1
|
Rossano‐Tapia M, Brown A. Quantum mechanical/molecular mechanical studies of photophysical properties of fluorescent proteins. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Alex Brown
- Department of Chemistry University of Alberta Edmonton Alberta Canada
| |
Collapse
|
2
|
Nikovics K, Favier AL. Macrophage Identification In Situ. Biomedicines 2021; 9:biomedicines9101393. [PMID: 34680510 PMCID: PMC8533306 DOI: 10.3390/biomedicines9101393] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding the processes of inflammation and tissue regeneration after injury is of great importance. For a long time, macrophages have been known to play a central role during different stages of inflammation and tissue regeneration. However, the molecular and cellular mechanisms by which they exert their effects are as yet mostly unknown. While in vitro macrophages have been characterized, recent progress in macrophage biology studies revealed that macrophages in vivo exhibited distinctive features. Actually, the precise characterization of the macrophages in vivo is essential to develop new healing treatments and can be approached via in situ analyses. Nowadays, the characterization of macrophages in situ has improved significantly using antigen surface markers and cytokine secretion identification resulting in specific patterns. This review aims for a comprehensive overview of different tools used for in situ macrophage identification, reporter genes, immunolabeling and in situ hybridization, discussing their advantages and limitations.
Collapse
|
3
|
Morikawa TJ, Nishiyama M, Yoshizawa K, Fujita H, Watanabe TM. Glycine insertion modulates the fluorescence properties of Aequorea victoria green fluorescent protein and its variants in their ambient environment. Biophys Physicobiol 2021; 18:145-158. [PMID: 34178565 PMCID: PMC8214926 DOI: 10.2142/biophysico.bppb-v18.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 12/04/2022] Open
Abstract
The green fluorescent protein (GFP) derived from Pacific Ocean jellyfish is an essential tool in biology. GFP-solvent interactions can modulate the fluorescent property of GFP. We previously reported that glycine insertion is an effective mutation in the yellow variant of GFP, yellow fluorescent protein (YFP). Glycine insertion into one of the β-strands comprising the barrel structure distorts its structure, allowing water molecules to invade near the chromophore, enhancing hydrostatic pressure or solution hydrophobicity sensitivity. However, the underlying mechanism of how glycine insertion imparts environmental sensitivity to YFP has not been elucidated yet. To unveil the relationship between fluorescence and β-strand distortion, we investigated the effects of glycine insertion on the dependence of the optical properties of GFP variants named enhanced-GFP (eGFP) and its yellow (eYFP) and cyan (eCFP) variants with respect to pH, temperature, pressure, and hydrophobicity. Our results showed that the quantum yield decreased depending on the number of inserted glycines in all variants, and the dependence on pH, temperature, pressure, and hydrophobicity was altered, indicating the invasion of water molecules into the β-barrel. Peak shifts in the emission spectrum were observed in glycine-inserted eGFP, suggesting a change of the electric state in the excited chromophore. A comparative investigation of the spectral shift among variants under different conditions demonstrated that glycine insertion rearranged the hydrogen bond network between His148 and the chromophore. The present results provide important insights for further understanding the fluorescence mechanism in GFPs and suggest that glycine insertion could be a potent approach for investigating the relationship between water molecules and the intra-protein chromophore.
Collapse
Affiliation(s)
- Takamitsu J Morikawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Graduate School of Frontier Bioscience, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Kindai University, Higashiosaka, Osaka 577-8502, Japan
| | - Keiko Yoshizawa
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Hyogo 650-0047, Japan.,Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| |
Collapse
|
4
|
Drobizhev M, Molina RS, Callis PR, Scott JN, Lambert GG, Salih A, Shaner NC, Hughes TE. Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins. Front Mol Biosci 2021; 8:633217. [PMID: 33763453 PMCID: PMC7983054 DOI: 10.3389/fmolb.2021.633217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022] Open
Abstract
Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.
Collapse
Affiliation(s)
- Mikhail Drobizhev
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Rosana S Molina
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| | - Patrik R Callis
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Gerard G Lambert
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Anya Salih
- Antares & Fluoresci Research, Dangar Island, NSW, Australia
| | - Nathan C Shaner
- Department of Neurosciences, UC San Diego, San Diego, CA, United States
| | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, MT, United States
| |
Collapse
|
5
|
Rossano-Tapia M, Olsen JMH, Brown A. Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM. Front Mol Biosci 2020; 7:111. [PMID: 32596253 PMCID: PMC7303285 DOI: 10.3389/fmolb.2020.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 11/13/2022] Open
Abstract
Multi-photon absorption properties, particularly two-photon absorption (2PA), of fluorescent proteins (FPs) have made them attractive tools in deep-tissue clinical imaging. Although the diversity of photophysical properties for FPs is wide, there are some caveats predominant among the existing FP variants that need to be overcome, such as low quantum yields and small 2PA cross-sections. From a computational perspective, Salem et al. (2016) suggested the inclusion of non-canonical amino acids in the chromophore of the red fluorescent protein DsRed, through the replacement of the tyrosine amino acid. The 2PA properties of these new non-canonical chromophores (nCCs) were determined in vacuum, i.e., without taking into account the protein environment. However, in the computation of response properties, such as 2PA cross-sections, the environment plays an important role. To account for environment and protein-chromophore coupling effects, quantum mechanical/molecular mechanical (QM/MM) schemes can be useful. In this work, the polarizable embedding (PE) model is employed along with time-dependent density functional theory to describe the 2PA properties of a selected set of chromophores made from non-canonical amino acids as they are embedded in the DsRed protein matrix. The objective is to provide insights to determine whether or not the nCCs could be developed and, thus, generate a new class of FPs. Results from this investigation show that within the DsRed environment, the nCC 2PA cross-sections are diminished relative to their values in vacuum. However, further studies toward understanding the 2PA limit of these nCCs using different protein environments are needed.
Collapse
Affiliation(s)
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, Tromsø, Norway
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
6
|
Back to the Future: Genetically Encoded Fluorescent Proteins as Inert Tracers of the Intracellular Environment. Int J Mol Sci 2020; 21:ijms21114164. [PMID: 32545175 PMCID: PMC7312867 DOI: 10.3390/ijms21114164] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
Over the past decades, the discovery and development of genetically encoded fluorescent proteins (FPs) has brought a revolution into our ability to study biologic phenomena directly within living matter. First, FPs enabled fluorescence-labeling of a variety of molecules of interest to study their localization, interactions and dynamic behavior at various scales-from cells to whole organisms/animals. Then, rationally engineered FP-based sensors facilitated the measurement of physicochemical parameters of living matter-especially at the intracellular level, such as ion concentration, temperature, viscosity, pressure, etc. In addition, FPs were exploited as inert tracers of the intracellular environment in which they are expressed. This oft-neglected role is made possible by two distinctive features of FPs: (i) the quite null, unspecific interactions of their characteristic β-barrel structure with the molecular components of the cellular environment; and (ii) their compatibility with the use of time-resolved fluorescence-based optical microscopy techniques. This review seeks to highlight the potential of such unique combinations of properties and report on the most significative and original applications (and related advancements of knowledge) produced to date. It is envisioned that the use of FPs as inert tracers of living matter structural organization holds a potential for several lines of further development in the next future, discussed in the last section of the review, which in turn can lead to new breakthroughs in bioimaging.
Collapse
|
7
|
Rossano-Tapia M, Brown A. Determination of Two-Photon-Absorption Cross Sections Using Time-Dependent Density Functional Theory Tight Binding: Application to Fluorescent Protein Chromophores. J Chem Theory Comput 2019; 15:3153-3161. [DOI: 10.1021/acs.jctc.9b00082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| |
Collapse
|
8
|
Ma Q, Ye L, Liu H, Shi Y, Zhou N. An overview of Ca 2+ mobilization assays in GPCR drug discovery. Expert Opin Drug Discov 2017; 12:511-523. [PMID: 28277837 DOI: 10.1080/17460441.2017.1303473] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Calcium ions (Ca2+) serve as a second messenger or universal signal transducer implicated in the regulation of a wide range of physiological processes. A change in the concentration of intracellular Ca2+ is an important step in intracellular signal transduction. G protein-coupled receptors (GPCRs), the largest and most versatile group of cell surface receptors, transduce extracellular signals into intracellular responses via their coupling to heterotrimeric G proteins. Since Ca2+ plays a crucial role in GPCR-induced signaling, measurement of intracellular Ca2+ has attracted more and more attention in GPCR-targeted drug discovery. Areas covered: This review focuses on the most popular functional assays measuring GPCRs-induced intracellular Ca2+ signaling. These include photoprotein-based, synthetic fluorescent indicator-based and genetically encoded calcium indicator (GECI)-based Ca2+ mobilization assays. A brief discussion of the design strategy of fluorescent probes in GPCR studies is also presented. Expert opinion: GPCR-mediated intracellular signaling is multidimensional. There is an urgent need for the development of multiple-readout screening assays capable of simultaneous detection of biased signaling and screening of both agonists and antagonists in the same assay. It is also necessary to develop GECIs offering low cost and consistent assays suitable for investigating GPCR activation in vivo.
Collapse
Affiliation(s)
- Qiang Ma
- a College of Life Sciences, Zijingang Campus , Zhejiang University, Institute of Biochemistry and Molecular Biology , Hangzhou , Zhejiang , China
| | - Lingyan Ye
- a College of Life Sciences, Zijingang Campus , Zhejiang University, Institute of Biochemistry and Molecular Biology , Hangzhou , Zhejiang , China
| | - Hongxia Liu
- b Department of Internal Medicine , Edong Healthcare Group , Huangshi , Hubei , China
| | - Ying Shi
- a College of Life Sciences, Zijingang Campus , Zhejiang University, Institute of Biochemistry and Molecular Biology , Hangzhou , Zhejiang , China
| | - Naiming Zhou
- a College of Life Sciences, Zijingang Campus , Zhejiang University, Institute of Biochemistry and Molecular Biology , Hangzhou , Zhejiang , China
| |
Collapse
|
9
|
Štěpánek P, Cowie TY, Šafařík M, Šebestík J, Pohl R, Bouř P. Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism. Chemphyschem 2016; 17:2348-54. [PMID: 27124359 DOI: 10.1002/cphc.201600313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Indexed: 11/08/2022]
Abstract
The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time-dependent density functional theory (TDDFT) computations and the sum-over-state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five-member ring, and methoxy groups can be used to further tune the electronic levels.
Collapse
Affiliation(s)
- Petr Štěpánek
- NMR Research Group, Faculty of Science, University of Oulu, PO Box 3000, 90014, Oulu, Finland
| | - Thomas Y Cowie
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Martin Šafařík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo náměstí 2, 166 10, Prague, Czech Republic.
| |
Collapse
|
10
|
Design and development of genetically encoded fluorescent sensors to monitor intracellular chemical and physical parameters. Biophys Rev 2016; 8:121-138. [PMID: 28510054 PMCID: PMC4884202 DOI: 10.1007/s12551-016-0195-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/09/2016] [Indexed: 01/26/2023] Open
Abstract
Over the past decades many researchers have made major contributions towards the development of genetically encoded (GE) fluorescent sensors derived from fluorescent proteins. GE sensors are now used to study biological phenomena by facilitating the measurement of biochemical behaviors at various scales, ranging from single molecules to single cells or even whole animals. Here, we review the historical development of GE fluorescent sensors and report on their current status. We specifically focus on the development strategies of the GE sensors used for measuring pH, ion concentrations (e.g., chloride and calcium), redox indicators, membrane potential, temperature, pressure, and molecular crowding. We demonstrate that these fluroescent protein-based sensors have a shared history of concepts and development strategies, and we highlight the most original concepts used to date. We believe that the understanding and application of these various concepts will pave the road for the development of future GE sensors and lead to new breakthroughs in bioimaging.
Collapse
|
11
|
Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning. Sci Rep 2015; 5:13223. [PMID: 26286372 PMCID: PMC4541067 DOI: 10.1038/srep13223] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/20/2015] [Indexed: 12/27/2022] Open
Abstract
The majority of protein functions are governed by their internal local electrostatics. Quantitative information about these interactions can shed light on how proteins work and allow for improving/altering their performance. Green fluorescent protein (GFP) and its mutation variants provide unique optical windows for interrogation of internal electric fields, thanks to the intrinsic fluorophore group formed inside them. Here we use an all-optical method, based on the independent measurements of transition frequency and one- and two-photon absorption cross sections in a number of GFP mutants to evaluate these internal electric fields. Two physical models based on the quadratic Stark effect, either with or without taking into account structural (bond-length) changes of the chromophore in varying field, allow us to separately evaluate the long-range and the total effective (short- and long-range) fields. Both types of the field quantitatively agree with the results of independent molecular dynamic simulations, justifying our method of measurement.
Collapse
|
12
|
Laurent AD, Adamo C, Jacquemin D. Dye chemistry with time-dependent density functional theory. Phys Chem Chem Phys 2015; 16:14334-56. [PMID: 24548975 DOI: 10.1039/c3cp55336a] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this perspective, we present an overview of the determination of excited-state properties of "real-life" dyes, and notably of their optical absorption and emission spectra, performed during the last decade with time-dependent density functional theory (TD-DFT). We discuss the results obtained with both vertical and adiabatic (vibronic) approximations, choosing relevant examples for several series of dyes. These examples include reproducing absorption wavelengths of numerous families of coloured molecules, understanding the specific band shape of amino-anthraquinones, optimising the properties of dyes used in solar cells, mimicking the fluorescence wavelengths of fluorescent brighteners and BODIPY dyes, studying optically active biomolecules and photo-induced proton transfer, as well as improving the properties of photochromes.
Collapse
Affiliation(s)
- Adèle D Laurent
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM), UMR CNRS no. 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
| | | | | |
Collapse
|
13
|
Laricheva EN, Goh GB, Dickson A, Brooks CL. pH-dependent transient conformational states control optical properties in cyan fluorescent protein. J Am Chem Soc 2015; 137:2892-900. [PMID: 25647152 PMCID: PMC4394632 DOI: 10.1021/ja509233r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently engineered mutant of cyan fluorescent protein (WasCFP) that exhibits pH-dependent absorption suggests that its tryptophan-based chromophore switches between neutral (protonated) and charged (deprotonated) states depending on external pH. At pH 8.1, the latter gives rise to green fluorescence as opposed to the cyan color of emission that is characteristic for the neutral form at low pH. Given the high energy cost of deprotonating the tryptophan at the indole nitrogen, this behavior is puzzling, even if the stabilizing effect of the V61K mutation in proximity to the protonation/deprotonation site is considered. Because of its potential to open new avenues for the development of optical sensors and photoconvertible fluorescent proteins, a mechanistic understanding of how the charged state in WasCFP can possibly be stabilized is thus important. Attributed to the dynamic nature of proteins, such understanding often requires knowledge of the various conformations adopted, including transiently populated conformational states. Transient conformational states triggered by pH are of emerging interest and have been shown to be important whenever ionizable groups interact with hydrophobic environments. Using a combination of the weighted-ensemble sampling method and explicit-solvent constant pH molecular dynamics (CPHMD(MSλD)) simulations, we have identified a solvated transient state, characterized by a partially open β-barrel where the chromophore pKa of 6.8 is shifted by over 20 units from that of the closed form (6.8 and 31.7, respectively). This state contributes a small population at low pH (12% at pH 6.1) but becomes dominant at mildly basic conditions, contributing as much as 53% at pH 8.1. This pH-dependent population shift between neutral (at pH 6.1) and charged (at pH 8.1) forms is thus responsible for the observed absorption behavior of WasCFP. Our findings demonstrate the conditions necessary to stabilize the charged state of the WasCFP chromophore (namely, local solvation at the deprotonation site and a partial flexibility of the protein β-barrel structure) and provide the first evidence that transient conformational states can control optical properties of fluorescent proteins.
Collapse
Affiliation(s)
- Elena N. Laricheva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Garrett B. Goh
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alex Dickson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
14
|
SAKAGUCHI M, MOCHIZUKI Y, WATANABE C, FUKUZAWA K. Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2015. [DOI: 10.2477/jccj.2015-0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Masataka SAKAGUCHI
- Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuji MOCHIZUKI
- Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Chiduru WATANABE
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori FUKUZAWA
- Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Dentistry at Matsudo, Nihon University, 2-870-1 Sakaemachi-Nishi, Matsudo 271-8571, Japan
| |
Collapse
|
15
|
Ichimura T, Jin T, Fujita H, Higuchi H, Watanabe TM. Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles. Front Physiol 2014; 5:273. [PMID: 25120488 PMCID: PMC4114191 DOI: 10.3389/fphys.2014.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/05/2014] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies.
Collapse
Affiliation(s)
- Taro Ichimura
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan
| | - Takashi Jin
- Laboratory for Nano-Bio Probes, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideaki Fujita
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| | - Hideo Higuchi
- Department of Physics, School of Science, The University of Tokyo Bunkyo, Tokyo, Japan
| | - Tomonobu M Watanabe
- Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center Suita, Osaka, Japan ; Graduate School of Frontier Biosciences, Osaka University Suita, Osaka, Japan ; WPI, Immunology Frontier Research Center, Osaka University Suita, Osaka, Japan
| |
Collapse
|
16
|
A theoretical study on magnetic properties of bis-TEMPO diradicals with possible application. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
17
|
Glycine insertion makes yellow fluorescent protein sensitive to hydrostatic pressure. PLoS One 2013; 8:e73212. [PMID: 24014139 PMCID: PMC3754940 DOI: 10.1371/journal.pone.0073212] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022] Open
Abstract
Fluorescent protein-based indicators for intracellular environment conditions such as pH and ion concentrations are commonly used to study the status and dynamics of living cells. Despite being an important factor in many biological processes, the development of an indicator for the physicochemical state of water, such as pressure, viscosity and temperature, however, has been neglected. We here found a novel mutation that dramatically enhances the pressure dependency of the yellow fluorescent protein (YFP) by inserting several glycines into it. The crystal structure of the mutant showed that the tyrosine near the chromophore flipped toward the outside of the β-can structure, resulting in the entry of a few water molecules near the chromophore. In response to changes in hydrostatic pressure, a spectrum shift and an intensity change of the fluorescence were observed. By measuring the fluorescence of the YFP mutant, we succeeded in measuring the intracellular pressure change in living cell. This study shows a new strategy of design to engineer fluorescent protein indicators to sense hydrostatic pressure.
Collapse
|
18
|
Watanabe TM, Fujii F, Jin T, Umemoto E, Miyasaka M, Fujita H, Yanagida T. Four-dimensional spatial nanometry of single particles in living cells using polarized quantum rods. Biophys J 2013; 105:555-64. [PMID: 23931303 PMCID: PMC3736678 DOI: 10.1016/j.bpj.2013.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/29/2022] Open
Abstract
Single particle tracking is widely used to study protein movement with high spatiotemporal resolution both in vitro and in cells. Quantum dots, which are semiconductor nanoparticles, have recently been employed in single particle tracking because of their intense and stable fluorescence. Although single particles inside cells have been tracked in three spatial dimensions (X, Y, Z), measurement of the angular orientation of a molecule being tracked would significantly enhance our understanding of the molecule's function. In this study, we synthesized highly polarized, rod-shaped quantum dots (Qrods) and developed a coating method that optimizes the Qrods for biological imaging. We describe a Qrod-based single particle tracking technique that blends optical nanometry with nanomaterial science to simultaneously measure the three-dimensional and angular movements of molecules. Using Qrods, we spatially tracked a membrane receptor in living cells in four dimensions with precision close to the single-digit range in nanometers and degrees.
Collapse
|
19
|
Nadal-Ferret M, Gelabert R, Moreno M, Lluch JM. How Does the Environment Affect the Absorption Spectrum of the Fluorescent Protein mKeima? J Chem Theory Comput 2013; 9:1731-42. [DOI: 10.1021/ct301003t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Marc Nadal-Ferret
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ricard Gelabert
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Miquel Moreno
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Departament
de Química and ‡Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| |
Collapse
|
20
|
List NH, Olsen JMH, Jensen HJA, Steindal AH, Kongsted J. Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore. J Phys Chem Lett 2012; 3:3513-3521. [PMID: 26290981 DOI: 10.1021/jz3014858] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a detailed study of the protein environmental effects on the one- and two-photon absorption (1PA and 2PA, respectively) properties of the S0-S1 transition in the DsRed protein using the polarizable embedding density functional theory formalism. We find that steric factors and chromophore-protein interactions act in concert to enhance the 2PA activity inside the protein while adversely blue-shifting the 1PA maximum. A two-state model reveals that the 2PA intensity gain is primarily governed by the increased change in the permanent dipole moment between the ground and the excited states acquired inside the protein. Our results indicate that this mainly is attributable to counter-directional contributions stemming from Lys163 and the conserved Arg95 with the former additionally identified as a key residue in the color tuning mechanism. The results provide new insight into the tuning mechanism of DsRed and suggest a possible strategy for simultaneous improvement of its 1PA and 2PA properties.
Collapse
Affiliation(s)
- Nanna H List
- †Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus H Olsen
- †Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hans Jørgen Aa Jensen
- †Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Arnfinn H Steindal
- ‡Centre of Theoretical and Computational Chemistry, Department of Chemistry, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- †Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| |
Collapse
|
21
|
Ansbacher T, Srivastava HK, Stein T, Baer R, Merkx M, Shurki A. Calculation of transition dipole moment in fluorescent proteins--towards efficient energy transfer. Phys Chem Chem Phys 2012; 14:4109-17. [PMID: 22331099 DOI: 10.1039/c2cp23351g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Förster Resonance Energy Transfer (FRET) between fluorescent proteins (FPs) is widely used to construct fluorescent sensor proteins, to study intracellular protein-protein interactions and to monitor conformational changes in multidomain proteins. Although FRET depends strongly on the orientation of the transition dipole moments (TDMs) of the donor and acceptor fluorophores, this orientation dependence is currently not taken into account in FRET sensor design. Similarly, studies that use FRET to derive structural constrains typically assume a κ(2) of 2/3 or use the TDM of green fluorescent protein, as this is the only FP for which the TDM has been determined experimentally. Here we used time-dependent density functional theory (TD-DFT) methods to calculate the TDM for a comprehensive list of commonly used fluorescent proteins. The method was validated against higher levels of calculation. Validation with model compounds and the experimentally determined TDM of GFP shows that the TDM is mostly determined by the structure of the π-conjugated fluorophore and is insensitive to non-conjugated side chains or the protein surrounding. Our calculations not only provide TDM for most of the currently used FPs, but also suggest an empirical rule that can be used to obtain the TDMs for newly developed fluorescent proteins in the future.
Collapse
Affiliation(s)
- Tamar Ansbacher
- Department of Medicinal Chemistry, Institute for Drug Research, The Lise-Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | | | | | | | | |
Collapse
|
22
|
Bhattacharya D, Panda A, Shil S, Goswami T, Misra A. A theoretical study on photomagnetic fluorescent protein chromophore coupled diradicals and their possible applications. Phys Chem Chem Phys 2012; 14:6905-13. [DOI: 10.1039/c2cp00053a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
|
23
|
Hasegawa JY, Fujimoto KJ, Nakatsuji H. Color tuning in photofunctional proteins. Chemphyschem 2011; 12:3106-15. [PMID: 21990164 DOI: 10.1002/cphc.201100452] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 08/24/2011] [Indexed: 11/11/2022]
Abstract
Depending on protein environment, a single photofunctional chromophore shows a wide variation of photoabsorption/emission energies. This photobiological phenomenon, known as color tuning, is observed in human visual cone pigments, firefly luciferase, and red fluorescent protein. We investigate the origin of color tuning by quantum chemical calculations on the excited states: symmetry-adapted cluster-configuration interaction (SAC-CI) method for excited states and a combined quantum mechanical (QM)/molecular mechanical (MM) method for protein environments. This Minireview summarizes our theoretical studies on the above three systems and explains a common feature of their color-tuning mechanisms. It also discuss the possibility of artificial color tuning toward a rational design of photoabsorption/emission properties.
Collapse
Affiliation(s)
- Jun-ya Hasegawa
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan.
| | | | | |
Collapse
|
24
|
Koseki J, Kita Y, Nagashima U, Tachikawa M. Theoretical study of the reversible photoconversion mechanism in Dronpa. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.procs.2011.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
25
|
Li X, Chung LW, Mizuno H, Miyawaki A, Morokuma K. Competitive Mechanistic Pathways for Green-to-Red Photoconversion in the Fluorescent Protein Kaede: A Computational Study. J Phys Chem B 2010; 114:16666-75. [DOI: 10.1021/jp1101779] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Hideaki Mizuno
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Atsushi Miyawaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| |
Collapse
|
26
|
Hasegawa JY, Ise T, Fujimoto KJ, Kikuchi A, Fukumura E, Miyawaki A, Shiro Y. Excited states of fluorescent proteins, mKO and DsRed: chromophore-protein electrostatic interaction behind the color variations. J Phys Chem B 2010; 114:2971-9. [PMID: 20131896 DOI: 10.1021/jp9099573] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The emitting states of green fluorescent protein (GFP), monomeric Kusabira orange (mKO), and Discosoma red (DsRed) were studied using QM/MM and SAC-CI methods. By comparing the electronic structures among the green-, orange-, and red-emitting states as well as their electrostatic and quantum mechanical interactions within the protein cavity, the basic mechanisms for determining emission colors have been clarified. We found that the orange and red emissions of mKO and DsRed, respectively, result from cancellation between two effects, the pi skeleton extension (red shift) and protein electrostatic potential (blue shift). The extension of the pi skeleton enhances the intramolecular charge-transfer character of the transition, which makes the fluorescence energy more sensitive to the protein's electrostatic potential. On the basis of this mechanism, we predicted amino acid mutations that could red shift the emission energy of DsRed. A novel single amino acid mutation, which was examined computationally, reduced the DsRed emission energy from 2.14 (579 nm) to 1.95 eV (636 nm), which is approaching near-infrared fluorescence.
Collapse
Affiliation(s)
- Jun-ya Hasegawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku-Katsura, Nshikyo-ku, Kyoto 615-8510, Japan.
| | | | | | | | | | | | | |
Collapse
|
27
|
Abstract
The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was recently confirmed by the assignment of two of the Nobel prizes in 2008: in chemistry for the discovery of GFP and in medicine for the discovery of HIV. Accordingly, these proteins were studied with essentially all of the available modeling techniques, making them ideal examples for studying the details of multiscale approaches in protein modeling.
Collapse
Affiliation(s)
- Valentina Tozzini
- NEST CNR-INFM, and Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
28
|
Effect of the Enhanced Cyan Fluorescent Protein framework on the UV/visible absorption spectra of some chromophores. Interdiscip Sci 2010; 2:38-47. [DOI: 10.1007/s12539-010-0084-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Revised: 11/09/2009] [Accepted: 11/10/2009] [Indexed: 10/19/2022]
|
29
|
Li X, Chung LW, Mizuno H, Miyawaki A, Morokuma K. A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman. J Phys Chem B 2009; 114:1114-26. [DOI: 10.1021/jp909947c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xin Li
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Lung Wa Chung
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Hideaki Mizuno
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Atsushi Miyawaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, and Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
| |
Collapse
|
30
|
Vallverdu G, Demachy I, Mérola F, Pasquier H, Ridard J, Lévy B. Relation between pH, structure, and absorption spectrum of Cerulean: A study by molecular dynamics and TD DFT calculations. Proteins 2009; 78:1040-54. [DOI: 10.1002/prot.22628] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
31
|
Drobizhev M, Tillo S, Makarov NS, Hughes TE, Rebane A. Color hues in red fluorescent proteins are due to internal quadratic Stark effect. J Phys Chem B 2009; 113:12860-4. [PMID: 19775174 PMCID: PMC2893592 DOI: 10.1021/jp907085p] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intrinsically fluorescent proteins (FPs) exhibit broad variations of absorption and emission colors and are available for different imaging applications. The physical cause of the absorption wavelength change from 540 to 590 nm in the Fruits series of red FPs has been puzzling because the mutations that cause the shifts do not disturb the pi-conjugation pathway of the chromophore. Here, we use two-photon absorption measurements to show that the different colors can be explained by quadratic Stark effect due to variations of the strong electric field within the beta barrel. This model brings simplicity to a bewildering diversity of fluorescent protein properties, and it suggests a new way to sense electrical fields in biological systems.
Collapse
|
32
|
Taguchi N, Mochizuki Y, Nakano T, Amari S, Fukuzawa K, Ishikawa T, Sakurai M, Tanaka S. Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits). J Phys Chem B 2009; 113:1153-61. [PMID: 19127982 DOI: 10.1021/jp808151c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.
Collapse
Affiliation(s)
- Naoki Taguchi
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima-ku, Tokyo 171-8501, Japan
| | | | | | | | | | | | | | | |
Collapse
|
33
|
González EM, Guidoni L, Molteni C. Chemical and protein shifts in the spectrum of the photoactive yellow protein: a time-dependent density functional theory/molecular mechanics study. Phys Chem Chem Phys 2009; 11:4556-63. [DOI: 10.1039/b902615k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
34
|
Luin S, Voliani V, Lanza G, Bizzarri R, Amat P, Tozzini V, Serresi M, Beltram F. Raman Study of Chromophore States in Photochromic Fluorescent Proteins. J Am Chem Soc 2008; 131:96-103. [DOI: 10.1021/ja804504b] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefano Luin
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Valerio Voliani
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Giacomo Lanza
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Ranieri Bizzarri
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Pietro Amat
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Valentina Tozzini
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Michela Serresi
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| | - Fabio Beltram
- NEST, Scuola Normale Superiore, CNR-INFM and Italian Institute of Technology, Piazza San Silvestro 12, 56124 Pisa, Italy
| |
Collapse
|
35
|
Voliani V, Bizzarri R, Nifosì R, Abbruzzetti S, Grandi E, Viappiani C, Beltram F. Cis−Trans Photoisomerization of Fluorescent-Protein Chromophores. J Phys Chem B 2008; 112:10714-22. [DOI: 10.1021/jp802419h] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Valerio Voliani
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Ranieri Bizzarri
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Riccardo Nifosì
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Stefania Abbruzzetti
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Elena Grandi
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Cristiano Viappiani
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| | - Fabio Beltram
- Scuola Normale Superiore, Italian Institute of Technology, Piazza dei Cavalieri 7, I-56126 Pisa, Italy, NEST, Scuola Normale Superiore and CNR-INFM, via della Faggiola 19, I-56126 Pisa, Italy, and NEST CNR-INFM, Dipartimento di Fisica, Università di Parma, viale G. P. Usberti 7A, I-43100 Parma, Italy
| |
Collapse
|
36
|
Nifosì R, Luo Y. Predictions of novel two-photon absorption bands in fluorescent proteins. J Phys Chem B 2007; 111:14043-50. [PMID: 18027922 DOI: 10.1021/jp075545v] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
By means of time-dependent density functional theory, we calculate the two-photon cross-sections for the lowest relevant excitations in some model chromophores of intrinsically fluorescent proteins. The two-photon strength of the first, one-photon active transition varies among the various chromophores, in line with experimental findings. Interestingly, additional transitions with large two-photon cross-sections are found in the 500-700 nm region arising from near-resonant enhancement, as revealed by few-state model analysis. Multiphoton excitation of fluorescent proteins in this spectral region can lead to relevant application for bioimaging.
Collapse
Affiliation(s)
- Riccardo Nifosì
- NEST-CNR INFM, Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa I-56126, Italy.
| | | |
Collapse
|