1
|
Shirley JC, Baiz CR. MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe. J Phys Chem B 2024; 128:5310-5319. [PMID: 38806061 DOI: 10.1021/acs.jpcb.4c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.
Collapse
Affiliation(s)
- Joseph C Shirley
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin 78712, Texas, United States
| |
Collapse
|
2
|
Streu K, Hunsberger S, Patel J, Wan X, Daly CA. Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch. J Chem Phys 2024; 160:074106. [PMID: 38364010 DOI: 10.1063/5.0185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024] Open
Abstract
The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.
Collapse
Affiliation(s)
- Kristina Streu
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Sara Hunsberger
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Jeanette Patel
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| | - Xiang Wan
- Department of Mathematics and Statistics, Loyola University Chicago, 1032 W. Sheridan Rd., Chicago, Illinois 60660, USA
| | - Clyde A Daly
- Department of Chemistry, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, USA
| |
Collapse
|
3
|
Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022; 61:e202204788. [PMID: 35704518 PMCID: PMC9542129 DOI: 10.1002/anie.202204788] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 11/06/2022]
Abstract
Recent advances in optical bioimaging have prompted the need for minimal chemical reporters that can retain the molecular recognition properties and activity profiles of biomolecules. As a result, several methodologies to reduce the size of fluorescent and Raman labels to a few atoms (e.g., single aryl fluorophores, Raman‐active triple bonds and isotopes) and embed them into building blocks (e.g., amino acids, nucleobases, sugars) to construct native‐like supramolecular structures have been described. The integration of small optical reporters into biomolecules has also led to smart molecular entities that were previously inaccessible in an expedite manner. In this article, we review recent chemical approaches to synthesize miniaturized optical tags as well as some of their multiple applications in biological imaging.
Collapse
Affiliation(s)
- Sam Benson
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
| | - Fabio de Moliner
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
| | - William Tipping
- Centre for Molecular Nanometrology The University of Strathclyde Glasgow G1 1RD UK
| | - Marc Vendrell
- Centre for Inflammation Research The University of Edinburgh Edinburgh EH16 4TJ UK
| |
Collapse
|
4
|
Benson S, de Moliner F, Tipping W, Vendrell M. Miniaturized Chemical Tags for Optical Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sam Benson
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - Fabio de Moliner
- The University of Edinburgh Centre for Inflammation Research UNITED KINGDOM
| | - William Tipping
- University of Strathclyde Centre for Molecular Nanometrology UNITED KINGDOM
| | - Marc Vendrell
- University of Edinburgh Centre for Inflammation Research 47 Little France Crescent EH16 4TJ Edinburgh UNITED KINGDOM
| |
Collapse
|
5
|
Flores ADR, Barber CC, Narayanamoorthy M, Gu D, Shen Y, Zhang W. Biosynthesis of Isonitrile- and Alkyne-Containing Natural Products. Annu Rev Chem Biomol Eng 2022; 13:1-24. [PMID: 35236086 PMCID: PMC9811556 DOI: 10.1146/annurev-chembioeng-092120-025140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural products are a diverse class of biologically produced compounds that participate in fundamental biological processes such as cell signaling, nutrient acquisition, and interference competition. Unique triple-bond functionalities like isonitriles and alkynes often drive bioactivity and may serve as indicators of novel chemical logic and enzymatic machinery. Yet, the biosynthetic underpinnings of these groups remain only partially understood, constraining the opportunity to rationally engineer biomolecules with these functionalities for applications in pharmaceuticals, bioorthogonal chemistry, and other value-added chemical processes. Here, we focus our review on characterized biosynthetic pathways for isonitrile and alkyne functionalities, their bioorthogonal transformations, and prospects for engineering their biosynthetic machinery for biotechnological applications.
Collapse
Affiliation(s)
- Antonio Del Rio Flores
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Colin C. Barber
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | | | - Di Gu
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuanbo Shen
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA,Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
6
|
Chen Y, Yan W, Guo D, Li Y, Li J, Liu H, Wei L, Yu N, Wang B, Zheng Y, Jing M, Zhao J, Ye Y. An Activity‐Based Sensing Fluorogenic Probe for Monitoring Ethylene in Living Cells and Plants. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yiliang Chen
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Wei Yan
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Duojing Guo
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Yu Li
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Ji Li
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center (ChemBIC) School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Hao Liu
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Lirong Wei
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Na Yu
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Biao Wang
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Ying Zheng
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Maofeng Jing
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry Chemistry and Biomedicine Innovation Center (ChemBIC) School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Yonghao Ye
- Key Laboratory of Plant Immunity, College of Plant Protection Nanjing Agricultural University Nanjing 210095 P. R. China
- State & Local Joint Engineering Research Center of Green Pesticide Invention and Application Nanjing Agricultural University Nanjing 210095 P. R. China
| |
Collapse
|
7
|
Wilson LT, Tipping WJ, Wetherill C, Henley Z, Faulds K, Graham D, Mackay SP, Tomkinson NCO. Mitokyne: A Ratiometric Raman Probe for Mitochondrial pH. Anal Chem 2021; 93:12786-12792. [PMID: 34505518 DOI: 10.1021/acs.analchem.1c03075] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial pH (pHmito) is intimately related to mitochondrial function, and aberrant values for pHmito are linked to several disease states. We report the design, synthesis, and application of mitokyne 1-the first small molecule pHmito sensor for stimulated Raman scattering (SRS) microscopy. This ratiometric probe can determine subtle changes in pHmito in response to external stimuli and the inhibition of both the electron transport chain and ATP synthase with small molecule inhibitors. In addition, 1 was also used to monitor mitochondrial dynamics in a time-resolved manner with subcellular spatial resolution during mitophagy providing a powerful tool for dissecting the molecular and cell biology of this critical organelle.
Collapse
Affiliation(s)
- Liam T Wilson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - William J Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Zoë Henley
- GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Simon P Mackay
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, United Kingdom
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| |
Collapse
|
8
|
Chen Y, Yan W, Guo D, Li Y, Li J, Liu H, Wei L, Yu N, Wang B, Zheng Y, Jing M, Zhao J, Ye Y. An Activity-Based Sensing Fluorogenic Probe for Monitoring Ethylene in Living Cells and Plants. Angew Chem Int Ed Engl 2021; 60:21934-21942. [PMID: 34291549 DOI: 10.1002/anie.202108335] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 02/06/2023]
Abstract
Ethylene (ET) is an important gaseous plant hormone. It is highly desirable to develop fluorescent probes for monitoring ethylene in living cells. We report an efficient RhIII -catalysed coupling of N-phenoxyacetamides to ethylene in the presence of an alcohol. The newly discovered coupling reaction exhibited a wide scope of N-phenoxyacetamides and excellent regioselectivity. We successfully developed three fluorophore-tagged RhIII -based fluorogenic coumarin-ethylene probes (CEPs) using this strategy for the selective and quantitative detection of ethylene. CEP-1 exhibited the highest sensitivity with a limit of detection of ethylene at 52 ppb in air. Furthermore, CEP-1 was successfully applied for imaging in living CHO-K1 cells and for monitoring endogenous-induced changes in ethylene biosynthesis in tobacco and Arabidopsis thaliana plants. These results indicate that CEP-1 has great potential to illuminate the spatiotemporal regulation of ethylene biosynthesis and ethylene signal transduction in living biological systems.
Collapse
Affiliation(s)
- Yiliang Chen
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Wei Yan
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Duojing Guo
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Yu Li
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Ji Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Hao Liu
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Lirong Wei
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Na Yu
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Biao Wang
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Ying Zheng
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Maofeng Jing
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yonghao Ye
- Key Laboratory of Plant Immunity, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China.,State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| |
Collapse
|