1
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Pamu R, Khomami B, Mukherjee D. Observation of anomalous carotenoid and blind chlorophyll activations in photosystem I under synthetic membrane confinements. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183930. [PMID: 35398026 DOI: 10.1016/j.bbamem.2022.183930] [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: 08/02/2021] [Revised: 03/27/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
The role of natural thylakoid membrane confinements in architecting the robust structural and electrochemical properties of PSI is not fully understood. Most PSI studies till date extract the proteins from their natural confinements that can lead to non-native conformations. Recently our group had successfully reconstituted PSI in synthetic lipid membranes using detergent-mediated liposome solubilizations. In this study, we investigate the alterations in chlorophylls and carotenoids interactions and reorganization in PSI based on spectral property changes induced by its confinement in anionic DPhPG and zwitterionic DPhPC phospholipid membranes. To this end, we employ a combination of absorption, fluorescence, and circular dichroism (CD) spectroscopic measurements. Our results indicate unique activation and alteration of photoresponses from the PSI carotenoid (Car) bands in PSI-DPhPG proteoliposomes that can tune the Excitation Energy Transfer (EET), otherwise absent in PSI at non-native environments. Specifically, we observe broadband light harvesting via enhanced absorption in the otherwise non-absorptive green region (500-580 nm) of the Chlorophylls (Chl) along with ~64% increase in the full-width half maximum of the Qy band (650-720 nm). The CD results indicate enhanced Chl-Chl and Chl-Car interactions along with conformational changes in protein secondary structures. Such distinct changes in the Car and Chl bands are not observed in PSI confined in DPhPC. The fundamental insights into membrane microenvironments tailoring PSI subunits reorganization and interactions provide novel strategies for tuning photoexcitation processes and rational designing of biotic-abiotic interfaces in PSI-based photoelectrochemical energy conversion systems.
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Affiliation(s)
- Ravi Pamu
- Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN 37996, USA; Nano-BioMaterials Laboratory for Energy, Energetics & Environment (nbml-E3), University of Tennessee, Knoxville, TN 37996, USA; Sustainable Energy Education and Research Center (SEERC), University of Tennessee, Knoxville, TN 37996, USA
| | - Bamin Khomami
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN 37996, USA; Sustainable Energy Education and Research Center (SEERC), University of Tennessee, Knoxville, TN 37996, USA.
| | - Dibyendu Mukherjee
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA; Nano-BioMaterials Laboratory for Energy, Energetics & Environment (nbml-E3), University of Tennessee, Knoxville, TN 37996, USA; Sustainable Energy Education and Research Center (SEERC), University of Tennessee, Knoxville, TN 37996, USA.
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2
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Lim B, Kim Y, Kim H, Park M, Yeo H, Koo S. 13,13′‐Diphenalkyl β
‐carotenes
as
pi‐stacking
models of chlorophylls and carotenoids in photosynthesis. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Boram Lim
- College of Bangmok Basic Education Myongji University Yongin Gyeonggi‐Do South Korea
| | - Young‐Hun Kim
- Department of Chemistry Myongji University Yongin Gyeonggi‐Do South Korea
| | - Hyein Kim
- Department of Chemistry Myongji University Yongin Gyeonggi‐Do South Korea
| | - Myeongnam Park
- Department of Chemistry Myongji University Yongin Gyeonggi‐Do South Korea
| | - Huisu Yeo
- Department of Chemistry Myongji University Yongin Gyeonggi‐Do South Korea
| | - Sangho Koo
- Department of Chemistry Myongji University Yongin Gyeonggi‐Do South Korea
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3
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Structural and physicochemical properties of composites between starch nanoparticles and β-carotene prepared via nanoprecipitation. Int J Biol Macromol 2022; 214:100-110. [PMID: 35705125 DOI: 10.1016/j.ijbiomac.2022.06.062] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/22/2022]
Abstract
To apply starch nanoparticles (SNP) as host materials for β-carotene encapsulation, aqueous SNP dispersions (10, 25, 50, and 100 mg/10 mL) and β-carotene in acetone (10, 50, 100, 150, and 200 μg/mL) were mixed. The acetone in the mixture was evaporated to prepare SNP and β-carotene composites, which were homogeneously dispersed in aqueous media with over 90 % solubility. When SNP content was higher than 50 mg, over 80 % of β-carotene was encapsulated in the composite matrix. X-ray diffraction, nuclear magnetic resonance spectroscopy, and transmission electron microscopic analyses confirmed the micellar-shaped composite particles with diameters <120 nm and an amorphous structure. High SNP content in the composites enhanced β-carotene stability under extremely hot and acidic conditions as well as against ultraviolet rays and oxidation reactions. The encapsulated β-carotene was not readily released in simulated gastric fluid, but was gradually released in simulated intestinal fluid via SNP digestion in the composites.
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4
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Mascoli V, Liguori N, Cupellini L, Elias E, Mennucci B, Croce R. Uncovering the interactions driving carotenoid binding in light-harvesting complexes. Chem Sci 2021; 12:5113-5122. [PMID: 34163750 PMCID: PMC8179543 DOI: 10.1039/d1sc00071c] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/14/2021] [Indexed: 11/25/2022] Open
Abstract
Carotenoids are essential constituents of plant light-harvesting complexes (LHCs), being involved in protein stability, light harvesting, and photoprotection. Unlike chlorophylls, whose binding to LHCs is known to require coordination of the central magnesium, carotenoid binding relies on weaker intermolecular interactions (such as hydrogen bonds and van der Waals forces), whose character is far more elusive. Here we addressed the key interactions responsible for carotenoid binding to LHCs by combining molecular dynamics simulations and polarizable quantum mechanics/molecular mechanics calculations on the major LHC, LHCII. We found that carotenoid binding is mainly stabilized by van der Waals interactions with the surrounding chlorophyll macrocycles rather than by hydrogen bonds to the protein, the latter being more labile than predicted from structural data. Furthermore, the interaction network in the binding pockets is relatively insensitive to the chemical structure of the embedded carotenoid. Our results are consistent with a number of experimental data and challenge the role played by specific interactions in the assembly of pigment-protein complexes.
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Affiliation(s)
- Vincenzo Mascoli
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Nicoletta Liguori
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Lorenzo Cupellini
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Eduard Elias
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
| | - Benedetta Mennucci
- Department of Chemistry, University of Pisa Via G. Moruzzi 13 56124 Pisa Italy
| | - Roberta Croce
- Department of Physics and Astronomy, Institute for Lasers, Life and Biophotonics, Faculty of Sciences, Vrije Universiteit Amsterdam De Boelelaan 1081 1081 HV Amsterdam The Netherlands
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5
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Zabelin AA, Fufina TY, Khristin AM, Khatypov RA, Shkuropatova VA, Shuvalov VA, Vasilieva LG, Shkuropatov AY. Effect of Leucine M196 Substitution by Histidine on Electronic Structure of the Primary Electron Donor and Electron Transfer in Reaction Centers from Rhodobacter sphaeroides. BIOCHEMISTRY (MOSCOW) 2019; 84:520-528. [PMID: 31234766 DOI: 10.1134/s0006297919050067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In our recent X-ray study, we demonstrated that substitution of the natural leucine residue M196 with histidine in the reaction center (RC) from Rhodobacter (Rba.) sphaeroides leads to formation of a close contact between the genetically introduced histidine and the primary electron donor P (bacteriochlorophylls (BChls) PA and PB dimer) creating a novel pigment-protein interaction that is not observed in native RCs. In the present work, the possible nature of this novel interaction and its effects on the electronic properties of P and the photochemical charge separation in isolated mutant RCs L(M196)H are investigated at room temperature using steady-state absorption spectroscopy, light-induced difference FTIR spectroscopy, and femtosecond transient absorption spectroscopy. The results are compared with the data obtained for the RCs from Rba. sphaeroides pseudo-wild type strain. It is shown that the L(M196)H mutation results in a decrease in intensity and broadening of the long-wavelength Qy absorption band of P at ~865 nm. Due to the mutation, there is also weakening of the electronic coupling between BChls in the radical cation P+ and increase in the positive charge localization on the PA molecule. Despite the significant perturbations of the electronic structure of P, the mutant RCs retain high electron transfer rates and quantum yield of the P+QA- state (QA is the primary quinone acceptor), which is close to the one observed in the native RCs. Comparison of our results with the literature data suggests that the imidazole group of histidine M196 forms a π-hydrogen bond with the π-electron system of the PB molecule in the P dimer. It is likely that the specific (T-shaped) spatial organization of the π-hydrogen interaction and its potential heterogeneity in relation to the bonding energy is, at least partially, the reason that this type of interaction between the protein and the pigment and quinone cofactors is not realized in the native RCs.
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Affiliation(s)
- A A Zabelin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - T Yu Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A M Khristin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - R A Khatypov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Shkuropatova
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Shuvalov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - L G Vasilieva
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A Ya Shkuropatov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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6
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Su Y. The effect of different light regimes on pigments in Coscinodiscus granii. PHOTOSYNTHESIS RESEARCH 2019; 140:301-310. [PMID: 30478709 DOI: 10.1007/s11120-018-0608-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
The influence of six different light regimes throughout the photosynthetically active radiation range (from 400 to 700 nm, including blue, green, yellow, red-orange, red, and white) at two intensities (100 and 300 µmol photons m-2 s-1) on pigmentation was assessed for the centric marine diatom Coscinodiscus granii for the first time. Chlorophyll (Chl) a and fucoxanthin were the dominating pigments in all treatments. The cellular concentrations of light harvesting pigment (Chl a, Chl c1 + c2, and fucoxanthin) were higher at 100 than at 300 µmol photons m-2 s-1 at all wavelengths, with the largest increases at red and blue light. The normalized concentrations of photoprotective pigments (violaxanthin, zeaxanthin, diadinoxanthin, and diatoxanthin) were higher at high light intensity than in cells grown at low light intensity. An increase in β-carotene in low light conditions is expected as the increased Chl a was related to increased photosynthetic subunits which require β-carotene (bound to photosystem core). At 300 µmol photons m-2 s-1, yellow light resulted in significantly lower concentration of most of the detected pigments than the other wavelengths. At 100 µmol photons m-2 s-1, W and B light led to statistically lower and higher concentration of most of the detected pigments than the other wavelengths, respectively.
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Affiliation(s)
- Yanyan Su
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
- Carlsberg Research Laboratory, Bjerregaardsvej 5, 2500, Valby, Denmark.
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7
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Fiedor L, Pilch M. Side Methyl Groups Control the Conformation and Contribute to Symmetry Breaking of Isoprenoid Chromophores. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Leszek Fiedor
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University Gronostajowa 7 30-387 Kraków Poland
| | - Mariusz Pilch
- Faculty of Biochemistry, Biophysics and BiotechnologyJagiellonian University Gronostajowa 7 30-387 Kraków Poland
- Faculty of ChemistryJagiellonian University Gronostajowa 2 30-387 Kraków Poland
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8
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Fiedor L, Pilch M. Side Methyl Groups Control the Conformation and Contribute to Symmetry Breaking of Isoprenoid Chromophores. Angew Chem Int Ed Engl 2018; 57:6501-6506. [PMID: 29601118 DOI: 10.1002/anie.201802094] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 01/02/2023]
Abstract
Ab initio DFT computations reveal that the essential structural and photophysical features of the conjugated π-electron system of retinal and carotenoids are dictated by "innocent" methyl substituents. These methyl groups shape the conformation and symmetry of the isoprenoid chromophores by causing a sigmoidal distortion of the polyene skeleton and increasing its flexibility, which facilitates fitting to their binding pockets in proteins. Comparison of in vacuo conformations of the chromophores with their native (protein-bound) conformations showed, surprisingly, that the peripheral groups and interactions with the protein environment are much less significant than the methyl side groups in tuning their structural features. The methyl side groups also contribute to a loss of symmetry elements specific to linear polyenes. In effect, the symmetry-imposed restrictions on the chromophore electronic properties are disabled, which is of tremendous relevance to their photophysics. This is evidenced by their non-negligible permanent dipole moments and by the simulated and experimentally measured circular dichroism spectra, which necessarily reflect the chirality of the conjugated π-electron system.
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Affiliation(s)
- Leszek Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Mariusz Pilch
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.,Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
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9
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Daskalakis V, Papadatos S. The Photosystem II Subunit S under Stress. Biophys J 2018; 113:2364-2372. [PMID: 29211990 DOI: 10.1016/j.bpj.2017.09.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 09/29/2017] [Indexed: 01/08/2023] Open
Abstract
Nonphotochemical quenching is the protective mechanism against overexcitation of photosystem II, triggered by excess ΔpH in photosynthetic membranes. The light-harvesting complexes (LHCs), the de-epoxidation of violaxanthin to zeaxanthin, and the photosystem II subunit S (PsbS) work in synergy for an optimized multilevel response. Understanding the fine details of this synergy has proven challenging to scientific research. Here, we employ large-scale, all-atom molecular simulations and beyond experimental insight, we proceed a step further in identifying the PsbS dynamics that could possibly be associated with this synergy. For the first time, to our knowledge, we probe the distinct behavior of PsbS under ΔpH that probes the details of the potential dimer-to-monomer transition, and in a violaxanthin/zeaxanthin-rich membrane, at an all-atom resolution. We propose that the lumen-exposed residues, threonine 162 and glutamic acid 173, form stabilizing hydrogen bonds between the PsbS monomers only at high lumen pH, whereas at low pH (excess ΔpH) this interaction is lost, and leads to higher flexibility of the protein and potentially to the dimer-to-monomer transition. Lastly, we discuss how conformational changes under the presence of ΔpH/zeaxanthin are related to the PsbS role in the current nonphotochemical quenching model in the literature. For the latter, we probe a PsbS-monomeric LHCII association. The association is proposed to potentially alter the monomeric LHCII sensitivity to ΔpH by changing the pKa values of interacting LHCII residues. This serves as an example where protonation-ligation events enhance protein-protein interactions fundamental to many life processes.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus.
| | - Sotiris Papadatos
- Department of Environmental Science and Technology, Cyprus University of Technology, Limassol, Cyprus
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10
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Herascu N, Hunter MS, Shafiei G, Najafi M, Johnson TW, Fromme P, Zazubovich V. Spectral Hole Burning in Cyanobacterial Photosystem I with P700 in Oxidized and Neutral States. J Phys Chem B 2016; 120:10483-10495. [PMID: 27661089 DOI: 10.1021/acs.jpcb.6b07803] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicoleta Herascu
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - Mark S. Hunter
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States
| | - Golia Shafiei
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - Mehdi Najafi
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
| | - T. Wade Johnson
- Department
of Chemistry, Susquehanna University, Selinsgrove, Pennsylvania, United States
| | - Petra Fromme
- Department
of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, United States
| | - Valter Zazubovich
- Department
of Physics, Concordia University, 7141 Sherbrooke Street West, Montreal, H4B 1R4, Quebec, Canada
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11
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Fiedor L, Fiedor J, Pilch M. Effects of Molecular Symmetry on the Electronic Transitions in Carotenoids. J Phys Chem Lett 2016; 7:1821-9. [PMID: 27138647 DOI: 10.1021/acs.jpclett.6b00637] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The aim of this work is the verification of symmetry effects on the electronic absorption spectra of carotenoids. The symmetry breaking in cis-β-carotenes and in carotenoids with nonlinear π-electron system is of virtually no effect on the dark transitions in these pigments, in spite of the loss of the inversion center and evident changes in their electronic structure. In the cis isomers, the S2 state couples with the higher excited states and the extent of this coupling depends on the position of the cis bend. A confrontation of symmetry properties of carotenoids with their electronic absorption and IR and Raman spectra shows that they belong to the C1 or C2 but not the C2h symmetry group, as commonly assumed. In these realistic symmetries all the electronic transitions are symmetry-allowed and the absence of some transitions, such as the dark S0 → S1 transition, must have another physical origin. Most likely it is a severe deformation of the carotenoid molecule in the S1 state, unachievable directly from the ground state, which means that the Franck-Condon factors for a vertical S0 → S1 transition are negligible because the final state is massively displaced along the vibrational coordinates. The implications of our findings have an impact on the understanding of the photophysics and functioning of carotenoids.
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Affiliation(s)
- Leszek Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Kraków, Poland
| | - Joanna Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Kraków, Poland
- Faculty of Physics and Applied Computer Science, AGH-University of Science and Technology , Mickiewicza 30, 30-059 Kraków, Poland
| | - Mariusz Pilch
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Gronostajowa 7, 30-387 Kraków, Poland
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
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12
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Parra MJ, Acuña KI, Sierra-Almeida A, Sanfuentes C, Saldaña A, Corcuera LJ, Bravo LA. Photosynthetic Light Responses May Explain Vertical Distribution of Hymenophyllaceae Species in a Temperate Rainforest of Southern Chile. PLoS One 2015; 10:e0145475. [PMID: 26699612 PMCID: PMC4699196 DOI: 10.1371/journal.pone.0145475] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 12/06/2015] [Indexed: 11/19/2022] Open
Abstract
Some epiphytic Hymenophyllaceae are restricted to lower parts of the host (< 60 cm; 10-100 μmol photons m(-2) s(-1)) in a secondary forest of Southern Chile; other species occupy the whole host height (≥ 10 m; max PPFD > 1000 μmol photons m(-2) s(-1)). Our aim was to study the photosynthetic light responses of two Hymenophyllaceae species in relation to their contrasting distribution. We determined light tolerance of Hymenoglossum cruentum and Hymenophyllum dentatum by measuring gas exchange, PSI and PSII light energy partitioning, NPQ components, and pigment contents. H. dentatum showed lower maximum photosynthesis rates (A max) than H. cruentum, but the former species kept its net rates (An) near Amax across a wide light range. In contrast, in the latter one, An declined at PPFDs > 60 μmol photons m(-2) s(-1). H. cruentum, the shadiest plant, showed higher chlorophyll contents than H. dentatum. Differences in energy partitioning at PSI and PSII were consistent with gas exchange results. H. dentatum exhibited a higher light compensation point of the partitioning of absorbed energy between photochemical Y(PSII) and non-photochemical Y(NPQ) processes. Hence, both species allocated energy mainly toward photochemistry instead of heat dissipation at their light saturation points. Above saturation, H. cruentum had higher heat dissipation than H. dentatum. PSI yield (YPSI) remained higher in H. dentatum than H. cruentum in a wider light range. In both species, the main cause of heat dissipation at PSI was a donor side limitation. An early dynamic photo-inhibition of PSII may have caused an over reduction of the Qa+ pool decreasing the efficiency of electron donation to PSI. In H. dentatum, a slight increase in heat dissipation due to acceptor side limitation of PSI was observed above 300 μmol photons m(-2)s(-1). Differences in photosynthetic responses to light suggest that light tolerance and species plasticity could explain their contrasting vertical distribution.
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Affiliation(s)
- María José Parra
- Departamento de Ciencias Biológicas y Químicas, Facultad de Ciencia, Universidad San Sebastián, Cruz 1577, Concepción, Chile
| | - Karina I. Acuña
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales. Facultad de Ciencias Agropecuarias y Forestales & Center of Plant, Soil Interactions and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Casilla 54-D, Temuco, Chile
| | - Angela Sierra-Almeida
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
- Instituto de Ecología y Biodiversidad (IEB), Casilla 653, Santiago, Chile
| | - Camila Sanfuentes
- Instituto de Ecología y Biodiversidad (IEB), Casilla 653, Santiago, Chile
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Chile
| | - Alfredo Saldaña
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Luis J. Corcuera
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - León A. Bravo
- Laboratorio de Fisiología y Biología Molecular Vegetal, Departamento de Ciencias Agronómicas y Recursos Naturales. Facultad de Ciencias Agropecuarias y Forestales & Center of Plant, Soil Interactions and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Casilla 54-D, Temuco, Chile
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13
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Dhanapal AP, Ray JD, Singh SK, Hoyos-Villegas V, Smith JR, Purcell LC, King CA, Fritschi FB. Association Mapping of Total Carotenoids in Diverse Soybean Genotypes Based on Leaf Extracts and High-Throughput Canopy Spectral Reflectance Measurements. PLoS One 2015; 10:e0137213. [PMID: 26368323 PMCID: PMC4569184 DOI: 10.1371/journal.pone.0137213] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/13/2015] [Indexed: 11/19/2022] Open
Abstract
Carotenoids are organic pigments that are produced predominantly by photosynthetic organisms and provide antioxidant activity to a wide variety of plants, animals, bacteria, and fungi. The carotenoid biosynthetic pathway is highly conserved in plants and occurs mostly in chromoplasts and chloroplasts. Leaf carotenoids play important photoprotective roles and targeted selection for leaf carotenoids may offer avenues to improve abiotic stress tolerance. A collection of 332 soybean [Glycine max (L.) Merr.] genotypes was grown in two years and total leaf carotenoid content was determined using three different methods. The first method was based on extraction and spectrophotometric determination of carotenoid content (eCaro) in leaf tissue, whereas the other two methods were derived from high-throughput canopy spectral reflectance measurements using wavelet transformed reflectance spectra (tCaro) and a spectral reflectance index (iCaro). An association mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify SNPs associated with total carotenoid content using a mixed linear model based on data from two growing seasons. A total of 28 SNPs showed a significant association with total carotenoid content in at least one of the three approaches. These 28 SNPs likely tagged 14 putative loci for carotenoid content. Six putative loci were identified using eCaro, five loci with tCaro, and nine loci with iCaro. Three of these putative loci were detected by all three carotenoid determination methods. All but four putative loci were located near a known carotenoid-related gene. These results showed that carotenoid markers can be identified in soybean using extract-based as well as by high-throughput canopy spectral reflectance-based approaches, demonstrating the utility of field-based canopy spectral reflectance phenotypes for association mapping.
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Affiliation(s)
- Arun Prabhu Dhanapal
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Jeffery D. Ray
- Crop Genetics Research Unit, USDA-ARS, Stoneville, Mississippi, United States of America
| | - Shardendu K. Singh
- Crop Systems and Global Change Lab, USDA-ARS, Beltsville, Maryland, United States of America
| | - Valerio Hoyos-Villegas
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - James R. Smith
- Crop Genetics Research Unit, USDA-ARS, Stoneville, Mississippi, United States of America
| | - Larry C. Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - C. Andy King
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Felix B. Fritschi
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
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Fufina TY, Vasilieva LG, Gabdulkhakov AG, Shuvalov VA. The L(M196)H mutation in Rhodobacter sphaeroides reaction center results in new electrostatic interactions. PHOTOSYNTHESIS RESEARCH 2015; 125:23-29. [PMID: 25480338 DOI: 10.1007/s11120-014-0062-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
New histidine residue was introduced in M196 position in the reaction center of Rhodobacter sphaeroides in order to alter polarity of the BChl dimer's protein environment and to study how it affects properties and structure of the primary electron donor P. It was shown that in the absorption spectrum of the mutant RC the 6 nm red shift of the Q Y P band was observed together with considerable decrease of its amplitude. The mid-point potential of P/P (+) in the mutant RC was increased by +65 (±15) mV as compared to the E m P/P (+) value in the wild-type RC suggesting that the mutation resulted in new pigment-protein interactions. Crystal structure of RC L(M196)H determined at 2.4 Å resolution implies that BChl Р В and introduced histidine-M196 organize new electrostatic contact that may be specified either as π-π staking or as hydrogen-π interaction. Besides, the structure of the mutants RC shows that His-M196 apparently became involved in hydrogen bond network existing in BChl Р В vicinity that may favor stability of the mutant RC.
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Affiliation(s)
- Tatiana Y Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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15
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Nishio M, Umezawa Y, Fantini J, Weiss MS, Chakrabarti P. CH-π hydrogen bonds in biological macromolecules. Phys Chem Chem Phys 2015; 16:12648-83. [PMID: 24836323 DOI: 10.1039/c4cp00099d] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This is a sequel to the previous Perspective "The CH-π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates", which featured in a PCCP themed issue on "Weak Hydrogen Bonds - Strong Effects?": Phys. Chem. Chem. Phys., 2011, 13, 13873-13900. Evidence that weak hydrogen bonds play an enormously important role in chemistry and biochemistry has now accumulated to an extent that the rigid classical concept of hydrogen bonds formulated by Pauling needs to be seriously revised and extended. The concept of a more generalized hydrogen bond definition is indispensable for understanding the folding mechanisms of proteins. The CH-π hydrogen bond, a weak molecular force occurring between a soft acid CH and a soft base π-electron system, among all is one of the most important and plays a functional role in defining the conformation and stability of 3D structures as well as in many molecular recognition events. This concept is also valuable in structure-based drug design efforts. Despite their frequent occurrence in organic molecules and bio-molecules, the importance of CH-π hydrogen bonds is still largely unknown to many chemists and biochemists. Here we present a review that deals with the evidence, nature, characteristics and consequences of the CH-π hydrogen bond in biological macromolecules (proteins, nucleic acids, lipids and polysaccharides). It is hoped that the present Perspective will show the importance of CH-π hydrogen bonds and stimulate interest in the interactions of biological macromolecules, one of the most fascinating fields in bioorganic chemistry. Implication of this concept is enormous and valuable in the scientific community.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338, Minamioya, Machida-shi, Tokyo 194-0031, Japan.
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16
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Qin X, Wang W, Chang L, Chen J, Wang P, Zhang J, He Y, Kuang T, Shen JR. Isolation and characterization of a PSI-LHCI super-complex and its sub-complexes from a siphonaceous marine green alga, Bryopsis Corticulans. PHOTOSYNTHESIS RESEARCH 2015; 123:61-76. [PMID: 25214185 DOI: 10.1007/s11120-014-0039-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 09/03/2014] [Indexed: 05/24/2023]
Abstract
A novel super-complex of photosystem I (PSI)-light-harvesting complex I (LHCI) was isolated from a siphonaceous marine green alga, Bryopsis corticulans. The super-complex contained 9-10 Lhca antennas as external LHCI bound to the core complex. The super-complex was further disintegrated into PSI core and LHCI sub-complexes, and analysis of the pigment compositions by high-performance liquid chromatography revealed unique characteristics of the B. corticulans PSI in that one PSI core contained around 14 α-carotenes and 1-2 ε-carotenes. This is in sharp contrast to the PSI core from higher plants and most cyanobacteria where only β-carotenes were present, and is the first report for an α-carotene-type PSI core complex among photosynthetic eukaryotes, suggesting a structural flexibility of the PSI core. Lhca antennas from B. corticulans contained seven kinds of carotenoids (siphonaxanthin, all-trans neoxanthin, 9'-cis neoxanthin, violaxanthin, siphonein, ε-carotene, and α-carotene) and showed a high carotenoid:chlorophyll ratio of around 7.5:13. PSI-LHCI super-complex and PSI core showed fluorescence emission peaks at 716 and 718 nm at 77 K, respectively; whereas two Lhca oligomers had fluorescence peaks at 681 and 684 nm, respectively. By comparison with spinach PSI preparations, it was found that B. corticulans PSI had less red chlorophylls, most of them are present in the core complex but not in the outer light-harvesting systems. These characteristics may contribute to the fine tuning of the energy transfer network, and to acclimate to the ever-changing light conditions under which the unique green alga inhabits.
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Affiliation(s)
- Xiaochun Qin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China,
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17
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Stamatakis K, Tsimilli-Michael M, Papageorgiou GC. On the question of the light-harvesting role of β-carotene in photosystem II and photosystem I core complexes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 81:121-7. [PMID: 24529497 DOI: 10.1016/j.plaphy.2014.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 01/22/2014] [Indexed: 05/24/2023]
Abstract
β-Carotene is the only carotenoid present in the core complexes of Photosystems I and II. Its proximity to chlorophyll a molecules enables intermolecular electronic interactions, including β-carotene to chlorophyll a electronic excitation transfers. However, it has been well documented that, compared to chlorophylls and to phycobilins, the light harvesting efficiency of β-carotenes for photosynthetic O2 evolution is poor. This is more evident in cyanobacteria than in plants and algae because they lack accessory light harvesting pigments with absorptions that overlap the β-carotene absorption. In the present work we investigated the light harvesting role of β-carotenes in the cyanobacterium Synechococcus sp. PCC 7942 using selective β-carotene excitation and selective Photosystem detection of photo-induced electron transport to and from the intersystem plastoquinones (the plastoquinone pool). We report that, although selectively excited β-carotenes transfer electronic excitation to the chlorophyll a of both photosystems, they enable only the oxidation of the plastoquinone pool by Photosystem I but not its reduction by Photosystem II. This may suggest a light harvesting role for the β-carotenes of the Photosystem I core complex but not for those of the Photosystem II core complex. According to the present investigation, performed with whole cyanobacterial cells, the lower photosynthesis yields measured with β-Car-absorbed light can be attributed to the different excitation trapping efficiencies in the reaction centers of PSI and PSII.
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Affiliation(s)
- Kostas Stamatakis
- Institute of Biosciences and Applications, National Center for Scentific Research Demokritos, Aghia Paraskevi, Attikis 15310, Greece.
| | | | - George C Papageorgiou
- Institute of Biosciences and Applications, National Center for Scentific Research Demokritos, Aghia Paraskevi, Attikis 15310, Greece
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18
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Pšenčík J, Butcher SJ, Tuma R. Chlorosomes: Structure, Function and Assembly. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Abstract
Chlorosomes are large light-harvesting complexes found in three phyla of anoxygenic photosynthetic bacteria. Chlorosomes are primarily composed of self-assembling pigment aggregates. In addition to the main pigment, bacteriochlorophyll c, d, or e, chlorosomes also contain variable amounts of carotenoids. Here, we use X-ray scattering and electron cryomicroscopy, complemented with absorption spectroscopy and pigment analysis, to compare the morphologies, structures, and pigment compositions of chlorosomes from Chloroflexus aurantiacus grown under two different light conditions and Chlorobaculum tepidum. High-purity chlorosomes from C. aurantiacus contain about 20% more carotenoid per bacteriochlorophyll c molecule when grown under low light than when grown under high light. This accentuates the light-harvesting function of carotenoids, in addition to their photoprotective role. The low-light chlorosomes are thicker due to the overall greater content of pigments and contain domains of lamellar aggregates. Experiments where carotenoids were selectively extracted from intact chlorosomes using hexane proved that they are located in the interlamellar space, as observed previously for species belonging to the phylum Chlorobi. A fraction of the carotenoids are localized in the baseplate, where they are bound differently and cannot be removed by hexane. In C. tepidum, carotenoids cannot be extracted by hexane even from the chlorosome interior. The chemical structure of the pigments in C. tepidum may lead to π-π interactions between carotenoids and bacteriochlorophylls, preventing carotenoid extraction. The results provide information about the nature of interactions between bacteriochlorophylls and carotenoids in the protein-free environment of the chlorosome interior.
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20
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Dall'Osto L, Piques M, Ronzani M, Molesini B, Alboresi A, Cazzaniga S, Bassi R. The Arabidopsis nox mutant lacking carotene hydroxylase activity reveals a critical role for xanthophylls in photosystem I biogenesis. THE PLANT CELL 2013; 25:591-608. [PMID: 23396829 PMCID: PMC3608780 DOI: 10.1105/tpc.112.108621] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 05/05/2023]
Abstract
Carotenes, and their oxygenated derivatives xanthophylls, are essential components of the photosynthetic apparatus. They contribute to the assembly of photosynthetic complexes and participate in light absorption and chloroplast photoprotection. Here, we studied the role of xanthophylls, as distinct from that of carotenes, by characterizing a no xanthophylls (nox) mutant of Arabidopsis thaliana, which was obtained by combining mutations targeting the four carotenoid hydroxylase genes. nox plants retained α- and β-carotenes but were devoid in xanthophylls. The phenotype included depletion of light-harvesting complex (LHC) subunits and impairment of nonphotochemical quenching, two effects consistent with the location of xanthophylls in photosystem II antenna, but also a decreased efficiency of photosynthetic electron transfer, photosensitivity, and lethality in soil. Biochemical analysis revealed that the nox mutant was specifically depleted in photosystem I function due to a severe deficiency in PsaA/B subunits. While the stationary level of psaA/B transcripts showed no major differences between genotypes, the stability of newly synthesized PsaA/B proteins was decreased and translation of psaA/B mRNA was impaired in nox with respect to wild-type plants. We conclude that xanthophylls, besides their role in photoprotection and LHC assembly, are also needed for photosystem I core translation and stability, thus making these compounds indispensable for autotrophic growth.
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Affiliation(s)
- Luca Dall'Osto
- Dipartimento di Biotecnologie, Università di Verona, 37134 Verona, Italy.
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21
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Landrum JT, Chatfield DC, Mebel AM, Alvarez-Calderon F, Fernandez MV. The conformation of end-groups is one determinant of carotenoid topology suitable for high fidelity molecular recognition: a study of beta- and epsilon-end-groups. Arch Biochem Biophys 2009; 493:169-74. [PMID: 19850003 DOI: 10.1016/j.abb.2009.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 10/13/2009] [Accepted: 10/15/2009] [Indexed: 11/18/2022]
Abstract
Conformation affects a carotenoid's ability to bind selectively to proteins. We calculated adiabatic energy profiles for rotating the ring end-groups around the C6C7 bond and for flexing of the ring with respect to the polyene chain. The choice of computational methods is important. A low, 4.2 kcal/mol barrier to rotation exists for a beta-ring. An 8.3 kcal/mol barrier exists for rotation of an epsilon-ring. Rotation of the epsilon-ring is sensitive to substitution at C3. In the absence of external forces neither beta- nor epsilon-rings are rotationally constrained. The nearly parallel alignment of the beta-ring to the C6C7 bond axis contrasts to the more perpendicular orientation of the epsilon-ring. Flexion of a beta-ring to the minimized epsilon-ring conformation requires approximately 23 kcal/mol; extension of the epsilon-ring to the minimized beta-ring conformation requires approximately 8 kcal/mol. Selectivity associated with beta- versus epsilon-rings is dominated by the inability of the beta-ring to flex to minimize protein/ring steric interactions and maximize van der Waal's attractions with the binding site.
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Affiliation(s)
- John T Landrum
- Florida International University, Department of Chemistry and Biochemistry, Miami, FL 33199, USA.
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22
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Fiedor J, Pilch M, Fiedor L. Tuning the Thermodynamics of Association of Transmembrane Helices. J Phys Chem B 2009; 113:12831-8. [DOI: 10.1021/jp903789y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joanna Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Gronostajowa 7, Poland, Department of Medical Physics and Biophysics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, 30-059 Kraków, Reymonta 19, Poland, and Higher Vocational School, 33-100 Tarnów, Mickiewicza 8, Poland
| | - Mariusz Pilch
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Gronostajowa 7, Poland, Department of Medical Physics and Biophysics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, 30-059 Kraków, Reymonta 19, Poland, and Higher Vocational School, 33-100 Tarnów, Mickiewicza 8, Poland
| | - Leszek Fiedor
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Gronostajowa 7, Poland, Department of Medical Physics and Biophysics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, 30-059 Kraków, Reymonta 19, Poland, and Higher Vocational School, 33-100 Tarnów, Mickiewicza 8, Poland
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23
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Liu WL, Wang ZG, Zheng ZR, Li AH, Su WH. Effect of β-Ring Rotation on the Structures and Vibrational Spectra of β-Carotene: Density Functional Theory Analysis. J Phys Chem A 2008; 112:10580-5. [PMID: 18821738 DOI: 10.1021/jp802024v] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Wei-Long Liu
- Center for Condensed Matter Science and Technology, Department of Physics, Harbin Institute of Technology, Harbin 150001, China, Institute of Atomic and Molecular Physics, Ji Lin University, Changchun 130012, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, and College of Physics, Ji Lin University, Changchun 130023, China
| | - Zhi-Gang Wang
- Center for Condensed Matter Science and Technology, Department of Physics, Harbin Institute of Technology, Harbin 150001, China, Institute of Atomic and Molecular Physics, Ji Lin University, Changchun 130012, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, and College of Physics, Ji Lin University, Changchun 130023, China
| | - Zhi-Ren Zheng
- Center for Condensed Matter Science and Technology, Department of Physics, Harbin Institute of Technology, Harbin 150001, China, Institute of Atomic and Molecular Physics, Ji Lin University, Changchun 130012, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, and College of Physics, Ji Lin University, Changchun 130023, China
| | - Ai-Hua Li
- Center for Condensed Matter Science and Technology, Department of Physics, Harbin Institute of Technology, Harbin 150001, China, Institute of Atomic and Molecular Physics, Ji Lin University, Changchun 130012, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, and College of Physics, Ji Lin University, Changchun 130023, China
| | - Wen-Hui Su
- Center for Condensed Matter Science and Technology, Department of Physics, Harbin Institute of Technology, Harbin 150001, China, Institute of Atomic and Molecular Physics, Ji Lin University, Changchun 130012, China, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China, and College of Physics, Ji Lin University, Changchun 130023, China
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24
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Ghosh D, Hachmann J, Yanai T, Chan GKL. Orbital optimization in the density matrix renormalization group, with applications to polyenes and β-carotene. J Chem Phys 2008; 128:144117. [DOI: 10.1063/1.2883976] [Citation(s) in RCA: 268] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hatfield MPD, Palermo NY, Csontos J, Murphy RF, Lovas S. Quantum chemical quantification of weakly polar interaction energies in the TC5b miniprotein. J Phys Chem B 2008; 112:3503-8. [PMID: 18303883 DOI: 10.1021/jp077674h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tertiary structure of the TC5b miniprotein is stabilized by inter-residue interactions of the Trp-cage, which is composed of a Tyr and several Pro residues surrounding a central Trp residue. The interactions include Ar-Ar (aromatic side-chain-aromatic side-chain), Ar-NH (aromatic side-chain-backbone amide), and CH-pi (aromatic side-chain-aliphatic hydrogen) interactions. In the present work, the strength of the weakly polar interactions found in the TC5b miniprotein was quantified using all of the available 38 NMR structures (1L2Y) from the Protein Data Bank with DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory and molecular fragmentation with capping of the partial structures. The energies of interaction between the individual residues of the Trp-cage range between -5.85+/-1.41 and -21.30+/-0.88 kcal mol(-1), leading to a significant total structural stabilization energy of -52.13+/-2.56 kcal mol(-1) of which about 50% is from the weakly polar interactions. Furthermore, the strengths of the individual weakly polar interactions are between -2.32+/-0.17 and -2.93+/-0.12 kcal mol(-1) for the CH-pi interactions, between -2.48+/-0.97 and -3.09+/-1.02 kcal mol(-1) for the Ar-NH interaction and -2.74+/-1.06 kcal mol(-1) for the Ar-Ar interaction.
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Zhao GJ, Han KL. Site-specific solvation of the photoexcited protochlorophyllide a in methanol: formation of the hydrogen-bonded intermediate state induced by hydrogen-bond strengthening. Biophys J 2007; 94:38-46. [PMID: 17827245 PMCID: PMC2134880 DOI: 10.1529/biophysj.107.113738] [Citation(s) in RCA: 371] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The site-specific solvation of the photoexcited protochlorophyllide a (Pchlide a) in methanol solvent was investigated using the time-dependent density functional theory method for the first time to our knowledge. The intermolecular site-specific coordination and hydrogen-bonding interactions between Pchlide a and methanol molecules play a very important role in the steady-state and time-resolved spectra. All the calculated absorption and fluorescence spectra of the isolated Pchlide a and its coordinated and hydrogen-bonded complexes with methanol demonstrate that the novel fluorescence shoulder at approximately 690 nm of Pchlide a in methanol should be ascribed to the coordinated and hydrogen-bonded Pchlide a-(MeOH)(4) complex. This coordinated and hydrogen-bonded complex can also account for the intermediate state found in the time-resolved spectroscopic studies. Herein, we have theoretically confirmed that the intermolecular coordination and hydrogen bonds between Pchlide a and methanol molecules can be strengthened in the electronically excited state of Pchlide a. Furthermore, the site-specific solvation of the photoexcited Pchlide a can be induced by the intermolecular coordination and hydrogen-bond strengthening upon photoexcitation. Then the hydrogen-bonded intermediate state is formed in 22-27 ps timescales after the site-specific solvation. All the steady-state and time-resolved spectral features of Pchlide a in different solvents can be explained by the formation of this hydrogen-bonded intermediate state after the site-specific solvation, which is induced by the coordination and hydrogen-bond strengthening.
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Affiliation(s)
- Guang-Jiu Zhao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, China.
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27
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Vokácová Z, Burda JV. Computational study on spectral properties of the selected pigments from various photosystems: structure-transition energy relationship. J Phys Chem A 2007; 111:5864-78. [PMID: 17555304 DOI: 10.1021/jp071639t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this study, the most important kinds of pigments (chlorophylls, bacteriochlorophylls, phycobilins, and carotenoids) from various photosystems were explored. For the most stable conformations, electronic transitions were determined at the TDDFT/6-31+G(d) level with the B3PW91 functional and compared to measured spectra. The group of carotenoids was also investigated at the TDA/TDDFT level with the BLYP functional. The energies of Qy transitions are systematically blue-shifted by about 50-100 nm in the case of (bacterio)chlorophyll and pheophytin molecules. Nevertheless, the correct relative order of the Q lines among various chlorophyll types was obtained through comparison with experimental results. Much better agreement was obtained for the Soret band, for which the differences between calculated and measured transitions were at most 35 nm. In the case of phycobilins, the first transition line was estimated to be at lower frequencies (around 500 nm) with a very similar blue shift of about 100 nm from experimental values. The influence of anchoring cysteine side chain(s) was found to be marginal. A dominant effect of the linear polyene chain on the determined spectral lines was found in the case of carotenoids. Nevertheless, the impact of beta-cycles and epoxy and keto groups is clearly visible as well. The high intensity of the first allowed transition matches different characters of the HOMO and LUMO. In the case of fucoxanthin, the TDA method also predicts the Bu- state to lie below the 1Bu+ state. Because the shift of electron transitions is approximately proportional to the size of the pi-conjugated system, the shift of the calculated transitions compared to experimental values is practically constant for the same excitations of (bacterio)chlorophyll and phycobilin molecules. However, this is not true for carotenoids, for which both the transition energy and the shift of the transition vary with the number of conjugated double bonds.
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Affiliation(s)
- Zuzana Vokácová
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16 Prague 2, Czech Republic
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Cuesta IG, Pedersen TB, Koch H, Sánchez de Merás A. Carbon Nanorings: A Challenge to Theoretical Chemistry. Chemphyschem 2006; 7:2503-7. [PMID: 17058312 DOI: 10.1002/cphc.200600362] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
High-level quantum-chemical methods show that the binding in the inclusion complex of hexamethylbenzene (HMB) in 6-cycloparaphenilacetylene (6-CPPA) cannot be explained only in terms of electrostatic interactions-caused by the polarization associated to curved pi-conjugated systems-and the inclusion of dispersion forces is definitely needed. The theoretical description of van der Waals interactions is notoriously complicated and in fact some DFT methods cannot even predict the existence of the relatively small supramolecular nanoring studied here. However, ab initio MP2 calculations agree with experimental data and show that, in the considered complex, the HMB fragment is placed at the center of the 6-CPPA ring. The binding energy, which is not available experimentally, is calculated to be around -14 kcal mol(-1) with a lower limit of -19 kcal mol(-1).
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Affiliation(s)
- I García Cuesta
- Instituto de Ciencia Molecular, Universidad de Valencia, PO Box 22085, 46071 Valencia, Spain.
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Billsten HH, Sundström V, Polívka T. Self-Assembled Aggregates of the Carotenoid Zeaxanthin: Time-Resolved Study of Excited States. J Phys Chem A 2005; 109:1521-9. [PMID: 16833473 DOI: 10.1021/jp044847j] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we present a way of controlling the formation of the two types of zeaxanthin aggregates in hydrated ethanol: J-zeaxanthin (head-to-tail aggregate, characteristic absorption band at 530 nm) and H-zeaxanthin (card-pack aggregate, characteristic absorption band at 400 nm). To control whether J- or H- zeaxanthin is formed, three parameters are important: (1) pH, that is, the ability to form a hydrogen bond; (2) the initial concentration of zeaxanthin, that is, the distance between zeaxanthin molecules; and (3) the ratio of ethanol/water. To create H-aggregates, the ability to form hydrogen bonds is crucial, while J-aggregates are preferentially formed when hydrogen-bond formation is prevented. Further, the formation of J-aggregates requires a high initial zeaxanthin concentration and a high ethanol/water ratio, while H-aggregates are formed under the opposite conditions. Time-resolved experiments revealed that excitation of the 530-nm band of J-zeaxanthin produces a different relaxation pattern than excitation at 485 and 400 nm, showing that the 530-nm band is not a vibrational band of the S2 state but a separate excited state formed by J-type aggregation. The excited-state dynamics of zeaxanthin aggregates are affected by annihilation that occurs in both J- and H-aggregates. In H-aggregates, the dominant annihilation component is on the subpicosecond time scale, while the main annihilation component for the J-aggregate is 5 ps. The S(1) lifetimes of aggregates are longer than in solution, yielding 20 and 30 ps for H- and J-zeaxanthin, respectively. In addition, H-type aggregation promotes a new relaxation channel that forms the zeaxanthin triplet state.
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