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The Mechanism of the AppABLUF Photocycle Probed by Site-Specific Incorporation of Fluorotyrosine Residues: The Effect of the Y21 pKa on the Forward and Reverse Ground State ReactionsAgnieszka Gil?,#, Allison Haigney?,#, Sergey P. Laptenok§, Richard Brust?, Andras Lukacs§, James Iuliano?, Jessica Jeng?, Eduard Melief?, Rui-Kun Zhao§, EunBin Yoon?, Ian Clark║, Michael Towrie║, Gregory M. Greetham║, Annabelle Ng?, James Truglio?, Jarrod French?,?, Stephen R. Meech§,* and Peter J. Tonge?,*?Department of Chemistry, and ?Biochemistry & Cell Biology, Stony Brook University, Stony Brook, New York 11794-3400, USA; ?William A. Shine Great Neck South High School, 341 Lakeville Rd, Great Neck, NY 11020, USA; §School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; ║Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, UK.*Authors to whom correspondence should be addressed: Email: s.meech@uea.ac.uk (SRM); peter.tonge@stonybrook.edu (PJT)#These authors contributed equally to this work.KEYWORDS AppA, BLUF, Fluorotyrosine, FAD, Photoactivation, kineticsABSTRACT The transcriptional antirepressor AppA is a blue light using flavin (BLUF) photoreceptor that releases the transcriptional repressor PpsR upon photoexcitation. Light activation of AppA involves changes in a hydrogen bonding network that surrounds the flavin chromophore on the nanosecond timescale, while the dark state of AppA is then recovered in a light independent reaction with a dramatically longer half-life of ~18 min. Residue Y21, a component of the hydrogen bonding network, is known to be essential for photoactivity. Here we directly explore the effect of the Y21 pKa on dark state recovery by replacing Y21 with fluorotyrosine analogs that increase the acidity of Y21 by 3.5 pH units. Ultrafast transient infrared measurements confirm that the structure of AppA is unperturbed by fluorotyrosine substitution, and that there is a small (3-fold) change in the photokinetics of the forward reaction over the fluorotyrosine series. However, reduction of 3.5 pH units in the pKa of Y21 increases the rate of dark state recovery by 4,000-fold with a Br?nsted coefficient of ~ 1, indicating that the Y21 proton is completely transferred in the transition state leading from light to dark adapted AppA. A large solvent isotope effect of ~6-8 is also observed on the rate of dark state recovery. These data establish that the acidity of Y21 is a crucial factor for stabilizing the light activated form of the protein, and have been used to propose a model for dark state recovery that will ultimately prove useful for tuning the properties of BLUF photosensors for optogenetic applications.INTRODUCTIONThe blue-light using FAD (BLUF) domain proteins are a class of photoreceptors that utilize a non-covalently bound flavin to sense and respond to light. ADDIN EN.CITE <EndNote><Cite><Author>Gomelsky</Author><Year>2002</Year><RecNum>3284</RecNum><DisplayText><style face="superscript">1</style></DisplayText><record><rec-number>3284</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966218">3284</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Gomelsky, M.</author><author>Klug, G.</author></authors></contributors><auth-address>Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA. gomelsky@uwyo.edu</auth-address><titles><title>BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms</title><secondary-title>Trends Biochem Sci</secondary-title></titles><periodical><full-title>Trends Biochem Sci</full-title><abbr-1>Trends in biochemical sciences</abbr-1></periodical><pages>497-500</pages><volume>27</volume><number>10</number><keywords><keyword>Amino Acid Sequence</keyword><keyword>*Bacterial Proteins</keyword><keyword>Binding Sites</keyword><keyword>Flavin-Adenine Dinucleotide/*metabolism</keyword><keyword>Flavoproteins/*chemistry/*metabolism</keyword><keyword>Molecular Sequence Data</keyword><keyword>Protein Binding</keyword><keyword>Protein Structure, Tertiary</keyword><keyword>Rhodobacter sphaeroides/metabolism</keyword><keyword>Sequence Alignment</keyword></keywords><dates><year>2002</year><pub-dates><date>Oct</date></pub-dates></dates><isbn>0968-0004 (Print)
0968-0004 (Linking)</isbn><accession-num>12368079</accession-num><urls><related-urls><url> BLUF domains are found in many species where they regulate the light dependent activity of a variety of biological processes through an output domain that is either fused to the BLUF domain or that forms a non-covalent complex with it.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5Hb21lbHNreTwvQXV0aG9yPjxZZWFyPjIwMDI8L1llYXI+
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ADDIN EN.CITE.DATA 1-5 The BLUF signaling state is formed on the nanosecond time scale and is characterized by a 10-15 nm red shift in the absorption spectrum of the flavin. Once formed, the photoactivated state returns to the dark state in a light independent reaction that occurs in seconds to minutes, depending on the BLUF domain. There is significant interest in understanding how light absorption leads to photoreceptor activation, partly because in AppA the flavin chromophore, unlike other photosensors, is unable to undergo large scale structural changes upon photoexcitation, but also more broadly because the BLUF domain proteins represent a model for determining how variations in light intensity lead to the control of gene expression in living organisms. AppA is the best characterized BLUF domain photoreceptor and is found in Rhodobacter sphaeroides where it acts as an antirepressor of photosystem biosynthesis. In the dark AppA binds PpsR, a transcription factor, forming an AppA-PpsR2 complex. When irradiated with blue light, the complex dissociates releasing PpsR, enabling it to bind to DNA and repress photosystem biosynthesis. ADDIN EN.CITE <EndNote><Cite><Author>Gomelsky</Author><Year>2002</Year><RecNum>3284</RecNum><DisplayText><style face="superscript">1</style></DisplayText><record><rec-number>3284</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966218">3284</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Gomelsky, M.</author><author>Klug, G.</author></authors></contributors><auth-address>Department of Molecular Biology, University of Wyoming, Laramie, WY 82071-3944, USA. gomelsky@uwyo.edu</auth-address><titles><title>BLUF: a novel FAD-binding domain involved in sensory transduction in microorganisms</title><secondary-title>Trends Biochem Sci</secondary-title></titles><periodical><full-title>Trends Biochem Sci</full-title><abbr-1>Trends in biochemical sciences</abbr-1></periodical><pages>497-500</pages><volume>27</volume><number>10</number><keywords><keyword>Amino Acid Sequence</keyword><keyword>*Bacterial Proteins</keyword><keyword>Binding Sites</keyword><keyword>Flavin-Adenine Dinucleotide/*metabolism</keyword><keyword>Flavoproteins/*chemistry/*metabolism</keyword><keyword>Molecular Sequence Data</keyword><keyword>Protein Binding</keyword><keyword>Protein Structure, Tertiary</keyword><keyword>Rhodobacter sphaeroides/metabolism</keyword><keyword>Sequence Alignment</keyword></keywords><dates><year>2002</year><pub-dates><date>Oct</date></pub-dates></dates><isbn>0968-0004 (Print)
0968-0004 (Linking)</isbn><accession-num>12368079</accession-num><urls><related-urls><url> Absorption of light leads to an ultrafast rearrangement of a hydrogen bonding network which ultimately leads to the signaling state of the protein.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj52YW4gZGVyIEhvcnN0PC9BdXRob3I+PFllYXI+MjAwNDwv
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ADDIN EN.CITE.DATA 7-9The hydrogen bonding network that surrounds the isoalloxazine ring in the dark and light states of AppA (dAppA and lAppA respectively) is shown in Figure 1. Y21 and Q63 are conserved in all BLUF proteins, and replacement of these residues with residues such as F, A (Y21) and N, E, L (Q63) results in a photoinactive protein.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwMzwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 9-12 Although W104 is not completely conserved, in AppA changes in interactions between this residue and the hydrogen bond network are thought to be important for photoactivation.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5HYXVkZW48L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 11 Indeed, while most W104 variants undergo the red shift in flavin spectrum, it was shown that W104A AppA is unable to function as competent photoreceptor,PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA3PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 13 consistent with the inability of light excitation to modulate the β-sheet structure in this mutant,PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA1PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 14 and with our own studies using ultrafast time-resolved multiple probe spectroscopy.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5CcnVzdDwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+PFJl
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ADDIN EN.CITE.DATA 15 In addition, W104A recovers the dark state much more rapidly than in the wild-type protein (half-life of 4 sec compared to 15 min).PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA1PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 14There are a number of mechanisms proposed for signaling state formation, which differ mainly in the roles of Y21 and Q63 in the photocycle (Figure 1). The first implicates electron transfer from Y21 to the flavin as the first step following blue light excitation, followed by rotation of Q63.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5BbmRlcnNvbjwvQXV0aG9yPjxZZWFyPjIwMDU8L1llYXI+
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ADDIN EN.CITE.DATA 6 A second suggests that direct proton transfer from Y21 to N5 of the flavin occurs.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwMzwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 9,15,16 and have also obtained data that argues against formation of a stable radical intermediate in dAppA.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MdWthY3M8L0F1dGhvcj48WWVhcj4yMDE0PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 17,18 Although the photoactivation process has been intensively studied, much less is known about the mechanism of light to dark state recovery in BLUF proteins, presenting a critical gap in knowledge that must be bridged if the BLUF proteins are to be used as optogenetic tools. Hellingwerf and coworkers speculated that formation of the basic form of Y21 might be involved in stabilization of the light state, based on the observation that the rate of recovery increased ~ 3-fold as the pH was increased from 8 to 11.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwMzwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 10 Subsequently, evidence has emerged that strongly supports proton transfer in the rate limiting step on the reaction coordinate from the light to the dark state. This includes observations that recovery of the AppA dark state occurs with a solvent isotope effect (variously reported as either ~ 2PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA1PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 20 we have introduced fluorotyrosine analogs specifically into the key residue Y21 of the AppA BLUF domain (AppABLUF). The fluorinated derivatives alter both the pKa and the redox potential of the tyrosine but are expected to cause little or no perturbation to the structure. ADDIN EN.CITE <EndNote><Cite><Author>Seyedsayamdost</Author><Year>2006</Year><RecNum>3512</RecNum><DisplayText><style face="superscript">21</style></DisplayText><record><rec-number>3512</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3512</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Seyedsayamdost, M. R.</author><author>Reece, S. Y.</author><author>Nocera, D. G.</author><author>Stubbe, J.</author></authors></contributors><auth-address>Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA.</auth-address><titles><title>Mono-, di-, tri-, and tetra-substituted fluorotyrosines: new probes for enzymes that use tyrosyl radicals in catalysis</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>1569-79</pages><volume>128</volume><number>5</number><edition>2006/02/02</edition><keywords><keyword>Catalysis</keyword><keyword>Escherichia coli/enzymology</keyword><keyword>Hydrogen-Ion Concentration</keyword><keyword>Kinetics</keyword><keyword>Nuclear Magnetic Resonance, Biomolecular</keyword><keyword>Oxidation-Reduction</keyword><keyword>Ribonucleotide Reductases/*chemistry/metabolism</keyword><keyword>Spectrophotometry, Ultraviolet</keyword><keyword>Tyrosine/*analogs & derivatives/chemistry/metabolism</keyword></keywords><dates><year>2006</year><pub-dates><date>Feb 8</date></pub-dates></dates><isbn>0002-7863 (Print)
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ADDIN EN.CITE.DATA 22 GFP, ADDIN EN.CITE <EndNote><Cite><Author>Ayyadurai</Author><Year>2011</Year><RecNum>3514</RecNum><DisplayText><style face="superscript">23</style></DisplayText><record><rec-number>3514</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3514</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Ayyadurai, N.</author><author>Prabhu, N. S.</author><author>Deepankumar, K.</author><author>Kim, A.</author><author>Lee, S. G.</author><author>Yun, H.</author></authors></contributors><auth-address>School of Biotechnology, Yeungnam University, Gyeongsan, South Korea.</auth-address><titles><title>Biosynthetic substitution of tyrosine in green fluorescent protein with its surrogate fluorotyrosine in Escherichia coli</title><secondary-title>Biotechnol Lett</secondary-title></titles><periodical><full-title>Biotechnol Lett</full-title></periodical><pages>2201-7</pages><volume>33</volume><number>11</number><edition>2011/07/12</edition><dates><year>2011</year><pub-dates><date>Nov</date></pub-dates></dates><isbn>1573-6776 (Electronic)
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ADDIN EN.CITE.DATA 29 In the present work we observe that replacement of Y21 in AppABLUF with mono, di and tri-substituted fluorotyrosines, which alter the pKa of the tyrosine in aqueous solution from 9.9 to 6.4, result in only a small change in the rate of light state formation, but dramatically accelerate the rate of dark state recovery. Specifically, the 3.5 unit reduction in pKa results in a 4,000-fold increase in the rate of recovery with a Br?nsted coefficient of 1.0, indicating that the Y21 proton is completely transferred in the rate-limiting transition state on the reaction coordinate for dark state recovery. Using this information we propose a mechanism for dark state recovery.EXPERIMENTAL SECTIONMaterials: 2-Fluorophenol, 3-fluorophenol and 2,6-difluorophenol were purchased from Sigma-Aldrich. 2,3-Difluorophenol was purchased from Acros Organics. 2,3,6-Trifluorophenol was purchased from Oakwood Chemical. Pyridoxal-5’-phosphate, flavin adenine dinucleotide and MEM vitamins were purchased from Sigma-Aldrich. M9 minimal media salts were from MP Biomedicals.Tyrosine Phenol Lyase (TPL) Purification: The gene encoding tyrosine phenol lyase (TPL) was amplified by PCR from Citrobacter freundii (ATCC: 29063) using the primers 5’-CTAGCTAGCATGAATTATCCGGCAGAACCC-3’ and 5’-CCGCTCGAGGATATAGTCAAAGCGTGCAGT-3’. The PCR product and pET23b expression vector were digested with NheI and XhoI and purified by electrophoresis (2% agarose gel). After gel extraction, the digested PCR product and pET23b vector were ligated overnight and then transformed into E. coli XL1-Blue cells. Colonies that grew on agar containing ampicillin (Amp) were cultured in LB-Amp media, and after harvesting the cells, the ligated plasmid was isolated using a Wizard mini-prep kit. The resulting plasmid was transformed into BL21(DE3)pLysS E. coli cells for protein expression. A single colony was used to inoculate 10 mL of LB media containing 0.5 mM Amp and 0.5 mM chloramphenicol (Cm), which was then incubated at 37 °C at 250 rpm overnight. This culture was then used to inoculate 1 L of LB/Amp/Cm media, in 4 L flasks, which were grown at 37 °C for ~2.5 h until the OD600 reached ~0.8. The temperature was then decreased to 25 °C for 30 min followed by addition of 0.5 mM IPTG to induce protein expression. After overnight incubation, the cells were harvested by centrifugation at 5,000 rpm (4 °C) and immediately processed to ensure maximum protein yield. The cell pellet was resuspended in lysis buffer (0.1 M NaH2PO4, 150 mM NaCl, 5 mM imidazole, 5 mM β-mercaptoethanol, 0.1 mM pyridoxal 5’phosphate buffer at pH 7.0) and the cells were lysed using sonication (6 x 45 seconds at 18 W and 1 min on ice between cycles). The cell debris was removed using centrifugation (33,000 rpm for 90 min) and TPL was purified using Ni-NTA chromatography (Qiagen). After loading the sample onto the Ni-NTA column, the column (50 mL total column volume/ 10 mL of resin) was washed with 0.1 M NaH2PO4, pH 7.0 buffer containing 150 mM NaCl and 5 mM β-mercaptoethanol, that also contained increasing amounts of imidazole (0, 10 and 20 mM), after which the protein was eluted with 5 mL fractions of the same buffer containing 250 mM imidazole. Fractions containing TPL were pooled and loaded onto a size exclusion column (Sephadex G-25) and chromatography was performed with 0.1 M NaH2PO4 pH 7.0 buffer containing 150 mM NaCl. Fractions containing TPL were pooled and the purity of the protein was determined using SDS-PAGE. After concentration to ~ 5 mg/mL, the purified TPL was stored at 4 °C in 20% glycerol. We found that protein could be stored under these conditions for no more than 7 days. Fluorotyrosine synthesis using Tyrosine Phenol Lyase (TPL): The fluorotyrosines were synthesized from the respective fluorophenols based on a method described by Stubbe and coworkers. ADDIN EN.CITE <EndNote><Cite><Author>Seyedsayamdost</Author><Year>2006</Year><RecNum>3512</RecNum><DisplayText><style face="superscript">21</style></DisplayText><record><rec-number>3512</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3512</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Seyedsayamdost, M. R.</author><author>Reece, S. Y.</author><author>Nocera, D. G.</author><author>Stubbe, J.</author></authors></contributors><auth-address>Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA.</auth-address><titles><title>Mono-, di-, tri-, and tetra-substituted fluorotyrosines: new probes for enzymes that use tyrosyl radicals in catalysis</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>1569-79</pages><volume>128</volume><number>5</number><edition>2006/02/02</edition><keywords><keyword>Catalysis</keyword><keyword>Escherichia coli/enzymology</keyword><keyword>Hydrogen-Ion Concentration</keyword><keyword>Kinetics</keyword><keyword>Nuclear Magnetic Resonance, Biomolecular</keyword><keyword>Oxidation-Reduction</keyword><keyword>Ribonucleotide Reductases/*chemistry/metabolism</keyword><keyword>Spectrophotometry, Ultraviolet</keyword><keyword>Tyrosine/*analogs & derivatives/chemistry/metabolism</keyword></keywords><dates><year>2006</year><pub-dates><date>Feb 8</date></pub-dates></dates><isbn>0002-7863 (Print)
0002-7863 (Linking)</isbn><accession-num>16448128</accession-num><urls><related-urls><url> Reaction mixtures (1 L) contained 10 mM fluorophenol, 60 mM pyruvic acid, 40 μM pyridoxal-5’-phosphate, 30 mM ammonium acetate, and 5 mM β-mercaptoethanol. The pH of the reaction mixture was adjusted to 8.0 using NH4OH, filtered using a 22 μm filter and 160 units/L (0.53 mg = 1 unit) of purified TPL were then added. The reaction mixture was stirred in the dark at room temperature for a minimum of 4 days and ~ 30 units of fresh TPL were added every other day. Purification of the fluorotyrosines was performed by first acidifying the mixture using 5% trichloroacetic acid to precipitate out TPL. The precipitated protein was removed by centrifugation at 5,000 rpm for 25 min (4 °C), or by gravity filtration, and the mixture was then extracted twice using an equal volume of ethyl acetate to remove excess phenol. The aqueous layer was heated to solubilize the product, cooled to room temperature and loaded onto a 200 mL cation exchange amberlite column activated with 50 mL of 2 N HCl. The column was then washed with 500 mL of distilled deionized water and the fluorotyrosines were eluted with 250 mL of 10% NH4OH. Fractions containing fluorotyrosine were identified using ninhydrin stain (4% ninhydrin), combined, concentrated using a rotary evaporator, lyophilized, and stored at 4 °C. This method was used to synthesize 2-fluoro-L-tyrosine (2-FY), 3-fluoro-L-tyrosine (3-FY), 2,3-difluoro-L-tyrosine (2,3-F2Y), 3,5-difluoro-L-tyrosine (3,5-F2Y), and 2,3,5-trifluoro-L-tyrosine (2,3,5-F3Y). During this process we discovered that the aqueous layer only had to be heated for purification of tyrosine because the lower pKa enabled solubilization of the modified tyrosines at room temperature. 2-FY, 3-FY, 2,3-F2Y, 3,5-F2Y, and 2,3,5-F3Y were characterized by mass spectrometry, 1H NMR, and 19F NMR spectroscopy (Figure S1 and S2).Preparation of AppABLUF(Y56F): Site-directed mutagenesis was used to introduce the Y56F mutation into a plasmid carrying the gene for AppABLUF (residues 5-125 in pet15b vector) using primers 5’-ACC GGC GCG CTC TTC TTC AGC CAG GGC GTC TTC-3’ (forward) and 5’-GAA GAC GCC CTG GCT GAA GAA GAG CGC GCC GGT-3’ (reverse). After verifying the sequence of the construct (AppABLUF(Y56F)), protein expression was performed as previously described. ADDIN EN.CITE <EndNote><Cite><Author>Stelling</Author><Year>2007</Year><RecNum>3356</RecNum><DisplayText><style face="superscript">9</style></DisplayText><record><rec-number>3356</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966219">3356</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Stelling, A. L.</author><author>Ronayne, K. L.</author><author>Nappa, J.</author><author>Tonge, P. J.</author><author>Meech, S. R.</author></authors></contributors><auth-address>Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.</auth-address><titles><title>Ultrafast structural dynamics in BLUF domains: transient infrared spectroscopy of AppA and its mutants</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>15556-64</pages><volume>129</volume><number>50</number><edition>2007/11/23</edition><keywords><keyword>Bacterial Proteins/*chemistry/genetics/*metabolism</keyword><keyword>Flavin-Adenine Dinucleotide/*chemistry/*metabolism</keyword><keyword>Flavoproteins/*chemistry/genetics/*metabolism</keyword><keyword>Kinetics</keyword><keyword>*Light</keyword><keyword>Molecular Structure</keyword><keyword>Mutation/*genetics</keyword><keyword>Spectrophotometry, Infrared</keyword><keyword>Time Factors</keyword></keywords><dates><year>2007</year><pub-dates><date>Dec 19</date></pub-dates></dates><isbn>1520-5126 (Electronic)
0002-7863 (Linking)</isbn><accession-num>18031038</accession-num><urls><related-urls><url> Briefly, the AppABLUF(Y56F) plasmid was transformed into BL21(DE3) E. coli cells and a single colony was used to inoculate a 10 mL culture of LB media containing 0.5 mM Amp. After incubating at 37 °C and 250 rpm overnight, this culture was used to inoculate 1 L of LB/Amp media in a 4 L flask. The 4 L flask was shaken at 37 °C until the OD600 reached ~ 0.8. Subsequently, the temperature was decreased to 18 °C followed by addition of 0.8 mM IPTG to induce protein expression overnight (16 h) in the dark. Incorporation of 2-FY: 2-FY is recognized by the tyrosyl–tRNA synthetase and can be incorporated by simply adding this amino acid analog to E. coli cells carrying the AppA plasmid and grown in minimal media. This method replaces every tyrosine in the expressed protein with 2-FY, and in order to incorporate 2-FY specifically into position 21, the Y56F AppA mutant (AppABLUF(Y56F)) was used to leave Y21 as the sole tyrosine. A single colony of BL21(DE3) E. coli cells carrying the AppABLUF(Y56F) plasmid was streaked on agar containing M9 minimal media, glucose (2.5 mg/mL) and Amp (200?g/mL). A colony from the M9 plate was then used to inoculate 500 mL of M9/Amp minimal media in a 4 L flask containing 5 g of sterile glucose and 5 mL of 100X MEM vitamin solution, which were added after autoclaving. The culture was shaken at 37 °C for 24 h until the OD600 reached ~ 0.8. The cells were then harvested by centrifugation, resuspended in fresh media containing 300 mg of 2-FY and incubated for a further 30 min at 18 °C. Subsequently 0.8 mM IPTG was used to induce protein expression for 5 h in the dark before harvesting. The cell pellet resulting from a 1 L culture was resuspended in 40 mL of buffer A (50 mM NaH2PO4, 10 mM NaCl, pH 8.0) to which was added 200 μL of the protease inhibitor, phenylmethanesulphonylfluoride (50 mM stock solution in ethanol), and 14 μL of β-mercaptoethanol. The cells were then lysed using sonication, cell debris was removed by centrifugation (33,000 rpm for 90 min), and the supernatant was incubated with 10 mg of FAD for 45 min on ice in the dark to ensure a homogeneous population of protein bound chromophore. Following incubation, the solution was loaded onto a Ni-NTA column (1x10 cm) that had been equilibrated with buffer A, and then washed with 50 mL of buffer A. The column was then washed with buffer A containing increasing concentrations of imidazole until AppABLUF(Y56F) 2-FY21 eluted at 250 mM imidazole. The fractions containing protein were pooled, dialyzed against buffer A overnight, and concentrated to 1.5 mM. Protein purity was assessed by SDS-PAGE and the chromophore content was determined from the ratio of the absorbance at 270 nm (protein and flavin) and 446 nm (flavin) (Figure S3). This ratio is 4.2 for wild-type AppABLUF (270 = 35,800 M-1 cm-1; 446 = 8,500 M-1cm-1). ADDIN EN.CITE <EndNote><Cite><Author>Laan</Author><Year>2004</Year><RecNum>3306</RecNum><DisplayText><style face="superscript">30</style></DisplayText><record><rec-number>3306</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966219">3306</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Laan, W.</author><author>Bednarz, T.</author><author>Heberle, J.</author><author>Hellingwerf, K. J.</author></authors></contributors><auth-address>Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Nieuwe Achtergracht 166, NL-1018 WV, Amsterdam, The Netherlands. Laan@science.uva.nl</auth-address><titles><title>Chromophore composition of a heterologously expressed BLUF-domain</title><secondary-title>Photochem Photobiol Sci</secondary-title></titles><periodical><full-title>Photochem Photobiol Sci</full-title><abbr-1>Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology</abbr-1></periodical><pages>1011-6</pages><volume>3</volume><number>11-12</number><keywords><keyword>Bacterial Proteins/chemistry/*genetics/radiation effects</keyword><keyword>Cloning, Molecular</keyword><keyword>Escherichia coli</keyword><keyword>Flavoproteins/chemistry/*genetics/radiation effects</keyword><keyword>Light</keyword><keyword>Recombinant Proteins/chemistry/radiation effects</keyword><keyword>Rhodobacter sphaeroides</keyword><keyword>Spectrometry, Fluorescence</keyword><keyword>Spectroscopy, Fourier Transform Infrared</keyword></keywords><dates><year>2004</year><pub-dates><date>Nov-Dec</date></pub-dates></dates><isbn>1474-905X (Print)
1474-905X (Linking)</isbn><accession-num>15570388</accession-num><urls><related-urls><url> To exchange the protein into D2O, samples of AppA were frozen in liquid N2, lyophilized overnight, re-dissolved in D2O, and allowed to incubate for 5 h after which this process was repeated 3-4 times. Both exchanged and unexchanged proteins were stored as lyophilized powders at 4 °C until needed. Percent incorporation of 2-fluorotyrosine was determined using a trypsin digest and MALDI mass spectroscopy showing >96% incorporation (Figure S4). Incorporation of fluorotyrosines using orthogonal aminoacyl-tRNA synthetases: In order to extend our study to fluorotyrosine analogs with lower pKa values, 3-FY, 2,3-F2Y, 3,5-F2Y and 2,3,5-F3Y were also incorporated into position 21 of AppABLUF(Y56F). These analogs are not recognized by tyrosyl–tRNA synthetase, and instead were introduced into the protein using two orthogonal polyspecific aminoacyl-tRNA synthetases, E3 and E11, generously provided by Prof. Stubbe. ADDIN EN.CITE <EndNote><Cite><Author>Minnihan</Author><Year>2011</Year><RecNum>3516</RecNum><DisplayText><style face="superscript">25</style></DisplayText><record><rec-number>3516</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3516</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Minnihan, E. C.</author><author>Young, D. D.</author><author>Schultz, P. G.</author><author>Stubbe, J.</author></authors></contributors><auth-address>Department of Chemistry and double daggerDepartment of Biology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.</auth-address><titles><title>Incorporation of Fluorotyrosines into Ribonucleotide Reductase Using an Evolved, Polyspecific Aminoacyl-tRNA Synthetase</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>15942-5</pages><volume>133</volume><number>40</number><edition>2011/09/15</edition><dates><year>2011</year><pub-dates><date>Oct 12</date></pub-dates></dates><isbn>1520-5126 (Electronic)
0002-7863 (Linking)</isbn><accession-num>21913683</accession-num><urls><related-urls><url> Since 2-FY was incorporated into the Y56F AppABLUF mutant, this variant was also used for the other fluorotyrosine analogs. Site-directed mutagenesis was first used to convert the codon for Y21 to the amber codon (TAG) in AppA(BLUF)(Y56F) 1-125. In addition, a C-terminal 6His-tag AppABLUF(Y56F) construct was used (pET20b) so that only protein with a fluorotyrosine incorporated at position 21 was able to bind to the Ni-NTA affinity purification resin. The AppABLUF(Y56F) plasmid with the Y21-TAG mutation was co-transformed into BL21(DE3) E.coli cells together with either the E3 or E11 pEVOL plasmid, and plated on LB agar containing both Amp (200 ?g/mL) and Cm (50 ?g/mL) to select cells harboring both plasmids. A colony from the LB/Amp/CM plate was used to start a 10 mL overnight culture, which was subsequently used to inoculate 500 mL 2XYT media containing Amp and Cm. The culture was grown until the OD600 reached ~ 0.4, and a fluorotyrosine analog dissolved with NaOH was added to the media to give a final concentration of ~1 mM. After ? hr incubation, 0.05% w/v arabinose was added to induce expression of the E3 or E11 synthetase. The culture was incubated at 37 °C (250 rpm) until the OD600 reached ~1.0, and then 0.8 mM IPTG was added to the media. After incubating overnight at 30 °C (250 rpm), the cells were harvested and purified using the same protocol as that described for the purification of AppABLUF(Y56F) 2-FY21 (above). Since a C-terminal His-tag is used, only fully translated protein can bind to the Ni-NTA resin, thus selecting against protein lacking an amino acid at position 21. Thus, as expected, MALDI analysis of tryptic peptides did not detect any native tyrosine in the fluorotyrosine substituted proteins except for the AppABLUF(Y56F) 3-FY21 where the sample contained ~1% of the native protein. Conservatively we estimate that the detection limit of this analytical method is 1% and so we are confident that the fluorotyrosine content of each variant was ≥99% (Figure S5). Time-resolved UV-Vis spectroscopy: Absorption spectra of each protein were obtained using an Ocean Optics USB2000+ spectrometer. This instrument collects spectra from 200-900 nm on the ms timescale using a diode array detector, with a minimum integration time of 10 ms. The white light source that was used during the recovery measurements was attenuated with a neutral density filter before it reached the sample to avoid saturating the spectrometer. In addition, it was shown that this source did not cause any photoconversion of the sample (Figure S6). Spectra of dark adapted AppABLUF(Y56F) and the fluorotyrosine substituted variants were first obtained, and then the sample was irradiated with ~500 mW of 455 (± 10) nm light until the photostationary state was generated. The light state spectrum were then acquired immediately after illumination was discontinued, except in the case of AppABLUF(Y56F) 2,3,5-F3Y which recovered so rapidly that the light state spectrum had to be acquired during illumination of the sample, resulting in an artefact in the light state spectrum around 455 nm due to scattered LED light. Subsequently, spectra were recorded as a function of time during the light to dark relaxation in the absence of irradiation. Time-resolved and steady-state FTIR spectroscopy: Light minus dark FTIR spectra were obtained with 1 cm-1 resolution on a Vertex 80v (Bruker) FTIR spectrometer using a Harrick liquid cell equipped with CaF2 windows and a 50 μm spacer. The light state was generated by 3 min irradiation using a 460 nm high power mounted LED (Prizmatix, Ltd.) placed in the sample compartment and focused onto the cell using an objective. The temperature of the sample holder was controlled using a circulating water bath and data were acquired at 20 °C. The spectrometer was operated in rapid scan mode to obtain spectra of the sample as a function of time once irradiation was initiated and then discontinued. This enabled the formation of the light state to be monitored and the rate of light state decay to be directly quantified. In each case a background spectrum of the dark adapted protein was acquired prior to initiating the photoreaction. Subsequently, light state formation was monitored by acquiring scans until the steady state was reached, and then recovery of the dark state was followed after terminating illumination. In general, scans were obtained every 200 ms. The background spectra were subtracted from the full dataset and time traces were fit to a single exponential function. The estimated rate constant for the recovery using rapid scan was determined from global analysis of the 1590 – 1710 cm-1. Measured protein samples were in D2O buffer (50 mM NaH2PO4, 10 mM NaCl, pD 8.0) at a concentration of ~ 1-2 mM where 80 μL of sample was used for each experiment.Ultrafast Time-Resolved Infrared Spectroscopy: Ultrafast time-resolved IR (TRIR) spectra were measured at the STFC Central Laser Facility with ~ 100 fs time resolution. ADDIN EN.CITE <EndNote><Cite><Author>Greetham</Author><Year>2010</Year><RecNum>3439</RecNum><DisplayText><style face="superscript">31</style></DisplayText><record><rec-number>3439</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966263">3439</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Greetham, G. M.</author><author>Burgos, P.</author><author>Cao, Q.</author><author>Clark, I. P.</author><author>Codd, P. S.</author><author>Farrow, R. C.</author><author>George, M. W.</author><author>Kogimtzis, M.</author><author>Matousek, P.</author><author>Parker, A. W.</author><author>Pollard, M. R.</author><author>Robinson, D. A.</author><author>Xin, Z. J.</author><author>Towrie, M.</author></authors></contributors><auth-address>Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0QX, UK. Greg.Greetham@stfc.ac.uk</auth-address><titles><title>ULTRA: A Unique Instrument for Time-Resolved Spectroscopy</title><secondary-title>Appl Spectrosc</secondary-title><alt-title>Applied spectroscopy</alt-title></titles><periodical><full-title>Appl Spectrosc</full-title></periodical><alt-periodical><full-title>Applied Spectroscopy</full-title><abbr-1>Appl. Spectrosc.</abbr-1></alt-periodical><pages>1311-9</pages><volume>64</volume><number>12</number><edition>2010/12/15</edition><dates><year>2010</year><pub-dates><date>Dec</date></pub-dates></dates><isbn>1943-3530 (Electronic)
0003-7028 (Linking)</isbn><accession-num>21144146</accession-num><urls><related-urls><url> TRIR spectra were acquired at 20 °C from 1400 – 1800 cm-1 at a resolution of 3 cm-1 per pixel. Data were obtained using a 50 ?m path length flow cell which was also rastered in the excitation beam in order to minimize photochemistry (photobleaching, photodegradation and photoconversion). The excitation beam of the 450 nm 100 fs 5 kHz pulses was focused to a spot size of ~ 100 μm and the pulse energy was kept below 400 nJ to avoid formation of the light state. Transient difference spectra (pump on – pump off) were recorded using the IR probe at time delays between 1 ps and 2 ns. After the measurements were recorded the extent of photoconversion was shown to be negligible using absorbance spectroscopy. Spectra were calibrated relative to the IR transmission of a pure cis stilbene standard sample placed at the sample position. Time Resolved Multiple Probe Spectroscopy (TRMPS): TRMPS spectra were obtained at 20 °C from 100 fs to 200 ?s at the STFC Central Laser Facility. ADDIN EN.CITE <EndNote><Cite><Author>Greetham</Author><Year>2009</Year><RecNum>62</RecNum><DisplayText><style face="superscript">32</style></DisplayText><record><rec-number>62</rec-number><foreign-keys><key app="EN" db-id="sxaxvw2tjdt2w5e22tkxp2tmrsxxrd5wf5es">62</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Greetham, Gregory M.</author><author>Burgos, Pierre</author><author>Cao, Qian</author><author>Clark, Ian P.</author><author>Codd, Peter S.</author><author>Farrow, Richard C.</author><author>George, Michael W.</author><author>Kogimtzis, Moschos</author><author>Matousek, Pavel</author><author>Parker, Anthony W.</author><author>Pollard, Mark R.</author><author>Robinson, David A.</author><author>Xin, Zhi-Jun</author><author>Towrie, Michael</author></authors></contributors><titles><title>ULTRA: A Unique Instrument for Time-Resolved Spectroscopy</title><secondary-title>Appl. Spectrosc.</secondary-title></titles><periodical><full-title>Appl. Spectrosc.</full-title></periodical><pages>1311-1319</pages><volume>64</volume><number>12</number><dates><year>2009</year></dates><publisher>OSA</publisher><urls><related-urls><url> The TRMPS method has been described, ADDIN EN.CITE <EndNote><Cite><Author>Greetham</Author><Year>2012</Year><RecNum>3457</RecNum><DisplayText><style face="superscript">33</style></DisplayText><record><rec-number>3457</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966280">3457</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Greetham, G. M.</author><author>Sole, D.</author><author>Clark, I. P.</author><author>Parker, A. W.</author><author>Pollard, M. R.</author><author>Towrie, M.</author></authors></contributors><auth-address>Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxfordshire, OX11 0QX, United Kingdom. greg.greetham@stfc.ac.uk</auth-address><titles><title>Time-resolved multiple probe spectroscopy</title><secondary-title>Rev Sci Instrum</secondary-title><alt-title>The Review of scientific instruments</alt-title></titles><periodical><full-title>Rev Sci Instrum</full-title><abbr-1>Rev Sci Instrum</abbr-1></periodical><pages>103107</pages><volume>83</volume><number>10</number><dates><year>2012</year><pub-dates><date>Oct</date></pub-dates></dates><isbn>1089-7623 (Electronic)
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ADDIN EN.CITE.DATA 15 Light sensitive samples were analysed using a rastered flow cell, and data were acquired using a 450 nm pump operated at 0.6-0.8 ?J per pulse and a repetition rate of 1 kHz. After the measurements were recorded, the extent of photoconversion was shown to be negligible using absorbance spectroscopy. The spectral resolution was 3 cm-1 and the temporal resolution was 200 fs. A typical measurement was acquired during 45 min of data collection. All samples were prepared at 1-2 mM concentration in D2O buffer (50 mM NaH2PO4, 10 mM NaCl, pD 8.0). Spectra were calibrated relative to the IR transmission of a pure cis stilbene standard sample placed at the sample position. Data were analysed globally using the sequential model with Glotaran. ADDIN EN.CITE <EndNote><Cite><Author>Snellenburg</Author><Year>2012</Year><RecNum>3508</RecNum><DisplayText><style face="superscript">34</style></DisplayText><record><rec-number>3508</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966296">3508</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Snellenburg, J. J.</author><author>Laptenok, S. P.</author><author>Seger, R.</author><author>Mullen, K. M.</author><author>van Stokkum, I. H. M.</author></authors></contributors><titles><title>Glotaran: A Java-Based Graphical User Interface for the R Package TIMP</title><secondary-title>J Stat Softw</secondary-title></titles><periodical><full-title>J Stat Softw</full-title></periodical><pages>1-22</pages><volume>49</volume><number>3</number><dates><year>2012</year><pub-dates><date>Jun</date></pub-dates></dates><isbn>1548-7660</isbn><accession-num>WOS:000305989900001</accession-num><urls><related-urls><url><Go to ISI>://WOS:000305989900001</url></related-urls></urls></record></Cite></EndNote>34RESULTSSynthesis and incorporation of fluorotyrosine residuesThe fluorotyrosine analogs were synthesized using tyrosine phenol lyase (TPL), which catalyzes the synthesis of tyrosine from phenol, ammonia and pyruvate.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NaW5uaWhhbjwvQXV0aG9yPjxZZWFyPjIwMTE8L1llYXI+
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ADDIN EN.CITE.DATA 21,25 TPL is able to accept a variety of tyrosine analogs, and this method was used to synthesize tyrosine substituted with fluorine at the 2 (2-FY), 3 (3-FY), 2,3 (2,3-F2Y), 3,5 (3,5-F2Y), and 2,3,5 (2,3,5-F3Y) positions. 2-FY was incorporated into position Y21 by feeding to bacteria expressing AppABLUF(Y56F), whereas the other fluorotyrosine analogs were incorporated into position 21 by amber codon mutagenesis using the E3 and E11 aminoacyl-tRNA synthetases. ADDIN EN.CITE <EndNote><Cite><Author>Minnihan</Author><Year>2011</Year><RecNum>3516</RecNum><DisplayText><style face="superscript">25</style></DisplayText><record><rec-number>3516</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3516</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Minnihan, E. C.</author><author>Young, D. D.</author><author>Schultz, P. G.</author><author>Stubbe, J.</author></authors></contributors><auth-address>Department of Chemistry and double daggerDepartment of Biology, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.</auth-address><titles><title>Incorporation of Fluorotyrosines into Ribonucleotide Reductase Using an Evolved, Polyspecific Aminoacyl-tRNA Synthetase</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>15942-5</pages><volume>133</volume><number>40</number><edition>2011/09/15</edition><dates><year>2011</year><pub-dates><date>Oct 12</date></pub-dates></dates><isbn>1520-5126 (Electronic)
0002-7863 (Linking)</isbn><accession-num>21913683</accession-num><urls><related-urls><url> The AppABLUF(Y56F) mutant was used so that feeding experiments only introduced 2-FY into position 21. Prior to these studies we first demonstrated that AppABLUF(Y56F) had a photocycle indistinguishable from that of the wild-type protein (Figure S5), in agreement with the findings of Iwata et al. ADDIN EN.CITE <EndNote><Cite><Author>Iwata</Author><Year>2011</Year><RecNum>4435</RecNum><DisplayText><style face="superscript">35</style></DisplayText><record><rec-number>4435</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1439866590">4435</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Iwata, T.</author><author>Watanabe, A.</author><author>Iseki, M.</author><author>Watanabe, M.</author><author>Kandori, H.</author></authors></contributors><titles><title>Strong Donation of the Hydrogen Bond of Tyrosine during Photoactivation of the BLUF Domain</title><secondary-title>J Phys Chem Lett</secondary-title></titles><periodical><full-title>J Phys Chem Lett</full-title><abbr-1>J Phys Chem Lett</abbr-1></periodical><pages>1015-1019</pages><volume>2</volume><number>9</number><dates><year>2011</year><pub-dates><date>May</date></pub-dates></dates><isbn>1948-7185</isbn><accession-num>WOS:000290372900017</accession-num><urls><related-urls><url><Go to ISI>://WOS:000290372900017</url></related-urls></urls><electronic-resource-num>10.1021/jz2003974</electronic-resource-num></record></Cite></EndNote>35 All proteins contained ≥ 99% fluorotyrosine based on MALDI mass spectrometry (Figure S4 and S5). Following purification, each labeled protein had an absorption spectrum indistinguishable from that of dark-adapted wild-type AppABLUF. In addition the absorbance spectrum of all five variants shifted to the red upon irradiation and then relaxed back to the position observed in the dark state, indicating that the proteins were photoactive. Representative data are shown in Figure 2.Analysis of the forward photoreaction As an initial step in gauging the impact of the fluorotyrosine substitutions on the photophysics of AppA, we characterized the forward photoreaction using ultrafast TRIR and time resolved multiple probe infrared spectroscopy (TRMPS).PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5CcnVzdDwvQXV0aG9yPjxZZWFyPjIwMTM8L1llYXI+PFJl
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ADDIN EN.CITE.DATA 15 Both TRIR and TRMPS are time-resolved infrared difference techniques that report on changes in the infrared spectrum of the chromophore and protein following photoexcitation, the main difference being that TRIR covers the ps to ns time domain whereas TRMPS makes measurements out to 1 ms. ADDIN EN.CITE <EndNote><Cite><Author>Greetham</Author><Year>2012</Year><RecNum>3457</RecNum><DisplayText><style face="superscript">33</style></DisplayText><record><rec-number>3457</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966280">3457</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Greetham, G. M.</author><author>Sole, D.</author><author>Clark, I. P.</author><author>Parker, A. W.</author><author>Pollard, M. R.</author><author>Towrie, M.</author></authors></contributors><auth-address>Central Laser Facility, Science and Technology Facilities Council, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Oxfordshire, OX11 0QX, United Kingdom. greg.greetham@stfc.ac.uk</auth-address><titles><title>Time-resolved multiple probe spectroscopy</title><secondary-title>Rev Sci Instrum</secondary-title><alt-title>The Review of scientific instruments</alt-title></titles><periodical><full-title>Rev Sci Instrum</full-title><abbr-1>Rev Sci Instrum</abbr-1></periodical><pages>103107</pages><volume>83</volume><number>10</number><dates><year>2012</year><pub-dates><date>Oct</date></pub-dates></dates><isbn>1089-7623 (Electronic)
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ADDIN EN.CITE.DATA 15 and in general TRIR was used only to confirm the sub-ns dynamics characterized by TRMPS. In Figure 3A we show the time evolution of the transient IR spectrum of AppABLUF(Y56F) following 450 nm excitation of the flavin (isoalloxazine) chromophore. Negative bands (bleaches) appearing at time zero are due to vibrational modes arising from photoinduced changes of the chromophore ground state, or from structural changes to the protein caused by photoexcitation. Positive bands (transients) arise from the electronic excited state of the chromophore, or from photoinduced changes in the protein modes. The TRMPS spectrum of AppABLUF(Y56F) is identical to that of wild-type AppABLUF (Figure S7). Major bleaches in the spectrum that appear within the time resolution of the experiment are observed at 1700, 1650, 1583 and 1548 cm-1. These bands have previously been assigned to the flavin C4=O and C2=O carbonyl groups (1700, 1650 cm-1) as well as C-N vibrations of the isoalloxazine ring (1583 and 1548 cm-1). In addition, several transients also appear instantaneously at 1383, 1420, 1610, 1630 and 1650 cm-1. The 1383 and 1420 cm-1 bands are excited state modes of the chromophore, whilst those at 1600 and 1630 cm-1 are protein modes perturbed upon excitation. As discussed previously, most of the flavin population has relaxed back to the electronic ground state by ~ 1 ns. This sub-nanosecond relaxation is adequately fit by a sum of two exponential functions (τ1 = 0.012 and τ2 = 0.145 ns) indicating the presence of more than one ground state structure with different relaxation rates (Figure 3, 4; Table 1). The spectrum that remains at 1 ns and 3 μs provides an estimate of the amount of the excited state that partitions to the light state. Analysis of the high wavenumber bleaches indicates that about 5% of the intensity remains at 1 ns and 3 μs compared to the intensity of the spectrum formed instantaneously following photoexcitation. This suggests a quantum yield significantly lower for both AppABLUF(Y56F) as well as wild-type AppABLUF than the value of 24% reported previously.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5HYXVkZW48L0F1dGhvcj48WWVhcj4yMDA1PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 36 The subsequent evolution of the spectrum remaining after 1 ns results from the structural dynamics in the protein leading to the final ground state photoactivated protein (lAppA). This evolution, from 1 ns to ~20 μs can again be adequately described by two exponential functions with time constants of 1 (τ3) and 3000 (τ4) ns (Figure 3, 4; Table 1). Evidence that the spectral evolution is complete by 40 μs is shown by the similarity between the TRMPS difference spectrum at 40 ?s for each protein and the corresponding steady state FTIR difference spectrum of AppABLUF(Y56F) (Figure 3C). For further comparison the TRMPS difference spectra of AppABLUF between 50 μs and 200 μs are included in Figure S8. The TRMPS data for AppABLUF(Y56F) are compared with the corresponding spectra of the fluorotyrosine-substituted proteins (Figure S9). The corresponding rate constants for spectral evolution obtained from the global analysis are given in Table 1. Two conclusions can be drawn from the data. Firstly the positions and amplitudes of the major bleaches and transients for each fluorotyrosine protein closely match those of AppABLUF(Y56F) suggesting that the incorporation of the unnatural amino acids has not had a significant effect on the protein structure and its interactions with the chromophore. Secondly, in each case spectral evolution can be adequately described by 4 rate constants, 2 for the initial sub-nanosecond ground state recovery, and 2 for the subsequent formation of the final photoactivated ground state. Thus, the inhomogeneity observed in wild-type AppABLUF as well as AppABLUF(Y56F), is also present for the fluorotyrosine mutants (Figures S7 and S9). Table 1 reveals a small effect resulting from alteration in the pKa and reduction potential of residue 21: as the pKa decreases by ~ 3.5 units from Y21 to 2,3,5-F3Y21 and the reduction potential Ep(Y●/Y?) increases by ~ 200mV, ADDIN EN.CITE <EndNote><Cite><Author>Seyedsayamdost</Author><Year>2006</Year><RecNum>3512</RecNum><DisplayText><style face="superscript">21</style></DisplayText><record><rec-number>3512</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966312">3512</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Seyedsayamdost, M. R.</author><author>Reece, S. Y.</author><author>Nocera, D. G.</author><author>Stubbe, J.</author></authors></contributors><auth-address>Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139-4307, USA.</auth-address><titles><title>Mono-, di-, tri-, and tetra-substituted fluorotyrosines: new probes for enzymes that use tyrosyl radicals in catalysis</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>1569-79</pages><volume>128</volume><number>5</number><edition>2006/02/02</edition><keywords><keyword>Catalysis</keyword><keyword>Escherichia coli/enzymology</keyword><keyword>Hydrogen-Ion Concentration</keyword><keyword>Kinetics</keyword><keyword>Nuclear Magnetic Resonance, Biomolecular</keyword><keyword>Oxidation-Reduction</keyword><keyword>Ribonucleotide Reductases/*chemistry/metabolism</keyword><keyword>Spectrophotometry, Ultraviolet</keyword><keyword>Tyrosine/*analogs & derivatives/chemistry/metabolism</keyword></keywords><dates><year>2006</year><pub-dates><date>Feb 8</date></pub-dates></dates><isbn>0002-7863 (Print)
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ADDIN EN.CITE.DATA 17Dark State RecoveryRecovery of the AppABLUF dark state was monitored using both absorption spectroscopy and rapid scan FTIR spectroscopy. Formation of the light state results in a red shift in the 450 nm flavin spectrum and the rate of dark state recovery was measured by following the relaxation of the red shifted spectrum using a spectrometer with a 1 ms time resolution (Figure 2 and 5). The recovery rate was measured in both H2O and D2O buffer (Table 2), and as a function of pH, by fitting the absorbance change measured at 480 – 510 nm to a single exponential equation (Table S1). We also used difference FTIR spectroscopy to monitor relaxation of the dark state for two representative variants, wild-type and AppABLUF(Y56F) 2,3-F2Y21. In both cases there was good correspondence between the rates obtained from FTIR with those determined from the UV-vis absorption spectra (Figure 5D). This indicates that the change in the electronic spectrum of the flavin and alteration in the protein structure observed by FTIR are reporting on the same structural change in the protein. The representative series of the recovery spectra taken for AppABLUF(Y56F) 2,3-F2Y21 using the rapid scan mode are shown in Figure S10. Variation of the pH had only a small impact on the rate of dark state recovery (Table S1), as reported previously for WT AppABLUF.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwMzwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 10 However, while modulation in the pKa of residue 21 had little effect on the forward reaction, the rate of dark state recovery in H2O increased 4,000-fold as the pKa decreased from 9.9 (Y21) to 6.4 (2,3,5-F3Y21). A plot of pKa against the log of the first order rate constant yielded a straight line (R = 0.99) with a slope of ~1.0 (Figure 6), consistent with a rate limiting proton transfer in the mechanism of dark state recovery. The Br?nsted coefficient of 1.0 indicates that the proton is completely transferred in the rate-limiting transition state. The Br?nsted plot in D2O was also linear with a slope of 1.09. The observation of a solvent isotope effect (SIE) on dark state recovery is consistent with previous reports for AppA (SIE 2-4.7)PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA1PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 37,38 supporting the importance of proton transfer in this step. The data in Table 2 also reveal a significant solvent isotope effect for dark state recovery that ranges from 5 for AppABLUF(Y56F) to almost 9 for 3-FY21 and to 2.3 for 2,3,5-F3Y21. DISCUSSIONAll BLUF-containing photoreceptors so far characterized operate through light driven formation of the photoactive state followed by recovery of the dark state through a light-independent reaction. Formation of the light state occurs rapidly and is complete within ~10’s of microseconds. Various mechanisms have been proposed for the forward reaction and for the best characterized BLUF protein AppA our data support a model in which the initial event involves light-induced keto-enol tautomerism of a conserved glutamine (Q63) leading ultimately to an alteration in the hydrogen bonding network that surrounds the flavin chromophore. In contrast to the rapid light-driven photoactivation, recovery of the dark state occurs through a light-independent pathway with a half-life of seconds to minutes depending on the specific BLUF protein. For AppA, dark state recovery occurs with a half-life of about 18 min. Previous studies on dark state recovery have provided evidence for rate limiting proton transfer through the observation of solvent isotope effects for AppA and PixD. However little else is known about the mechanism of dark state recovery.In the present work we have replaced Y21 with a series of mono, di and tri-substituted fluorotyrosines that range in pKa from 9.9 (Y21) to 6.4 (2,3,5-F3Y21). These experiments were performed in the AppABLUF(Y56F) background so that only Y21 was replaced in the one variant (2-FY) that could not be produced via amber codon mutagenesis. The similarities in the vibrational peak positions from the time-resolved (TRMPS) and steady-state IR difference spectra obtained for the different variants suggests that the fluorine substituents do not significantly perturb the overall environment of the flavin or the protein structure. The forward photoreaction was examined using TRMPS and revealed a ~ 3 fold increase in the time constants that characterize spectral evolution over ~7 decades in time (1 ps to 20 μs). Thus the ~3,200-fold change in tyrosine acidity and 200 mV change in reduction potential has only a ~3-fold modest impact on the rate of light state formation, suggesting that proton or electron transfer to or from the hydroxyl group of this residue does not play a significant role in the rate determining step(s) that lead to formation of the signaling state of the protein.In contrast to the forward reaction, the rate of dark state recovery exhibits a very strong dependence on acidity of the Y21 hydroxyl group. Specifically, the increase in Y21 acidity through the fluorotyrosine series correlates with a 4,000-fold increase in the rate of recovery in H2O and 8,800-fold increase in the rate in D2O. This correlation is well described by a linear free energy relationship with a Br?nsted coefficient of 1.0, indicating a direct connection between Y21 acidity and the mechanism of dark state recovery (Figure 6). In addition, the Br?nsted coefficient of 1 indicates complete proton transfer in the rate-limiting transition state on the reaction coordinate leading from light to dark AppABLUF. The above data allow us to propose a detailed mechanism for the light to dark state recovery of wild-type AppA (Figure 7) where proton transfer from Y21 to Q63 is hypothesized to be the rate determining step in the recovery. In formulating this model we assume that the Q63 side chain has rotated during formation of the light statePEVuZE5vdGU+PENpdGU+PEF1dGhvcj5KdW5nPC9BdXRob3I+PFllYXI+MjAwNjwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 6,12 and that, like the photoactivation mechanism (Figure 1), the recovery mechanism also involves keto-enol tautomerism. In addition, although several theoretical studiesPEVuZE5vdGU+PENpdGU+PEF1dGhvcj5TYWRlZ2hpYW48L0F1dGhvcj48WWVhcj4yMDA4PC9ZZWFy
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ADDIN EN.CITE.DATA 39-42 support our original proposal ADDIN EN.CITE <EndNote><Cite><Author>Stelling</Author><Year>2007</Year><RecNum>3356</RecNum><DisplayText><style face="superscript">9</style></DisplayText><record><rec-number>3356</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966219">3356</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Stelling, A. L.</author><author>Ronayne, K. L.</author><author>Nappa, J.</author><author>Tonge, P. J.</author><author>Meech, S. R.</author></authors></contributors><auth-address>Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA.</auth-address><titles><title>Ultrafast structural dynamics in BLUF domains: transient infrared spectroscopy of AppA and its mutants</title><secondary-title>J Am Chem Soc</secondary-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><pages>15556-64</pages><volume>129</volume><number>50</number><edition>2007/11/23</edition><keywords><keyword>Bacterial Proteins/*chemistry/genetics/*metabolism</keyword><keyword>Flavin-Adenine Dinucleotide/*chemistry/*metabolism</keyword><keyword>Flavoproteins/*chemistry/genetics/*metabolism</keyword><keyword>Kinetics</keyword><keyword>*Light</keyword><keyword>Molecular Structure</keyword><keyword>Mutation/*genetics</keyword><keyword>Spectrophotometry, Infrared</keyword><keyword>Time Factors</keyword></keywords><dates><year>2007</year><pub-dates><date>Dec 19</date></pub-dates></dates><isbn>1520-5126 (Electronic)
0002-7863 (Linking)</isbn><accession-num>18031038</accession-num><urls><related-urls><url> for Q63 keto-enol tautomerism occurring during photoactivation, in the model proposed here we assume that final ground state structures in both dark and light-adapted AppA is the more stable keto tautomer. In the light state keto tautomer (i) (lAppAketo) Y21 is hydrogen bonded to the Q63 carbonyl group, consistent with NMR data that shows the presence of a well-defined hydrogen bond between Y21 and a neighboring residue. ADDIN EN.CITE <EndNote><Cite><Author>Grinstead</Author><Year>2006</Year><RecNum>3295</RecNum><DisplayText><style face="superscript">43</style></DisplayText><record><rec-number>3295</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966219">3295</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Grinstead, J. S.</author><author>Avila-Perez, M.</author><author>Hellingwerf, K. J.</author><author>Boelens, R.</author><author>Kaptein, R.</author></authors></contributors><auth-address>Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</auth-address><titles><title>Light-induced flipping of a conserved glutamine sidechain and its orientation in the AppA BLUF domain</title><secondary-title>J. Am. Chem. Soc.</secondary-title></titles><periodical><full-title>J. Am. Chem. Soc.</full-title><abbr-1>J. Am. Chem. Soc.</abbr-1></periodical><pages>15066-7</pages><volume>128</volume><number>47</number><keywords><keyword>Bacterial Proteins/ chemistry</keyword><keyword>Conserved Sequence</keyword><keyword>Flavin-Adenine Dinucleotide/chemistry</keyword><keyword>Flavoproteins/ chemistry</keyword><keyword>Glutamine/chemistry</keyword><keyword>Kinetics</keyword><keyword>Light</keyword><keyword>Models, Molecular</keyword><keyword>Nuclear Magnetic Resonance, Biomolecular</keyword><keyword>Photochemistry</keyword><keyword>Photoreceptors, Microbial/ chemistry</keyword><keyword>Protein Conformation</keyword><keyword>Protein Structure, Tertiary</keyword></keywords><dates><year>2006</year><pub-dates><date>Nov 29</date></pub-dates></dates><isbn>0002-7863 (Print)</isbn><accession-num>17117839</accession-num><urls><related-urls><url> In the rate-determining step, we suggest that Y21 protonates Q63 leading to formation of the Q63 enol. This is envisaged in Figure 7 as proton transfer to the enolate resonance form of the Q63 sidechain (ii). After formation of the enol (iv), Q63 rotates, breaking the hydrogen bond to the C4=O of the flavin, and forming a new hydrogen bond with the flavin N5 atom (v). The last step involves a second tautomerization to return to the more stable keto state of Q63 (vi). In our mechanism we assign (iv) to lAppAenol and (v) to dAppAenol although we do not know at what stage the protein structure will relax back to that found in the dark state. In (v) Y21 will now be solvent accessible and thus able to abstract a proton from the solvent. Abstraction of the proton from Y21 by Q63 (ii to iv) is the rate determining step of the light to dark recovery, consistent with the isotope effect observed for recovery in deuterated buffer. In addition, the Br?nsted coefficient of 1 indicates that proton transfer is complete in the rate-limiting transition state (iii). This mechanism also enables us to envisage a role for a base such as imidazole, which has been shown to accelerate the rate of dark state recovery.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwNjwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 8 For instance, general base catalysis could assist in the formation of the enol species (iv) by abstracting a proton from the Q63 NH2 group. While the mechanism in Figure 7 rationalizes the essential role that Y21 plays in the AppA photocycle, it also provides a basis for discussing the impact of W104 on light to dark state recovery. Although W104 is critical for coupling the change in the hydrogen bonding network around the flavin to the alteration in protein structure that accompanies photoactivation, the exact position of W104 in the dark and light states is controversial (see Collette et al. ADDIN EN.CITE <EndNote><Cite><Author>Collette</Author><Year>2014</Year><RecNum>3871</RecNum><DisplayText><style face="superscript">42</style></DisplayText><record><rec-number>3871</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1409501115">3871</key><key app="ENWeb" db-id="">0</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Collette, F.</author><author>Renger, T.</author><author>Schmidt Am Busch, M.</author></authors></contributors><titles><title>Revealing the Functional States in the Active Site of BLUF Photoreceptors from Electrochromic Shifts Calculations</title><secondary-title>J Phys Chem B</secondary-title><alt-title>The journal of physical chemistry. B</alt-title></titles><periodical><full-title>J Phys Chem B</full-title></periodical><dates><year>2014</year><pub-dates><date>Aug 25</date></pub-dates></dates><isbn>1520-5207 (Electronic)
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ADDIN EN.CITE.DATA 14 suggests that W104 interacts with Q63 to either stabilize the keto form of lAppA (i) and/ or destabilize the rate limiting transition state (iii) involved in the proton transfer step. This would suggest that W104 is close to Q63 in the light state, potentially arguing against large scale motion of W104 during photoactivation such that W104 occupies a Trpin conformation in both dark and light states, or that W104 is in the ‘out’ configuration in the dark state and in the ‘in’ configuration in the light state. Finally we can return to the solvent isotope effect on dark state recovery. Apart from 2,3,5-F3Y AppABLUF(Y56F), the solvent isotope effect ranges from ~5-9 which is unusually large for a single proton transfer step. However, conversion of the light state to the dark state must be coupled to an alteration in the conformation of the protein, since only dark adapted AppA is able to bind the transcriptional repressor PpsR, and in this regard we note that large solvent isotope effects have been reported for protein conformational changes. ADDIN EN.CITE <EndNote><Cite><Author>Wang</Author><Year>1975</Year><RecNum>4442</RecNum><DisplayText><style face="superscript">44</style></DisplayText><record><rec-number>4442</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1440187113">4442</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Wang, M. S.</author><author>Gandour, R. D.</author><author>Rodgers, J.</author><author>Haslam, J. L.</author><author>Schowen, R. L.</author></authors></contributors><auth-address>Univ Kansas,Dept Chem,Lawrence,Ks 66045</auth-address><titles><title>Transition-State Structure for a Conformation Change of Ribonuclease</title><secondary-title>Bioorg Chem</secondary-title><alt-title>Bioorg Chem</alt-title></titles><periodical><full-title>Bioorg Chem</full-title></periodical><alt-periodical><full-title>Bioorg Chem</full-title></alt-periodical><pages>392-406</pages><volume>4</volume><number>4</number><dates><year>1975</year><pub-dates><date>1975</date></pub-dates></dates><isbn>0045-2068</isbn><accession-num>WOS:A1975BF70700009</accession-num><urls><related-urls><url><Go to ISI>://WOS:A1975BF70700009</url></related-urls></urls><electronic-resource-num>Doi 10.1016/0045-2068(75)90050-4</electronic-resource-num><language>English</language></record></Cite></EndNote>44 The present studies have focused on the BLUF domain of AppA and one important extension of this work will be to explore how variation in tyrosine pKa modulates the forward and reverse reactions in the context of full-length AppA and the AppA:PpsR2 complex. In parallel, additional experiments will seek to determine whether the mechanism proposed here for AppABLUF translates to other BLUF proteins. Solvent isotope effects are also observed on the rate of dark state recovery for the BLUF proteins PixD (4)PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5NYXN1ZGE8L0F1dGhvcj48WWVhcj4yMDA0PC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 46 Thus significant differences may exist in the mechanism of dark state recovery throughout the BLUF domain family.SUMMARYWe have used unnatural amino acid incorporation to probe the mechanism of photoactivation and ground state recovery in AppA. The vibrational spectra recorded in TRMPS demonstrate that replacement of Y21 with fluorotyrosine analogues neither causes a structural perturbation in the environment of the flavin chromophore nor greatly modifies the forward photokinetics. Modulation of the Y21 pKa does, however, have a dramatic effect on the rate of light to dark state recovery following AppA photoactivation, where an increase in Y21 acidity is found to correlate with an increase in the recovery rate. A Br?nsted analysis of the data indicates that the Y21 proton is almost completely transferred in the transition state leading from the light to the dark state. Rate limiting proton transfer is consistent with the solvent isotope effect reported previously and has been incorporated into a mechanism for AppA recovery that involves tautomerization of residue Q63. This light to dark ground state recovery mechanism, which highlights the importance of Y21 in the photocycle, has not been elucidated previously. The ability to control the light to dark recovery rate may have great importance in optogenetic applications of the BLUF photosensors, since the delay in recovery and/or life-time of the signaling state could directly influence the magnitude and duration of downstream biological events triggered by photoactivation.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5CYWNjaHVzPC9BdXRob3I+PFllYXI+MjAxMjwvWWVhcj48
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ADDIN EN.CITE.DATA 47,48 ASSOCIATED CONTENTSupporting Information Available: Analytical data (MS, 1H NMR, and 19F NMR) for the synthesized fluorotyrosines: 2-FY, 3-FY, 2,3-F2Y, 3,5-F2Y, and 2,3,5-F3Y. Full UV-Vis spectrum of AppABLUF(Y56F) in the dark state showing the ratio of the absorbance of 260 nm to 446 nm. MALDI mass analysis of fluorotyrosine incorporation into AppABLUFY56F. Time-resolved UV-Vis control absorbance measurements. Additional TRMPS datasets and pH dependence on the recovery of the dark state. Rapid scan FTIR representative spectra. This material is available free of charge via the Internet at . AUTHOR INFORMATIONCorresponding Authors*PJT: Telephone: (631) 632-7907; Fax: (631) 632-7960; Email: peter.tonge@stonybrook.edu; SRM:44(0)1603 593141; Fax: 44(0)1603 592004; Email: s.meech@uea.ac.ukACKNOWLEDGMENTFunded by the EPSRC (EP/G002916 to SRM) and NSF (CHE-1223819 to PJT). We are grateful to STFC for access to the ULTRA laser facility. We are grateful to Professor Ray Owens and Anil Verma for assistance in protein preparation and access to the Oxford Protein Production Facility – UK. JI was supported by an NIH Chemistry-Biology Interface training grant (T32GM092714).REFERENCES ADDIN EN.REFLIST (1) Gomelsky, M.; Klug, G. Trends Biochem Sci 2002, 27, 497.(2) Okajima, K.; Yoshihara, S.; Fukushima, Y.; Geng, X.; Katayama, M.; Higashi, S.; Watanabe, M.; Sato, S.; Tabata, S.; Shibata, Y.; Itoh, S.; Ikeuchi, M. J Biochem 2005, 137, 741.(3) Zirak, P.; Penzkofer, A.; Schiereis, T.; Hegemann, P.; Jung, A.; Schlichting, I. J Photochem Photobiol B 2006, 83, 180.(4) Rajagopal, S.; Key, J. M.; Purcell, E. B.; Boerema, D. J.; Moffat, K. Photochem Photobiol 2004, 80, 542.(5) van der Horst, M. A.; Hellingwerf, K. J. Acc Chem Res 2004, 37, 13.(6) Anderson, S.; Dragnea, V.; Masuda, S.; Ybe, J.; Moffat, K.; Bauer, C. Biochemistry 2005, 44, 7998.(7) Masuda, S.; Bauer, C. E. 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Spectral evolution from the TRMPS data.τ1 /nsτ2 /nsτ3 /nsτ4 /nsAppABLUF(Y56F)0.0120.1451.030002-FY21 AppABLUF(Y56F)0.030.331.548503-FY21 AppABLUF(Y56F)0.0160.422.641502,3-F2Y21 AppABLUF(Y56F)0.080.542.472002,3,5-F2Y21 AppABLUF(Y56F)0.0650.62.78200Data were globally analyzed using Glotaran, ADDIN EN.CITE <EndNote><Cite><Author>Snellenburg</Author><Year>2012</Year><RecNum>3508</RecNum><DisplayText><style face="superscript">34</style></DisplayText><record><rec-number>3508</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966296">3508</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Snellenburg, J. J.</author><author>Laptenok, S. P.</author><author>Seger, R.</author><author>Mullen, K. M.</author><author>van Stokkum, I. H. M.</author></authors></contributors><titles><title>Glotaran: A Java-Based Graphical User Interface for the R Package TIMP</title><secondary-title>J Stat Softw</secondary-title></titles><periodical><full-title>J Stat Softw</full-title></periodical><pages>1-22</pages><volume>49</volume><number>3</number><dates><year>2012</year><pub-dates><date>Jun</date></pub-dates></dates><isbn>1548-7660</isbn><accession-num>WOS:000305989900001</accession-num><urls><related-urls><url><Go to ISI>://WOS:000305989900001</url></related-urls></urls></record></Cite></EndNote>34 and in each case 4 time constants plus the final spectrum were required to adequately describe the data.Table 2. Dark state recovery rate constants.pKakH2O /s-1kD2O /s-1Solvent isotope effectAppABLUF(Y56F)9.90.00065 0.000060.00013 0.000015.0 1 2-FY21 AppABLUF(Y56F)9.00.011 0.0010.0018 0.00026.2 1.23-FY21 AppABLUF(Y56F)8.40.034 0.0020.0039 0.00018.8 0.72,3-F2Y21 AppABLUF(Y56F)7.80.22 0.010.040 0.0015.5 0.23,5-F2Y21 AppABLUF(Y56F)7.20.63 0.020.11 0.015.8 0.32,3,5-F3Y21 AppABLUF(Y56F)6.42.6 0.11.15 0.032.2 0.1Recovery rate constants were obtained from the change in absorption spectra once irradiation at 455 nm had been terminated by fitting the data to a single exponential function. Errors are based on measurements made in triplicate or quadruplicate. Recovery rates were also measured in D2O for the wild-type and AppABLUF(Y56F) 2,3-F2Y21 using fast scan FTIR. The rate constants obtained from fitting of the FTIR data were 0.00015 and 0.038 respectively which agrees within experimental error to those measured by monitoring the change in the electronic spectrum of the flavin.FIGURES Figure 1. Mechanism of AppA Light State Formation.The flavin chromophore is surrounded by a hydrogen bonding network that includes Y21, Q63, W014. W104 is shown close to the hydrogen bonding network in both the dark and light states, however the position of this residue in both states remains to be fully elucidated. Photoactivation of dark adapted AppA (dAppA) is proposed to proceed via keto-enol tautomerism of Q63 resulting ultimately in rotation of Q63 in the light state (lAppA).PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MdWthY3M8L0F1dGhvcj48WWVhcj4yMDExPC9ZZWFyPjxS
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ADDIN EN.CITE.DATA 9,16 Hydrogen bonds are shown as dashed lines and formation of lAppA results in an additional hydrogen bond with the flavin C4=O.Figure 2. Absorption Spectra of fluorotyrosine-substituted AppABLUF(Y56F).A: Comparison of the absorption spectra of wild-type AppABLUF(Y56F), and the fluorotyrosine-substituted variants in the dark state. The dark state spectra of all the fluorotyrosine-substituted proteins are very similar to each other and to that of wild-type AppABLUF(Y56F). B: Light adapted absorption spectra of wild-type AppABLUF(Y56F), and the fluorotyrosine-substituted variants measured at the photostationary state. In each case the flavin absorption spectrum was found to red shift relative to the dark state spectra (dashed). The extent of the red shift varied for each protein based on the different photostationary state, which in-turn depends on irradiation intensity and the rate of recovery of the dark state. The trace for AppABLUF(Y56F) 2,3,5-F3Y21 has lower signal:noise because of the very fast light to dark recovery (see experimental). Protein concentrations were ~ 60 μM and the absorption spectra have been normalized. Figure 3. TRMPS and steady state IR Spectra of dAppABLUF(Y56F).A: Temporal evolution of transient IR data for wild-type AppABLUF(Y56F). B: Evolution associated difference spectra (EADS) of wild-type AppABLUF(Y56F). Data were globally analyzed using the sequential model. The four time constants required (in addition to a final spectrum) to adequately describe the data were : 11 ps, 145 ps, 1 ns and 3 μs. C: Comparison of the spectra at 40 ?s for wild-type and 2-FY21, 2,3-F2Y21 and 2,3,5-F3Y21 AppABLUF(Y56F), together with the steady state FTIR difference spectrum of wild-type AppABLUF(Y56F).Figure 4. Ground state recovery at 1548 cm-1 from the TRMPS data.The dashed lines are the results of global analysis and the solid lines are the raw data. The first ns of the data are plotted on a linear scale while the remainder are plotted on a logarithmic scale. The time constants for each protein are given in Table 1. Figure 5. Dark state recovery kinetics.Dark state recovery kinetics were obtained by monitoring the visible absorption spectrum of AppA. A: spectral evolution of AppABLUF(Y56F), following irradiation at 455 nm. B: Recovery kinetics in D2O buffer. C: Comparison of the recovery kinetics in H2O and D2O buffer for selected proteins. D: Comparison of the recovery kinetics of AppABLUF(Y56F) 2,3-F2Y21 in D2O obtained by monitoring the change in electronic absorption spectrum (estimated recovery rate 0.04 s-1) or the change in the FTIR spectrum at 1686 cm-1 (estimated recovery rate 0.038 s-1 from global analysis of the 1590 – 1710 cm-1 spectral region) as a function of time. In each case time constants for the recovery kinetics were obtained by fitting the data to a single exponential function. Protein concentration was ~ 60 μM for the UV-vis absorption measurements or ~ 1.5 mM for the FTIR spectroscopy. Figure 6: Br?nsted plots in H2O and D2O.Recovery rate constants (log k) for the AppABLUF(Y56F) variants plotted against the corresponding ?pKa values for tyrosine and the fluorotyrosines. Data have been fit to a linear function. A: Data obtained in D2O (pD 8.0). B: Data obtained in H2O (pH 8.0). Figure 7. Mechanism of light to dark state recovery in AppABLUF. In the ground state of lAppABLUF the Q63 side chain exists as a mixture of keto (i) and enol (ii) resonance structures. ADDIN EN.CITE <EndNote><Cite><Author>Lukacs</Author><Year>2011</Year><RecNum>3464</RecNum><DisplayText><style face="superscript">16</style></DisplayText><record><rec-number>3464</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966280">3464</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Lukacs, A.</author><author>Haigney, A.</author><author>Brust, R.</author><author>Zhao, R. K.</author><author>Stelling, A. L.</author><author>Clark, I. P.</author><author>Towrie, M.</author><author>Greetham, G. M.</author><author>Meech, S. R.</author><author>Tonge, P. J.</author></authors></contributors><auth-address>School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.</auth-address><titles><title>Photoexcitation of the blue light using FAD photoreceptor AppA results in ultrafast changes to the protein matrix</title><secondary-title>J Am Chem Soc</secondary-title><alt-title>Journal of the American Chemical Society</alt-title></titles><periodical><full-title>J Am Chem Soc</full-title></periodical><alt-periodical><full-title>Journal of the American Chemical Society</full-title></alt-periodical><pages>16893-900</pages><volume>133</volume><number>42</number><edition>2011/09/09</edition><keywords><keyword>Flavin-Adenine Dinucleotide/*chemistry</keyword><keyword>Hydrogen Bonding</keyword><keyword>*Light</keyword><keyword>Molecular Structure</keyword><keyword>Photoreceptor Cells/*chemistry</keyword><keyword>Spectrophotometry, Infrared</keyword><keyword>Spectrum Analysis, Raman</keyword></keywords><dates><year>2011</year><pub-dates><date>Oct 26</date></pub-dates></dates><isbn>1520-5126 (Electronic)
0002-7863 (Linking)</isbn><accession-num>21899315</accession-num><urls><related-urls><url> Consistent with NMR solution studies, ADDIN EN.CITE <EndNote><Cite><Author>Grinstead</Author><Year>2006</Year><RecNum>3295</RecNum><DisplayText><style face="superscript">43</style></DisplayText><record><rec-number>3295</rec-number><foreign-keys><key app="EN" db-id="svwxtt9r0rp2xoes5w0520v7a0wfr220zxw2" timestamp="1382966219">3295</key></foreign-keys><ref-type name="Journal Article">17</ref-type><contributors><authors><author>Grinstead, J. S.</author><author>Avila-Perez, M.</author><author>Hellingwerf, K. J.</author><author>Boelens, R.</author><author>Kaptein, R.</author></authors></contributors><auth-address>Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.</auth-address><titles><title>Light-induced flipping of a conserved glutamine sidechain and its orientation in the AppA BLUF domain</title><secondary-title>J. Am. Chem. Soc.</secondary-title></titles><periodical><full-title>J. Am. Chem. Soc.</full-title><abbr-1>J. Am. Chem. Soc.</abbr-1></periodical><pages>15066-7</pages><volume>128</volume><number>47</number><keywords><keyword>Bacterial Proteins/ chemistry</keyword><keyword>Conserved Sequence</keyword><keyword>Flavin-Adenine Dinucleotide/chemistry</keyword><keyword>Flavoproteins/ chemistry</keyword><keyword>Glutamine/chemistry</keyword><keyword>Kinetics</keyword><keyword>Light</keyword><keyword>Models, Molecular</keyword><keyword>Nuclear Magnetic Resonance, Biomolecular</keyword><keyword>Photochemistry</keyword><keyword>Photoreceptors, Microbial/ chemistry</keyword><keyword>Protein Conformation</keyword><keyword>Protein Structure, Tertiary</keyword></keywords><dates><year>2006</year><pub-dates><date>Nov 29</date></pub-dates></dates><isbn>0002-7863 (Print)</isbn><accession-num>17117839</accession-num><urls><related-urls><url> this state is characterized by a hydrogen bond between Q63 and the Y21 amide carbonyl that is essential for stabilization of lAppABLUF. We propose that the rate determining step (RDS) for recovery of the dark state involves proton transfer from Y21 to Q63 leading to formation of the enol form of Q63 in which the Q63 hydroxyl group is hydrogen bonded to the Y21 anion (iv). The Br?nsted coefficient of 1 indicates that this proton transfer is almost complete in the rate determining transition state (iii). During the conversion of (ii) to (iv) the Q63 amide must also lose a proton. Under normal conditions this proton may be transferred directly to solvent, however in our mechanism we show a base B abstracting the proton indicating one potential way in which imidazole could act as a general base to catalyze the reaction.PEVuZE5vdGU+PENpdGU+PEF1dGhvcj5MYWFuPC9BdXRob3I+PFllYXI+MjAwNjwvWWVhcj48UmVj
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ADDIN EN.CITE.DATA 8 The enol tautomer (iv) then rotates (v) and returns to the more stable keto form (vi), breaking the hydrogen bond with the C4=O of the flavin and forming a new hydrogen bond with the N5 atom of the flavin. In this mechanism we show protonation of Y21 in the final dAppABLUF species although the pKa of this residue is likely around 8 in the dark state. State v is labeled as dAppAenol although we do not know at what stage the overall protein structure relaxes from that found in lAppA to that in dAppA. TOC Graphic ................
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