1
|
Yabushita A, Cheng CY, Ko YK, Kobayashi T, Iwakura I, Jimenez R. Excited State Vibrational Dynamics Reveals a Photocycle That Enhances the Photostability of the TagRFP-T Fluorescent Protein. J Phys Chem B 2024; 128:1188-1193. [PMID: 38282329 PMCID: PMC10860143 DOI: 10.1021/acs.jpcb.3c07212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
High photostability is a desirable property of fluorescent proteins (FPs) for imaging, yet its molecular basis is poorly understood. We performed ultrafast spectroscopy on TagRFP and its 9-fold more photostable variant TagRFP-T (TagRFP S158T) to characterize their initial photoreactions. We find significant differences in their electronic and vibrational dynamics, including faster excited-state proton transfer and transient changes in the frequency of the v520 mode in the excited electronic state of TagRFP-T. The frequency of v520, which is sensitive to chromophore planarity, downshifts within 0.58 ps and recovers within 0.87 ps. This vibrational mode modulates the distance from the chromophore phenoxy to the side chain of residue N143, which we suggest can trigger cis/trans photoisomerization. In TagRFP, the dynamics of v520 is missing, and this FP therefore lacks an important channel for chromophore isomerization. These dynamics are likely to be a key mechanism differentiating the photostability of the two FPs.
Collapse
Affiliation(s)
- Atsushi Yabushita
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Research Institute for Engineering, Kanagawa University, Yokohama 2210802, Japan
| | - Chia-Yun Cheng
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Ying Kuan Ko
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Takayoshi Kobayashi
- Department of Electrophysics, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Advanced Ultrafast Laser Research Center, The University of Electro-Communications, Chofu 1828585, Japan
| | - Izumi Iwakura
- Department of Chemistry, Faculty of Engineering, Kanagawa University, Yokohama 2218686, Japan
| | - Ralph Jimenez
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
2
|
Fusco F, Pires MC, Lopes APY, Alves VDS, Gonçalves VM. Influence of the mRNA initial region on protein production: a case study using recombinant detoxified pneumolysin as a model. Front Bioeng Biotechnol 2024; 11:1304965. [PMID: 38260740 PMCID: PMC10800503 DOI: 10.3389/fbioe.2023.1304965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
Recombinant proteins are of great importance in modern society, mostly as biopharmaceutical products. However, challenging and complex processes with low production yield are major drawbacks. Normally, the optimization to overcome these obstacles is focused on bioreactor and purification processes, and the biomolecular aspects are neglected, seen as less important. In this work, we present how the 5' mRNA secondary structure region can be relevant for translation and, therefore, protein production. For this, Escherichia coli BL21(DE3) clones, producing recombinant detoxified pneumolysin (PdT) with and without the N-terminal His-tag, were cultivated in 10-L bioreactors. Another version of the pdt gene (version 2) with synonymous changes in the 5'-end nucleotide sequence was also obtained. Protein production, plasmid stability, carbon sources, and acetic acid were quantified during the cultures. Furthermore, in silico mRNA analyses were performed using TIsigner and RNAfold. The results showed that the His-tag presence at the N-terminus generated a minimum 1.5-fold increase in target protein synthesis, which was explained by the in silico mRNA analyses that returned an mRNA secondary structure easier to translate and, therefore, higher protein production than without the His-tag. The pdt gene version 2 showed lower 5' mRNA opening energy than version 1, allowing higher PdT production even without a tag. This work reveals that simple mRNA analyses during heterologous gene design and production steps can help reach high-recombinant protein titers in a shorter time than using only traditional bioprocess optimization strategies.
Collapse
Affiliation(s)
- Filipe Fusco
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuella Cazelato Pires
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | | - Vítor dos Santos Alves
- Laboratory of Vaccine Development, Butantan Institute, Sao Paulo, Brazil
- Interunits Graduate Program in Biotechnology, University of Sao Paulo, Sao Paulo, Brazil
| | | |
Collapse
|
3
|
Schneider F, Sych T, Eggeling C, Sezgin E. Influence of nanobody binding on fluorescence emission, mobility, and organization of GFP-tagged proteins. iScience 2021; 24:101891. [PMID: 33364580 PMCID: PMC7753935 DOI: 10.1016/j.isci.2020.101891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/02/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022] Open
Abstract
Advanced fluorescence microscopy studies require specific and monovalent molecular labeling with bright and photostable fluorophores. This necessity led to the widespread use of fluorescently labeled nanobodies against commonly employed fluorescent proteins (FPs). However, very little is known how these nanobodies influence their target molecules. Here, we tested commercially available nanobodies and observed clear changes of the fluorescence properties, mobility and organization of green fluorescent protein (GFP) tagged proteins after labeling with the anti-GFP nanobody. Intriguingly, we did not observe any co-diffusion of fluorescently labeled nanobodies with the GFP-labeled proteins. Our results suggest significant binding of the nanobodies to a non-emissive, likely oligomerized, form of the FPs, promoting disassembly into monomeric form after binding. Our findings have significant implications on the application of nanobodies and GFP labeling for studying dynamic and quantitative protein organization in the plasma membrane of living cells using advanced imaging techniques.
Collapse
Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
- Jena Center of Soft Matters, Friedrich-Schiller-University Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, 171 65 Solna, Sweden
| |
Collapse
|
4
|
Paley MA, Prescher JA. Bioluminescence: a versatile technique for imaging cellular and molecular features. MEDCHEMCOMM 2014; 5:255-267. [PMID: 27594981 PMCID: PMC5006753 DOI: 10.1039/c3md00288h] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioluminescence is a ubiquitous imaging modality for visualizing biological processes in vivo. This technique employs visible light and interfaces readily with most cell and tissue types, making it a versatile technology for preclinical studies. Here we review basic bioluminescence imaging principles, along with applications of the technology that are relevant to the medicinal chemistry community. These include noninvasive cell tracking experiments, analyses of protein function, and methods to visualize small molecule metabolites. In each section, we also discuss how bioluminescent tools have revealed insights into experimental therapies and aided drug discovery. Last, we highlight the development of new bioluminescent tools that will enable more sensitive and multi-component imaging experiments and, thus, expand our broader understanding of living systems.
Collapse
Affiliation(s)
- Miranda A. Paley
- Department of Chemistry, University of California, Irvine, CA, USA
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| |
Collapse
|
5
|
Kuchmiy AA, Efimov GA, Nedospasov SA. Methods for in vivo molecular imaging. BIOCHEMISTRY (MOSCOW) 2013; 77:1339-53. [PMID: 23244729 DOI: 10.1134/s0006297912120012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Visualization of single molecules and specific subsets of cells is widely used for studies of biological processes and particularly in immunological research. Recent technological advances have provided a qualitative change in biological visualization from studying of "snapshot" pictures to real-time continuous observation of cellular dynamics in vivo. Contemporary methods of in vivo imaging make it possible to localize specific cells within organs and tissues, to study their differentiation, migration, and cell-to-cell interactions, and to follow some intracellular events. Fluorescence intravital microscopy plays an especially important role in high resolution molecular imaging. The methods of intravital microscopy are quickly advancing thanks to improvements in molecular sensors, labeling strategies, and detection approaches. Novel techniques allow simultaneous detection of various probes with better resolution and depth of imaging. In this review, we describe current methods for in vivo imaging, with special accent on fluorescence approaches, and discuss their applications for medical and biological studies.
Collapse
Affiliation(s)
- A A Kuchmiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova st. 32, 119991 Moscow, Russia.
| | | | | |
Collapse
|
6
|
Cuyvers S, Hendrix J, Dornez E, Engelborghs Y, Delcour JA, Courtin CM. Both Substrate Hydrolysis and Secondary Substrate Binding Determine Xylanase Mobility as Assessed by FRAP. J Phys Chem B 2011; 115:4810-7. [DOI: 10.1021/jp110963f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 20 - box 2463, B-3001 Leuven, Belgium
| | - Jelle Hendrix
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G - box 2403, B-3001 Leuven, Belgium
| | - Emmie Dornez
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 20 - box 2463, B-3001 Leuven, Belgium
| | - Yves Engelborghs
- Laboratory of Biomolecular Dynamics, Katholieke Universiteit Leuven, Celestijnenlaan 200G - box 2403, B-3001 Leuven, Belgium
| | - Jan A. Delcour
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 20 - box 2463, B-3001 Leuven, Belgium
| | - Christophe M. Courtin
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Kasteelpark Arenberg 20 - box 2463, B-3001 Leuven, Belgium
| |
Collapse
|
7
|
De Backer P, De Waele D, Van Speybroeck L. Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut? Acta Biotheor 2010; 58:15-49. [PMID: 19855930 DOI: 10.1007/s10441-009-9089-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 09/17/2009] [Indexed: 01/24/2023]
Abstract
The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.
Collapse
Affiliation(s)
- Philippe De Backer
- VIB, Department of Molecular Genetics/Department of Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | | | | |
Collapse
|
8
|
Vrzheshch EP, Dmitrienko DV, Rudanov GS, Zagidullin VE, Paschenko VZ, Razzhivin AP, Saletsky AM, Vrzheshch PV. Optical properties of the monomeric red fluorescent protein mRFP1. ACTA ACUST UNITED AC 2008. [DOI: 10.3103/s0096392508030036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Abstract
The ability to sense and respond to the environment is a hallmark of living systems. These processes occur at the levels of the organism, cells and individual molecules. Sensing of extracellular changes could result in a structural or chemical alteration in a molecule, which could in turn trigger a cascade of intracellular signals or regulated trafficking of molecules at the cell surface. These and other such processes allow cells to sense and respond to environmental changes. Often, these changes and the responses to them are spatially and/or temporally localized, and visualization of such events necessitates the use of high-resolution imaging approaches. Here we discuss optical imaging approaches and tools for imaging individual events at the cell surface with improved speed and resolution.
Collapse
Affiliation(s)
- Jyoti K Jaiswal
- The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
| | | |
Collapse
|
10
|
Stafforst T, Diederichsen U. Synthesis of Alaninyl andN-(2-Aminoethyl)glycinyl Amino Acid Derivatives Containing the Green Fluorescent Protein Chromophore in Their Side Chains for Incorporation into Peptides and Peptide Nucleic Acids. European J Org Chem 2007. [DOI: 10.1002/ejoc.200600729] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
11
|
Chudakov DM, Lukyanov S, Lukyanov KA. Fluorescent proteins as a toolkit for in vivo imaging. Trends Biotechnol 2005; 23:605-13. [PMID: 16269193 DOI: 10.1016/j.tibtech.2005.10.005] [Citation(s) in RCA: 345] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2005] [Revised: 07/21/2005] [Accepted: 10/12/2005] [Indexed: 10/25/2022]
Abstract
Green fluorescent protein (GFP) from the jellyfish Aequorea victoria, and its mutant variants, are the only fully genetically encoded fluorescent probes available and they have proved to be excellent tools for labeling living specimens. Since 1999, numerous GFP homologues have been discovered in Anthozoa, Hydrozoa and Copepoda species, demonstrating the broad evolutionary and spectral diversity of this protein family. Mutagenic studies gave rise to diversified and optimized variants of fluorescent proteins, which have never been encountered in nature. This article gives an overview of the GFP-like proteins developed to date and their most common applications to study living specimens using fluorescence microscopy.
Collapse
Affiliation(s)
- Dmitriy M Chudakov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | | | | |
Collapse
|