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Nakamura T, Singh M, Sugiura M, Kato S, Yamamoto R, Kandori H, Furutani Y. SNap Bond, a Crucial Hydrogen Bond Between Ser in Helix 3 and Asn in Helix 4, Regulates the Structural Dynamics of Heliorhodopsin. J Mol Biol 2024; 436:168666. [PMID: 38880378 DOI: 10.1016/j.jmb.2024.168666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/18/2024]
Abstract
Heliorhodopsin (HeR) is a new rhodopsin family discovered in 2018 through functional metagenomic analysis. Similar to microbial rhodopsins, HeR has an all-trans retinal chromophore, and its photoisomerization to the 13-cis form triggers a relatively slow photocycle with sequential intermediate states (K, M, and O intermediates). The O intermediate has a relatively long lifetime and is a putative active state for transferring signals or regulating enzymatic reactions. Although the first discovered HeR, 48C12, was found in bacteria and the second HeR (TaHeR) was found in archaea, their key amino acid residues and molecular architectures have been recognized to be well conserved. Nevertheless, the rise and decay kinetics of the O intermediate are faster in 48C12 than in TaHeR. Here, using a new infrared spectroscopic technique with quantum cascade lasers, we clarified that the hydrogen bond between transmembrane helices (TM) 3 and 4 is essential for the altered O kinetics (Ser112 and Asn138 in 48C12). Interconverting mutants of 48C12 and TaHeR clearly revealed that the hydrogen bond is important for regulating the dynamics of the O intermediate. Overall, our study sheds light on the importance of the hydrogen bond between TM3 and TM4 in heliorhodopsins, similar to the DC gate in channelrhodopsins.
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Affiliation(s)
- Toshiki Nakamura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Manish Singh
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Soichiro Kato
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Ryo Yamamoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.
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2
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Liang S, Fu K, Li X, Wang Z. Unveiling the spatiotemporal dynamics of membrane fouling: A focused review on dynamic fouling characterization techniques and future perspectives. Adv Colloid Interface Sci 2024; 328:103179. [PMID: 38754212 DOI: 10.1016/j.cis.2024.103179] [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: 08/25/2023] [Revised: 03/12/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Membrane technology has emerged as a crucial method for obtaining clean water from unconventional sources in the face of water scarcity. It finds wide applications in wastewater treatment, advanced treatment, and desalination of seawater and brackish water. However, membrane fouling poses a huge challenge that limits the development of membrane-based water treatment technologies. Characterizing the dynamics of membrane fouling is crucial for understanding its development, mechanisms, and effective mitigation. Instrumental techniques that enable in situ or real-time characterization of the dynamics of membrane fouling provide insights into the temporal and spatial evolution of fouling, which play a crucial role in understanding the fouling mechanism and the formulation of membrane control strategies. This review consolidates existing knowledge about the principal advanced instrumental analysis technologies employed to characterize the dynamics of membrane fouling, in terms of membrane structure, morphology, and intermolecular forces. Working principles, applications, and limitations of each technique are discussed, enabling researchers to select appropriate methods for their specific studies. Furthermore, prospects for the future development of dynamic characterization techniques for membrane fouling are discussed, underscoring the need for continued research and innovation in this field to overcome the challenges posed by membrane fouling.
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Affiliation(s)
- Shuling Liang
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
| | - Kunkun Fu
- School of Aerospace Engineering and Applied Mechanics, Tongji University, Shanghai 200092, China
| | - Xuesong Li
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China.
| | - Zhiwei Wang
- School of Environmental Science and Engineering, Shanghai Institute of Pollution Control and Ecological Security, State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092, China
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3
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Odeyemi I, Douglas TA, Igie NF, Hargrove JA, Hamilton G, Bradley BB, Thai C, Le B, Unjia M, Wicherts D, Ferneyhough Z, Pillai A, Koirala S, Hagge LM, Polara H, Trievel RC, Fick RJ, Stelling AL. An optimized purification protocol for enzymatically synthesized S-adenosyl-L-methionine (SAM) for applications in solution state infrared spectroscopic studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 309:123816. [PMID: 38198991 DOI: 10.1016/j.saa.2023.123816] [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: 05/02/2023] [Revised: 11/07/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
S-adenosyl-L-methionine (SAM) is an abundant biomolecule used by methyltransferases to regulate a wide range of essential cellular processes such as gene expression, cell signaling, protein functions, and metabolism. Despite considerable effort, there remain many specificity challenges associated with designing small molecule inhibitors for methyltransferases, most of which exhibit off-target effects. Interestingly, NMR evidence suggests that SAM undergoes conformeric exchange between several states when free in solution. Infrared spectroscopy can detect different conformers of molecules if present in appreciable populations. When SAM is noncovalently bound within enzyme active sites, the nature and the number of different conformations of the molecule are likely to be altered from when it is free in solution. If there are unique structures or different numbers of conformers between different methyltransferase active sites, solution-state information may provide promising structural leads to increase inhibitor specificity for a particular methyltransferase. Toward this goal, frequencies measured in SAM's infrared spectra must be assigned to the motions of specific atoms via isotope incorporation at discrete positions. The incorporation of isotopes into SAM's structure can be accomplished via an established enzymatic synthesis using isotopically labeled precursors. However, published protocols produced an intense and highly variable IR signal which overlapped with many of the signals from SAM rendering comparison between isotopes challenging. We observed this intense absorption to be from co-purifying salts and the SAM counterion, producing a strong, broad signal at 1100 cm-1. Here, we report a revised SAM purification protocol that mitigates the contaminating salts and present the first IR spectra of isotopically labeled CD3-SAM. These results provide a foundation for isotopic labeling experiments of SAM that will define which atoms participate in individual molecular vibrations, as a means to detect specific molecular conformations.
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Affiliation(s)
- Isaiah Odeyemi
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Teri A Douglas
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Nosakhare F Igie
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - James A Hargrove
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Grace Hamilton
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Brianna B Bradley
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Cathy Thai
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Brendan Le
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Maitri Unjia
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Dylan Wicherts
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Zackery Ferneyhough
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Anjali Pillai
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Shailendra Koirala
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Laurel M Hagge
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Himanshu Polara
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Raymond C Trievel
- University of Michigan, 1150 W. Medical Center Dr., Ann Arbor, 48109, MI, USA
| | - Robert J Fick
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA
| | - Allison L Stelling
- The University of Texas at Dallas, 800 W. Campbell Rd., Richardson, 75080, TX, USA.
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4
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Agarwala N, Hastings G. Time-resolved FTIR difference spectroscopy for the study of photosystem I with high potential naphthoquinones incorporated into the A 1 binding site 2: Identification of neutral state quinone bands. PHOTOSYNTHESIS RESEARCH 2023; 158:1-11. [PMID: 37477846 DOI: 10.1007/s11120-023-01036-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
Time-resolved step-scan FTIR difference spectroscopy at 77 K has been used to study photosystem I (PSI) from Synechocystis sp. PCC 6803 with four high-potential, 1,4-naphthoquinones (NQs) incorporated into the A1 binding site. The incorporated quinones are 2-chloro-NQ (2ClNQ), 2-bromo-NQ (2BrNQ), 2,3-dichloro-NQ (Cl2NQ), and 2,3-dibromo-NQ (Br2NQ). For completeness 2-methyl-NQ (2MNQ) was also incorporated and studied. Previously, PSI with the same quinones incorporated were studied in the, so-called, anion spectral region between 1550 and 1400 cm-1 (Agarwala et al. in Biochim Biophys Acta 1864(1):148918, 2023). Here we focus on spectra in the previously unexplored 1400-1200 cm-1 spectral region. In this region several bands are identified and assigned to the neutral state of the incorporated quinones. This is important as identification of neutral state quinone bands in the regular 1700-1600 cm-1 region has proven difficult in the past. For neutral PhQ in PSI a broad, intense band appears at ~ 1300 cm-1. For the symmetric di-substituted NQs (Cl2NQ/Br2NQ) a single intense neutral state band is found at ~ 1280/1269 cm-1, respectively. For both mono-substituted NQs, 2ClNQ and 2BrNQ, however, two neutral state bands are observed at ~ 1280 and ~ 1250 cm-1, respectively. These observations from time-resolved spectra agree well with conclusions drawn from absorption spectra of the NQs in THF, which are also presented here. Density functional theory based vibrational frequency calculations were undertaken allowing an identification of the normal modes associated with the neutral state quinone bands.
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Affiliation(s)
- Neva Agarwala
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA, USA
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Gary Hastings
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA, USA.
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5
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Mann D, Labudda K, Zimmermann S, Vocke KU, Gasper R, Kötting C, Hofmann E. ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. Biol Chem 2023:hsz-2023-0122. [PMID: 37185095 DOI: 10.1515/hsz-2023-0122] [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: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of gram negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.
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Affiliation(s)
- Daniel Mann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons / ER-C-3: Structural Biology, D-52425 Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology, D-52425 Jülich, Germany
| | - Kristin Labudda
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Sophie Zimmermann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Kai Ulrich Vocke
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Max Planck Institute of Molecular Physiology, Crystallography and Biophysics Facility, D-44227 Dortmund, Germany
| | - Carsten Kötting
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
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6
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Hanai S, Nagata T, Katayama K, Inukai S, Koyanagi M, Inoue K, Terakita A, Kandori H. Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K. Biochemistry 2023; 62:1347-1359. [PMID: 37001008 DOI: 10.1021/acs.biochem.3c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D2O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.
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7
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Hu T, Yamaura M, Pham DM, Kasai T, Katayama A. Wide distribution of extracellular electron transfer functionality in natural proteinaceous organic materials for microbial reductive dehalogenation. J Biosci Bioeng 2023; 135:238-249. [PMID: 36646568 DOI: 10.1016/j.jbiosc.2022.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/23/2022] [Accepted: 12/09/2022] [Indexed: 01/16/2023]
Abstract
Extracellular electron transfer materials (EETMs) in the environment, such as humic substances and biochar, are formed from the humification/heating of natural organic materials. However, the distribution of extracellular electron transfer (EET) functionality in fresh natural organic materials has not yet been explored. In the present study, we reveal the wide distribution of EET functionality in proteinaceous materials for the first time using an anaerobic pentachlorophenol dechlorinating consortium, whose activity depends on EETM. Out of 11 natural organic materials and 13 reference compounds, seven proteinaceous organic materials (albumin, beef, milk, pork, soybean, yolk, and bovine serum albumin) functioned as EETMs. Carbohydrates and lipids did not function as EETMs. Comparative spectroscopic analyses suggested that a β-sheet secondary structure was essential for proteins to function as EETMs, regardless of water solubility. A high content of reduced sulfur was potentially involved in EET functionality. Although proteinaceous materials have thus far been considered simply as nutrients, the wide distribution of EET functionality in these materials provides new insights into their impact on biogeochemical cycles. In addition, structural information on EET functionality can provide a scientific basis for the development of eco-friendly EETMs.
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Affiliation(s)
- Tingting Hu
- Graduate School of Engineering, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan
| | - Mirai Yamaura
- Graduate School of Engineering, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan
| | - Duyen Minh Pham
- Institute of Materials and Systems for Sustainability, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan
| | - Takuya Kasai
- Graduate School of Engineering, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan; Institute of Materials and Systems for Sustainability, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan
| | - Arata Katayama
- Graduate School of Engineering, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan; Institute of Materials and Systems for Sustainability, Nagoya University, Tokai National Higher Education and Research System, Chikusa, Nagoya 464-8603, Japan.
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8
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Lento C, Wilson DJ. Subsecond Time-Resolved Mass Spectrometry in Dynamic Structural Biology. Chem Rev 2021; 122:7624-7646. [PMID: 34324314 DOI: 10.1021/acs.chemrev.1c00222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Life at the molecular level is a dynamic world, where the key players-proteins, oligonucleotides, lipids, and carbohydrates-are in a perpetual state of structural flux, shifting rapidly between local minima on their conformational free energy landscapes. The techniques of classical structural biology, X-ray crystallography, structural NMR, and cryo-electron microscopy (cryo-EM), while capable of extraordinary structural resolution, are innately ill-suited to characterize biomolecules in their dynamically active states. Subsecond time-resolved mass spectrometry (MS) provides a unique window into the dynamic world of biological macromolecules, offering the capacity to directly monitor biochemical processes and conformational shifts with a structural dimension provided by the electrospray charge-state distribution, ion mobility, covalent labeling, or hydrogen-deuterium exchange. Over the past two decades, this suite of techniques has provided important insights into the inherently dynamic processes that drive function and pathogenesis in biological macromolecules, including (mis)folding, complexation, aggregation, ligand binding, and enzyme catalysis, among others. This Review provides a comprehensive account of subsecond time-resolved MS and the advances it has enabled in dynamic structural biology, with an emphasis on insights into the dynamic drivers of protein function.
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Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, Ontario M3J 1P3, Canada
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9
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Pirisi K, Nag L, Fekete Z, Iuliano JN, Tolentino Collado J, Clark IP, Pécsi I, Sournia P, Liebl U, Greetham GM, Tonge PJ, Meech SR, Vos MH, Lukacs A. Identification of the vibrational marker of tyrosine cation radical using ultrafast transient infrared spectroscopy of flavoprotein systems. Photochem Photobiol Sci 2021; 20:369-378. [PMID: 33721272 DOI: 10.1007/s43630-021-00024-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/09/2021] [Indexed: 11/29/2022]
Abstract
Tryptophan and tyrosine radical intermediates play crucial roles in many biological charge transfer processes. Particularly in flavoprotein photochemistry, short-lived reaction intermediates can be studied by the complementary techniques of ultrafast visible and infrared spectroscopy. The spectral properties of tryptophan radical are well established, and the formation of neutral tyrosine radicals has been observed in many biological processes. However, only recently, the formation of a cation tyrosine radical was observed by transient visible spectroscopy in a few systems. Here, we assigned the infrared vibrational markers of the cationic and neutral tyrosine radical at 1483 and 1502 cm-1 (in deuterated buffer), respectively, in a variant of the bacterial methyl transferase TrmFO, and in the native glucose oxidase. In addition, we studied a mutant of AppABLUF blue-light sensor domain from Rhodobacter sphaeroides in which only a direct formation of the neutral radical was observed. Our studies highlight the exquisite sensitivity of transient infrared spectroscopy to low concentrations of specific radicals.
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Affiliation(s)
- Katalin Pirisi
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - Lipsa Nag
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - James N Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | | | - Ian P Clark
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0QX, Oxon, UK
| | - Ildikó Pécsi
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary
| | - Pierre Sournia
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0QX, Oxon, UK
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Marten H Vos
- Laboratoire d'Optique et Biosciences, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France.
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti Str. 12, 7624, Pecs, Hungary.
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10
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Kandori H. Structure/Function Study of Photoreceptive Proteins by FTIR Spectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200109] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry & OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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11
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Pettersson P, Barth A. Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins. RSC Adv 2020; 10:4715-4724. [PMID: 35495230 PMCID: PMC9049017 DOI: 10.1039/c9ra10366j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 12/02/2022] Open
Abstract
Density functional theory calculations were used to establish correlations between the structure and the vibrational spectrum of the phosphate group in model compounds for phosphorylated amino acids. The model compounds were acetyl phosphate, methyl phosphate, and p-tolyl phosphate, which represented the phosphorylated amino acids aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. The compounds were placed in different environments consisting of one or several HF or H2O molecules, which modeled interactions of phosphorylated amino acids in the protein environment. The calculations were performed with the B3LYP functional and the 6-311++G(3df, 3pd) basis set. In general, the wavenumbers (or frequencies) of the stretching vibrations of the terminal P–O bonds correlated better with bond lengths of the phosphate group than with its bond angles. The best correlations were obtained with the shortest and the mean terminal P–O bond lengths with standard deviations from the trend line of only 0.2 pm. Other useful correlations were observed with the bond length difference between the shortest and longest terminal P–O bond and with the bond length of the bridging P–O bond. Vibrational frequencies of phosphate are sensitive to bond length changes on the sub-picometer scale.![]()
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Affiliation(s)
- Pontus Pettersson
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics
- Arrhenius Laboratories
- Stockholm University
- 10691 Stockholm
- Sweden
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12
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Rudolph G, Virtanen T, Ferrando M, Güell C, Lipnizki F, Kallioinen M. A review of in situ real-time monitoring techniques for membrane fouling in the biotechnology, biorefinery and food sectors. J Memb Sci 2019. [DOI: 10.1016/j.memsci.2019.117221] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Katayama K, Imai H, Kandori H. FTIR Study of S180A Mutant of Primate Red-sensitive Pigment. CHEM LETT 2019. [DOI: 10.1246/cl.190458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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14
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Calculated vibrational properties of semiquinones in the A1 binding site in photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:699-707. [DOI: 10.1016/j.bbabio.2019.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 06/03/2019] [Accepted: 07/10/2019] [Indexed: 11/17/2022]
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15
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Mezzetti A, Alexandre M, Thurotte A, Wilson A, Gwizdala M, Kirilovsky D. Two-Step Structural Changes in Orange Carotenoid Protein Photoactivation Revealed by Time-Resolved Fourier Transform Infrared Spectroscopy. J Phys Chem B 2019; 123:3259-3266. [DOI: 10.1021/acs.jpcb.9b01242] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alberto Mezzetti
- Sorbonne Université, CNRS, Laboratoire Réactivité de Surface, UMR CNRS 7197, F-75252 Paris, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Maxime Alexandre
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Department of Physics and Astronomy, Faculty of Sciences, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Adrien Thurotte
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Metabolism, Engineering of Microalgal Molecules and Applications (MIMMA) Team, Mer, Molécules, Santé/Sea, Molecules & Health (EA2160), Département de Biologie et Géosciences, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans cedex 9, France
| | - Adjelé Wilson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Michal Gwizdala
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
- Department of Physics, Faculty of Natural and Agricultural Sciences, University of Pretoria, Private bag X20, 0028 Hatfield, South Africa
- Department of Physics and Astronomy, Faculty of Sciences, VU University, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
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16
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Massarczyk M, Schlitter J, Kötting C, Rudack T, Gerwert K. Monitoring transient events in infrared spectra using local mode analysis. Proteins 2018; 86:1013-1019. [PMID: 30019772 DOI: 10.1002/prot.25536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 01/10/2023]
Abstract
Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.
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Affiliation(s)
| | - Jürgen Schlitter
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
| | - Klaus Gerwert
- Department of Biophysics, Ruhr University Bochum, Bochum, Germany.,Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), Shanghai, China
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17
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Schwaighofer A, Montemurro M, Freitag S, Kristament C, Culzoni MJ, Lendl B. Beyond Fourier Transform Infrared Spectroscopy: External Cavity Quantum Cascade Laser-Based Mid-infrared Transmission Spectroscopy of Proteins in the Amide I and Amide II Region. Anal Chem 2018; 90:7072-7079. [DOI: 10.1021/acs.analchem.8b01632] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Andreas Schwaighofer
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
| | - Milagros Montemurro
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
- Laboratorio de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra de Química Analítica I, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral-CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
| | - Stephan Freitag
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
| | - Christian Kristament
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
| | - María J. Culzoni
- Laboratorio de Desarrollo Analítico y Quimiometría (LADAQ), Cátedra de Química Analítica I, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral-CONICET, Ciudad Universitaria, 3000 Santa Fe, Argentina
| | - Bernhard Lendl
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164-UPA, 1060 Vienna, Austria
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18
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Li Y, Zhang Y, Großerüschkamp F, Stephan S, Cui Q, Kötting C, Xia F, Gerwert K. Specific Substates of Ras To Interact with GAPs and Effectors: Revealed by Theoretical Simulations and FTIR Experiments. J Phys Chem Lett 2018; 9:1312-1317. [PMID: 29488771 PMCID: PMC6692134 DOI: 10.1021/acs.jpclett.8b00342] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The oncogenic Ras protein adopts various specific conformational states to execute its function in signal transduction. The large number of Ras structures obtained from X-ray and NMR experiments illustrates the diverse conformations that Ras adopts. It is difficult, however, to connect specific structural features with Ras functions. We report the free-energy landscape of Ras·GTP based on extensive explicit solvent simulations. The free-energy map clearly shows that the functional state 2 of Ras·GTP in fact has two distinct substates, denoted here as "Tyr32in" and "Tyr32out". Unbiased MD simulations show that the two substrates interconvert on the submicrosecond scale in solution, pointing to a novel mechanism for Ras·GTP to selectively interact with GAPs and effectors. This proposal is further supported by time-resolved FTIR experiments, which demonstrate that Tyr32 destabilizes the Ras·GAP complex and facilitates an efficient termination of Ras signaling.
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Affiliation(s)
- Yang Li
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
- School of Information Science and Engineering , Shandong Agricultural University , Taian 271018 , China
| | - Yuwei Zhang
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
| | | | - Sara Stephan
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute , University of Wisconsin , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Carsten Kötting
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
| | - Fei Xia
- School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062 , China
| | - Klaus Gerwert
- Department of Biophysics , Ruhr-University Bochum , ND 04 North , 44780 Bochum , Germany
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19
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Pavlou A, Yoshimura H, Aono S, Pinakoulaki E. Protein Dynamics of the Sensor Protein HemAT as Probed by Time-Resolved Step-Scan FTIR Spectroscopy. Biophys J 2018; 114:584-591. [PMID: 29414704 DOI: 10.1016/j.bpj.2017.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/06/2017] [Accepted: 12/11/2017] [Indexed: 12/09/2022] Open
Abstract
The heme-based aerotactic transducer (HemAT) is an oxygen-sensor protein consisting of a sensor and a signaling domain in the N- and C-terminal regions, respectively. Time-resolved step-scan FTIR spectroscopy was employed to characterize protein intermediate states obtained by photolysis of the carbon monoxide complexes of sensor-domain, full-length HemAT, and the Y70F (B-helix), L92A (E-helix), T95A (E-helix), and Y133F (G-helix) HemAT mutants. We assign the spectral components to discrete substructures, which originate from a helical structure that is solvated (1638 cm-1) and a native helix that is protected from solvation by interhelix tertiary interactions (1654 cm-1). The full-length protein is characterized by an additional amide I absorbance at 1661 cm-1, which is attributed to disordered structure suggesting that further protein conformational changes occur in the presence of the signaling domain in the full-length protein. The kinetics monitored within the amide I absorbance of the polypeptide backbone in the sensor domain exhibit two distinct relaxation phases (t1 = 24 and t2 = 694 μs), whereas that of the full-length protein exhibits monophasic behavior for all substructures in a time range of t = 1253-2090 μs. These observations can be instrumental in monitoring helix motion and the role of specific mutants in controlling the dynamics in the communication pathway from the sensor to the signaling domain. The kinetics observed for the amide I relaxation for the full-length protein indicate that the discrete substructures within full-length HemAT, unlike those of the sensor domain, relax independently.
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Affiliation(s)
- Andrea Pavlou
- Department of Chemistry, University of Cyprus, Nicosia, Cyprus
| | - Hideaki Yoshimura
- Institute for Molecular Science, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan
| | - Shigetoshi Aono
- Institute for Molecular Science, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Myodaiji, Okazaki, Japan
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20
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Mezzetti A, Leibl W. Time-resolved infrared spectroscopy in the study of photosynthetic systems. PHOTOSYNTHESIS RESEARCH 2017; 131:121-144. [PMID: 27678250 DOI: 10.1007/s11120-016-0305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.
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Affiliation(s)
- Alberto Mezzetti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7197, Laboratoire de Réactivité de Surfaces, 4 Pl. Jussieu, 75005, Paris, France.
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Winfried Leibl
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
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21
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Neehaul Y, Kriegel S, Barquera B, Hellwig P. Functional Studies on Membrane Proteins by Means of H/D Exchange in Infrared: Structural Changes in Na + NQR from V. cholerae in the Presence of Lipids. Methods Mol Biol 2017; 1635:247-257. [PMID: 28755373 DOI: 10.1007/978-1-4939-7151-0_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
H/D exchange kinetics at the level of the amide proton in the mid infrared (1700-1500 cm-1) make it possible to study the conformational flexibility of membrane proteins, independent of size or the presence of detergent or lipids. Slow, medium, and fast exchanging domains are distinguished, which reveal a different accessibility to the solvent. Whereas amide hydrogens undergo rapid exchange with solvent in an open structure, hydrogens experience much slower exchange when involved in H-bonded structures or when sterically inaccessible to the solvent. Here, we describe the protocol that was used to study the effect of phospholipids on the overall structure of the Na+ NQR from V. cholerae, a sodium pumping membrane protein.
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Affiliation(s)
- Yashvin Neehaul
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
- Mauritius Oceanography Institute, Avenue des Anchois, Albion, Mauritius
| | - Sebastien Kriegel
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France
| | - Blanca Barquera
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, 4 rue Blaise Pascal, Strasbourg, France.
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22
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Guo Z, Barry BA. Cryogenic Trapping and Isotope Editing Identify a Protonated Water Cluster as an Intermediate in the Photosynthetic Oxygen-Evolving Reaction. J Phys Chem B 2016; 120:8794-808. [DOI: 10.1021/acs.jpcb.6b05283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhanjun Guo
- School of Chemistry and Biochemistry
and Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- School of Chemistry and Biochemistry
and Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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23
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Gavriljuk K, Schartner J, Seidel H, Dickhut C, Zahedi RP, Hedberg C, Kötting C, Gerwert K. Unraveling the Phosphocholination Mechanism of the Legionella pneumophila Enzyme AnkX. Biochemistry 2016; 55:4375-85. [PMID: 27404583 DOI: 10.1021/acs.biochem.6b00524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intracellular pathogen Legionella pneumophila infects lung macrophages and injects numerous effector proteins into the host cell to establish a vacuole for proliferation. The necessary interference with vesicular trafficking of the host is achieved by modulation of the function of Rab GTPases. The effector protein AnkX chemically modifies Rab1b and Rab35 by covalent phosphocholination of serine or threonine residues using CDP-choline as a donor. So far, the phosphoryl transfer mechanism and the relevance of observed autophosphocholination of AnkX remained disputable. We designed tailored caged compounds to make this type of enzymatic reaction accessible for time-resolved Fourier transform infrared difference spectroscopy. By combining spectroscopic and biochemical methods, we determined that full length AnkX is autophosphocholinated at Ser521, Thr620, and Thr943. However, autophosphocholination loses specificity for these sites in shortened constructs and does not appear to be relevant for the catalysis of the phosphoryl transfer. In contrast, transient phosphocholination of His229 in the conserved catalytic motif might exist as a short-lived reaction intermediate. Upon substrate binding, His229 is deprotonated and locked in this state, being rendered capable of a nucleophilic attack on the pyrophosphate moiety of the substrate. The proton that originated from His229 is transferred to a nearby carboxylic acid residue. Thus, our combined findings support a ping-pong mechanism involving phosphocholination of His229 and subsequent transfer of phosphocholine to the Rab GTPase. Our approach can be extended to the investigation of further nucleotidyl transfer reactions, which are currently of reemerging interest in regulatory pathways of host-pathogen interactions.
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Affiliation(s)
- Konstantin Gavriljuk
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Jonas Schartner
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Hans Seidel
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Rene P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Christian Hedberg
- Department of Chemistry and Umeå Center for Microbial Research, Umeå University , SE-90187 Umeå, Sweden
| | - Carsten Kötting
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-Universität Bochum , Universitätsstrasse 150, 44801 Bochum, Germany
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24
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Süss B, Ringleb F, Heberle J. New ultrarapid-scanning interferometer for FT-IR spectroscopy with microsecond time-resolution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:063113. [PMID: 27370432 DOI: 10.1063/1.4953658] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel Fourier-transform infrared (FT-IR) rapid-scan spectrometer has been developed (patent pending EP14194520.4) which yields 1000 times higher time resolution as compared to conventional rapid-scanning spectrometers. The central element to achieve faster scanning rates is based on a sonotrode whose front face represents the movable mirror of the interferometer. A prototype spectrometer with a time resolution of 13 μs was realized, capable of fully automated long-term measurements with a flow cell for liquid samples, here a photosynthetic membrane protein in solution. The performance of this novel spectrometer is demonstrated by recording the photoreaction of bacteriorhodopsin initiated by a short laser pulse that is synchronized to the data recording. The resulting data are critically compared to those obtained by step-scan spectroscopy and demonstrate the relevance of performing experiments on proteins in solution. The spectrometer allows for future investigations of fast, non-repetitive processes, whose investigation is challenging to step-scan FT-IR spectroscopy.
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Affiliation(s)
- B Süss
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - F Ringleb
- Institute for Crystal Growth, Max-Born Straße 2, 12489 Berlin, Germany
| | - J Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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25
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Nabers A, Ollesch J, Schartner J, Kötting C, Genius J, Haußmann U, Klafki H, Wiltfang J, Gerwert K. An infrared sensor analysing label-free the secondary structure of the Abeta peptide in presence of complex fluids. JOURNAL OF BIOPHOTONICS 2016; 9:224-234. [PMID: 25808829 DOI: 10.1002/jbio.201400145] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/19/2015] [Accepted: 03/01/2015] [Indexed: 06/04/2023]
Abstract
The secondary structure change of the Abeta peptide to beta-sheet was proposed as an early event in Alzheimer's disease. The transition may be used for diagnostics of this disease in an early state. We present an Attenuated Total Reflection (ATR) sensor modified with a specific antibody to extract minute amounts of Abeta peptide out of a complex fluid. Thereby, the Abeta peptide secondary structure was determined in its physiological aqueous environment by FTIR-difference-spectroscopy. The presented results open the door for label-free Alzheimer diagnostics in cerebrospinal fluid or blood. It can be extended to further neurodegenerative diseases. An immunologic ATR-FTIR sensor for Abeta peptide secondary structure analysis in complex fluids is presented.
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Affiliation(s)
- Andreas Nabers
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Julian Ollesch
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Jonas Schartner
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Carsten Kötting
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany
| | - Just Genius
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Ute Haußmann
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Hans Klafki
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
| | - Jens Wiltfang
- Protein Research Unit Ruhr within Europe (PURE), LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty University of Duisburg-Essen, 45147, Essen, Germany
- University Medical Center, Department of Psychiatry and Psychotherapy, Georg-August-University, 37073, Göttingen, Germany
| | - Klaus Gerwert
- Protein Research Unit Ruhr within Europe (PURE), Ruhr-University Bochum, Department of Biophysics ND04-596, Universitätsstraße 150, 44780, Bochum, Germany.
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26
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Nabers A, Ollesch J, Schartner J, Kötting C, Genius J, Hafermann H, Klafki H, Gerwert K, Wiltfang J. Amyloid-β-Secondary Structure Distribution in Cerebrospinal Fluid and Blood Measured by an Immuno-Infrared-Sensor: A Biomarker Candidate for Alzheimer's Disease. Anal Chem 2016; 88:2755-62. [PMID: 26828829 DOI: 10.1021/acs.analchem.5b04286] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The misfolding of the Amyloid-beta (Aβ) peptide into β-sheet enriched conformations was proposed as an early event in Alzheimer's Disease (AD). Here, the Aβ peptide secondary structure distribution in cerebrospinal fluid (CSF) and blood plasma of 141 patients was measured with an immuno-infrared-sensor. The sensor detected the amide I band, which reflects the overall secondary structure distribution of all Aβ peptides extracted from the body fluid. We observed a significant downshift of the amide I band frequency of Aβ peptides in Dementia Alzheimer type (DAT) patients, which indicated an overall shift to β-sheet. The secondary structure distribution of all Aβ peptides provides a better marker for DAT detection than a single Aβ misfold or the concentration of a specific oligomer. The discrimination between DAT and disease control patients according to the amide I frequency was in excellent agreement with the clinical diagnosis (accuracy 90% for CSF and 84% for blood). The amide I band maximum above or below the decisive marker frequency appears as a novel spectral biomarker candidate of AD. Additionally, a preliminary proof-of-concept study indicated an amide I band shift below the marker band already in patients with mild cognitive impairment due to AD. The presented immuno-IR-sensor method represents a promising, simple, robust, and label-free diagnostic tool for CSF and blood analysis.
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Affiliation(s)
- Andreas Nabers
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Julian Ollesch
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Jonas Schartner
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Just Genius
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany
| | - Henning Hafermann
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany
| | - Hans Klafki
- Department of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical Center , 37099 Göttingen, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum , 44780 Bochum, Germany
| | - Jens Wiltfang
- Clinics for Psychiatry and Psychotherapy, LVR-Clinical Center Essen , 45147 Essen, Germany.,Department of Psychiatry and Psychotherapy, Georg-August-University Göttingen, University Medical Center , 37099 Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE) , 37099 Göttingen, Germany
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Yamada D, Yamamoto J, Zhang Y, Iwata T, Hitomi K, Getzoff ED, Iwai S, Kandori H. Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase. Biochemistry 2016; 55:715-23. [PMID: 26719910 DOI: 10.1021/acs.biochem.5b01111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Yu Zhang
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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Hellwig P, Kriegel S, Friedrich T. Infrared spectroscopic studies on reaction induced conformational changes in the NADH ubiquinone oxidoreductase (complex I). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:922-7. [PMID: 26702948 DOI: 10.1016/j.bbabio.2015.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
Abstract
Redox-dependent conformational changes are currently discussed to be a crucial part of the reaction mechanism of the respiratory complex I. Specialized difference Fourier transform infrared techniques allow the detection of side-chain movements and minute secondary structure changes. For complex I, (1)H/(2)H exchange kinetics of the amide modes revealed a better accessibility of the backbone in the presence of NADH and quinone. Interestingly, the presence of phospholipids, that is crucial for the catalytic activity of the isolated enzyme complex, changes the overall conformation. When comparing complex I samples from different species, very similar electrochemically induced FTIR difference spectra and very similar rearrangements are reported. Finally, the information obtained with variants and from Zn(2+) inhibited samples for the conformational reorganization of complex I upon electron transfer are discussed in this review. This article is part of a Special Issue entitled Respiratory complex I, edited by Volker Zickermann and Ulrich Brandt.
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Affiliation(s)
- Petra Hellwig
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Sébastien Kriegel
- Laboratoire de bioelectrochimie et spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg-CNRS, Strasbourg, France
| | - Thorsten Friedrich
- Albert-Ludwigs-Universität Freiburg, Institut für Biochemie, Albertstr. 21, 79104 Freiburg i. Br., Germany
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Kurihara M, Sudo Y. Microbial rhodopsins: wide distribution, rich diversity and great potential. Biophys Physicobiol 2015; 12:121-9. [PMID: 27493861 PMCID: PMC4736836 DOI: 10.2142/biophysico.12.0_121] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/13/2015] [Indexed: 02/04/2023] Open
Abstract
One of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. Taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. Rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. In this review, we summarize progress of microbial rhodopsin research from the viewpoint of distribution, diversity and potential.
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Affiliation(s)
- Marie Kurihara
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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Resler T, Schultz BJ, Lórenz-Fonfría VA, Schlesinger R, Heberle J. Kinetic and vibrational isotope effects of proton transfer reactions in channelrhodopsin-2. Biophys J 2015; 109:287-97. [PMID: 26200864 PMCID: PMC4621815 DOI: 10.1016/j.bpj.2015.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-gated cation channels. After blue-light excitation, the protein undergoes a photocycle with different intermediates. Here, we have recorded transient absorbance changes of ChR2 from Chlamydomonas reinhardtii in the visible and infrared regions with nanosecond time resolution, the latter being accomplished using tunable quantum cascade lasers. Because proton transfer reactions play a key role in channel gating, we determined vibrational as well as kinetic isotope effects (VIEs and KIEs) of carboxylic groups of various key aspartic and glutamic acid residues by monitoring their C=O stretching vibrations in H2O and in D2O. D156 exhibits a substantial KIE (>2) in its deprotonation and reprotonation, which substantiates its role as the internal proton donor to the retinal Schiff base. The unusual VIE of D156, upshifted from 1736 cm(-1) to 1738 cm(-1) in D2O, was scrutinized by studying the D156E variant. The C=O stretch of E156 shifted down by 8 cm(-1) in D2O, providing evidence for the accessibility of the carboxylic group. The C=O stretching band of E90 exhibits a VIE of 9 cm(-1) and a KIE of ∼2 for the de- and the reprotonation reactions during the lifetime of the late desensitized state. The KIE of 1 determined in the time range from 20 ns to 5 ms is incompatible with early deprotonation of E90.
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Affiliation(s)
- Tom Resler
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | | | | | - Ramona Schlesinger
- Genetic Biophysics at Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany.
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Schartner J, Hoeck N, Güldenhaupt J, Mavarani L, Nabers A, Gerwert K, Kötting C. Chemical Functionalization of Germanium with Dextran Brushes for Immobilization of Proteins Revealed by Attenuated Total Reflection Fourier Transform Infrared Difference Spectroscopy. Anal Chem 2015; 87:7467-75. [PMID: 26102158 DOI: 10.1021/acs.analchem.5b01823] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein immobilization studied by attenuated total reflection Fourier transform infrared (ATR-FT-IR) difference spectroscopy is an emerging field enabling the study of proteins at atomic detail. Gold or glass surfaces are frequently used for protein immobilization. Here, we present an alternative method for protein immobilization on germanium. Because of its high refractive index and broad spectral window germanium is the best material for ATR-FT-IR spectroscopy of thin layers. So far, this technique was mainly used for protein monolayers, which lead to a limited signal-to-noise ratio. Further, undesired protein-protein interactions can occur in a dense layer. Here, the germanium surface was functionalized with thiols and stepwise a dextran brush was generated. Each step was monitored by ATR-FT-IR spectroscopy. We compared a 70 kDa dextran with a 500 kDa dextran regarding the binding properties. All surfaces were characterized by atomic force microscopy, revealing thicknesses between 40 and 110 nm. To analyze the capability of our system we utilized N-Ras on mono-NTA (nitrilotriacetic acid) functionalized dextran, and the amount of immobilized Ras corresponded to several monolayers. The protein stability and loading capacity was further improved by means of tris-NTA for immobilization. Small-molecule-induced changes were revealed with an over 3 times higher signal-to-noise ratio compared to monolayers. This improvement may allow the observation of very small and so far hidden changes in proteins upon stimulus. Furthermore, we immobilized green fluorescent protein (GFP) and mCherry simultaneously enabling an analysis of the surface by fluorescence microscopy. The absence of a Förster resonance energy transfer (FRET) signal demonstrated a large protein-protein distance, indicating an even distribution of the protein within the dextran.
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Affiliation(s)
- Jonas Schartner
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Nina Hoeck
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Jörn Güldenhaupt
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Laven Mavarani
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Andreas Nabers
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr-University, 44801 Bochum, Germany
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Ritter E, Puskar L, Bartl FJ, Aziz EF, Hegemann P, Schade U. Time-resolved infrared spectroscopic techniques as applied to channelrhodopsin. Front Mol Biosci 2015. [PMID: 26217670 PMCID: PMC4493399 DOI: 10.3389/fmolb.2015.00038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Among optogenetic tools, channelrhodopsins, the light gated ion channels of the plasma membrane from green algae, play the most important role. Properties like channel selectivity, timing parameters or color can be influenced by the exchange of selected amino acids. Although widely used, in the field of neurosciences for example, there is still little known about their photocycles and the mechanism of ion channel gating and conductance. One of the preferred methods for these studies is infrared spectroscopy since it allows observation of proteins and their function at a molecular level and in near-native environment. The absorption of a photon in channelrhodopsin leads to retinal isomerization within femtoseconds, the conductive states are reached in the microsecond time scale and the return into the fully dark-adapted state may take more than minutes. To be able to cover all these time regimes, a range of different spectroscopical approaches are necessary. This mini-review focuses on time-resolved applications of the infrared technique to study channelrhodopsins and other light triggered proteins. We will discuss the approaches with respect to their suitability to the investigation of channelrhodopsin and related proteins.
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Affiliation(s)
- Eglof Ritter
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ljiljana Puskar
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
| | - Franz J Bartl
- Institut für medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin Berlin, Germany
| | - Emad F Aziz
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany ; Fachbereich Physik, Freie Universität Berlin Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt-Universität zu Berlin Berlin, Germany
| | - Ulrich Schade
- Methods for Material Development, Helmholtz-Zentrum für Materialien und Energie GmbH Berlin, Germany
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Light-Induced Infrared Difference Spectroscopy in the Investigation of Light Harvesting Complexes. Molecules 2015; 20:12229-49. [PMID: 26151118 PMCID: PMC6332223 DOI: 10.3390/molecules200712229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/24/2023] Open
Abstract
Light-induced infrared difference spectroscopy (IR-DS) has been used, especially in the last decade, to investigate early photophysics, energy transfer and photoprotection mechanisms in isolated and membrane-bound light harvesting complexes (LHCs). The technique has the definite advantage to give information on how the pigments and the other constituents of the biological system (proteins, membranes, etc.) evolve during a given photoreaction. Different static and time-resolved approaches have been used. Compared to the application of IR-DS to photosynthetic Reaction Centers (RCs), however, IR-DS applied to LHCs is still in an almost pioneering age: very often sophisticated techniques (step-scan FTIR, ultrafast IR) or data analysis strategies (global analysis, target analysis, multivariate curve resolution) are needed. In addition, band assignment is usually more complicated than in RCs. The results obtained on the studied systems (chromatophores and RC-LHC supercomplexes from purple bacteria; Peridinin-Chlorophyll-a-Proteins from dinoflagellates; isolated LHCII from plants; thylakoids; Orange Carotenoid Protein from cyanobacteria) are summarized. A description of the different IR-DS techniques used is also provided, and the most stimulating perspectives are also described. Especially if used synergically with other biophysical techniques, light-induced IR-DS represents an important tool in the investigation of photophysical/photochemical reactions in LHCs and LHC-containing systems.
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34
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Kötting C, Gerwert K. What vibrations tell us about GTPases. Biol Chem 2015; 396:131-44. [DOI: 10.1515/hsz-2014-0219] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 07/29/2014] [Indexed: 01/30/2023]
Abstract
Abstract
In this review, we discuss how time-resolved Fourier transform infrared (FTIR) spectroscopy is used to understand how GTP hydrolysis is catalyzed by small GTPases and their cognate GTPase-activating proteins (GAPs). By interaction with small GTPases, GAPs regulate important signal transduction pathways and transport mechanisms in cells. The GTPase reaction terminates signaling and controls transport. Dysfunctions of GTP hydrolysis in these proteins are linked to serious diseases including cancer. Using FTIR, we resolved both the intrinsic and GAP-catalyzed GTPase reaction of the small GTPase Ras with high spatiotemporal resolution and atomic detail. This provided detailed insight into the order of events and how the active site is completed for catalysis. Comparisons of Ras with other small GTPases revealed conservation and variation in the catalytic mechanisms. The approach was extended to more nearly physiological conditions at a membrane. Interactions of membrane-anchored GTPases and their extraction from the membrane are studied using the attenuated total reflection (ATR) technique.
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35
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Hellwig P. Infrared spectroscopic markers of quinones in proteins from the respiratory chain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:126-33. [PMID: 25026472 DOI: 10.1016/j.bbabio.2014.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 01/12/2023]
Abstract
In bioenergetic systems quinones play a central part in the coupling of electron and proton transfer. The specific function of each quinone binding site is based on the protein-quinone interaction that can be described by means of reaction induced FTIR difference spectroscopy, induced for example by light or electrochemically. The identification of sites in enzymes from the respiratory chain is presented together with the analysis of the accommodation of different types of quinones to the same enzyme and the possibility to monitor the interaction with inhibitors. Reaction induced FTIR difference spectroscopy is shown to give an essential information on the general geometry of quinone binding sites, the conformation of the ring and of the substituents as well as essential structural information on the identity of the amino-acid residues lining this site. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Affiliation(s)
- Petra Hellwig
- Laboratoire de bioélectrochimie et spectroscopie, UMR 7140, Chimie de la matière complexe, Université de Strasbourg, 1, rue Blaise Pascal, 67008 Strasbourg, France.
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Offenbacher AR, Watson RA, Pagba CV, Barry BA. Redox-dependent structural coupling between the α2 and β2 subunits in E. coli ribonucleotide reductase. J Phys Chem B 2014; 118:2993-3004. [PMID: 24606240 DOI: 10.1021/jp501121d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the production of deoxyribonucleotides in all cells. In E. coli class Ia RNR, a transient α2β2 complex forms when a ribonucleotide substrate, such as CDP, binds to the α2 subunit. A tyrosyl radical (Y122O•)-diferric cofactor in β2 initiates substrate reduction in α2 via a long-distance, proton-coupled electron transfer (PCET) process. Here, we use reaction-induced FT-IR spectroscopy to describe the α2β2 structural landscapes, which are associated with dATP and hydroxyurea (HU) inhibition. Spectra were acquired after mixing E. coli α2 and β2 with a substrate, CDP, and the allosteric effector, ATP. Isotopic chimeras, (13)Cα2β2 and α2(13)Cβ2, were used to define subunit-specific structural changes. Mixing of α2 and β2 under turnover conditions yielded amide I (C═O) and II (CN/NH) bands, derived from each subunit. The addition of the inhibitor, dATP, resulted in a decreased contribution from amide I bands, attributable to β strands and disordered structures. Significantly, HU-mediated reduction of Y122O• was associated with structural changes in α2, as well as β2. To define the spectral contributions of Y122O•/Y122OH in the quaternary complex, (2)H4 labeling of β2 tyrosines and HU editing were performed. The bands of Y122O•, Y122OH, and D84, a unidentate ligand to the diferric cluster, previously identified in isolated β2, were observed in the α2β2 complex. These spectra also provide evidence for a conformational rearrangement at an additional β2 tyrosine(s), Yx, in the α2β2/CDP/ATP complex. This study illustrates the utility of reaction-induced FT-IR spectroscopy in the study of complex enzymes.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of amino acid side chain IR absorptions in the amide I' region. Biopolymers 2014; 101:536-48. [DOI: 10.1002/bip.22416] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/05/2013] [Accepted: 09/16/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Benjamin A. Anderson
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Alex Literati
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Borden Ball
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, 1000 E University Ave; Laramie WY 82071
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Lin J, Gerwert K, Kötting C. A modified infrared spectrometer with high time resolution and its application for investigating fast conformational changes of the GTPase Ras. APPLIED SPECTROSCOPY 2014; 68:531-535. [PMID: 25014595 DOI: 10.1366/13-07320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Time-resolved infrared spectroscopy is a valuable tool for the investigation of proteins and protein interactions. The investigation of many biological processes is possible by means of caged compounds, which set free biologically active substances upon light activation. Some caged compounds could provide sub-nanosecond time resolution, e.g., para-hydroxyphenacyl-guanosine 5'-triphosphate (GTP) forms GTP in picoseconds. However, the time resolution in single shot experiments with rapid-scan Fourier transform infrared (FT-IR) spectrometers is limited to about 10 ms. Here we use an infrared diode laser instead of the conventional globar and achieve a time resolution of 100 ns. This allows for the time-resolved measurement of the fast Ras(off) to Ras(on) conformational change at room temperature. We quantified the activation parameters for this reaction and found that the free energy of activation for this reaction is mainly enthalpic. Investigation of the same reaction in the presence of the Ras binding domain of the effector Raf (RafRBD) reveals a four orders of magnitude faster reaction, indicating that Ras·RafRBD complex formation directly induces the conformational change. Recent developments of broadly tunable quantum cascade lasers will further improve time resolution and usability of the setup. The reported 100 ns time resolution is the best achieved for a non-repetitive experiment so far.
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Affiliation(s)
- Jie Lin
- Department of Biophysics, Ruhr-University Bochum, Universitäetsstr. 150, Bochum 44801, Germany
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum, Universitäetsstr. 150, Bochum 44801, Germany
| | - Carsten Kötting
- Department of Biophysics, Ruhr-University Bochum, Universitäetsstr. 150, Bochum 44801, Germany
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Abstract
Light-induced difference Fourier transform infrared (FTIR) spectroscopy is a powerful, sensitive, and informative method to study structure-function relationships in photoreceptive proteins. Strong absorption of water in the IR region is always problematic in this method, but if water content in the sample is controlled during measurements, this method can provide useful information on a single protein-bound water molecule. We established three kinds of sample preparations: hydrated film, redissolved sample, and concentrated solution. Hydrated films were used for the measurements of LOV and BLUF domains, where accurate difference FTIR spectra were obtained in the whole mid-IR region (4,000-800 cm(-1)). Vibrations of S-H stretch of cysteine, O-H stretch of water, and O-H stretch of tyrosine provide important information on hydrogen bonds in these proteins. Redissolved samples were used for the measurements of (6-4) photolyase, in which enzymatic turnover takes place. From the illumination time-dependence of excess amount of substrate, it is possible to isolate the signal originating from the binding of enzyme to substrate. If proteins are less tolerant to drying, as for example cryptochromes of the DASH type, concentrated solution is used. Detailed methodological aspects in light-induced difference FTIR spectroscopy are reviewed by mainly focusing on our results.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
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Eremina N, Barth A. Use of Creatine Kinase To Induce Multistep Reactions in Infrared Spectroscopic Experiments. J Phys Chem B 2013; 117:14967-72. [DOI: 10.1021/jp409599p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadejda Eremina
- Department
of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural
Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Andreas Barth
- Department
of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural
Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
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Mehlhorn J, Steinocher H, Beck S, Kennis JTM, Hegemann P, Mathes T. A set of engineered Escherichia coli expression strains for selective isotope and reactivity labeling of amino acid side chains and flavin cofactors. PLoS One 2013; 8:e79006. [PMID: 24223875 PMCID: PMC3815312 DOI: 10.1371/journal.pone.0079006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/21/2013] [Indexed: 11/18/2022] Open
Abstract
Biological reactions are facilitated by delicate molecular interactions between proteins, cofactors and substrates. To study and understand their dynamic interactions researchers have to take great care not to influence or distort the object of study. As a non-invasive alternative to a site-directed mutagenesis approach, selective isotope labeling in combination with vibrational spectroscopy may be employed to directly identify structural transitions in wild type proteins. Here we present a set of customized Escherichia coli expression strains, suitable for replacing both the flavin cofactor and/or selective amino acids with isotope enriched or chemically modified substrates. For flavin labeling we report optimized auxotrophic strains with significantly enhanced flavin uptake properties. Labeled protein biosynthesis using these strains was achieved in optimized cultivation procedures using high cell density fermentation. Finally, we demonstrate how this approach is used for a clear assignment of vibrational spectroscopic difference signals of apoprotein and cofactor of a flavin containing photoreceptor of the BLUF (Blue Light receptors Using FAD) family.
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Affiliation(s)
- Jennifer Mehlhorn
- Institut für Biologie/Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Helena Steinocher
- Institut für Biologie/Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sebastian Beck
- Institut für Chemie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - John T. M. Kennis
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie/Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tilo Mathes
- Institut für Biologie/Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
- Biophysics Group, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands
- * E-mail:
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Hammaecher C, Joris B, Goormaghtigh E, Marchand-Brynaert J. Photoactivable Nonsymmetrical Bifunctional Linkers for Protein Immobilization on Attenuated Total Reflectance FTIR Optical Devices. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300939] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Geibel S, Lörinczi È, Bamberg E, Friedrich T. Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate. PLoS One 2013; 8:e73338. [PMID: 24019918 PMCID: PMC3760879 DOI: 10.1371/journal.pone.0073338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum is tightly regulated by the [H(+)] gradient and transmembrane potential. BR exhibits optoelectric properties, since spectral changes during the photocycle are kinetically controlled by voltage, which predestines BR for optical storage or processing devices. BR mutants with prolonged lifetime of the blue-shifted M intermediate would be advantageous, but the optoelectric properties of such mutants are still elusive. Using expression in Xenopus oocytes and two-electrode voltage-clamping, we analyzed photocurrents of BR mutants with kinetically destabilized (F171C, F219L) or stabilized (D96N, D96G) M intermediate in response to green light (to probe H(+) pumping) and blue laser flashes (to probe accumulation/decay of M). These mutants have divergent M lifetimes. As for BR-WT, this strictly correlates with the voltage dependence of H(+) pumping. BR-F171C and BR-F219L showed photocurrents similar to BR-WT. Yet, BR-F171C showed a weaker voltage dependence of proton pumping. For both mutants, blue laser flashes applied during and after green-light illumination showed reduced M accumulation and shorter M lifetime. In contrast, BR-D96G and BR-D96N exhibited small photocurrents, with nonlinear current-voltage curves, which increased strongly in the presence of azide. Blue laser flashes showed heavy M accumulation and prolonged M lifetime, which accounts for the strongly reduced H(+) pumping rate. Hyperpolarizing potentials augmented these effects. The combination of M-stabilizing and -destabilizing mutations in BR-D96G/F171C/F219L (BR-tri) shows that disruption of the primary proton donor Asp-96 is fatal for BR as a proton pump. Mechanistically, M destabilizing mutations cannot compensate for the disruption of Asp-96. Accordingly, BR-tri and BR-D96G photocurrents were similar. However, BR-tri showed negative blue laser flash-induced currents even without actinic green light, indicating that Schiff base deprotonation in BR-tri exists in the dark, in line with previous spectroscopic investigations. Thus, M-stabilizing mutations, including the triple mutation, drastically interfere with electrochemical H(+) gradient generation.
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Affiliation(s)
- Sven Geibel
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Èva Lörinczi
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Thomas Friedrich
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
- Technical University of Berlin, Institute of Chemistry, Berlin, Germany
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Kubo M, Nakashima S, Yamaguchi S, Ogura T, Mochizuki M, Kang J, Tateno M, Shinzawa-Itoh K, Kato K, Yoshikawa S. Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system. J Biol Chem 2013; 288:30259-30269. [PMID: 23996000 DOI: 10.1074/jbc.m113.473983] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O2 binding to the second heme (heme a3) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of α-helices of CcO in H2O medium. The present results indicate that migration of CO from heme a3 to CuB in the O2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including CuB, O2, heme a3, and two helix turns extending to Ser-382, CuB induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O2 transfer from CuB to heme a3.
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Affiliation(s)
| | | | - Satoru Yamaguchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and
| | - Takashi Ogura
- From the Picobiology Institute,; Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Masaru Tateno
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Shinya Yoshikawa
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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Offenbacher AR, Polander BC, Barry BA. An intrinsically disordered photosystem II subunit, PsbO, provides a structural template and a sensor of the hydrogen-bonding network in photosynthetic water oxidation. J Biol Chem 2013; 288:29056-68. [PMID: 23940038 DOI: 10.1074/jbc.m113.487561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Photosystem II (PSII) is a membrane-bound enzyme that utilizes solar energy to catalyze the photooxidation of water. Molecular oxygen is evolved after four sequential light-driven oxidation reactions at the Mn4CaO5 oxygen-evolving complex, producing five sequentially oxidized states, Sn. PSII is composed of 17 membrane-spanning subunits and three extrinsic subunits, PsbP, PsbQ, and PsbO. PsbO is intrinsically disordered and plays a role in facilitation of the water oxidizing cycle. Native PsbO can be removed and substituted with recombinant PsbO, thereby restoring steady-state activity. In this report, we used reaction-induced Fourier transform infrared spectroscopy to obtain information concerning the role of PsbP, PsbQ, and PsbO during the S state cycle. Light-minus-dark difference spectra were acquired, monitoring structural changes associated with each accessible flash-induced S state transition in a highly purified plant PSII preparation (Triton X-100, octylthioglucoside). A comparison of S2 minus S1 spectra revealed that removal of PsbP and PsbQ had no significant effect on the data, whereas amide frequency and intensity changes were associated with PsbO removal. These data suggest that PsbO acts as an organizational template for the PSII reaction center. To identify any coupled conformational changes arising directly from PsbO, global (13)C-PsbO isotope editing was employed. The reaction-induced Fourier transform infrared spectra of accessible S states provide evidence that PsbO spectral contributions are temperature (263 and 277 K) and S state dependent. These experiments show that PsbO undergoes catalytically relevant structural dynamics, which are coupled over long distance to hydrogen-bonding changes at the Mn4CaO5 cluster.
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Affiliation(s)
- Adam R Offenbacher
- From the School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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Offenbacher AR, Burns LA, Sherrill CD, Barry BA. Redox-linked conformational control of proton-coupled electron transfer: Y122 in the ribonucleotide reductase β2 subunit. J Phys Chem B 2013; 117:8457-68. [PMID: 23822111 DOI: 10.1021/jp404757r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl radicals play essential roles in biological proton-coupled electron transfer (PCET) reactions. Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides and is vital in DNA replication in all organisms. Class Ia RNRs consist of α2 and β2 homodimeric subunits. In class Ia RNR, such as the E. coli enzyme, an essential tyrosyl radical (Y122O(•))-diferric cofactor is located in β2. Although Y122O(•) is extremely stable in free β2, Y122O(•) is highly reactive in the quaternary substrate-α2β2 complex and serves as a radical initiator in catalytic PCET between β2 and α2. In this report, we investigate the structural interactions that control the reactivity of Y122O(•) in a model system, isolated E. coli β2. Y122O(•) was reduced with hydroxyurea (HU), a radical scavenger that quenches the radical in a clinically relevant reaction. In the difference FT-IR spectrum, associated with this PCET reaction, amide I (CO) and amide II (CN/NH) bands were observed. Specific (13)C-labeling of the tyrosine C1 carbon assigned a component of these bands to the Y122-T123 amide bond. Comparison to density functional calculations on a model dipeptide, tyrosine-threonine, and structural modeling demonstrated that PCET is associated with a Y122 rotation and a 7.2 Å translation of the Y122 phenolic oxygen. To test for the functional consequences of this structural change, a proton inventory defined the origin of the large solvent isotope effect (SIE = 16.7 ± 1.0 at 25 °C) on this reaction. These data suggest that the one-electron, HU-mediated reduction of Y122O(•) is associated with two, rate-limiting (full or partial) proton transfer reactions. One is attributable to HU oxidation (SIE = 11.9, net H atom transfer), and the other is attributable to coupled, hydrogen-bonding changes in the Y122O(•)-diferric cofactor (SIE = 1.4). These results illustrate the importance of redox-linked changes to backbone and ring dihedral angles in high potential PCET and provide evidence for rate-limiting, redox-linked hydrogen-bonding interactions between Y122O(•) and the iron cluster.
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Affiliation(s)
- Adam R Offenbacher
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Spudich JL, Sineshchekov OA, Govorunova EG. Mechanism divergence in microbial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:546-52. [PMID: 23831552 DOI: 10.1016/j.bbabio.2013.06.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 10/26/2022]
Abstract
A fundamental design principle of microbial rhodopsins is that they share the same basic light-induced conversion between two conformers. Alternate access of the Schiff base to the outside and to the cytoplasm in the outwardly open "E" conformer and cytoplasmically open "C" conformer, respectively, combined with appropriate timing of pKa changes controlling Schiff base proton release and uptake make the proton path through the pumps vectorial. Phototaxis receptors in prokaryotes, sensory rhodopsins I and II, have evolved new chemical processes not found in their proton pump ancestors, to alter the consequences of the conformational change or modify the change itself. Like proton pumps, sensory rhodopsin II undergoes a photoinduced E→C transition, with the C conformer a transient intermediate in the photocycle. In contrast, one light-sensor (sensory rhodopsin I bound to its transducer HtrI) exists in the dark as the C conformer and undergoes a light-induced C→E transition, with the E conformer a transient photocycle intermediate. Current results indicate that algal phototaxis receptors channelrhodopsins undergo redirected Schiff base proton transfers and a modified E→C transition which, contrary to the proton pumps and other sensory rhodopsins, is not accompanied by the closure of the external half-channel. The article will review our current understanding of how the shared basic structure and chemistry of microbial rhodopsins have been modified during evolution to create diverse molecular functions: light-driven ion transport and photosensory signaling by protein-protein interaction and light-gated ion channel activity. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- John L Spudich
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, 6431 Fannin St., MSB6.130, Houston, TX 77030, USA.
| | - Oleg A Sineshchekov
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, 6431 Fannin St., MSB6.130, Houston, TX 77030, USA
| | - Elena G Govorunova
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Medical School, 6431 Fannin St., MSB6.130, Houston, TX 77030, USA
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Detection of an intermediary, protonated water cluster in photosynthetic oxygen evolution. Proc Natl Acad Sci U S A 2013; 110:10634-9. [PMID: 23757501 DOI: 10.1073/pnas.1306532110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In photosynthesis, photosystem II evolves oxygen from water by the accumulation of photooxidizing equivalents at the oxygen-evolving complex (OEC). The OEC is a Mn4CaO5 cluster, and its sequentially oxidized states are termed the Sn states. The dark-stable state is S1, and oxygen is released during the transition from S3 to S0. In this study, a laser flash induces the S1 to S2 transition, which corresponds to the oxidation of Mn(III) to Mn(IV). A broad infrared band, at 2,880 cm(-1), is produced during this transition. Experiments using ammonia and (2)H2O assign this band to a cationic cluster of internal water molecules, termed "W5(+)." Observation of the W5(+) band is dependent on the presence of calcium, and flash dependence is observed. These data provide evidence that manganese oxidation during the S1 to S2 transition results in a coupled proton transfer to a substrate-containing, internal water cluster in the OEC hydrogen-bonded network.
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50
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The dynamics of the catalytic site in small GTPases, variations on a common motif. FEBS Lett 2013; 587:2025-7. [DOI: 10.1016/j.febslet.2013.05.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 05/06/2013] [Indexed: 12/14/2022]
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