1
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Abstract
Photoactive yellow protein (PYP) is a model photoreceptor. It binds a p-coumaric acid as a chromophore, thus enabling blue light sensing. The first discovered single-domain PYP from Halorhodospira halophila has been studied thoroughly in terms of its structural dynamics and photochemical properties. However, the evolutionary origins and biological role of PYP homologs are not well understood. Here, we show that PYP is an evolutionarily novel domain family of the ubiquitous PAS (Per-Arnt-Sim) superfamily. It likely originated from the phylum Myxococcota and was then horizontally transferred to representatives of a few other bacterial phyla. We show that PYP is associated with signal transduction either by domain fusion or by genome context. Key cellular functions modulated by PYP-initiated signal transduction pathways likely involve gene expression, motility, and biofilm formation. We identified three clades of the PYP family, one of which is poorly understood and potentially has novel functional properties. The Tyr42, Glu46, and Cys69 residues that are involved in p-coumaric acid binding in the model PYP from H. halophila are well conserved in the PYP family. However, we also identified cases where substitutions in these residues might have led to neofunctionalization, such as the proposed transition from light to redox sensing. Overall, this study provides definition, a newly built hidden Markov model, and the current genomic landscape of the PYP family and sets the stage for the future exploration of its signaling mechanisms and functional diversity. IMPORTANCE Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms.
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2
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Mix LT, Hara M, Fuzell J, Kumauchi M, Kaledhonkar S, Xie A, Hoff WD, Larsen DS. Not All Photoactive Yellow Proteins Are Built Alike: Surprises and Insights into Chromophore Photoisomerization, Protonation, and Thermal Reisomerization of the Photoactive Yellow Protein Isolated from Salinibacter ruber. J Am Chem Soc 2021; 143:19614-19628. [PMID: 34780163 DOI: 10.1021/jacs.1c08910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We demonstrate that the Halorhodospira halophila (Hhal) photoactive yellow protein (PYP) is not representative of the greater PYP family. The photodynamics of the PYP isolated from Salinibacter ruber (Srub) is characterized with a comprehensive range of spectroscopic techniques including ultrafast transient absorption, photostationary light titrations, Fourier transform infrared, and cryokinetics spectroscopies. We demonstrate that the dark-adapted pG state consists of two subpopulations differing in the protonation state of the chromophore and that both are photoactive, with the protonated species undergoing excited-state proton transfer. However, the primary I0 photoproduct observed in the Hhal PYP photocycle is absent in the Srub PYP photodynamics, which indicates that this intermediate, while important in Hhal photodynamics, is not a critical intermediate in initiating all PYP photocycles. The excited-state lifetime of Srub PYP is the longest of any PYP resolved to date (∼30 ps), which we ascribe to the more constrained chromophore binding pocket of Srub PYP and the absence of the critical Arg52 residue found in Hhal PYP. The final stage of the Srub PYP photocycle involves the slowest known thermal dark reversion of a PYP (∼40 min vs 350 ms in Hhal PYP). This property allowed the characterization of a pH-dependent equilibrium between the light-adapted pB state with a protonated cis chromophore and a newly resolved pG' intermediate with a deprotonated cis chromophore and pG-like protein conformation. This result demonstates that protein conformational changes and chromophore deprotonation precede chromophore reisomerization during the thermal recovery of the PYP photocycle.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Miwa Hara
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jack Fuzell
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Sandip Kaledhonkar
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Aihua Xie
- Department of Physics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States.,Center for Advanced Infrared Biology College of Arts and Sciences, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S Larsen
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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3
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Zhang TS, Fang YG, Song XF, Fang WH, Cui G. Hydrogen-Bonding Interaction Regulates Photoisomerization of a Single-Bond-Rotation Locked Photoactive Yellow Protein Chromophore in Protein. J Phys Chem Lett 2020; 11:2470-2476. [PMID: 32150415 DOI: 10.1021/acs.jpclett.0c00294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We have employed the QM(CASPT2//CASSCF)/MM method to explore the excited-state isomerization and decay mechanism of a single-bond-rotation locked photoactive yellow protein (PYP) chromophore in wild-type and mutant proteins. The S1 state is a spectroscopically bright state in the Franck-Condon region. In this state, there exist two excited-state isomerization pathways separately related to the clockwise and anticlockwise rotations of the C=C bond. The clockwise path is favorable because of a small barrier of 2 kcal/mol and uses a novel bicycle-pedal unidirectional photoisomerization mechanism in which the involved two dihedral angles rotate asynchronously because of the reinforced hydrogen-bonding interaction between the chromophore and Cys69. Near the twisted S1 minimum, the chromophore hops to the S0 state via the S1/S0 conical intersection. Finally, the R52A mutation has small effects on the excited-state properties and photoisomerization of the locked PYP chromophore. The present work provides new insights for understanding the photochemistry of PYP chromophores in protein surroundings.
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Affiliation(s)
- Teng-Shuo Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ye-Guang Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Xiu-Fang Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Chemistry College, Beijing Normal University, Beijing 100875, P.R. China
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4
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Amoruso G, Taylor VCA, Duchi M, Goodband E, Oliver TAA. Following Bimolecular Excited-State Proton Transfer between Hydroxycoumarin and Imidazole Derivatives. J Phys Chem B 2019; 123:4745-4756. [DOI: 10.1021/acs.jpcb.9b01475] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Giordano Amoruso
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Victoria C. A. Taylor
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, United Kingdom
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Bristol BS8 1TH, United Kingdom
| | - Marta Duchi
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Emma Goodband
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Thomas A. A. Oliver
- School of Chemistry, Cantock’s Close, University of Bristol, Bristol BS8 1TS, United Kingdom
- Bristol Centre for Functional Nanomaterials, School of Physics, University of Bristol, Bristol BS8 1TH, United Kingdom
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5
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Bull JN, Silva GD, Scholz MS, Carrascosa E, Bieske EJ. Photoinitiated Intramolecular Proton Transfer in Deprotonated para-Coumaric Acid. J Phys Chem A 2019; 123:4419-4430. [DOI: 10.1021/acs.jpca.9b02023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- James N. Bull
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
- School of Chemistry, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Gabriel da Silva
- Department of Chemical Engineering, University of Melbourne, Parkville, VIC 3010, Australia
| | - Michael S. Scholz
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Eduardo Carrascosa
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Evan J. Bieske
- School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
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6
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Mix LT, Carroll EC, Morozov D, Pan J, Gordon WR, Philip A, Fuzell J, Kumauchi M, van Stokkum I, Groenhof G, Hoff WD, Larsen DS. Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila. Biochemistry 2018; 57:1733-1747. [PMID: 29465990 DOI: 10.1021/acs.biochem.7b01114] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photoactive yellow proteins (PYPs) make up a diverse class of blue-light-absorbing bacterial photoreceptors. Electronic excitation of the p-coumaric acid chromophore covalently bound within PYP results in triphasic quenching kinetics; however, the molecular basis of this behavior remains unresolved. Here we explore this question by examining the excitation-wavelength dependence of the photodynamics of the PYP from Halorhodospira halophila via a combined experimental and computational approach. The fluorescence quantum yield, steady-state fluorescence emission maximum, and cryotrapping spectra are demonstrated to depend on excitation wavelength. We also compare the femtosecond photodynamics in PYP at two excitation wavelengths (435 and 475 nm) with a dual-excitation-wavelength-interleaved pump-probe technique. Multicompartment global analysis of these data demonstrates that the excited-state photochemistry of PYP depends subtly, but convincingly, on excitation wavelength with similar kinetics with distinctly different spectral features, including a shifted ground-state beach and altered stimulated emission oscillator strengths and peak positions. Three models involving multiple excited states, vibrationally enhanced barrier crossing, and inhomogeneity are proposed to interpret the observed excitation-wavelength dependence of the data. Conformational heterogeneity was identified as the most probable model, which was supported with molecular mechanics simulations that identified two levels of inhomogeneity involving the orientation of the R52 residue and different hydrogen bonding networks with the p-coumaric acid chromophore. Quantum calculations were used to confirm that these inhomogeneities track to altered spectral properties consistent with the experimental results.
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Affiliation(s)
- L Tyler Mix
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elizabeth C Carroll
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Dmitry Morozov
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Jie Pan
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | | | | | - Jack Fuzell
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Ivo van Stokkum
- Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1081 , 1081 HV Amsterdam , The Netherlands
| | - Gerrit Groenhof
- Department of Chemistry and NanoScience Center , University of Jyväskylä , P.O. Box 35, 40014 Jyväskylä , Finland
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics , Oklahoma State University , Stillwater , Oklahoma 74078 , United States
| | - Delmar S Larsen
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
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7
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Yu P, Song L, Qin J, Wang J. Capturing the photo-signaling state of a photoreceptor in a steady-state fashion by binding a transition metal complex. Protein Sci 2017; 26:2249-2256. [PMID: 28856755 DOI: 10.1002/pro.3284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/26/2017] [Indexed: 11/08/2022]
Abstract
Binding a small molecule to proteins causes conformational changes, but often to a limited extent. Here, we demonstrate that the interaction of a CO-releasing molecule (CORM3) with a photoreceptor photoactive yellow protein (PYP) drives large structural changes in the latter. The interaction of CORM3 and a mutant of PYP, Met100Ala, not only trigger the isomerization of its chromophore, p-coumaric acid, from its anionic trans configuration to a protonated cis configuration, but also increases the content of β-sheet at the cost of α-helix and random coil in the secondary structure of the protein. The CORM3 derived Met100Ala is found to highly resemble the signaling state, which is one of the key photo-intermediates of this photoactive protein, in both protein local conformation and chromophore configuration. The organometallic reagents hold promise as protein engineering tools. This work highlights a novel approach to structurally accessing short lived intermediates of proteins in a steady-state fashion.
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Affiliation(s)
- Pengyun Yu
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine; National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, 102206, People's Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences; Molecular Reaction Dynamics Laboratory; CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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8
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Mix LT, Kirpich J, Kumauchi M, Ren J, Vengris M, Hoff WD, Larsen DS. Bifurcation in the Ultrafast Dynamics of the Photoactive Yellow Proteins from Leptospira biflexa and Halorhodospira halophila. Biochemistry 2016; 55:6138-6149. [DOI: 10.1021/acs.biochem.6b00547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- L. Tyler Mix
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Julia Kirpich
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Masato Kumauchi
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Jie Ren
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Mikas Vengris
- Faculty
of Physics, Laser Research Centre, Vilnius University, Sauletekio
10, LT-10233 Vilnius, Lithuania
| | - Wouter D. Hoff
- Department
of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
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9
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Andersen LH, Bochenkova AV, Houmøller J, Kiefer HV, Lattouf E, Stockett MH. A PYP chromophore acts as a 'photoacid' in an isolated hydrogen bonded complex. Phys Chem Chem Phys 2016; 18:9909-13. [PMID: 27009407 DOI: 10.1039/c6cp00433d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The light-induced response of a neutral Photoactive Yellow Protein chromophore in a hydrogen-bonded complex with a proton acceptor has been studied by dual-detection action absorption spectroscopy and density functional theory. We show that the chromophore is a 'photoacid' and that ultrafast excited-state proton transfer might be operative in an isolated complex.
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Affiliation(s)
- Lars H Andersen
- Department of Physics and Astronomy, Aarhus University, DK-8000 Aarhus C, Denmark.
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10
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Wang X, Wang D, Guo Y, Yang C, Iqbal A, Liu W, Qin W, Yan D, Guo H. Imidazole derivative-functionalized carbon dots: using as a fluorescent probe for detecting water and imaging of live cells. Dalton Trans 2015; 44:5547-54. [PMID: 25697218 DOI: 10.1039/c5dt00128e] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A highly sensitive carbon dot-imidazole (CD-imidazole) nanoprobe is prepared through covalently conjugating imidazole group onto the surface of carbon dots for water fluorescence. In organic solvents, quenching of fluorescence occurs via photoinduced electron transfer (PET) process from the imidazole nitrogen to the CD acceptor. Addition of a trace amount of water into CD nanocomposites in various organic solvents leads to a fluorescence turn-on response, which can be attributed to the suppression of PET due to the formation of the "free" ion pair by proton transfer from the carboxyl groups that are on the CDs surface to the imidazole nitrogen through a water-bridge. This phenomenon can be used for the highly selective detection of trace amounts of water in organic solvents. Laser confocal microscope experiment shows the potential utilization of CD-imidazole for the probed proton-transfer reactions in living cells.
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Affiliation(s)
- Xudong Wang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province and State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, P. R. China.
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11
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Kumar A, Woolley GA. Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein. Photochem Photobiol 2015; 91:985-91. [PMID: 25946641 DOI: 10.1111/php.12464] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/26/2015] [Indexed: 12/11/2022]
Abstract
Numerous single-site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark-adapted states. The structural basis for the occurrence of this shoulder, called the "intermediate spectral form," has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E-cPYP). The M121 site in M121E-cPYP corresponds to the M100 site in wild-type H. halophila PYP. High-resolution NMR measurements with a salt-tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
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12
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Vegh RB, Bloch DA, Bommarius AS, Verkhovsky M, Pletnev S, Iwaï H, Bochenkova AV, Solntsev KM. Hidden photoinduced reactivity of the blue fluorescent protein mKalama1. Phys Chem Chem Phys 2015; 17:12472-85. [DOI: 10.1039/c5cp00887e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report a complete photocycle of the blue fluorescent protein exhibiting two delayed branches coupled to hidden proton transfer events.
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Affiliation(s)
- Russell B. Vegh
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Dmitry A. Bloch
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Andreas S. Bommarius
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
- Petit Institute of Bioengineering and Bioscience
| | - Michael Verkhovsky
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | - Sergei Pletnev
- Synchrotron Radiation Research Section
- Macromolecular Crystallography Laboratory
- National Cancer Institute
- Argonne
- USA
| | - Hideo Iwaï
- Research Program in Structural Biology and Biophysics
- Institute of Biotechnology
- University of Helsinki
- Helsinki 00014
- Finland
| | | | - Kyril M. Solntsev
- School of Chemistry and Biochemistry
- Georgia Institute of Technology
- Atlanta
- USA
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13
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Ishikita H, Saito K. Proton transfer reactions and hydrogen-bond networks in protein environments. J R Soc Interface 2013; 11:20130518. [PMID: 24284891 DOI: 10.1098/rsif.2013.0518] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In protein environments, proton transfer reactions occur along polar or charged residues and isolated water molecules. These species consist of H-bond networks that serve as proton transfer pathways; therefore, thorough understanding of H-bond energetics is essential when investigating proton transfer reactions in protein environments. When the pKa values (or proton affinity) of the H-bond donor and acceptor moieties are equal, significantly short, symmetric H-bonds can be formed between the two, and proton transfer reactions can occur in an efficient manner. However, such short, symmetric H-bonds are not necessarily stable when they are situated near the protein bulk surface, because the condition of matching pKa values is opposite to that required for the formation of strong salt bridges, which play a key role in protein-protein interactions. To satisfy the pKa matching condition and allow for proton transfer reactions, proteins often adjust the pKa via electron transfer reactions or H-bond pattern changes. In particular, when a symmetric H-bond is formed near the protein bulk surface as a result of one of these phenomena, its instability often results in breakage, leading to large changes in protein conformation.
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Affiliation(s)
- Hiroshi Ishikita
- Department of Biological Sciences, Graduate School of Science, Osaka University, , Machikaneyama-cho 1-1, Toyonaka 560-0043, Japan
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14
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Gottlieb SM, Kim PW, Rockwell NC, Hirose Y, Ikeuchi M, Lagarias JC, Larsen DS. Primary Photodynamics of the Green/Red-Absorbing Photoswitching Regulator of the Chromatic Adaptation E Domain from Fremyella diplosiphon. Biochemistry 2013; 52:8198-208. [DOI: 10.1021/bi400946q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean M. Gottlieb
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Peter W. Kim
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
| | - Nathan C. Rockwell
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Yuu Hirose
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Masahiko Ikeuchi
- Electronics-Inspired
Interdisciplinary Research Institute, Toyohashi University of Technology, 1-1 Hibarigaoka Tempaku, Toyohashi, Aichi 441-8580, Japan
- Department
of Life Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - J. Clark Lagarias
- Department
of Molecular and Cell Biology, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Delmar S. Larsen
- Department
of Chemistry, University of California, One Shields Avenue, Davis, California 95616, United States
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15
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Khistyaev K, Golan A, Bravaya KB, Orms N, Krylov AI, Ahmed M. Proton Transfer in Nucleobases is Mediated by Water. J Phys Chem A 2013; 117:6789-97. [DOI: 10.1021/jp406029p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirill Khistyaev
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Amir Golan
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ksenia B. Bravaya
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Natalie Orms
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los
Angeles, California 90089-0482, United States
| | - Musahid Ahmed
- Chemical Sciences
Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Kennis JTM, van Stokkum IHM, Peterson DS, Pandit A, Wachter RM. Ultrafast proton shuttling in Psammocora cyan fluorescent protein. J Phys Chem B 2013; 117:11134-43. [PMID: 23534404 DOI: 10.1021/jp401114e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cyan, green, yellow, and red fluorescent proteins (FPs) homologous to green fluorescent protein (GFP) are used extensively as model systems to study fundamental processes in photobiology, such as the capture of light energy by protein-embedded chromophores, color tuning by the protein matrix, energy conversion by Förster resonance energy transfer (FRET), and excited-state proton transfer (ESPT) reactions. Recently, a novel cyan fluorescent protein (CFP) termed psamFP488 was isolated from the genus Psammocora of reef building corals. Within the cyan color class, psamFP488 is unusual because it exhibits a significantly extended Stokes shift. Here, we applied ultrafast transient absorption and pump-dump-probe spectroscopy to investigate the mechanistic basis of psamFP488 fluorescence, complemented with fluorescence quantum yield and dynamic light scattering measurements. Transient absorption spectroscopy indicated that, upon excitation at 410 nm, the stimulated cyan emission rises in 170 fs. With pump-dump-probe spectroscopy, we observe a very short-lived (110 fs) ground-state intermediate that we assign to the deprotonated, anionic chromophore. In addition, a minor fraction (14%) decays with 3.5 ps to the ground state. Structural analysis of homologous proteins indicates that Glu-167 is likely positioned in sufficiently close vicinity to the chromophore to act as a proton acceptor. Our findings support a model where unusually fast ESPT from the neutral chromophore to Glu-167 with a time constant of 170 fs and resulting emission from the anionic chromophore forms the basis of the large psamFP488 Stokes shift. When dumped to the ground state, the proton on neutral Glu is very rapidly shuttled back to the anionic chromophore in 110 fs. Proton shuttling in excited and ground states is a factor of 20-4000 faster than in GFP, which probably results from a favorable hydrogen-bonding geometry between the chromophore phenolic oxygen and the glutamate acceptor, possibly involving a short hydrogen bond. At any time in the reaction, the proton is localized on either the chromophore or Glu-167, which implies that most likely no low-barrier hydrogen bond exists between these molecular groups. This work supports the notion that proton transfer in biological systems, be it in an electronic excited or ground state, can be an intrinsically fast process that occurs on a 100 fs time scale. PsamFP488 represents an attractive model system that poses an ultrafast proton transfer regime in discrete steps. It constitutes a valuable model system in addition to wild type GFP, where proton transfer is relatively slow, and the S65T/H148D GFP mutant, where the effects of low-barrier hydrogen bonds dominate.
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Affiliation(s)
- John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Sciences, Vrije Universiteit , De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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Saito K, Ishikita H. Formation of an unusually short hydrogen bond in photoactive yellow protein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012. [PMID: 23201477 DOI: 10.1016/j.bbabio.2012.11.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The photoactive chromophore of photoactive yellow protein (PYP) is p-coumaric acid (pCA). In the ground state, the pCA chromophore exists as a phenolate anion, which is H-bonded by protonated Glu46 (O(Glu46)-O(pCA)=~2.6Å) and protonated Tyr42. On the other hand, the O(Glu46)-O(pCA) H-bond was unusually short (O(Glu46)-O(pCA)=2.47Å) in the intermediate pR(CW) state observed in time-resolved Laue diffraction studies. To understand how the existence of the unusually short H-bond is energetically possible, we analyzed the H-bond energetics adopting a quantum mechanical/molecular mechanical (QM/MM) approach based on the atomic coordinates of the PYP crystal structures. In QM/MM calculations, the O(Glu46)-O(pCA) bond is 2.60Å in the ground state, where Tyr42 donates an H-bond to pCA. In contrast, when the hydroxyl group of Tyr42 is flipped away from pCA, the H-bond was significantly shortened to 2.49Å in the ground state. The same H-bond pattern reproduced the unusually short H-bond in the pR(CW) structure (O(Glu46)-O(pCA)=2.49Å). Intriguingly, the potential-energy profile resembles that of a single-well H-bond, suggesting that the pK(a) values of the donor (Glu46) and acceptor (pCA) moieties are nearly equal. The present results indicate that the "equal pK(a)" requirement for formation of single-well or low-barrier H-bond (LBHB) is satisfied only when Tyr42 does not donate an H-bond to pCA, and argue against the possibility that the O(Glu46)-O(pCA) bond is an LBHB in the ground state, where Tyr42 donates an H-bond to pCA.
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Affiliation(s)
- Keisuke Saito
- Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
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19
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Lincoln CN, Fitzpatrick AE, van Thor JJ. Photoisomerisation quantum yield and non-linear cross-sections with femtosecond excitation of the photoactive yellow protein. Phys Chem Chem Phys 2012; 14:15752-64. [PMID: 23090503 DOI: 10.1039/c2cp41718a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quantum yield of photoisomerisation of the photoactive yellow protein (PYP) strongly depends on peak power and wavelength with femtosecond optical excitation. Using systematic power titrations and addition of second order dispersion resulting in 140, 300 and 600 fs pulse durations, the one and multi-photon cross-sections at 400, 450 and 490 nm have been assessed from transient absorption spectroscopy and additionally the Z-scan technique. Applying a target model that incorporates photoselection theory, estimates for the cross-sections for stimulated emission and absorption of the first excited state, the amount of ultrafast internal conversion and the underlying species associated dynamics have been determined. The final quantum yields for photoisomerisation were found to be 0.06, 0.14-0.19 and 0.02 for excitation wavelengths 400, 450 and 490 nm and found to increase with increasing pulse durations. Transient absorption measurements and Z-scan measurements at 450 nm, coinciding with the maximum wavelength of the ground state absorption, indicate that the photochemical quantum yield is intrinsically limited by an ultrafast internal conversion reaction as well as by stimulated emission cross-section. With excitation at 400 nm photoisomerisation quantum yield is further significantly limited by competing multi-photon excitation into excited state absorption at 385 nm previously proposed to result in photoionisation. With excitation at 490 nm the photoisomerisation quantum yield is predominantly limited further by the significantly higher stimulated emission cross-section compared to ground state cross-section as well as multi-photon processes. In addition to photoionisation, a second product of multi-photon excitation is identified and characterised by an induced absorption at 500 nm and a time constant of 2 ps for relaxation. With power densities up to 138 GW cm(-2) the measurements have not provided indication for coherent multi-photon absorption of PYP. In the saturation regime with 450 nm excitation, the limit for the photoisomerisation quantum yield was found to be 0.14-0.19 and the excited state absorption cross-section 6.1 × 10(-17) cm(2) or 0.36 times the ground state cross-section of 1.68 × 10(-16) cm(2) per molecule. This places a fundamental restriction on the maximum populations and sample penetration that may be achieved for instance in femtosecond pump-probe experiments with molecular crystals of PYP.
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Affiliation(s)
- Craig N Lincoln
- Imperial College London, Division of Molecular Biosciences, South Kensington campus, SW7 2AZ, London, UK
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Oktaviani NA, Pool TJ, Kamikubo H, Slager J, Scheek RM, Kataoka M, Mulder FAA. Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophys J 2012; 102:579-86. [PMID: 22325281 DOI: 10.1016/j.bpj.2011.12.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/23/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022] Open
Abstract
Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14 kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that closely matches the bacterium's motility spectrum. In the electronic ground state, the para-coumaric acid (pCA) chromophore of PYP is negatively charged and forms two short hydrogen bonds to the side chains of Glu-46 and Tyr-42. The resulting acid triad is central to the marked pH dependence of the optical-absorption relaxation kinetics of PYP. Here, we describe an NMR approach to sequence-specifically follow all tyrosine side-chain protonation states in PYP from pH 3.41 to 11.24. The indirect observation of the nonprotonated (13)C(γ) resonances in sensitive and well-resolved two-dimensional (13)C-(1)H spectra proved to be pivotal in this effort, as observation of other ring-system resonances was hampered by spectral congestion and line-broadening due to ring flips. We observe three classes of tyrosine residues in PYP that exhibit very different pK(a) values depending on whether the phenolic side chain is solvent-exposed, buried, or hydrogen-bonded. In particular, our data show that Tyr-42 remains fully protonated in the pH range of 3.41-11.24, and that pH-induced changes observed in the photocycle kinetics of PYP cannot be caused by changes in the charge state of Tyr-42. It is therefore very unlikely that the pCA chromophore undergoes changes in its electrostatic interactions in the electronic ground state.
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Affiliation(s)
- Nur Alia Oktaviani
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Femtosecond Photodynamics of the Red/Green Cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 1. Forward Dynamics. Biochemistry 2012; 51:608-18. [DOI: 10.1021/bi201507k] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter W. Kim
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
| | - Lucy H. Freer
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
| | - Nathan C. Rockwell
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
| | - Shelley S. Martin
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
| | - J. Clark Lagarias
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
| | - Delmar S. Larsen
- Department
of Chemistry and ‡Department of Molecular and Cell Biology, University of California, One Shields Avenue, Davis,
California
95616, United States
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Kim PW, Freer LH, Rockwell NC, Martin SS, Lagarias JC, Larsen DS. Femtosecond photodynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. 2. reverse dynamics. Biochemistry 2012; 51:619-30. [PMID: 22148731 DOI: 10.1021/bi2017365] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Phytochromes are red/far-red photosensory proteins that utilize photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert reversibly between red- and far-red-absorbing forms (P(r) and P(fr), respectively). Cyanobacteriochromes (CBCRs) are related photosensory proteins with more diverse spectral sensitivity. The mechanisms that underlie this spectral diversity have not yet been fully elucidated. One of the main CBCR subfamilies photoconverts between a red-absorbing 15Z ground state, like the familiar P(r) state of phytochromes, and a green-absorbing photoproduct ((15E)P(g)). We have previously used the red/green CBCR NpR6012g4 from the cyanobacterium Nostoc punctiforme to examine ultrafast photodynamics of the forward photoreaction. Here, we examine the reverse reaction. Using excitation-interleaved transient absorption spectroscopy with broadband detection and multicomponent global analysis, we observed multiphasic excited-state dynamics. Interleaved excitation allowed us to identify wavelength-dependent shifts in the ground-state bleach that equilibrated on a 200 ps time scale, indicating ground-state heterogeneity. Compared to the previously studied forward reaction, the reverse reaction has much faster excited-state decay time constants and significantly higher photoproduct yield. This work thus demonstrates striking differences between the forward and reverse reactions of NpR6012g4 and provides clear evidence of ground-state heterogeneity in the phytochrome superfamily.
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Affiliation(s)
- Peter W Kim
- Department of Chemistry, University of California, Davis, California 95616, United States
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Kumpulainen T, Brouwer AM. Excited-state proton transfer and ion pair formation in a Cinchona organocatalyst. Phys Chem Chem Phys 2012; 14:13019-26. [DOI: 10.1039/c2cp41483j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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