1
|
Habanjar O, Maurin AC, Vituret C, Vachias C, Longechamp L, Garnier C, Decombat C, Bourgne C, Diab-Assaf M, Caldefie-Chezet F, Delort L. A bicellular fluorescent ductal carcinoma in situ (DCIS)-like tumoroid to study the progression of carcinoma: practical approaches and optimization. Biomater Sci 2023; 11:3308-3320. [PMID: 36946175 DOI: 10.1039/d2bm01470j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Recently, many types of 3D culture systems have been developed to preserve the physicochemical environment and biological characteristics of the original tumors better than the conventional 2D monolayer culture system. There are various types of models belonging to this culture, such as the culture based on non-adherent and/or scaffold-free matrices to form the tumors. Agarose mold has been widely used to facilitate tissue spheroid assembly, as it is essentially non-biodegradable, bio-inert, biocompatible, low-cost, and low-attachment material that can promote cell spheroidization. As no studies have been carried out on the development of a fluorescent bicellular tumoroid mimicking ductal carcinoma in situ (DCIS) using human cell lines, our objective was to detail the practical approaches developed to generate this model, consisting of a continuous layer of myoepithelial cells (MECs) around a previously formed in situ breast tumor. The practical approaches developed to generate a bi-cellular tumoroid mimicking ductal carcinoma in situ (DCIS), consisting of a continuous layer of myoepithelial cells (MECs) around a previously formed in situ breast tumoroid. Firstly, the optimal steps and conditions of spheroids generation using a non-adherent agarose gel were described, in particular, the appropriate medium, seeding density of each cell type and incubation period. Next, a lentiviral transduction approach to achieve stable fluorescent protein expression (integrative system) was used to characterize the different cell lines and to track tumoroid generation through immunofluorescence, the organization of the two cell types was validated, specific merits and drawbacks were compared to lentiviral transduction. Two lentiviral vectors expressing either EGFP (Enhanced Green Fluorescent Protein) or m-Cherry (Red Fluorescent Protein) were used. Various rates of a multiplicity of infection (MOI) and multiple types of antibodies (anti-p63, anti-CK8, anti-Maspin, anti-Calponin) for immunofluorescence analysis were tested to determine the optimal conditions for each cell line. At MOI 40 (GFP) and MOI 5 (m-Cherry), the signals were almost homogeneously distributed in the cells which could then be used to generate the DCIS-like tumoroids. Images of the tumoroids in agarose molds were captured with a confocal microscope Micro Zeiss Cell Observer Spinning Disk or with IncuCyte® to follow the progress of the generation. Measurement of protumoral cytokines such as IL-6, IL8 and leptin confirmed their secretion in the supernatants, indicating that the properties of our cells were not altered. Finally the advantages and disadvantages of each fluorescent approach were discussed. This model could also be used for other solid malignancies to study the complex relationship between different cells such as tumor and myoepithelial cells in various microenvironments (inflammatory, adipose and tumor, obesity, etc.). Although, this new model is well established to monitor drug screening applications and perform pharmacokinetic and pharmacodynamic analyses.
Collapse
Affiliation(s)
- Ola Habanjar
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| | | | - Cyrielle Vituret
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| | - Caroline Vachias
- iGReD (Institute of Genetics, Reproduction and Development), Université Clermont Auvergne, UMR CNRS 6293 - INSERM U1103, Faculté de Médecine, 28 Place Henri-Dunant, 63000, Clermont-Ferrand, France
| | - Lucie Longechamp
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| | - Cécile Garnier
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| | - Caroline Decombat
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| | - Céline Bourgne
- Plate-forme CMF, Service d'Hématologie biologique, CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | - Mona Diab-Assaf
- Equipe Tumorigénèse Pharmacologie moléculaire et anticancéreuse, Faculté des Sciences II, Université libanaise Fanar, Beirut, Lebanon
| | | | - Laetitia Delort
- Université Clermont-Auvergne, INRAE, UNH, 63000 Clermont-Ferrand, France.
| |
Collapse
|
2
|
Roldán‐Salgado A, Muslinkina L, Pletnev S, Pletneva N, Pletnev V, Gaytán P. A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins. Protein Sci 2022; 31:688-700. [PMID: 34936154 PMCID: PMC8862416 DOI: 10.1002/pro.4265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
We describe an engineered violet fluorescent protein from the lancelet Branchiostoma floridae (bfVFP). This is the first example of a GFP-like fluorescent protein with a stable fluorescent chromophore lacking an imidazolinone ring; instead, it consists of oxidized tyrosine 68 flanked by glycine 67 and alanine 69. bfVFP contains the simplest chromophore reported in fluorescent proteins and was generated from the yellow protein lanFP10A2 by two synergetic mutations, S148H and C166I. The chromophore structure was confirmed crystallographically and by high-resolution mass spectrometry. The photophysical characteristics of bfVFP (323/430 nm, quantum yield 0.33, and Ec 14,300 M-1 cm-1 ) make it potentially useful for multicolor experiments to expand the excitation range of available FP biomarkers and Förster resonance energy transfer with blue and cyan fluorescent protein acceptors.
Collapse
Affiliation(s)
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies BranchNational Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMarylandUSA
| | - Nadya Pletneva
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Vladimir Pletnev
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussian Federation
| | - Paul Gaytán
- Instituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| |
Collapse
|
3
|
Zamora RA, Fuentes-Lemus E, Barrias P, Herrera-Morande A, Mura F, Guixé V, Castro-Fernandez V, Rojas T, López-Alarcón C, Aguirre P, Rivas-Aravena A, Aspée A. Free radicals derived from γ-radiolysis of water and AAPH thermolysis mediate oxidative crosslinking of eGFP involving Tyr-Tyr and Tyr-Cys bonds: the fluorescence of the protein is conserved only towards peroxyl radicals. Free Radic Biol Med 2020; 150:40-52. [PMID: 32081747 DOI: 10.1016/j.freeradbiomed.2020.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/29/2020] [Accepted: 02/08/2020] [Indexed: 10/25/2022]
Abstract
The enhanced green fluorescent protein (eGFP) is one of the most employed variants of fluorescent proteins. Nonetheless little is known about the oxidative modifications that this protein can undergo in the cellular milieu. The present work explored the consequences of the exposure of eGFP to free radicals derived from γ-radiolysis of water, and AAPH thermolysis. Results demonstrated that protein crosslinking was the major pathway of modification of eGFP towards these oxidants. As evidenced by HPLC-FLD and UPLC-MS, eGFP crosslinking would occur as consequence of a mixture of pathways including the recombination of two protein radicals, as well as secondary reactions between nucleophilic residues (e.g. lysine, Lys) with protein carbonyls. The first mechanism was supported by detection of dityrosine and cysteine-tyrosine bonds, whilst evidence of formation of protein carbonyls, along with Lys consumption, would suggest the formation and participation of Schiff bases in the crosslinking process. Despite of the degree of oxidative modifications elicited by peroxyl radicals (ROO•) generated from the thermolysis of AAPH, and free radicals generated from γ-radiolysis of water, that were evidenced at amino acidic level, only the highest dose of γ-irradiation (10 kGy) triggered significant changes in the secondary structure of eGFP. These results were accompanied by the complete loss of fluorescence arising from the chromophore unit of eGFP in γ-irradiation-treated samples, whereas it was conserved in ROO•-treated samples. These data have potential biological significance, as this fluorescent protein is widely employed to study interactions between cytosolic proteins; consequently, the formation of fluorescent eGFP dimers could act as artifacts in such experiments.
Collapse
Affiliation(s)
- Ricardo A Zamora
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile
| | - Eduardo Fuentes-Lemus
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile
| | - Pablo Barrias
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile
| | - Alejandra Herrera-Morande
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile; Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco Mura
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile
| | - Victoria Guixé
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Tomás Rojas
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile
| | - Camilo López-Alarcón
- Departamento de Química Física, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Aguirre
- Comisión Chilena de Energía Nuclear, Departamento de Tecnología Nucleares, Nueva Bilbao 12501, Santiago, 7600713, Chile
| | - Andrea Rivas-Aravena
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Lota 2465, Providencia, Santiago, 7510157, Chile.
| | - Alexis Aspée
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Casilla 40 Correo 33, Santiago, Chile.
| |
Collapse
|
4
|
Gao A, Wang M, Ding J. Ultrafasttrans-cisphotoisomerization of the neutral chromophore in green fluorescent proteins: Surface-hopping dynamics simulation. J Chem Phys 2018; 149:074304. [DOI: 10.1063/1.5043246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Junxia Ding
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| |
Collapse
|
5
|
Girija V, Malaikozhundan B, Vaseeharan B, Vijayakumar S, Gobi N, Del Valle Herrera M, Chen JC, Santhanam P. In vitro antagonistic activity and the protective effect of probiotic Bacillus licheniformis Dahb1 in zebrafish challenged with GFP tagged Vibrio parahaemolyticus Dahv2. Microb Pathog 2017; 114:274-280. [PMID: 29198821 DOI: 10.1016/j.micpath.2017.11.058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/25/2017] [Accepted: 11/27/2017] [Indexed: 11/30/2022]
Abstract
In vitro antagonistic activity and the protective effect of probiotic Bacillus licheniformis Dahb1 in zebrafish (Danio rerio) challenged with GFP tagged Vibrio parahaemolyticus Dahv2 was studied. The cell free extract of probiotic B. licheniformis Dahb1 at 100 μg mL-1 showed growth inhibition of V. parahaemolyticus Dahv2 in vitro. B. licheniformis Dahb1 also inhibited the biofilm growth of GFP tagged V. parahaemolyticus Dahv2 at 100 μg mL-1 in vitro. The growth and survival of zebrafish was tested using probiotic B. licheniformis Dahb1. Weight (1.28 g) of zebrafish that received the cell free extract was much higher than in control (1.04 g). The mortality of zebrafish infected with GFP tagged V. parahaemolyticus Dahv2 at 107 Cfu mL-1 (Group IV) was 100%, whereas a complete survival of zebrafish that received the cell free extract of B. licheniformis Dahb1 at 107 Cfu mL-1 (Group VII) was observed after 30 days. The number of GFP tagged V. parahaemolyticus Dahv2 colonies in the intestine and gills significantly reduced after treatment with the cell free extract of B. licheniformis Dahb1. Furthermore, a significant decrease in the fluorescent colonies of GFP tagged V. parahaemolyticus Dahv2 was observed after treatment with the cell free extract of B. licheniformis Dahb1 under confocal laser scanning microscopy (CLSM). In conclusion, the cell free extract of B. licheniformis Dahb1 could prevent Vibrio infection by enhancing the growth and survival of zebrafish.
Collapse
Affiliation(s)
- Vairavan Girija
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Science Campus 6(th) Floor, Burma Colony, Karaikudi 630004, Tamil Nadu, India
| | - Balasubramanian Malaikozhundan
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Science Campus 6(th) Floor, Burma Colony, Karaikudi 630004, Tamil Nadu, India
| | - Baskaralingam Vaseeharan
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Science Campus 6(th) Floor, Burma Colony, Karaikudi 630004, Tamil Nadu, India.
| | - Sekar Vijayakumar
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Science Campus 6(th) Floor, Burma Colony, Karaikudi 630004, Tamil Nadu, India
| | - Narayanan Gobi
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Science Campus 6(th) Floor, Burma Colony, Karaikudi 630004, Tamil Nadu, India
| | - Marian Del Valle Herrera
- Centro de Investigación en Alimentación y Desarrollo, A.C, Av. Sábalo-Cerritos s/n. Estero del Yugo, Mazatlán Sinaloa 82000 Mexico
| | - Jiann-Chu Chen
- Department of Aquaculture, College of Life Sciences, Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Perumal Santhanam
- Department of Marine Science, School of Marine Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| |
Collapse
|
6
|
Shorter SA, Pettit MW, Dyer PDR, Coakley Youngs E, Gorringe-Pattrick MAM, El-Daher S, Richardson S. Green fluorescent protein (GFP): is seeing believing and is that enough? J Drug Target 2017; 25:809-817. [PMID: 28743200 DOI: 10.1080/1061186x.2017.1358725] [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] [Indexed: 01/28/2023]
Abstract
Intracellular compartmentalisation is a significant barrier to the successful nucleocytosolic delivery of biologics. The endocytic system has been shown to be responsible for compartmentalisation, providing an entry point, and trigger(s) for the activation of drug delivery systems. Consequently, many of the technologies used to understand endocytosis have found utility within the field of drug delivery. The use of fluorescent proteins as markers denoting compartmentalisation within the endocytic system has become commonplace. Several of the limitations associated with the use of green fluorescent protein (GFP) within the context of drug delivery have been explored here by asking a series of related questions: (1) Are molecules that regulate fusion to a specific compartment (i.e. Rab- or SNARE-GFP fusions) a good choice of marker for that compartment? (2) How reliable was GFP-marker overexpression when used to define a given endocytic compartment? (3) Can glutathione-s-transferase (GST) fused in frame with GFP (GST-GFP) act as a fluid phase endocytic probe? (4) Was GFP fluorescence a robust indicator of (GFP) protein integrity? This study concluded that there are many appropriate and useful applications for GFP; however, thought and an understanding of the biological and physicochemical character of these markers are required for the generation of meaningful data.
Collapse
Affiliation(s)
- Susan A Shorter
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Marie W Pettit
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Paul D R Dyer
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Emma Coakley Youngs
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Monique A M Gorringe-Pattrick
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Samer El-Daher
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| | - Simon Richardson
- a IDS Laboratory, Department of Life and Sports Science, Faculty of Engineering and Science , University of Greenwich , Chatham , Kent , UK
| |
Collapse
|
7
|
Bose S, Chakrabarty S, Ghosh D. Electrostatic Origin of the Red Solvatochromic Shift of DFHBDI in RNA Spinach. J Phys Chem B 2017; 121:4790-4798. [DOI: 10.1021/acs.jpcb.7b02445] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials
Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| |
Collapse
|
8
|
Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
Collapse
Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| |
Collapse
|
9
|
Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| |
Collapse
|
10
|
Abstract
![]()
A family
of extended 5-modified-6-aza-uridines was obtained via
Suzuki coupling reactions with a common brominated precursor. Extending
the conjugated-6-aza-uridines with substituted aryl rings increases
the push–pull interactions yielding enhanced bathochromic shifts
and solvatochromism compared to the parent nucleosides. For example,
the methoxy substituted derivative 1d displays λmax abs around 375 nm, with visible emission maxima at
486 nm (Φ = 0.74) and 525 nm (Φ = 0.02) in dioxane and
water, respectively.
Collapse
Affiliation(s)
- Patrycja A Hopkins
- Department of Chemistry and Biochemistry, University of California , San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | | | | |
Collapse
|
11
|
Spectral and structural comparison between bright and dim green fluorescent proteins in Amphioxus. Sci Rep 2014; 4:5469. [PMID: 24968921 PMCID: PMC4073121 DOI: 10.1038/srep05469] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 05/23/2014] [Indexed: 11/09/2022] Open
Abstract
The cephalochordate Amphioxus naturally co-expresses fluorescent proteins (FPs) with different brightness, which thus offers the rare opportunity to identify FP molecular feature/s that are associated with greater/lower intensity of fluorescence. Here, we describe the spectral and structural characteristics of green FP (bfloGFPa1) with perfect (100%) quantum efficiency yielding to unprecedentedly-high brightness, and compare them to those of co-expressed bfloGFPc1 showing extremely-dim brightness due to low (0.1%) quantum efficiency. This direct comparison of structure-function relationship indicated that in the bright bfloGFPa1, a Tyrosine (Tyr159) promotes a ring flipping of a Tryptophan (Trp157) that in turn allows a cis-trans transformation of a Proline (Pro55). Consequently, the FP chromophore is pushed up, which comes with a slight tilt and increased stability. FPs are continuously engineered for improved biochemical and/or photonic properties, and this study provides new insight to the challenge of establishing a clear mechanistic understanding between chromophore structural environment and brightness level.
Collapse
|
12
|
Addison K, Heisler IA, Conyard J, Dixon T, Bulman Page PC, Meech SR. Ultrafast excited state dynamics of the green fluorescent protein chromophore and its kindling fluorescent protein analogue. Faraday Discuss 2013; 163:277-96; discussion 393-432. [DOI: 10.1039/c3fd00019b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
13
|
Ghosh D, Acharya A, Tiwari SC, Krylov AI. Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects. J Phys Chem B 2012; 116:12398-405. [PMID: 22978512 DOI: 10.1021/jp305022t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The redox properties of model chromophores from the green fluorescent protein family are characterized computationally using density functional theory with a long-range corrected functional, the equation-of-motion coupled-cluster method, and implicit solvation models. The analysis of electron-donating abilities of the chromophores reveals an intricate interplay between the size of the chromophore, conjugation, resonance stabilization, presence of heteroatoms, and solvent effects. Our best estimates of the gas-phase vertical/adiabatic detachment energies of the deprotonated (i.e., anionic) model red, green, and blue chromophores are 3.27/3.15, 2.79/2.67, and 2.75/2.35 eV, respectively. Vertical/adiabatic ionization energies of the respective protonated (i.e., neutral) species are 7.64/7.35, 7.38/7.15, and 7.70/7.32 eV, respectively. The standard reduction potentials (E(red)(0)) of the anionic (Chr•/Chr–) and neutral (Chr+•/Chr) model chromophores in acetonitrile are 0.34/1.40 V (red), 0.22/1.24 V (green), and −0.12/1.02 V (blue), suggesting, counterintuitively, that the red chromophore is more difficult to oxidize than the green and blue ones (in both neutral and deprotonated forms). The respective redox potentials in water follow a similar trend but are more positive than the acetonitrile values.
Collapse
Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | | | | |
Collapse
|
14
|
Shinzato C, Shoguchi E, Tanaka M, Satoh N. Fluorescent protein candidate genes in the coral Acropora digitifera genome. Zoolog Sci 2012; 29:260-4. [PMID: 22468836 DOI: 10.2108/zsj.29.260] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The vivid coloration of corals depends on fluorescent proteins that include cyan (CFP), green (GFP) and red (RFP) fluorescent proteins, and a non-fluorescent blue/purple chromoprotein. We examined how many genes encoding fluorescent proteins are present in the recently sequenced genome of the coral Acropora digitifera. Based on molecular phylogenetic analysis, we found one, five, one, and three candidate genes for CFP, GFP, RFP, and chromoprotein, respectively. The CFP and GFP genes are clustered in a ~80-kb-long genomic region, suggesting that they originated from an ancestral gene by tandem duplication. Since CFP and GFP possess the same chromophore, the gene clustering may provide the first genomic evidence for a common origin of the two proteins. Comparison between the fluorescent protein genes of closely related coral species suggests an expansion of chromoprotein genes in the A. digitifera genome, and of RFP genes in the A. millepora genome. The A. digitifera fluorescent protein genes are expressed during embryonic and larval developmental stages and in adults, suggesting that the genes play a variety of roles in coral physiology.
Collapse
Affiliation(s)
- Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | | | | | | |
Collapse
|
15
|
Grigorenko BL, Nemukhin AV, Morozov DI, Polyakov IV, Bravaya KB, Krylov AI. Toward Molecular-Level Characterization of Photoinduced Decarboxylation of the Green Fluorescent Protein: Accessibility of the Charge-Transfer States. J Chem Theory Comput 2012; 8:1912-20. [DOI: 10.1021/ct300043e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bella L. Grigorenko
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991,
Russia
| | - Alexander V. Nemukhin
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991,
Russia
- Institute of Biochemical
Physics, Russian Academy of Sciences, Moscow
119334, Russia
| | - Dmitry I. Morozov
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991,
Russia
| | - Igor V. Polyakov
- Department
of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991,
Russia
| | - Ksenia B. Bravaya
- Department
of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California
90089-0482, United States
| |
Collapse
|
16
|
Bravaya KB, Grigorenko BL, Nemukhin AV, Krylov AI. Quantum chemistry behind bioimaging: insights from ab initio studies of fluorescent proteins and their chromophores. Acc Chem Res 2012; 45:265-75. [PMID: 21882809 DOI: 10.1021/ar2001556] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The unique properties of green fluorescent protein (GFP) have been harnessed in a variety of bioimaging techniques, revolutionizing many areas of the life sciences. Molecular-level understanding of the underlying photophysics provides an advantage in the design of new fluorescent proteins (FPs) with improved properties; however, because of its complexity, many aspects of the GFP photocycle remain unknown. In this Account, we discuss computational studies of FPs and their chromophores that provide qualitative insights into mechanistic details of their photocycle and the structural basis for their optical properties. In a reductionist framework, studies of well-defined model systems (such as isolated chromophores) help to understand their intrinsic properties, while calculations including protein matrix and/or solvent demonstrate, on the atomic level, how these properties are modulated by the environment. An interesting feature of several anionic FP chromophores in the gas phase is their low electron detachment energy. For example, the bright excited ππ* state of the model GFP chromophore (2.6 eV) lies above the electron detachment continuum (2.5 eV). Thus, the excited state is metastable with respect to electron detachment. This autoionizing character needs to be taken into account in interpreting gas-phase measurements and is very difficult to describe computationally. Solvation (and even microsolvation by a single water molecule) stabilizes the anionic states enough such that the resonance excited state becomes bound. However, even in stabilizing environments (such as protein or solution), the anionic chromophores have relatively low oxidation potentials and can act as light-induced electron donors. Protein appears to affect excitation energies very little (<0.1 eV), but alters ionization or electron detachment energies by several electron volts. Solvents (especially polar ones) have a pronounced effect on the chromophore's electronic states; for example, the absorption wavelength changes considerably, the ground-state barrier for cis-trans isomerization is reduced, and fluorescence quantum yield drops dramatically. Calculations reveal that these effects can be explained in terms of electrostatic interactions and polarization, as well as specific interactions such as hydrogen bonding. The availability of efficient computer implementations of predictive electronic structure methods is essential. Important challenges include developing faster codes (to enable better equilibrium sampling and excited-state dynamics modeling), creating algorithms for properties calculations (such as nonlinear optical properties), extending standard excited-state methods to autoionizing (resonance) states, and developing accurate QM/MM schemes. The results of sophisticated first-principle calculations can be interpreted in terms of simpler, qualitative molecular orbital models to explain general trends. In particular, an essential feature of the anionic GFP chromophore is an almost perfect resonance (mesomeric) interaction between two Lewis structures, giving rise to charge delocalization, bond-order scrambling, and, most importantly, allylic frontier molecular orbitals spanning the methine bridge. We demonstrate that a three-center Hückel-like model provides a useful framework for understanding properties of FPs. It can explain changes in absorption wavelength upon protonation or other structural modifications of the chromophore, the magnitude of transition dipole moment, barriers to isomerization, and even non-Condon effects in one- and two-photon absorption.
Collapse
Affiliation(s)
- Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Bella L. Grigorenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander V. Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
17
|
Jonasson G, Teuler JM, Vallverdu G, Mérola F, Ridard J, Lévy B, Demachy I. Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale. J Chem Theory Comput 2011; 7:1990-7. [DOI: 10.1021/ct200150r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gabriella Jonasson
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Jean-Marie Teuler
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Germain Vallverdu
- Equipe de Chimie-Physique, IPREM, UMR5254, Université de Pau et des Pays de l′Adour, 64000 Pau, France
| | - Fabienne Mérola
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Jacqueline Ridard
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| |
Collapse
|
18
|
Lobo LA, Smith CJ, Rocha ER. Flavin mononucleotide (FMN)-based fluorescent protein (FbFP) as reporter for gene expression in the anaerobe Bacteroides fragilis. FEMS Microbiol Lett 2011; 317:67-74. [PMID: 21223361 DOI: 10.1111/j.1574-6968.2011.02212.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this study, we show the expression of flavin mononucleotide-based fluorescent protein (FbFP) BS2 as a marker for gene expression in the opportunistic human anaerobic pathogen Bacteroides fragilis. Bacteroides fragilis 638R strain carrying osu∷bs2 constructs showed inducible fluorescence following addition of maltose anaerobically compared with nonfluorescent cells under glucose-repressed conditions. Bacteria carrying ahpC∷bs2 or dps∷bs2 constructs were fluorescent following induction by oxygen compared with nonfluorescent cells from the anaerobic control cultures. In addition, when these transcriptional fusion constructs were mobilized into B. fragilis IB263, a constitutive peroxide response strain, fluorescent BS2, was detected in both anaerobic and aerobic cultures, confirming the unique properties of the FbFP BS2 to yield fluorescent signal in B. fragilis in the presence and in the absence of oxygen. Moreover, intracellular expression of BS2 was also detected when cell culture monolayers of J774.1 macrophages were incubated with B. fragilis ahpC∷bs2 or dps∷bs2 strains within an anaerobic chamber. This suggests that ahpC and dps are induced following internalization by macrophages. Thus, we show that BS2 is a suitable tool for the detection of gene expression in obligate anaerobic bacteria in in vivo studies.
Collapse
Affiliation(s)
- Leandro A Lobo
- Instituto de Microbiologia Paulo de Gois, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | |
Collapse
|
19
|
Lopes AM, Magalhães PO, Mazzola PG, Rangel-Yagui CO, de Carvalho JCM, Penna TC, Pessoa A. LPS removal from an E. coli fermentation broth using aqueous two-phase micellar system. Biotechnol Prog 2010; 26:1644-53. [DOI: 10.1002/btpr.463] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
20
|
Titushin MS, Feng Y, Stepanyuk GA, Li Y, Markova SV, Golz S, Wang BC, Lee J, Wang J, Vysotski ES, Liu ZJ. NMR-derived topology of a GFP-photoprotein energy transfer complex. J Biol Chem 2010; 285:40891-900. [PMID: 20926380 DOI: 10.1074/jbc.m110.133843] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Förster resonance energy transfer within a protein-protein complex has previously been invoked to explain emission spectral modulation observed in several bioluminescence systems. Here we present a spatial structure of a complex of the Ca(2+)-regulated photoprotein clytin with its green-fluorescent protein (cgGFP) from the jellyfish Clytia gregaria, and show that it accounts for the bioluminescence properties of this system in vitro. We adopted an indirect approach of combining x-ray crystallography determined structures of the separate proteins, NMR spectroscopy, computational docking, and mutagenesis. Heteronuclear NMR spectroscopy using variously (15)N,(13)C,(2)H-enriched proteins enabled assignment of backbone resonances of more than 94% of the residues of both proteins. In a mixture of the two proteins at millimolar concentrations, complexation was inferred from perturbations of certain (1)H-(15)N HSQC-resonances, which could be mapped to those residues involved at the interaction site. A docking computation using HADDOCK was employed constrained by the sites of interaction, to deduce an overall spatial structure of the complex. Contacts within the clytin-cgGFP complex and electrostatic complementarity of interaction surfaces argued for a weak protein-protein complex. A weak affinity was also observed by isothermal titration calorimetry (K(D) = 0.9 mM). Mutation of clytin residues located at the interaction site reduced the degree of protein-protein association concomitant with a loss of effectiveness of cgGFP in color-shifting the bioluminescence. It is suggested that this clytin-cgGFP structure corresponds to the transient complex previously postulated to account for the energy transfer effect of GFP in the bioluminescence of aequorin or Renilla luciferase.
Collapse
Affiliation(s)
- Maxim S Titushin
- National Laboratory of Biomacromolecules, Institute of Biophysics Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Wachter RM, Watkins JL, Kim H. Mechanistic diversity of red fluorescence acquisition by GFP-like proteins. Biochemistry 2010; 49:7417-27. [PMID: 20666493 DOI: 10.1021/bi100901h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review aims to summarize our current state of knowledge of several post-translational modification mechanisms known to yield red fluorescence in the family of GFP-like (green fluorescent protein-like) proteins. We begin with a brief review of the maturation mechanism that leads to green fluorescence in GFPs. The main body of this article is focused on a series of main chain redox and beta-elimination reactions mediated by light and O(2), ultimately yielding a red-emitting chromophore. In all GFP-like proteins, a tyrosine-derived phenolic group constitutes an essential building block of the chromophore's skeleton. Two major classes of red-emitting species have been identified in naturally occurring fluorescent proteins. In the DsRed type, an acylimine moiety is found to be conjugated to the GFP-like chromophore. Recent evidence has suggested that two mechanistic pathways, a green branch and a red branch, diverge from an early cyclic intermediate that bears a standard tyrosine side chain. Therefore, the long-standing notion that all FP colors originate from modifications of the GFP-like chromophore may need to be revised. In the Kaede-type green-to-red photoconvertible class of FPs, a light-mediated main chain elimination reaction partakes in the formation of a three-ring chromophore that involves the incorporation of a histidine residue into the conjugated system. A mechanistic role for photoexcitation of the GFP-like chromophore is undisputed; however, the nature of associated proton transfer steps and the charge state of the critical imidazole group remain controversial. In addition to the two major classes of red fluorescent proteins, we briefly describe yellow fluorescence arising from modifications of DsRed-type intermediates, and the less well understood photoactivated oxidative redding phenomenon.
Collapse
Affiliation(s)
- Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.
| | | | | |
Collapse
|
22
|
Ikmi A, Gibson MC. Identification and in vivo characterization of NvFP-7R, a developmentally regulated red fluorescent protein of Nematostella vectensis. PLoS One 2010; 5:e11807. [PMID: 20668556 PMCID: PMC2910727 DOI: 10.1371/journal.pone.0011807] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 06/30/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In recent years, the sea anemone Nematostella vectensis has emerged as a critical model organism for comparative genomics and developmental biology. Although Nematostella is a member of the anthozoan cnidarians (known for producing an abundance of diverse fluorescent proteins (FPs)), endogenous patterns of Nematostella fluorescence have not been described and putative FPs encoded by the genome have not been characterized. METHODOLOGY/PRINCIPAL FINDINGS We described the spatiotemporal expression of endogenous red fluorescence during Nematostella development. Spatially, there are two patterns of red fluorescence, both restricted to the oral endoderm in developing polyps. One pattern is found in long fluorescent domains associated with the eight mesenteries and the other is found in short fluorescent domains situated between tentacles. Temporally, the long domains appear simultaneously at the 12-tentacle stage. In contrast, the short domains arise progressively between the 12- and 16-tentacle stage. To determine the source of the red fluorescence, we used bioinformatic approaches to identify all possible putative Nematostella FPs and a Drosophila S2 cell culture assay to validate NvFP-7R, a novel red fluorescent protein. We report that both the mRNA expression pattern and spectral signature of purified NvFP-7R closely match that of the endogenous red fluorescence. Strikingly, the red fluorescent pattern of NvFP-7R exhibits asymmetric expression along the directive axis, indicating that the nvfp-7r locus senses the positional information of the body plan. At the tissue level, NvFP-7R exhibits an unexpected subcellular localization and a complex complementary expression pattern in apposed epithelia sheets comprising each endodermal mesentery. CONCLUSIONS/SIGNIFICANCE These experiments not only identify NvFP-7R as a novel red fluorescent protein that could be employed as a research tool; they also uncover an unexpected spatio-temporal complexity of gene expression in an adult cnidarian. Perhaps most importantly, our results define Nematostella as a new model organism for understanding the biological function of fluorescent proteins in vivo.
Collapse
Affiliation(s)
- Aissam Ikmi
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Matthew C. Gibson
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Anatomy and Cell Biology, Kansas University Medical School, Kansas City, Kansas, United States of America
| |
Collapse
|
23
|
Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| |
Collapse
|
24
|
Field SF, Matz MV. Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Mol Biol Evol 2010; 27:225-33. [PMID: 19793832 PMCID: PMC2877551 DOI: 10.1093/molbev/msp230] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proteins of the green fluorescent protein family represent a convenient experimental model to study evolution of novelty at the molecular level. Here, we focus on the origin of Kaede-like red fluorescent proteins characteristic of the corals of the Faviina suborder. We demonstrate, using an original approach involving resurrection and analysis of the library of possible evolutionary intermediates, that it takes on the order of 12 mutations, some of which strongly interact epistatically, to fully recapitulate the evolution of a red fluorescent phenotype from the ancestral green. Five of the identified mutations would not have been found without the help of ancestral reconstruction, because the corresponding site states are shared between extant red and green proteins due to their recent descent from a dual-function common ancestor. Seven of the 12 mutations affect residues that are not in close contact with the chromophore and thus must exert their effect indirectly through adjustments of the overall protein fold; the relevance of these mutations could not have been anticipated from the purely theoretical analysis of the protein's structure. Our results introduce a powerful experimental approach for comparative analysis of functional specificity in protein families even in the cases of pronounced epistasis, provide foundation for the detailed studies of evolutionary trajectories leading to novelty and complexity, and will help rational modification of existing fluorescent labels.
Collapse
Affiliation(s)
| | - Mikhail V. Matz
- Section of Integrative Biology, University of Texas at Austin
| |
Collapse
|
25
|
Zhang K, Li X, Ma Y, Zou S, Yang L, Zhang M. A curve fitting method of quantifying green fluorescent protein expression level in Escherichia coli. J Microbiol Methods 2010; 80:172-7. [DOI: 10.1016/j.mimet.2009.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Revised: 12/04/2009] [Accepted: 12/06/2009] [Indexed: 10/20/2022]
|
26
|
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]
|
27
|
|
28
|
Hering VR, Faulin TES, Triboni ER, Rodriguez SD, Bernik DL, Schumacher RI, Mammana VP, Faljoni-Alario A, Abdalla DSP, Gibson G, Politi MJ. Violet ZnSe/ZnS as an Alternative to Green CdSe/ZnS in Nanocrystal−Fluorescent Protein FRET Systems. Bioconjug Chem 2009; 20:1237-41. [DOI: 10.1021/bc9001085] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vitor R. Hering
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Tanize E. S. Faulin
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Eduardo R. Triboni
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Silvio D. Rodriguez
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Delia L. Bernik
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Robert I. Schumacher
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Victor P. Mammana
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Adelaide Faljoni-Alario
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Dulcineia S. P. Abdalla
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Gary Gibson
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| | - Mário J. Politi
- Department of Biochemistry, Chemistry Institute, University of São Paulo, São Paulo, SP 05513-970, Brazil, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, SP 05508-900, Brazil, Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires, BA 1428EGA, Argentina, Renato Archer Information Technology Center, Campinas, SP 13069-901, Brazil, Natural and, Human Sciences Center, Federal University of ABC, Santo André, SP 09210-170, Brazil, and Hewlett-Packard
| |
Collapse
|
29
|
Albertazzi L, Arosio D, Marchetti L, Ricci F, Beltram F. Quantitative FRET Analysis With the E0GFP-mCherry Fluorescent Protein Pair. Photochem Photobiol 2009; 85:287-97. [PMID: 18764891 DOI: 10.1111/j.1751-1097.2008.00435.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lorenzo Albertazzi
- Scuola Normale Superiore and Istituto Italiano di Tecnologia, Pisa, Italy.
| | | | | | | | | |
Collapse
|
30
|
Samarkina ON, Popova AG, Gvozdik EY, Chkalina AV, Zvyagin IV, Rylova YV, Rudenko NV, Lusta KA, Kelmanson IV, Gorokhovatsky AY, Vinokurov LM. Universal and rapid method for purification of GFP-like proteins by the ethanol extraction. Protein Expr Purif 2008; 65:108-13. [PMID: 19084068 DOI: 10.1016/j.pep.2008.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 11/15/2008] [Accepted: 11/17/2008] [Indexed: 11/17/2022]
Abstract
GFP-like fluorescent proteins (FPs) are crucial in biological and biomedical studies. The majority of FP purification techniques either include multiple time-consuming chromatography steps with a low yield of the desired product or require prior protein modification (addition of special tags). In the present work, we propose an alternative ethanol extraction-based technique previously used for GFP purification and then modified for diverse FPs originated from different sources. The following recombinant FPs were expressed using Escherichia coli M15 (pREP4) strain as a host transformed with pQE30 plasmid bearing one of the target FP genes: TagCFP, TagGFP, TagYFP, TagRFP, TurboGFP, TurboRFP, Dendra2, TurboFP602 and KillerRed. Despite their diversity, all tested recombinant FPs were successfully purified and yielded a highly homogeneous product. The method is easily scalable for purification of any amount of protein and requires no expensive reagents and equipment.
Collapse
Affiliation(s)
- Olga N Samarkina
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Nauki Prosp. 6, 142290 Pushchino, Moscow Region, Russia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Pouwels LJ, Zhang L, Chan NH, Dorrestein PC, Wachter RM. Kinetic isotope effect studies on the de novo rate of chromophore formation in fast- and slow-maturing GFP variants. Biochemistry 2008; 47:10111-22. [PMID: 18759496 DOI: 10.1021/bi8007164] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The maturation process of green fluorescent protein (GFP) entails a protein oxidation reaction triggered by spontaneous backbone condensation. The chromophore is generated by full conjugation of the Tyr66 phenolic group with the heterocycle, a process that requires C-H bond scission at the benzylic carbon. We have prepared isotope-enriched protein bearing tyrosine residues deuterated at the beta carbon, and have determined kinetic isotope effects (KIEs) on the GFP self-processing reaction. Progress curves for the production of H 2O 2 and the mature chromophore were analyzed by global curve fitting to a three-step mechanism describing preoxidation, oxidation and postoxidation events. Although a KIE for protein oxidation could not be discerned ( k H/ k D = 1.1 +/- 0.2), a full primary KIE of 5.9 (+/-2.8) was extracted for the postoxidation step. Therefore, the exocyclic carbon is not involved in the reduction of molecular oxygen. Rather, C-H bond cleavage proceeds from the oxidized cyclic imine form, and is the rate-limiting event of the final step. Substantial pH-dependence of maturation was observed upon substitution of the catalytic glutamate (E222Q), indicating an apparent p K a of 9.4 (+/-0.1) for the base catalyst. For this variant, a KIE of 5.8 (+/-0.4) was determined for the intrinsic time constant that is thought to describe the final step, as supported by ultra-high resolution mass spectrometric results. The data are consistent with general base catalysis of the postoxidation events yielding green color. Structural arguments suggest a mechanism in which the highly conserved Arg96 serves as catalytic base in proton abstraction from the Tyr66-derived beta carbon.
Collapse
Affiliation(s)
- Lauren J Pouwels
- The Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA
| | | | | | | | | |
Collapse
|
32
|
Alieva NO, Konzen KA, Field SF, Meleshkevitch EA, Hunt ME, Beltran-Ramirez V, Miller DJ, Wiedenmann J, Salih A, Matz MV. Diversity and evolution of coral fluorescent proteins. PLoS One 2008; 3:e2680. [PMID: 18648549 PMCID: PMC2481297 DOI: 10.1371/journal.pone.0002680] [Citation(s) in RCA: 202] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 06/15/2008] [Indexed: 11/18/2022] Open
Abstract
GFP-like fluorescent proteins (FPs) are the key color determinants in reef-building corals (class Anthozoa, order Scleractinia) and are of considerable interest as potential genetically encoded fluorescent labels. Here we report 40 additional members of the GFP family from corals. There are three major paralogous lineages of coral FPs. One of them is retained in all sampled coral families and is responsible for the non-fluorescent purple-blue color, while each of the other two evolved a full complement of typical coral fluorescent colors (cyan, green, and red) and underwent sorting between coral groups. Among the newly cloned proteins are a "chromo-red" color type from Echinopora forskaliana (family Faviidae) and pink chromoprotein from Stylophora pistillata (Pocilloporidae), both evolving independently from the rest of coral chromoproteins. There are several cyan FPs that possess a novel kind of excitation spectrum indicating a neutral chromophore ground state, for which the residue E167 is responsible (numeration according to GFP from A. victoria). The chromoprotein from Acropora millepora is an unusual blue instead of purple, which is due to two mutations: S64C and S183T. We applied a novel probabilistic sampling approach to recreate the common ancestor of all coral FPs as well as the more derived common ancestor of three main fluorescent colors of the Faviina suborder. Both proteins were green such as found elsewhere outside class Anthozoa. Interestingly, a substantial fraction of the all-coral ancestral protein had a chromohore apparently locked in a non-fluorescent neutral state, which may reflect the transitional stage that enabled rapid color diversification early in the history of coral FPs. Our results highlight the extent of convergent or parallel evolution of the color diversity in corals, provide the foundation for experimental studies of evolutionary processes that led to color diversification, and enable a comparative analysis of structural determinants of different colors.
Collapse
Affiliation(s)
- Naila O. Alieva
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Karen A. Konzen
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, Florida, United States of America
| | - Steven F. Field
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Ella A. Meleshkevitch
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, Florida, United States of America
| | - Marguerite E. Hunt
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Victor Beltran-Ramirez
- ARC Centre of Excellence in Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - David J. Miller
- ARC Centre of Excellence in Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Jörg Wiedenmann
- National Oceanography Centre, University of Southampton, Southampton, United Kingdom
- Institute of General Zoology and Endocrinology, University of Ulm, Ulm, Germany
| | - Anya Salih
- School of Natural Sciences, University of Western Sydney, Penrith South DC, New South Wales, Australia
| | - Mikhail V. Matz
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| |
Collapse
|
33
|
Green fluorescent protein is superior to blue fluorescent protein as a quantitative reporter of promoter activity in E. coli. Mol Biol Rep 2008; 36:1107-12. [DOI: 10.1007/s11033-008-9285-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 06/11/2008] [Indexed: 01/13/2023]
|
34
|
Malo GD, Wang M, Wu D, Stelling AL, Tonge PJ, Wachter RM. Crystal structure and Raman studies of dsFP483, a cyan fluorescent protein from Discosoma striata. J Mol Biol 2008; 378:871-86. [PMID: 18395223 DOI: 10.1016/j.jmb.2008.02.069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 02/28/2008] [Indexed: 10/22/2022]
Abstract
To better understand the diverse mechanisms of spectral tuning operational in fluorescent proteins (FPs), we determined the 2.1-A X-ray structure of dsFP483 from the reef-building coral Discosoma. This protein is a member of the cyan class of Anthozoa FPs and exhibits broad, double-humped excitation and absorbance bands, with a maximum at 437-440 nm and a shoulder at 453 nm. Although these features support a heterogeneous ground state for the protein-intrinsic chromophore, peak fluorescence occurs at 483 nm for all excitation wavelengths, suggesting a common emissive state. Optical properties are insensitive to changes in pH over the entire range of protein stability. The refined crystal structure of the biological tetramer (space group C2) demonstrates that all protomers bear a cis-coplanar chromophore chemically identical with that in green fluorescent protein (GFP). To test the roles of specific residues in color modulation, we investigated the optical properties of the H163Q and K70M variants. Although absorbance bands remain broad, peak excitation maxima are red shifted to 455 and 460 nm, emitting cyan light and green light, respectively. To probe chromophore ground-state features, we collected Raman spectra using 752-nm excitation. Surprisingly, the positions of key Raman bands of wild-type dsFP483 are most similar to those of the neutral GFP chromophore, whereas the K70M spectra are more closely aligned with the anionic form. The Raman data provide further evidence of a mixed ground state with chromophore populations that are modulated by mutation. Possible internal protonation equilibria, structural heterogeneity in the binding sites, and excited-state proton transfer mechanisms are discussed. Structural alignments of dsFP483 with the homologs DsRed, amFP486, and zFP538-K66M suggest that natural selection for cyan is an exquisitely fine-tuned and highly cooperative process involving a network of electrostatic interactions that may vary substantially in composition and arrangement.
Collapse
Affiliation(s)
- Gabrielle D Malo
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | | | | | | | | | | |
Collapse
|
35
|
Hering VR, Gibson G, Schumacher RI, Faljoni-Alario A, Politi MJ. Energy Transfer between CdSe/ZnS Core/Shell Quantum Dots and Fluorescent Proteins. Bioconjug Chem 2007; 18:1705-8. [PMID: 17900163 DOI: 10.1021/bc700147j] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent proteins from the green fluorescent protein (GFP) family interact strongly with CdSe/ZnS quantum dots. Photoluminescence of GFP5 is suppressed by red-emitting CdSe/ZnS quantum dots with high efficiency in a pH-dependent manner. The elevated degree of quenching, around 90%, makes it difficult to analyze the remaining signal, and it is not clear yet whether FRET is the reason behind the quenching. When the donor is a green-emitting CdSe/ZnS quantum dot and the acceptor is the HcRed1 protein, it is possible to detect quenching of the donor and sensitized emission from the acceptor. It was verified that the sensitized emission has the low anisotropy characteristic of FRET. The present characterization identifies donor-acceptor pairs formed by fluorescent proteins and CdSe/ZnS quantum dots that are suitable for the exploration of cellular events. These donor-acceptor pairs take advantage of the exceptional photochemical properties of quantum dots allied with the unique ability of fluorescent proteins to act as gene-based fluorescent probes.
Collapse
Affiliation(s)
- Vitor R Hering
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
| | | | | | | | | |
Collapse
|
36
|
Arosio D, Garau G, Ricci F, Marchetti L, Bizzarri R, Nifosì R, Beltram F. Spectroscopic and structural study of proton and halide ion cooperative binding to gfp. Biophys J 2007; 93:232-44. [PMID: 17434942 PMCID: PMC1914440 DOI: 10.1529/biophysj.106.102319] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Accepted: 03/13/2007] [Indexed: 11/18/2022] Open
Abstract
This study reports the influence of halogens on fluorescence properties of the Aequorea victoria Green Fluorescent Protein variant S65T/T203Y (E(2)GFP). Halide binding forms a specific nonfluorescent complex generating a substantial drop of the fluorescence via static quenching. Spectroscopic analysis under different solution conditions reveals high halogen affinity, which is strongly dependent on the pH. This evidences the presence in E(2)GFP of interacting binding sites for halide ions and for protons. Thermodynamic link and cooperative interaction are assessed demonstrating that binding of one halide ion is associated with the binding of one proton in a cooperative fashion with the formation, in the pH range 4.5-10, of a single fully protonated E(2)GFP.halogen complex. To resolve the structural determinants of E(2)GFP sensitivity to halogens, high-resolution crystallographic structures were obtained for the halide-free and I(-), Br(-), and Cl(-) bound E(2)GFP. Remarkably the first high-resolution (1.4 A) crystallographic structure of a chloride-bound GFP is reported. The chloride ion occupies a specific and unique binding pocket in direct contact (3.4 A) with the chromophore imidazolidinone aromatic ring. Unanticipated flexibility, strongly modulated by halide ion interactions, is observed in the region surrounding the chromophore. Furthermore molecular dynamics simulations identified E222 residue (along with the chromophore Y66 residue) being in the protonated state when E(2)GFP.halogen complex is formed. The impact of these results on high-sensitivity biosensor design will be discussed.
Collapse
Affiliation(s)
- Daniele Arosio
- Scuola Normale Superiore, National Enterprise for nanoScience and nanoTechnology-Consiglio Nazionale delle Ricerche-Instituto Nazionale di Fisica della Materia, Pisa, Italy.
| | | | | | | | | | | | | |
Collapse
|
37
|
Barakat NH, Love JJ. Molecular diversity in engineered protein libraries. Curr Opin Chem Biol 2007; 11:335-41. [PMID: 17548238 DOI: 10.1016/j.cbpa.2007.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 05/17/2007] [Indexed: 11/26/2022]
Abstract
Engineered protein libraries, defined here as a collection of different mutant variants of a single specific protein, are intentionally designed to be rich in molecular diversity and can span ranges from as little as 400 different variants to greater than 10(12) members per library. The goal of engineering libraries is to generate new protein variants, identified upon screening, that possess desired novel properties. Exploitation of the natural organization of the genetic code has led to 'focused' libraries that are lower in overall complexity yet biased towards variants with preferred biophysical properties. An emerging trend, in which computational algorithms are blended with in vivo screens, is also leading towards greater and more rapid success in the field of protein design.
Collapse
Affiliation(s)
- Nora H Barakat
- Department of Chemistry and Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, USA
| | | |
Collapse
|
38
|
Abstract
Recent advances in our understanding of the mechanism of chromophore formation in green fluorescent protein (GFP) are presented. GFP is the best-studied member of the family of GFP-like proteins, proteins that exhibit bright coloration spanning most of the visible spectrum. GFPs undergo a post-translational self-modification process that yields an intrinsic fluorophore constructed from an internal main-chain cross-link that is susceptible to air oxidation. A combination of protein X-ray crystallographic and kinetic experiments has led to the development of a mechanistic model that entails conformational pre-organization, electrophilic and base catalysis, and production of hydrogen peroxide upon protein oxidation. The process is concluded by a slow proton abstraction step from a tyrosine-derived carbon acid.
Collapse
Affiliation(s)
- Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, USA.
| |
Collapse
|