1
|
Hartley SM, Tiernan KA, Ahmetaj G, Cretu A, Zhuang Y, Zimmer M. AlphaFold2 and RoseTTAFold predict posttranslational modifications. Chromophore formation in GFP-like proteins. PLoS One 2022; 17:e0267560. [PMID: 35709156 PMCID: PMC9202861 DOI: 10.1371/journal.pone.0267560] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/12/2022] [Indexed: 11/26/2022] Open
Abstract
AlphaFold2 and RoseTTAfold are able to predict, based solely on their sequence whether GFP-like proteins will post-translationally form a chromophore (the part of the protein responsible for fluorescence) or not. Their training has not only taught them protein structure and folding, but also chemistry. The structures of 21 sequences of GFP-like fluorescent proteins that will post-translationally form a chromophore and of 23 GFP-like non-fluorescent proteins that do not have the residues required to form a chromophore were determined by AlphaFold2 and RoseTTAfold. The resultant structures were mined for a series of geometric measurements that are crucial to chromophore formation. Statistical analysis of these measurements showed that both programs conclusively distinguished between chromophore forming and non-chromophore forming proteins. A clear distinction between sequences capable of forming a chromophore and those that do not have the residues required for chromophore formation can be obtained by examining a single measurement—the RMSD of the overlap of the central alpha helices of the crystal structure of S65T GFP and the AlphaFold2 determined structure. Only 10 of the 578 GFP-like proteins in the pdb have no chromophore, yet when AlphaFold2 and RoseTTAFold are presented with the sequences of 44 GFP-like proteins that are not in the pdb they fold the proteins in such a way that one can unequivocally distinguish between those that can and cannot form a chromophore.
Collapse
|
2
|
Dean Cho CC, Blankenship LR, Ma X, Xu S, Liu W. The Pyrrolysyl-tRNA Synthetase Activity can be Improved by a P188 Mutation that Stabilizes the Full-Length Enzyme. J Mol Biol 2022; 434:167453. [PMID: 35033561 PMCID: PMC9018550 DOI: 10.1016/j.jmb.2022.167453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/18/2021] [Accepted: 01/09/2022] [Indexed: 11/24/2022]
Abstract
The amber suppression-based noncanonical amino acid (ncAA) mutagenesis technique has been widely used in both basic and applied research. So far more than two hundred ncAAs have been genetically encoded by amber codon in both prokaryotes and eukaryotes using wild-type and engineered pyrrolysyl-tRNA synthetase (PylRS)-tRNAPyl (PylT) pairs. Methanosarcina mazei PylRS (MmPylRS) is arguably one of two most used PylRS variants. However, it contains an unstable N-terminal domain that is usually cleaved from the full-length protein during expression and therefore leads to a low enzyme activity. We discovered that the cleavage takes place after A189 and this cleavage is inhibited when MmPylRS is co-expressed with Ca. Methanomethylophilus alvus tRNAPyl (CmaPylT). In the presence of CmaPylT, MmPylRS is cleaved after an alternative site K110. MmPylRS is active toward CmaPylT. Its combined use with CmaPylT leads to enhanced incorporation of Nε-Boc-lysine (BocK) at amber codon. To prevent MmPylRS from cleavage after A189 in the presence of its cognate M. mazei tRNAPyl (MmPylT), we introduced mutations at P188. Our results indicated that the P188G mutation stabilizes MmPylRS. We showed that the P188G mutation in wild-type MmPylRS or its engineered variants allows enhanced incorporation of BocK and other noncanonical amino acids including Nε-acetyl-lysine when they are co-expressed with MmPylT.
Collapse
Affiliation(s)
- Chia-Chuan Dean Cho
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Lauren R Blankenship
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Xinyu Ma
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Liu
- The Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
3
|
Nwafor J, Salguero C, Welcome F, Durmus S, Glasser RN, Zimmer M, Schneider TL. Why Are Gly31, Gly33, and Gly35 Highly Conserved in All Fluorescent Proteins? Biochemistry 2021; 60:3762-3770. [PMID: 34806355 DOI: 10.1021/acs.biochem.1c00587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Green fluorescent protein (GFP)-like fluorescent proteins have been found in more than 120 species. Although the proteins have little sequence identity, Gly31, 33, and 35 are 87, 100, and 95% conserved across all species, respectively. All GFP-like proteins have a β-barrel structure composed of 11 β-sheets, and the 3 conserved glycines are located in the second β-sheet. Molecular dynamics (MD) simulations have shown that mutating one or more of the glycines to alanines most likely does not reduce chromophore formation in correctly folded immature fluorescent proteins. MD and protein characterization of alanine mutants indicate that mutation of the conserved glycines leads to misfolding. Gly31, 33, and 35 are essential to maintain the integrity of the β1-3 triad that is the last structural element to slot in place in the formation of the canonical fluorescent protein β-barrel. Glycines located in β-sheets may have a similar role in the formation of other non-GFP β-barrels.
Collapse
Affiliation(s)
- Justin Nwafor
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Christian Salguero
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Franceine Welcome
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Sercan Durmus
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Rachel N Glasser
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Marc Zimmer
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| | - Tanya L Schneider
- Chemistry Department, Connecticut College, New London, Connecticut 06320, United States
| |
Collapse
|
4
|
Olenginski GM, Piacentini J, Harris DR, Runko NA, Papoutsis BM, Alter JR, Hess KR, Brewer SH, Phillips-Piro CM. Structural and spectrophotometric investigation of two unnatural amino-acid altered chromophores in the superfolder green fluorescent protein. Acta Crystallogr D Struct Biol 2021; 77:1010-1018. [PMID: 34342274 PMCID: PMC8329867 DOI: 10.1107/s2059798321006525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
The spectrophotometric properties of the green fluorescent protein (GFP) result from the post-translationally cyclized chromophore composed of three amino acids including a tyrosine at the center of the β-barrel protein. Altering the amino acids in the chromophore or the nearby region has resulted in numerous GFP variants with differing photophysical properties. To further examine the effect of small atomic changes in the chromophore on the structure and photophysical properties of GFP, the hydroxyl group of the chromophore tyrosine was replaced with a nitro or a cyano group. The structures and spectrophotometric properties of these superfolder GFP (sfGFP) variants with the unnatural amino acids (UAAs) 4-nitro-L-phenylalanine or 4-cyano-L-phenylalanine were explored. Notably, the characteristic 487 nm absorbance band of wild-type (wt) sfGFP is absent in both unnatural amino-acid-containing protein constructs (Tyr66pNO2Phe-sfGFP and Tyr66pCNPhe-sfGFP). Consequently, neither Tyr66pNO2Phe-sfGFP nor Tyr66pCNPhe-sfGFP exhibited the characteristic emission of wt sfGFP centered at 511 nm when excited at 487 nm. Tyr66pNO2Phe-sfGFP appeared orange due to an absorbance band centered at 406 nm that was not present in wt sfGFP, while Tyr66pCNPhe-sfGFP appeared colorless with an absorbance band centered at 365 nm. Mass spectrometry and X-ray crystallography confirmed the presence of a fully formed chromophore and no significant structural changes in either of these UAA-containing protein constructs, signaling that the change in the observed photophysical properties of the proteins is the result of the presence of the UAA in the chromophore.
Collapse
Affiliation(s)
- Gregory M. Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Juliana Piacentini
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Darcy R. Harris
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Nicolette A. Runko
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Brianna M. Papoutsis
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Jordan R. Alter
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | | |
Collapse
|
5
|
Pletneva NV, Maksimov EG, Protasova EA, Mamontova AV, Simonyan TR, Ziganshin RH, Lukyanov KA, Muslinkina L, Pletnev S, Bogdanov AM, Pletnev VZ. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Comput Struct Biotechnol J 2021; 19:2950-2959. [PMID: 34136094 PMCID: PMC8163865 DOI: 10.1016/j.csbj.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023] Open
Abstract
For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.
Collapse
Key Words
- Ala (A), alanine
- Arg (R), arginine
- Asn (R), asparagine
- Chromophore maturation
- DTT, dithiothreitol
- EC, extinction coefficient
- EET, excitation energy transfer
- EGFP, enhanced green fluorescent protein
- ESET, excited-state electron transfer
- EYFP
- EYFP, enhanced yellow fluorescent protein
- Excitation energy transfer
- FLIM, fluorescence lifetime imaging microscopy
- FP, fluorescent protein
- FQY, fluorescence quantum yield
- FRET, Förster resonance energy transfer
- FTIR, Fourier-transform infrared (spectroscopy
- Femtosecond spectroscopy
- Fluorescent proteins
- GFP, green fluorescent protein
- GYG, glycine-tyrosine-glycine
- Gln (Q), glutamine
- Glu (E), glutamic acid
- Gly (G), glycine
- His (H), histidine
- IVA-cloning, in vivo assembly cloning
- Leu (L), leucine
- PBS, phosphate buffered saline
- PCR, polymerase chain reaction
- Phe (F), phenylalanine
- REACh, resonance energy-accepting chromoprotein
- Ser (S), serine
- Structure-guided mutagenesis
- Trp (W), tryptophan
- Tryptophan fluorescence
- Tyr (Y), tyrosine
- Val (V), valine
- X-ray structure
- avGFP, Aequorea victoria green fluorescent protein
- sfGFP, superfolder GFP
Collapse
Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Tatiana R. Simonyan
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| |
Collapse
|
6
|
Sen T, Mamontova AV, Titelmayer AV, Shakhov AM, Astafiev AA, Acharya A, Lukyanov KA, Krylov AI, Bogdanov AM. Influence of the First Chromophore-Forming Residue on Photobleaching and Oxidative Photoconversion of EGFP and EYFP. Int J Mol Sci 2019; 20:E5229. [PMID: 31652505 DOI: 10.3390/ijms20205229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022] Open
Abstract
Enhanced green fluorescent protein (EGFP)—one of the most widely applied genetically encoded fluorescent probes—carries the threonine-tyrosine-glycine (TYG) chromophore. EGFP efficiently undergoes green-to-red oxidative photoconversion (“redding”) with electron acceptors. Enhanced yellow fluorescent protein (EYFP), a close EGFP homologue (five amino acid substitutions), has a glycine-tyrosine-glycine (GYG) chromophore and is much less susceptible to redding, requiring halide ions in addition to the oxidants. In this contribution we aim to clarify the role of the first chromophore-forming amino acid in photoinduced behavior of these fluorescent proteins. To that end, we compared photobleaching and redding kinetics of EGFP, EYFP, and their mutants with reciprocally substituted chromophore residues, EGFP-T65G and EYFP-G65T. Measurements showed that T65G mutation significantly increases EGFP photostability and inhibits its excited-state oxidation efficiency. Remarkably, while EYFP-G65T demonstrated highly increased spectral sensitivity to chloride, it is also able to undergo redding chloride-independently. Atomistic calculations reveal that the GYG chromophore has an increased flexibility, which facilitates radiationless relaxation leading to the reduced fluorescence quantum yield in the T65G mutant. The GYG chromophore also has larger oscillator strength as compared to TYG, which leads to a shorter radiative lifetime (i.e., a faster rate of fluorescence). The faster fluorescence rate partially compensates for the loss of quantum efficiency due to radiationless relaxation. The shorter excited-state lifetime of the GYG chromophore is responsible for its increased photostability and resistance to redding. In EYFP and EYFP-G65T, the chromophore is stabilized by π-stacking with Tyr203, which suppresses its twisting motions relative to EGFP.
Collapse
|
7
|
Nemukhin AV, Grigorenko BL, Khrenova MG, Krylov AI. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. J Phys Chem B 2019; 123:6133-6149. [DOI: 10.1021/acs.jpcb.9b00591] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Alexander V. Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Bella L. Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G. Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Federal Research Center of Biotechnology, Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russian
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| |
Collapse
|
8
|
Grabarek D, Andruniów T. Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores. J Chem Theory Comput 2018; 15:490-508. [PMID: 30485096 DOI: 10.1021/acs.jctc.8b00769] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S1 state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.
Collapse
Affiliation(s)
- Dawid Grabarek
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| | - Tadeusz Andruniów
- Advanced Materials Engineering and Modelling Group , Wroclaw University of Science and Technology , Wyb. Wyspianskiego 27 , 50-370 Wroclaw , Poland
| |
Collapse
|
9
|
Ganini D, Leinisch F, Kumar A, Jiang J, Tokar EJ, Malone CC, Petrovich RM, Mason RP. Fluorescent proteins such as eGFP lead to catalytic oxidative stress in cells. Redox Biol 2017; 12:462-468. [PMID: 28334681 PMCID: PMC5362137 DOI: 10.1016/j.redox.2017.03.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022] Open
Abstract
Fluorescent proteins are an important tool that has become omnipresent in life sciences research. They are frequently used for localization of proteins and monitoring of cells [1,2]. Green fluorescent protein (GFP) was the first and has been the most used fluorescent protein. Enhanced GFP (eGFP) was optimized from wild-type GFP for increased fluorescence yield and improved expression in mammalian systems [3]. Many GFP-like fluorescent proteins have been discovered, optimized or created, such as the red fluorescent protein TagRFP [4]. Fluorescent proteins are expressed colorless and immature and, for eGFP, the conversion to the fluorescent form, mature, is known to produce one equivalent of hydrogen peroxide (H2O2) per molecule of chromophore [5,6]. Even though it has been proposed that this process is non-catalytic and generates nontoxic levels of H2O2 [6], this study investigates the role of fluorescent proteins in generating free radicals and inducing oxidative stress in biological systems. Immature eGFP and TagRFP catalytically generate the free radical superoxide anion (O2•-) and H2O2 in the presence of NADH. Generation of the free radical O2•- and H2O2 by eGFP in the presence of NADH affects the gene expression of cells. Many biological pathways are altered, such as a decrease in HIF1α stabilization and activity. The biological pathways altered by eGFP are known to be implicated in the pathophysiology of many diseases associated with oxidative stress; therefore, it is critical that such experiments using fluorescent proteins are validated with alternative methodologies and the results are carefully interpreted. Since cells inevitably experience oxidative stress when fluorescent proteins are expressed, the use of this tool for cell labeling and in vivo cell tracing also requires validation using alternative methodologies.
Collapse
Affiliation(s)
- Douglas Ganini
- Free Radical Biology, Immunity, Inflammation & Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Fabian Leinisch
- Free Radical Biology, Immunity, Inflammation & Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ashutosh Kumar
- Free Radical Biology, Immunity, Inflammation & Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - JinJie Jiang
- Free Radical Biology, Immunity, Inflammation & Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Erik J Tokar
- Stem Cell Toxicology Group, National Toxicology Program Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Christine C Malone
- Protein Expression Core Facility, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Robert M Petrovich
- Protein Expression Core Facility, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ronald P Mason
- Free Radical Biology, Immunity, Inflammation & Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
10
|
Grigorenko BL, Krylov AI, Nemukhin AV. Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein. J Am Chem Soc 2017; 139:10239-10249. [DOI: 10.1021/jacs.7b00676] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bella L. Grigorenko
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V. Nemukhin
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel
Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119991, Russia
| |
Collapse
|
11
|
Ma Y, Sun Q, Smith SC. The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study. Phys Chem Chem Phys 2017; 19:12942-12952. [DOI: 10.1039/c6cp07983k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DFT calculations suggested that the thermodynamically unfavourable cyclized product was trapped by oxidation.
Collapse
Affiliation(s)
- Yingying Ma
- Institue of Mining Technology
- Inner Mongolia University of Technology
- Hohhot 010051
- P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation
| | - Qiao Sun
- School of Radiation Medicine and Radiation Protection
- Soochow University
- Suzhou 215123
- P. R. China
| | - Sean C. Smith
- Integrated Materials Design Centre
- School of Chemical Engineering
- The University of New South Wales
- Sydney
- Australia
| |
Collapse
|
12
|
Ma Y, Zhang H, Sun Q, Smith SC. New Insights on the Mechanism of Cyclization in Chromophore Maturation of Wild-Type Green Fluorescence Protein: A Computational Study. J Phys Chem B 2016; 120:5386-94. [DOI: 10.1021/acs.jpcb.6b04406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yingying Ma
- Institue
of Mining Technology, Inner Mongolia University of Technology, Hohhot 010051, P. R. China
- Inner Mongolia Key Laboratory of Theoretical and Computational Chemistry Simulation, Hohhot 010051, P. R. China
| | - Hao Zhang
- College
of Life Science and Engineering, Northwest University for Nationalities, Lanzhou 730030, P. R. China
| | - Qiao Sun
- School
of Radiation Medicine and Radiation Protection, Soochow University, Suzhou 215123, P. R. China
| | - Sean C. Smith
- Integrated
Materials Design Centre, School of Chemical Engineering, The University of New South Wales, NSW2052, Sydney, Australia
| |
Collapse
|
13
|
Ma Y, Yu JG, Sun Q, Li Z, Smith SC. The mechanism of dehydration in chromophore maturation of wild-type green fluorescent protein: A theoretical study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
14
|
Ohba Y, Fujioka Y, Nakada S, Tsuda M. Fluorescent protein-based biosensors and their clinical applications. Prog Mol Biol Transl Sci. 2013;113:313-348. [PMID: 23244794 DOI: 10.1016/B978-0-12-386932-6.00008-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Green fluorescent protein and its relatives have shed their light on a wide range of biological problems. To date, with a color palette consisting of fluorescent proteins with different spectra, researchers can "paint" living cells as they desire. Moreover, sophisticated biosensors engineered to contain single or multiple fluorescent proteins, including FRET-based biosensors, spatiotemporally unveil molecular mechanisms underlying physiological processes. Although such molecules have contributed considerably to basic research, their abilities to be used in applied life sciences have yet to be fully explored. Here, we review the molecular bases of fluorescent proteins and fluorescent protein-based biosensors and focus on approaches aimed at applying such proteins to the clinic.
Collapse
|
15
|
WEI JING, ZHANG MINYI, WANG JINYUN, CHAI GUOLIANG, LIN CHENSHENG, CHENG WENDAN. SECOND-HARMONIC GENERATION OF FLUORESCENT PROTEINS. J Theor Comput Chem 2013. [DOI: 10.1142/s0219633613410071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We theoretically study the second-order nonlinear optical properties of six fluorescent proteins (FPs), such as green fluorescent protein (GFP), BFP, enhanced BFP (eBFP), CFP, YFP, and DsRed. To begin with, the geometries of all these FP chromophores are optimized at B3LYP/6-311++G** level in a water medium and the polarized continuum model (PCM in water) method is adopted. Using a time-dependent density functional theory (TDDFT) method, the electronic structures and excited-state properties of chromophores are determined. Here we employ TDDFT combining with the sum-over-states (SOS) method to calculate the first-order hyperpolarizability for second-harmonic generation (SHG) optical process. Moreover, we discuss the origin of the nonlinear optical response and determine what caused the variation of first-order hyperpolarizability. Our calculations show that the charge transfers of π → π* in the central conjugated structure and p → π* charge transfers from the side chain R1 to conjugated structure of chromophores markedly affect the first-order hyperpolarizability.
Collapse
Affiliation(s)
- JING WEI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - MIN-YI ZHANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - JIN-YUN WANG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - GUO-LIANG CHAI
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - CHEN-SHENG LIN
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - WEN-DAN CHENG
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| |
Collapse
|
16
|
Zhang MY, Li GS, Li LP. First-principles study of one and two-photon absorption of an artificial fluorescent protein chromophore by 5-hydroxytryptophan substitution. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
17
|
Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. Int Rev Cell Mol Biol 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
Collapse
Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | | |
Collapse
|
18
|
Battad JM, Traore DAK, Byres E, Rossjohn J, Devenish RJ, Olsen S, Wilce MCJ, Prescott M. A green fluorescent protein containing a QFG tri-peptide chromophore: optical properties and X-ray crystal structure. PLoS One 2012; 7:e47331. [PMID: 23071789 PMCID: PMC3468514 DOI: 10.1371/journal.pone.0047331] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/12/2012] [Indexed: 01/07/2023] Open
Abstract
Rtms5 is an deep blue weakly fluorescent GFP-like protein ([Formula: see text], 592 nm; [Formula: see text], 630nm; Φ(F), 0.004) that contains a (66)Gln-Tyr-Gly chromophore tripeptide sequence. We investigated the optical properties and structure of two variants, Rtms5(Y67F) and Rtms5(Y67F/H146S) in which the tyrosine at position 67 was substituted by a phenylalanine. Compared to the parent proteins the optical spectra for these new variants were significantly blue-shifted. Rtms5(Y67F) spectra were characterised by two absorbing species ([Formula: see text], 440 nm and 513 nm) and green fluorescence emission ([Formula: see text], 440 nm; [Formula: see text], 508 nm; Φ(F), 0.11), whilst Rtms5(Y67F/H146S) spectra were characterised by a single absorbing species ([Formula: see text], 440 nm) and a relatively high fluorescence quantum yield (Φ(F,) 0.75; [Formula: see text], 440 nm; [Formula: see text], 508 nm). The fluorescence emissions of each variant were remarkably stable over a wide range of pH (3-11). These are the first GFP-like proteins with green emissions (500-520 nm) that do not have a tyrosine at position 67. The X-ray crystal structure of each protein was determined to 2.2 Å resolution and showed that the benzylidine ring of the chromophore, similar to the 4-hydroxybenzylidine ring of the Rtms5 parent, is non-coplanar and in the trans conformation. The results of chemical quantum calculations together with the structural data suggested that the 513 nm absorbing species in Rtms5(Y67F) results from an unusual form of the chromophore protonated at the acylimine oxygen. These are the first X-ray crystal structures for fluorescent proteins with a functional chromophore containing a phenylalanine at position 67.
Collapse
Affiliation(s)
- Jion M. Battad
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Daouda A. K. Traore
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Emma Byres
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Rodney J. Devenish
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Seth Olsen
- School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew C. J. Wilce
- The Structural Biology Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
| | - Mark Prescott
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
- * E-mail: (MP); (MW)
| |
Collapse
|
19
|
Stepanenko OV, Stepanenko OV, Shcherbakova DM, Kuznetsova IM, Turoverov KK, Verkhusha VV. Modern fluorescent proteins: from chromophore formation to novel intracellular applications. Biotechniques 2012; 51:313-4, 316, 318 passim. [PMID: 22054544 DOI: 10.2144/000113765] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 09/29/2011] [Indexed: 01/24/2023] Open
Abstract
The diverse biochemical and photophysical properties of fluorescent proteins (FPs) have enabled the generation of a growing palette of colors, providing unique opportunities for their use in a variety of modern biology applications. Modulation of these FP characteristics is achieved through diversity in both the structure of the chromophore as well as the contacts between the chromophore and the surrounding protein barrel. Here we review our current knowledge of blue, green, and red chromophore formation in permanently emitting FPs, photoactivatable FPs, and fluorescent timers. Progress in understanding the interplay between FP structure and function has allowed the engineering of FPs with many desirable features, and enabled recent advances in microscopy techniques such as super-resolution imaging of single molecules, imaging of protein dynamics, photochromic FRET, deep-tissue imaging, and multicolor two-photon microscopy in live animals.
Collapse
Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
| | | | | | | | | | | |
Collapse
|
20
|
Fernandez-Lima FA, Eller MJ, DeBord JD, Levy MJ, Verkhoturov SV, Della-Negra S, Schweikert EA. Analysis of Fluorescent Proteins with a Nanoparticle Probe. J Phys Chem Lett 2012; 3:337-341. [PMID: 22308203 PMCID: PMC3270945 DOI: 10.1021/jz201547x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This letter presents the first application of high energy, single nanoparticle probes (e.g., 520 keV Au(400) 2nm NP) in the characterization of surfaces containing fluorescent proteins (e.g., GFP variants) by their co-emitted photon, electron and secondary ion signals. NP induced protein luminescence increases with the NP incident energy, is originated by the NP impact and is transferred to the protein fluorophor via electronic energy transfer. Multi-electron emission is observed per single NP impacts and their distributions are specific to the target morphology and composition. Fragment ions of protein sub-units consisting of 2-7 amino acid peptides are observed under individual NP impacts that can be correlated to the random protein orientation relative to the impact site (e.g., outer layer or "skin" of the protein).
Collapse
Affiliation(s)
| | - Michael J. Eller
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - J. Daniel DeBord
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | - Michaella J. Levy
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| | | | | | - Emile A. Schweikert
- Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255
| |
Collapse
|
21
|
Ma Y, Sun Q, Li Z, Yu JG, Smith SC. Theoretical studies of chromophore maturation in the wild-type green fluorescent protein: ONIOM(DFT:MM) investigation of the mechanism of cyclization. J Phys Chem B 2012; 116:1426-36. [PMID: 22212013 DOI: 10.1021/jp208749v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The availability of a gene encoding green fluorescence immediately stimulates interest in the puzzle of autocatalytic formation of the green fluorescent protein (GFP) chromophore. Numerous experimental and theoretical studies have indicated that cyclization is the first and most important step in the maturation process of the GFP. In our previous paper based on cluster models [J. Phys. Chem. B2010, 114, 9698-9705], two possible mechanisms have been investigated with the conclusion that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 α-carbon. However, the impact of the protein environment on the reaction mechanism remains to be explored. In this paper, we investigated the two possible mechanisms with inclusion of protein environmental effects by using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Our calculations reveal no hydrogen bonding network that would facilitate deprotonation of the amide nitrogen of Gly67, although it is the lower energy pathway in the cluster model system. Contrastingly, there is a hydrogen bonding network between Tyr66 α-carbon and Glu222, which is in good agreement with X-ray data. The ONIOM studies show that proton transfer from Tyr66 α-carbon to Glu222 is a long-distance charge transfer process. The charge distribution of the MM region has a significant perturbation to the wave function for the QM region, with the QM energy for the proton transfer product being increased under the influence of the electrostatic protein environment. The barrier for the rate-limiting step in cyclization is quite high, about 40.0 kcal/mol in the case of ONIOM-EE.
Collapse
Affiliation(s)
- Yingying Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | | | | | | |
Collapse
|
22
|
Reeder PJ, Huang YM, Dordick JS, Bystroff C. A rewired green fluorescent protein: folding and function in a nonsequential, noncircular GFP permutant. Biochemistry 2010; 49:10773-9. [PMID: 21090791 DOI: 10.1021/bi100975z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequential order of secondary structural elements in proteins affects the folding and activity to an unknown extent. To test the dependence on sequential connectivity, we reconnected secondary structural elements by their solvent-exposed ends, permuting their sequential order, called "rewiring". This new protein design strategy changes the topology of the backbone without changing the core side chain packing arrangement. While circular and noncircular permutations have been observed in protein structures that are not related by sequence homology, to date no one has attempted to rationally design and construct a protein with a sequence that is noncircularly permuted while conserving three-dimensional structure. Herein, we show that green fluorescent protein can be rewired, still functionally fold, and exhibit wild-type fluorescence excitation and emission spectra.
Collapse
Affiliation(s)
- Philippa J Reeder
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, United States
| | | | | | | |
Collapse
|
23
|
Ma Y, Sun Q, Zhang H, Peng L, Yu JG, Smith SC. The mechanism of cyclization in chromophore maturation of green fluorescent protein: a theoretical study. J Phys Chem B 2010; 114:9698-705. [PMID: 20593847 DOI: 10.1021/jp1039817] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An intriguing aspect of the green fluorescent protein (GFP) is the autocatalytic post-translational modification that results in the formation of its chromophore. Numerous experimental and theoretical studies indicate that cyclization is the first and the most important step in the maturation process. In this work, two proposed mechanisms for the cyclization were investigated by using the hybrid density functional theory method B3LYP. Cluster models corresponding to the two mechanisms proposed by Wachter et al. [J. Biol. Chem. 2005, 280, 26248-26255] are constructed on the basis of the X-ray crystal structure (PDB entry 2AWJ) and corresponding reaction path potential energy profiles for the two cyclization mechanisms are presented. Our results suggest that the backbone condensation initiated by deprotonation of the Gly67 amide nitrogen is easier than deprotonation of the Tyr66 alpha-carbon. Moreover, Arg96 fulfills the role of stabilizing the enolate moiety, and Glu222 plays the role of a general base. The formation of the cyclized product is found to be 16.0 and 18.6 kcal/mol endothermic with respect to the two models, which is in agreement with experimental observation.
Collapse
Affiliation(s)
- Yingying Ma
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | | | | | | | | | | |
Collapse
|
24
|
Chudakov DM, Matz MV, Lukyanov S, Lukyanov KA. Fluorescent proteins and their applications in imaging living cells and tissues. Physiol Rev 2010; 90:1103-63. [PMID: 20664080 DOI: 10.1152/physrev.00038.2009] [Citation(s) in RCA: 915] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Green fluorescent protein (GFP) from the jellyfish Aequorea victoria and its homologs from diverse marine animals are widely used as universal genetically encoded fluorescent labels. Many laboratories have focused their efforts on identification and development of fluorescent proteins with novel characteristics and enhanced properties, resulting in a powerful toolkit for visualization of structural organization and dynamic processes in living cells and organisms. The diversity of currently available fluorescent proteins covers nearly the entire visible spectrum, providing numerous alternative possibilities for multicolor labeling and studies of protein interactions. Photoactivatable fluorescent proteins enable tracking of photolabeled molecules and cells in space and time and can also be used for super-resolution imaging. Genetically encoded sensors make it possible to monitor the activity of enzymes and the concentrations of various analytes. Fast-maturing fluorescent proteins, cell clocks, and timers further expand the options for real time studies in living tissues. Here we focus on the structure, evolution, and function of GFP-like proteins and their numerous applications for in vivo imaging, with particular attention to recent techniques.
Collapse
|
25
|
Subach FV, Patterson GH, Renz M, Lippincott-Schwartz J, Verkhusha VV. Bright monomeric photoactivatable red fluorescent protein for two-color super-resolution sptPALM of live cells. J Am Chem Soc 2010; 132:6481-91. [PMID: 20394363 PMCID: PMC2866019 DOI: 10.1021/ja100906g] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rapidly emerging techniques of super-resolution single-molecule microscopy of living cells rely on the continued development of genetically encoded photoactivatable fluorescent proteins. On the basis of monomeric TagRFP, we have developed a photoactivatable TagRFP protein that is initially dark but becomes red fluorescent after violet light irradiation. Compared to other monomeric dark-to-red photoactivatable proteins including PAmCherry, PATagRFP has substantially higher molecular brightness, better pH stability, substantially less sensitivity to blue light, and better photostability in both ensemble and single-molecule modes. Spectroscopic analysis suggests that PATagRFP photoactivation is a two-step photochemical process involving sequential one-photon absorbance by two distinct chromophore forms. True monomeric behavior, absence of green fluorescence, and single-molecule performance in live cells make PATagRFP an excellent protein tag for two-color imaging techniques, including conventional diffraction-limited photoactivation microscopy, super-resolution photoactivated localization microscopy (PALM), and single particle tracking PALM (sptPALM) of living cells. Two-color sptPALM imaging was demonstrated using several PATagRFP tagged transmembrane proteins together with PAGFP-tagged clathrin light chain. Analysis of the resulting sptPALM images revealed that single-molecule transmembrane proteins, which are internalized into a cell via endocytosis, colocalize in space and time with plasma membrane domains enriched in clathrin light-chain molecules.
Collapse
Affiliation(s)
- Fedor V. Subach
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - George H. Patterson
- Biophotonics Section, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892
| | - Malte Renz
- Section on Organelle Biology, Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892
| | - Jennifer Lippincott-Schwartz
- Section on Organelle Biology, Cell Biology and Metabolism Program, National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| |
Collapse
|
26
|
Pletnev S, Subach FV, Dauter Z, Wlodawer A, Verkhusha VV. Understanding blue-to-red conversion in monomeric fluorescent timers and hydrolytic degradation of their chromophores. J Am Chem Soc 2010; 132:2243-53. [PMID: 20121102 DOI: 10.1021/ja908418r] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast-FT is a fluorescent timer (FT) engineered from DsRed-like fluorescent protein mCherry. Crystal structures of Fast-FT (chromophore Met66-Tyr67-Gly68) and its precursor with blocked blue-to-red conversion Blue102 (chromophore Leu66-Tyr67-Gly68) have been determined at the resolution of 1.15 A and 1.81 A, respectively. Structural data suggest that blue-to-red conversion, taking place in Fast-FT and in related FTs, is associated with the oxidation of Calpha2-Cbeta2 bond of Tyr67. Site directed mutagenesis revealed a crucial role of Arg70 and Tyr83 in the delayed oxidation of Calpha2-Cbeta2 bond, introducing the timing factor in maturation of the timer. Substitutions Ser217Ala and Ser217Cys in Fast-FT substantially slow down formation of an intermediate blue chromophore but do not affect much blue-to-red conversion, whereas mutations Arg70Lys or Trp83Leu, having little effect on the blue chromophore formation rate, markedly accelerates formation of the red chromophore. The chromophore of FTs adopts a cis-conformation stabilized by a hydrogen bond between its phenolate oxygen and the side chain hydroxyl of Ser146. In Blue102, a bulky side chain of Ile146 precludes the chromophore from adopting a "cis-like" conformation, blocking its blue-to-red conversion. Both Fast-FT and Blue102 structures revealed hydrolytic degradation of the chromophores. In Fast-FT, chromophore-forming Met66 residue is eliminated from the polypeptide chain, whereas Leu66 in Blue102 is cleaved out from the chromophore, decarboxylated and remains attached to the preceding Phe65. Hydrolysis of the chromophore competes with chromophore maturation and is driven by the same residues that participate in chromophore maturation.
Collapse
Affiliation(s)
- Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois 60439, USA.
| | | | | | | | | |
Collapse
|
27
|
Liu P, O'Mara BW, Warrack BM, Wu W, Huang Y, Zhang Y, Zhao R, Lin M, Ackerman MS, Hocknell PK, Chen G, Tao L, Rieble S, Wang J, Wang-Iverson DB, Tymiak AA, Grace MJ, Russell RJ. A tris (2-carboxyethyl) phosphine (TCEP) related cleavage on cysteine-containing proteins. J Am Soc Mass Spectrom 2010; 21:837-844. [PMID: 20189823 DOI: 10.1016/j.jasms.2010.01.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 01/13/2010] [Accepted: 01/14/2010] [Indexed: 05/28/2023]
Abstract
Introduced in the late 1980s as a reducing reagent, Tris (2-carboxyethyl) phosphine (TCEP) has now become one of the most widely used protein reductants. To date, only a few studies on its side reactions have been published. We report the observation of a side reaction that cleaves protein backbones under mild conditions by fracturing the cysteine residues, thus generating heterogeneous peptides containing different moieties from the fractured cysteine. The peptide products were analyzed by high performance liquid chromatography and tandem mass spectrometry (LC/MS/MS). Peptides with a primary amine and a carboxylic acid as termini were observed, and others were found to contain amidated or formamidated carboxy termini, or formylated or glyoxylic amino termini. Formamidation of the carboxy terminus and the formation of glyoxylic amino terminus were unexpected reactions since both involve breaking of carbon-carbon bonds in cysteine.
Collapse
Affiliation(s)
- Peiran Liu
- Department of Biologics Product and Process Development, Bristol-Myers Squibb Technical Operations, Princeton, New Jersey 08543, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Subach OM, Malashkevich VN, Zencheck WD, Morozova KS, Piatkevich KD, Almo SC, Verkhusha VV. Structural characterization of acylimine-containing blue and red chromophores in mTagBFP and TagRFP fluorescent proteins. Chem Biol 2010; 17:333-41. [PMID: 20416505 PMCID: PMC2862997 DOI: 10.1016/j.chembiol.2010.03.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/23/2010] [Accepted: 03/05/2010] [Indexed: 11/28/2022]
Abstract
We determined the 2.2 A crystal structures of the red fluorescent protein TagRFP and its derivative, the blue fluorescent protein mTagBFP. The crystallographic analysis is consistent with a model in which TagRFP has the trans coplanar anionic chromophore with the conjugated pi-electron system, similar to that of DsRed-like chromophores. Refined conformation of mTagBFP suggests the presence of an N-acylimine functionality in its chromophore and single C(alpha)-C(beta) bond in the Tyr64 side chain. Mass spectrum of mTagBFP chromophore-bearing peptide indicates a loss of 20 Da upon maturation, whereas tandem mass spectrometry reveals that the C(alpha)-N bond in Leu63 is oxidized. These data indicate that mTagBFP has a new type of the chromophore, N-[(5-hydroxy-1H-imidazole-2-yl)methylidene]acetamide. We propose a chemical mechanism in which the DsRed-like chromophore is formed via the mTagBFP-like blue intermediate.
Collapse
Affiliation(s)
- Oksana M. Subach
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, U.S.A
| | - Vladimir N. Malashkevich
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, U.S.A
| | - Wendy D. Zencheck
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, U.S.A
| | - Kateryna S. Morozova
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, U.S.A
| | - Kiryl D. Piatkevich
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, U.S.A
| | - Steven C. Almo
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, U.S.A
| | - Vladislav V. Verkhusha
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Bronx, New York 10461, U.S.A
| |
Collapse
|
29
|
Merola F, Levy B, Demachy I, Pasquier H. Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family. Springer Series on Fluorescence 2010. [DOI: 10.1007/978-3-642-04702-2_11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
|
30
|
Abstract
The prolific use of green fluorescent protein and its variants throughout cellular biology relies on the post-translational formation of the chromophore, which proceeds without the need for any additional enzymes or cofactors, except molecular oxygen. In order to form the mature chromophore, the polypeptide backbone must undergo four distinct processes: folding, cyclisation, oxidation and dehydration. This tutorial review looks in detail at the proposed mechanisms for chromophore formation arising out of experimental and computational studies. The folding process is discussed, and the role that the native state plays in catalysing the initial cyclisation and subsequent chemistry is analysed. The specific functions of four conserved residues (Y66, G67, R96 and E222) in the maturation process are also presented. A greater understanding of the maturation process of fluorescent proteins from both jellyfish and coral species will profit the ongoing quest for brighter, faster maturing, genetically-encodable fluorescent probes of all colours, thus increasing their utility throughout the biomedical sciences.
Collapse
Affiliation(s)
- Timothy D Craggs
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews, UK KY16 9SS.
| |
Collapse
|
31
|
Aleksic J, Lazic R, Müller I, Russell SR, Adryan B. Biases in Drosophila melanogaster protein trap screens. BMC Genomics 2009; 10:249. [PMID: 19476619 PMCID: PMC2695487 DOI: 10.1186/1471-2164-10-249] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 05/28/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ability to localise or follow endogenous proteins in real time in vivo is of tremendous utility for cell biology or systems biology studies. Protein trap screens utilise the random genomic insertion of a transposon-borne artificial reporter exon (e.g. encoding the green fluorescent protein, GFP) into an intron of an endogenous gene to generate a fluorescent fusion protein. Despite recent efforts aimed at achieving comprehensive coverage of the genes encoded in the Drosophila genome, the repertoire of genes that yield protein traps is still small. RESULTS We analysed the collection of available protein trap lines in Drosophila melanogaster and identified potential biases that are likely to restrict genome coverage in protein trap screens. The protein trap screens investigated here primarily used P-element vectors and thus exhibit some of the same positional biases associated with this transposon that are evident from the comprehensive Drosophila Gene Disruption Project. We further found that protein trap target genes usually exhibit broad and persistent expression during embryonic development, which is likely to facilitate better detection. In addition, we investigated the likely influence of the GFP exon on host protein structure and found that protein trap insertions have a significant bias for exon-exon boundaries that encode disordered protein regions. 38.8% of GFP insertions land in disordered protein regions compared with only 23.4% in the case of non-trapping P-element insertions landing in coding sequence introns (p < 10(-4)). Interestingly, even in cases where protein domains are predicted, protein trap insertions frequently occur in regions encoding surface exposed areas that are likely to be functionally neutral. Considering the various biases observed, we predict that less than one third of intron-containing genes are likely to be amenable to trapping by the existing methods. CONCLUSION Our analyses suggest that the utility of P-element vectors for protein trap screens has largely been exhausted, and that approximately 2,800 genes may still be amenable using piggyBac vectors. Thus protein trap strategies based on current approaches are unlikely to offer true genome-wide coverage. We suggest that either transposons with reduced insertion bias or recombineering-based targeting techniques will be required for comprehensive genome coverage in Drosophila.
Collapse
Affiliation(s)
- Jelena Aleksic
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
| | | | | | | | | |
Collapse
|
32
|
|
33
|
Affiliation(s)
- Luis A. Alvarez
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Fabienne Merola
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Marie Erard
- Laboratoire de Chimie Physique,
Université Paris-Sud 11, UMR 8000 CNRS, F-91405 Orsay Cedex,
France
| | - Filippo Rusconi
- Laboratoire de biophysique, Muséum national d’Histoire naturelle, CNRS UMR5153-INSERM U565-MNHN USM0503, 57 rue Cuvier, Case postale 26, F-75231 Paris Cedex 05, France
| |
Collapse
|
34
|
Pakhomov AA, Martynov VI. GFP Family: Structural Insights into Spectral Tuning. ACTA ACUST UNITED AC 2008; 15:755-64. [DOI: 10.1016/j.chembiol.2008.07.009] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/02/2008] [Accepted: 07/07/2008] [Indexed: 10/21/2022]
|
35
|
Lemay NP, Morgan AL, Archer EJ, Dickson LA, Megley CM, Zimmer M. The Role of the Tight-Turn, Broken Hydrogen Bonding, Glu222 and Arg96 in the Post-translational Green Fluorescent Protein Chromophore Formation. Chem Phys 2008; 348:152-160. [PMID: 19079566 DOI: 10.1016/j.chemphys.2008.02.055] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Green Fluorescent Proteins (GFP) and GFP-like proteins all undergo an autocatalytic post-translational modification to form a centrally located chromophore. Structural analyses of all the GFP and GFP-like proteins in the protein databank were undertaken to determine the role of the tight-turn, broken hydrogen bonding, Gly67, Glu222 and Arg96 in the biosynthesis of the imidazolone group from 65SYG67. The analysis was supplemented by computational generation of the conformation adopted by uncyclized wild-type GFP. The data analysis suggests that Arg96 interacts with the Tyr66 carbonyl, stabilizing the reduced enolate intermediate that is required for cyclization; the carboxylate of Glu 222 acts as a base facilitating, through a network of two waters, the abstraction of a hydrogen from the alpha-carbon of Tyr66; a tight-turn conformation is required for autocatalytic cyclization. This conformation is responsible for a partial reduction in the hydrogen bonding network around the chromophore-forming region of the immature protein.
Collapse
Affiliation(s)
- Nathan P Lemay
- Dept. of Chemistry, Connecticut College, New London, CT 06320
| | | | | | | | | | | |
Collapse
|