10.1021/jp504625d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Fluorescence
of 2-(N,N-dimethylamino)-6-propionylnaphthalene
dyes Badan and Prodan is quenched by tryptophan in Brij 58 micelles
as well as in two cytochrome P450 proteins (CYP102, CYP119) with Badan
covalently attached to a cysteine residue. Formation of nonemissive
complexes between a dye molecule and tryptophan accounts for about
76% of the fluorescence intensity quenching in micelles, the rest
is due to diffusive encounters. In the absence of tryptophan, fluorescence
of Badan-labeled cytochromes decays with triexponential kinetics characterized
by lifetimes of about 100 ps, 700–800 ps, and 3 ns. Site mutation
of a histidine residue in the vicinity of the Badan label by tryptophan
results in shortening of all three decay lifetimes. The relative amplitude
of the fastest component increases at the expense of the two slower
ones. The average quenching rate constants are 4.5 × 108 s–1 (CYP102) and 3.7 × 108 s–1 (CYP119), at 288 K. Cyclic voltammetry of Prodan
in MeCN shows a reversible reduction peak at −1.85 V vs NHE
that becomes chemically irreversible and shifts positively upon addition
of water. A quasireversible reduction at −0.88 V was observed
in an aqueous buffer (pH 7.3). The excited-state reduction potential
of Prodan (and Badan) is estimated to vary from about +0.6 V (vs NHE)
in polar aprotic media (MeCN) to approximately +1.6 V in water. Tryptophan
quenching of Badan/Prodan fluorescence in CYPs and Brij 58 micelles
is exergonic by ≤0.5 V and involves tryptophan oxidation by
excited Badan/Prodan, coupled with a fast reaction between the reduced
dye and water. Photoreduction is a new quenching mechanism for 2-(N,N-dimethylamino)-6-propionylnaphthalene
dyes that are often used as solvatochromic polarity probes, FRET donors
and acceptors, as well as reporters of solvation dynamics.
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Affiliation(s)
- Petr Pospíšil
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3, CZ-182 23 Prague, Czech Republic
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67
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Petersson EJ, Goldberg JM, Wissner RF. On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability. Phys Chem Chem Phys 2014; 16:6827-37. [PMID: 24598971 DOI: 10.1039/c3cp55525a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our laboratory has developed thioamide analogs of the natural amino acids as minimally-perturbing fluorescence quenching probes that can be placed at many locations in a protein sequence. We have shown that the mechanism of quenching can be either Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), depending on the identity of the donor fluorophore. Furthermore, we have shown that one can use a combination of semi-synthetic methods to label full-sized proteins with fluorophore-thioamide pairs. These probes can be used to study protein-protein interactions, protein folding or misfolding, and proteolysis.
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Affiliation(s)
- E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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68
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Goldberg JM, Chen X, Meinhardt N, Greenbaum DC, Petersson EJ. Thioamide-based fluorescent protease sensors. J Am Chem Soc 2014; 136:2086-93. [PMID: 24472041 PMCID: PMC3985465 DOI: 10.1021/ja412297x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Thioamide
quenchers can be paired with compact fluorophores to
design “turn-on” fluorescent protease substrates. We
have used this method to study a variety of serine-, cysteine-, carboxyl-,
and metallo-proteases, including trypsin, chymotrypsin, pepsin, thermolysin,
papain, and calpain. Since thioamides quench some fluorophores red-shifted
from those naturally occurring in proteins, this technique can be
used for real time monitoring of protease activity in crude preparations
of virtually any protease. We demonstrate the value of this method
in three model applications: (1) characterization of papain enzyme
kinetics using rapid-mixing experiments, (2) selective monitoring
of cleavage at a single site in a peptide with multiple proteolytic
sites, and (3) analysis of the specificity of an inhibitor of calpain
in cell lysates.
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Affiliation(s)
- Jacob M Goldberg
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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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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