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Rohani L, Lamichhane HP, Hastings G. Calculated vibrational properties of pigments in protein binding sites 2: Semiquinones in photosynthetic proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 295:122518. [PMID: 36996613 DOI: 10.1016/j.saa.2023.122518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/03/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
[QA- - QA] Fourier transform infrared difference spectra have previously been obtained using purple bacterial reaction centers from Rhodobacter sphaeroides with unlabeled, 18O and 13C isotope labeled phylloquinone (PhQ, also known as vitamin K1) incorporated into the QA protein binding site (Breton, (1997), Proc. Natl. Acad. Sci. USA94 11318-11323). The nature of the bands in these spectra and the isotope induced band shifts are poorly understood, especially for the phyllosemiquinone anion (PhQ-) state. To aid in the interpretation of the bands in these experimental spectra, ONIOM type QM/MM vibrational frequency calculations were undertaken. Calculations were also undertaken for PhQ- in solution. Surprisingly, both sets of calculated spectra are similar and agree well with the experimental spectra. This similarity suggests pigment-protein interactions do not perturb the electronic structure of the semiquinone in the QA binding site. This is not found to be the case for the neutral PhQ species in the same protein binding site. PhQ also occupies the A1 protein binding site in photosystem I, and the vibrational properties of PhQ- in the QA and A1 binding sites are compared and shown to exhibit considerable differences. These differences probably arise because of changes in the degree of asymmetry of hydrogen bonding of PhQ- in the A1 and QA binding sites.
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Affiliation(s)
- Leyla Rohani
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Hari P Lamichhane
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA.
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Askelson PG, Meloni SL, Hoffnagle AM, Anna JM. Resolving the Impact of Hydrogen Bonding on the Phylloquinone Cofactor through Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2022; 126:10120-10135. [PMID: 36444999 DOI: 10.1021/acs.jpcb.2c03556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two-dimensional infrared spectroscopy (2DIR) was applied to phylloquinone (PhQ), an important biological cofactor, to elucidate the impact of hydrogen bonding on the ultrafast dynamics and energetics of the carbonyl stretching modes. 2DIR measurements were performed on PhQ dissolved in hexanol, which served as the hydrogen bonding solvent, and hexane, which served as a non-hydrogen bonding control. Molecular dynamics simulations and quantum chemical calculations were performed to aid in spectral assignment and interpretation. From the position of the peaks in the 2DIR spectra, we extracted the transition frequencies for the fundamental, overtone, and combination bands of hydrogen bonded and non-hydrogen bonded carbonyl groups of PhQ in the 1635-1680 cm-1 region. We find that hydrogen bonding to a single carbonyl group acts to decouple the two carbonyl units of PhQ. Through analysis of the time-resolved 2DIR data, we find that hydrogen bonding leads to faster vibrational relaxation as well as an increase in the inhomogeneous broadening of the carbonyl groups. Overall, this work demonstrates how hydrogen bonding to the carbonyl groups of PhQ presents in the 2DIR spectra, laying the groundwork to use PhQ as a 2DIR probe to characterize the ultrafast fluctuations in the local environment of natural photosynthetic complexes.
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Affiliation(s)
- Phoebe G Askelson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Stephen L Meloni
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Alexander M Hoffnagle
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
| | - Jessica M Anna
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania19104, United States
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Agarwala N, Rohani L, Hastings G. Experimental and calculated infrared spectra of disubstituted naphthoquinones. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 268:120674. [PMID: 34894562 DOI: 10.1016/j.saa.2021.120674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 10/21/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
In recent years there has been interest in incorporating substituted 1,4-naphthoquinones (NQs) into the A1 binding site in photosystem I (PSI) photosynthetic protein complexes. This interest in part stems from the considerably altered bioenergetics of electron transfer that occur in PSI with such substitutions. Time resolved FTIR studies of PSI complexes with disubstituted NQs incorporated have and currently are being undertaken, and with this in mind it is worth considering FTIR absorption spectra of these disubstituted NQs in solution. Here we present FTIR absorbance spectra for 2-bromo-3-methyl-1,4-naphthoquinone (BrMeNQ), 2-chloromethyl-3-methyl-1,4-naphthoquinone (CMMeNQ) and 2-ethylthio-3-methyl-1,4-naphthoquinone (ETMeNQ) in tetrahydrofuran (THF). The FTIR spectra of these di-substituted naphthoquinones (NQs) were compared to FTIR spectra of 2-methyl-3-phytyl-1,4-naphthoquinone [phylloquinone (PhQ)], 2,3-dimethyl-1,4-naphthoquinone (DMNQ), and 2-methyl-1,4-naphthoquinone (2MNQ). To aid in the assignment of bands in the experimental spectra, density functional theory (DFT) based vibrational frequency calculations for all the substituted NQs in solution were undertaken. The calculated and experimental spectra agree well. By calculating normal mode potential energy distributions, unambiguous quantitative band assignments were made. The calculated and experimental spectra together make predictions about what may be observable in time resolved FTIR difference spectra obtained using PSI with the different NQs incorporated. Time resolved FTIR difference spectra are presented that support these predictions.
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Affiliation(s)
- Neva Agarwala
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Leyla Rohani
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA.
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Assessment of the orientation and conformation of pigments in protein binding sites from infrared difference spectra. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148366. [PMID: 33385342 DOI: 10.1016/j.bbabio.2020.148366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 01/01/2023]
Abstract
Time resolved FTIR difference spectroscopy (DS) has been used to study photosystem I (PSI) with the disubstituted 1,4-naphthoquinones acequinocyl (AcQ) and lapachol (Lpc) incorporated into the A1 binding site. AcQ is a 2-acetoxy-3-dodecyl-1,4-naphthoquinone, Lpc is a 2-hydroxy-3-(3-methyl-2-butenyl)-1,4-naphthoquinone. To assess whether the experimental spectra are specific to different orientations of the quinone and their substitutions ONIOM-type QM/MM vibrational frequency calculations were undertaken for various orientations of the pigments and side-chain conformations in the A1 binding site. Comparison of calculated and experimental spectra for the reduced species (semiquinone anion) suggests that the orientation for the naphthoquinone ring in the binding site and specific side-chain conformations can be identified based on the spectra. In native PSI phylloquinone (PhQ) in the A1 binding site binds with its phytyl chain ortho to the hydrogen bonded carbonyl group. This is not found to be the case for the hydrocarbon tail of AcQ, which is meta to the H-bonded carbonyl group. In contrast, Lpc in PSI binds with its hydrocarbon tail also ortho to the H-bonded carbonyl group. Furthermore, comparison of calculated and experimental spectra indicates which conformations the acetoxy group of AcQ and the hydroxy group of Lpc adopt in the A1 binding site.
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Makita H, Hastings G. Time-resolved FTIR difference spectroscopy for the study of quinones in the A 1 binding site in photosystem I: Identification of neutral state quinone bands. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148173. [PMID: 32059842 DOI: 10.1016/j.bbabio.2020.148173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 11/24/2022]
Abstract
Infrared absorption bands associated with the neutral state of quinones in the A1 binding site in photosystem I (PSI) have been difficult to identify in the past. This problem is addressed here, where time-resolved step-scan FTIR difference spectroscopy at 77 K has been used to study PSI with six different quinones incorporated into the A1 binding site. (P700+A1- - P700A1) and (A1- - A1) FTIR difference spectra (DS) were obtained for PSI with the different quinones incorporated, and several double-difference spectra (DDS) were constructed from the DS. From analysis of the DS and DDS, in combination with density functional theory based vibrational frequency calculations of the quinones, the neutral state bands of the incorporated quinones are identified and assigned. For neutral PhQ in the A1 binding site, infrared absorption bands were identified near 1665 and 1635 cm-1, that are due to the C1O and C4O stretching vibrations of the incorporated PhQ, respectively. These assignments indicate a 30 cm-1 separation between the C1O and C4O modes, considerably less than the ~80 cm-1 found for similar modes of PhQ-. The C4O mode downshifts due to hydrogen bonding, so the suggestion is that hydrogen bonding is weaker for the neutral state compared to the anion state, indicating radical-induced proton dynamics associated with the quinone in the A1 binding site in PSI.
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Affiliation(s)
- Hiroki Makita
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, USA.
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Makita H, Hastings G. Time-resolved step-scan FTIR difference spectroscopy for the study of photosystem I with different benzoquinones incorporated into the A1 binding site. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:1199-1206. [DOI: 10.1016/j.bbabio.2018.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/16/2018] [Accepted: 08/21/2018] [Indexed: 11/28/2022]
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Zhao N, Lamichhane HP, Hastings G. Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site. FRONTIERS IN PLANT SCIENCE 2013; 4:328. [PMID: 24009618 PMCID: PMC3757576 DOI: 10.3389/fpls.2013.00328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 08/02/2013] [Indexed: 06/02/2023]
Abstract
Previously we have shown that ONIOM type (QM/MM) calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and (18)O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0), 2,3,5,6-tetramethyl-1, 4-benzoquinone (duroquinone, DQ), and 2,3-dimethyl-l,4-naphthoquinone (DMNQ) incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites. The normal modes that contribute to the bands in the calculated spectra, their composition, frequency, and intensity, and how these quantities are modified upon (18)O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10-13 cm(-1) separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry in H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are "tail-less." Spectra were also calculated for reaction centers with corresponding "tail" containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated spectra.
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Affiliation(s)
- Nan Zhao
- Department of Physics and Astronomy, Georgia State University Atlanta, GA, USA
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Jones MR. Structural Plasticity of Reaction Centers from Purple Bacteria. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_16] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Bender SL, Keough JM, Boesch SE, Wheeler RA, Barry BA. The Vibrational Spectrum of the Secondary Electron Acceptor, A1, in Photosystem I. J Phys Chem B 2008; 112:3844-52. [DOI: 10.1021/jp0775146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shana L. Bender
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - James M. Keough
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Scott E. Boesch
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Ralph A. Wheeler
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
| | - Bridgette A. Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, and Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019
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Lancaster CR, Michel H. Refined crystal structures of reaction centres from Rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid. J Mol Biol 1999; 286:883-98. [PMID: 10024457 DOI: 10.1006/jmbi.1998.2532] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled with the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). It has been established by X-ray crystallography that the triazine herbicide terbutryn binds to the QB site. However, the exact description of protein-triazine interactions has had to await the refinement of higher-resolution structures. In addition, there is also interest in the role of chirality in the activity of herbicides. Here, we report the structural characterisation of triazine binding by crystallographic refinement of complexes of the RC either with the triazine inhibitor atrazine (Protein Data Bank (PDB) entry 5PRC) or with the chiral atrazine derivatives, DG-420314 (S(-) enantiomer, PDB entry 6PRC) or DG-420315 (R(+) enantiomer, PDB entry 7PRC). Due to the high quality of the data collected, it has been possible to describe the exact nature of triazine binding and its effect on the structure of the protein at high-resolution limits of 2.35 A (5PRC), 2.30 A (6PRC), and 2.65 A (7PRC), respectively. In addition to two previously implied hydrogen bonds, a third hydrogen bond, binding the distal side of the inhibitors to the protein, and four additional hydrogen bonds mediated by two tightly bound water molecules on the proximal side of the inhibitors, are apparent. Based on the high quality data collected on the RC complexes of the two chiral atrazine derivatives, unequivocal assignment of the structure at the chiral centres was possible, even though the differences in structures of the substituents are small. The structures provide explanations for the relative binding affinities of the two chiral compounds. Although it was not an explicit goal of this work, the new data were of sufficient quality to improve the original model also regarding the structure of the bound carotenoid 1,2-dihydroneurosporene. A carotenoid model with a cis double bond at the 15,15' position fits the electron density better than the original model with a 13,14-cis double bond.
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Affiliation(s)
- C R Lancaster
- Abteilung Molekulare Membranbiologie, Max-Planck-Institut für Biophysik, Heinrich-Hoffmann-Str. 7, Frankfurt am Main, D-60528, Germany
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