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Schulz V, Freibert SA, Boss L, Mühlenhoff U, Stehling O, Lill R. Mitochondrial [2Fe-2S] ferredoxins: new functions for old dogs. FEBS Lett 2023; 597:102-121. [PMID: 36443530 DOI: 10.1002/1873-3468.14546] [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: 10/20/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/02/2022]
Abstract
Ferredoxins (FDXs) comprise a large family of iron-sulfur proteins that shuttle electrons from NADPH and FDX reductases into diverse biological processes. This review focuses on the structure, function and specificity of mitochondrial [2Fe-2S] FDXs that are related to bacterial FDXs due to their endosymbiotic inheritance. Their classical function in cytochrome P450-dependent steroid transformations was identified around 1960, and is exemplified by mammalian FDX1 (aka adrenodoxin). Thirty years later the essential function in cellular Fe/S protein biogenesis was discovered for the yeast mitochondrial FDX Yah1 that is additionally crucial for the formation of haem a and ubiquinone CoQ6 . In mammals, Fe/S protein biogenesis is exclusively performed by the FDX1 paralog FDX2, despite the high structural similarity of both proteins. Recently, additional and specific roles of human FDX1 in haem a and lipoyl cofactor biosyntheses were described. For lipoyl synthesis, FDX1 transfers electrons to the radical S-adenosyl methionine-dependent lipoyl synthase to kickstart its radical chain reaction. The high target specificity of the two mammalian FDXs is contained within small conserved sequence motifs, that upon swapping change the target selection of these electron donors.
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Affiliation(s)
- Vinzent Schulz
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Linda Boss
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Oliver Stehling
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany.,Zentrum für Synthetische Mikrobiologie Synmikro, Marburg, Germany
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2
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Kim S, Koo J. Recent advances in utilization of ferredoxins for biosynthesis of valuable compounds. World J Microbiol Biotechnol 2022; 38:178. [PMID: 35941298 DOI: 10.1007/s11274-022-03371-9] [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: 07/02/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022]
Abstract
Ferredoxin (Fd) is a small metalloprotein holding one or two Fe-S clusters in its inner shell. Like many other metalloproteins, Fd is redox active and involved in electron transfer during cellular metabolism. The electrons from reduced Fd are mostly used to regenerate NADPH under physiological conditions. Increasing number of attempts have been reported, however, where Fd delivers electrons to enable biosynthesis of valuable compounds. Various compounds ranging from H2 to vitamin D3 have been synthesized successfully using electrons mediated by Fd molecules. In this review, we provide an overview of the engineering studies utilizing Fd for biosynthesis of targeted molecules. The emphasis is on the role and activity of Fd as well as the methods used to improve the rate of electron transfer. Both microbial and electrochemical biosynthesis technologies are described and compared with respect to productivity and the compound being produced. In addition to the ferredoxins from the microbial organisms, artificially designed de novo types are described, highlighting the potential of the emerging computational methods used in metabolic and protein engineering. We believe that the recent advances in utilization of Fd for biosynthesis can result in breakthrough innovation across the biotechnology industry.
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Affiliation(s)
- Seongwon Kim
- Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Jamin Koo
- Department of Chemical Engineering, Hongik University, Seoul, 04066, Republic of Korea.
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3
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Zakharov SD, Savikhin S, Misumi Y, Kurisu G, Cramer WA. Isothermal titration calorimetry of membrane protein interactions: FNR and the cytochrome b 6f complex. Biophys J 2022; 121:300-308. [PMID: 34902329 PMCID: PMC8790201 DOI: 10.1016/j.bpj.2021.12.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/03/2021] [Accepted: 12/09/2021] [Indexed: 01/21/2023] Open
Abstract
Ferredoxin-NADP+ reductase (FNR) was previously inferred to bind to the cytochrome b6f complex in the electron transport chain of oxygenic photosynthesis. In the present study, this inference has been examined through analysis of the thermodynamics of the interaction between FNR and the b6f complex. Isothermal titration calorimetry (ITC) was used to characterize the physical interaction of FNR with b6f complex derived from two plant sources (Spinacia oleracea and Zea maize). ITC did not detect a significant interaction of FNR with the b6f complex in detergent solution nor with the complex reconstituted in liposomes. A previous inference of a small amplitude but defined FNR-b6f interaction is explained by FNR interaction with micelles of the undecyl β-D maltoside (UDM) detergent micelles used to purify b6f. Circular dichroism, employed to analyze the effect of detergent on the FNR structure, did not reveal significant changes in secondary or tertiary structures of FNR domains in the presence of UDM detergent. However, thermodynamic analysis implied a significant decrease in an interaction between the N-terminal FAD-binding and C-terminal NADP+-binding domains of FNR caused by detergent. The enthalpy, ΔHo, and the entropy, ΔSo, associated with FNR unfolding decreased four-fold in the presence of 1 mM UDM at pH 6.5. In addition to the conclusion regarding the absence of a binding interaction of significant amplitude between FNR and the b6f complex, these studies provide a precedent for consideration of significant background protein-detergent interactions in ITC analyses involving integral membrane proteins.
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Affiliation(s)
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana
| | - Yuko Misumi
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Suita, Osaka
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.
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4
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Kawakami T, Yu LJ, Liang T, Okazaki K, Madigan MT, Kimura Y, Wang-Otomo ZY. Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP. Nat Commun 2021; 12:1104. [PMID: 33597527 PMCID: PMC7889895 DOI: 10.1038/s41467-021-21397-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 01/26/2021] [Indexed: 11/12/2022] Open
Abstract
Photosynthetic electron transfers occur through multiple components ranging from small soluble proteins to large integral membrane protein complexes. Co-crystallization of a bacterial photosynthetic electron transfer complex that employs weak hydrophobic interactions was achieved by using high-molar-ratio mixtures of a soluble donor protein (high-potential iron-sulfur protein, HiPIP) with a membrane-embedded acceptor protein (reaction center, RC) at acidic pH. The structure of the co-complex offers a snapshot of a transient bioenergetic event and revealed a molecular basis for thermodynamically unfavorable interprotein electron tunneling. HiPIP binds to the surface of the tetraheme cytochrome subunit in the light-harvesting (LH1) complex-associated RC in close proximity to the low-potential heme-1 group. The binding interface between the two proteins is primarily formed by uncharged residues and is characterized by hydrophobic features. This co-crystal structure provides a model for the detailed study of long-range trans-protein electron tunneling pathways in biological systems. The high potential iron-sulfur (HiPIP) proteins are direct electron donors to the light-harvesting-reaction center complexes (LH1-RC) in photosynthetic β- and γ-Proteobacteria. Here, the authors present the 2.9 Å crystal structure of the HiPIP-bound LH1-RC complex from the thermophilic purple sulfur bacterium Thermochromatium tepidum and discuss mechanistic implications for the electron transfer pathway.
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Affiliation(s)
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
| | - Tai Liang
- Faculty of Science, Ibaraki University, Mito, Japan
| | | | - Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, USA
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Japan.
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5
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Anoz-Carbonell E, Rivero M, Polo V, Velázquez-Campoy A, Medina M. Human riboflavin kinase: Species-specific traits in the biosynthesis of the FMN cofactor. FASEB J 2020; 34:10871-10886. [PMID: 32649804 DOI: 10.1096/fj.202000566r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/26/2020] [Accepted: 06/05/2020] [Indexed: 11/11/2022]
Abstract
Human riboflavin kinase (HsRFK) catalyzes vitamin B2 (riboflavin) phosphorylation to flavin mononucleotide (FMN), obligatory step in flavin cofactor synthesis. HsRFK expression is related to protection from oxidative stress, amyloid-β toxicity, and some malignant cancers progression. Its downregulation alters expression profiles of clock-controlled metabolic-genes and destroys flavins protection on stroke treatments, while its activity reduction links to protein-energy malnutrition and thyroid hormones decrease. We explored specific features of the mechanisms underlying the regulation of HsRFK activity, showing that both reaction products regulate it through competitive inhibition. Fast-kinetic studies show that despite HsRFK binds faster and preferably the reaction substrates, the complex holding both products is kinetically most stable. An intricate ligand binding landscape with all combinations of substrates/products competing with the catalytic complex and exhibiting moderate cooperativity is also presented. These data might contribute to better understanding the molecular bases of pathologies coursing with aberrant HsRFK availability, and envisage that interaction with its client-apoproteins might favor FMN release. Finally, HsRFK parameters differ from those of the so far evaluated bacterial counterparts, reinforcing the idea of species-specific mechanisms in RFK catalysis. These observations support HsRFK as potential therapeutic target because of its key functions, while also envisage bacterial RFK modules as potential antimicrobial targets.
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Affiliation(s)
- Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Maribel Rivero
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Victor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Departamento de Química Física, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain.,Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain.,Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (GBsC-CSIC and BIFI-IQFR Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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6
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Srivastava AP, Mishra N, Prasad RLA, Rajesh P, Knaff DB. Thermodynamics of ferredoxin binding to cyanobacterial nitrate reductase. PHOTOSYNTHESIS RESEARCH 2020; 144:73-84. [PMID: 32222887 DOI: 10.1007/s11120-020-00738-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/20/2020] [Indexed: 06/10/2023]
Abstract
The role of the seven negatively charged amino acids of Synechocystis sp. PCC 6803 ferredoxin (Fd), i.e., Glu29, Glu30, Asp60, Asp65, Asp66, Glu92, and Glu93, predicted to form complex with nitrate reductase (NR), was investigated using site-directed mutagenesis and isothermal titration calorimetry (ITC). These experiments identified four Fd amino acids, i.e., Glu29, Asp60, Glu92, and Glu93, that are essential for the Fd binding and efficient electron transfer to the NR. ITC measurements showed that the most likely stoichiometry for the wild-type NR/wild-type Fd complex is 1:1, a Kd value 4.7 μM for the complex at low ionic strength residues and both the enthalpic and entropic components are associated with complex formation. ITC titrations of wild-type NR with four Fd variants, E29N, D60N, E92Q, and E93N demonstrated that the complex formation, although favorable, was less energetically favorable when compared to complex formation between the two wild-type proteins, suggesting that these negatively charged Fd residues at these positions are important for the effective and productive interaction with wild-type enzyme.
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Affiliation(s)
- Anurag P Srivastava
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA.
| | - Neelam Mishra
- Department of Botany, St. Joseph's College, Bangalore, Karnataka, India
| | | | - Preethi Rajesh
- Department of Life Sciences, Garden City University, Bangalore, Karnataka, India.
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
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7
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Seo D, Muraki N, Kurisu G. Kinetic and structural insight into a role of the re-face Tyr328 residue of the homodimer type ferredoxin-NADP + oxidoreductase from Rhodopseudomonas palustris in the reaction with NADP +/NADPH. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1861:148140. [PMID: 31838096 DOI: 10.1016/j.bbabio.2019.148140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/08/2019] [Accepted: 12/05/2019] [Indexed: 11/28/2022]
Abstract
Among the thioredoxin reductase-type ferredoxin-NAD(P)+ oxidoreductase (FNR) family, FNR from photosynthetic purple non‑sulfur bacterium Rhodopseudomonas palustris (RpFNR) is distinctive because the predicted residue on the re-face of the isoalloxazine ring portion of the FAD prosthetic group is a tyrosine. Here, we report the crystal structure of wild type RpFNR and kinetic analyses of the reaction of wild type, and Y328F, Y328H and Y328S mutants with NADP+/NADPH using steady state and pre-steady state kinetic approaches. The obtained crystal structure of wild type RpFNR confirmed the presence of Tyr328 on the re-face of the isoalloxazine ring of the FAD prosthetic group through the unique hydrogen bonding of its hydroxyl group. In the steady state assays, the substitution results in the decrease of Kd for NADP+ and KM for NADPH in the diaphorase assay; however, the kcat values also decreased significantly. In the stopped-flow spectrophotometry, mixing oxidized RpFNRs with NADPH and reduced RpFNRs with NADP+ resulted in rapid charge transfer complex formation followed by hydride transfer. The observed rate constants for the hydride transfer in both directions were comparable (>400 s-1). The substitution did not drastically affect the rate of hydride transfer, but substantially slowed down the subsequent release and re-association of NADP+/NADPH in both directions. The obtained results suggest that Tyr328 stabilizes the stacking of C-terminal residues on the isoalloxazine ring portion of the FAD prosthetic group, which impedes the access of NADP+/NADPH on the isoalloxazine ring portions, in turn, enhancing the release of the NADP+/NADPH and/or reaction with electron transfer proteins.
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Affiliation(s)
- Daisuke Seo
- Division of Material Science, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
| | - Norifumi Muraki
- Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan; Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Department of Life Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan; Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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8
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Kimata-Ariga Y, Chikuma Y, Saitoh T, Miyata M, Yanagihara Y, Yamane K, Hase T. NADP(H) allosterically regulates the interaction between ferredoxin and ferredoxin-NADP + reductase. FEBS Open Bio 2019; 9:2126-2136. [PMID: 31665566 PMCID: PMC6886308 DOI: 10.1002/2211-5463.12752] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/17/2022] Open
Abstract
Ferredoxin‐NADP+ reductase (FNR) in plants receives electrons from ferredoxin (Fd) at the end of the photosynthetic electron transfer chain and converts NADP+ to NADPH. The interaction between Fd and FNR in plants was previously shown to be attenuated by NADP(H). Here, we investigated the molecular mechanism of this phenomenon using maize FNR and Fd, as the three‐dimensional structure of this complex is available. NADPH, NADP+, and 2′5′‐ADP differentially affected the interaction, as revealed through kinetic and physical binding analyses. Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction to that for NADPH. We propose that the binding of NADP(H) causes a conformational change of FNR which is transferred to the Fd‐binding region through different domains of FNR, resulting in allosteric changes in the affinity for Fd. The interaction between ferredoxin (Fd) and Fd‐NADP+ reductase (FNR) in plants is attenuated by NADP(H). Site‐directed mutations of FNR which change the affinity for NADPH altered the affinity for Fd in the opposite direction. We propose that the binding of NADP(H) leads to conformational changes of FNR, resulting in allosteric changes in the affinity for Fd.![]()
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Affiliation(s)
- Yoko Kimata-Ariga
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Yutaro Chikuma
- Laboratory of Regulation of Biological Reactions, Division of Protein Chemistry, Institute for Protein Research, Osaka University, Suita, Japan
| | - Takashi Saitoh
- Division of Pharmaceutics, Hokkaido Pharmaceutical University School of Pharmacy, Sapporo, Japan
| | - Masayuki Miyata
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Yuetsu Yanagihara
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Kazukiyo Yamane
- Department of Biological Chemistry, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yoshida, Japan
| | - Toshiharu Hase
- Laboratory of Regulation of Biological Reactions, Division of Protein Chemistry, Institute for Protein Research, Osaka University, Suita, Japan
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9
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Pérez-Amigot D, Taleb V, Boneta S, Anoz-Carbonell E, Sebastián M, Velázquez-Campoy A, Polo V, Martínez-Júlvez M, Medina M. Towards the competent conformation for catalysis in the ferredoxin-NADP + reductase from the Brucella ovis pathogen. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148058. [PMID: 31394095 DOI: 10.1016/j.bbabio.2019.148058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/19/2019] [Accepted: 08/02/2019] [Indexed: 02/02/2023]
Abstract
Brucella ovis encodes a bacterial subclass 1 ferredoxin-NADP(H) reductase (BoFPR) that, by similarity with other FPRs, is expected either to deliver electrons from NADPH to the redox-based metabolism and/or to oxidize NADPH to regulate the soxRS regulon that protects bacteria against oxidative damage. Such potential roles for the pathogen survival under infection conditions make of interest to understand and to act on the BoFPR mechanism. Here, we investigate the NADP+/H interaction and NADPH oxidation by hydride transfer (HT) to BoFPR. Crystal structures of BoFPR in free and in complex with NADP+ hardly differ. The latter shows binding of the NADP+ adenosine moiety, while its redox-reactive nicotinamide protrudes towards the solvent. Nonetheless, pre-steady-state kinetics show formation of a charge-transfer complex (CTC-1) prior to the hydride transfer, as well as conversion of CTC-1 into a second charge-transfer complex (CTC-2) concomitantly with the HT event. Thus, during catalysis nicotinamide and flavin reacting rings stack. Kinetic data also identify the HT itself as the rate limiting step in the reduction of BoFPR by NADPH, as well as product release limiting the overall reaction. Using all-atom molecular dynamics simulations with a thermal effect approach we are able to visualise a potential transient catalytically competent interaction of the reacting rings. Simulations indicate that the architecture of the FAD folded conformation in BoFPR might be key in catalysis, pointing to its adenine as an element to orient the reactive atoms in conformations competent for HT.
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Affiliation(s)
- Daniel Pérez-Amigot
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Víctor Taleb
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Sergio Boneta
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Sebastián
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Aragon Institute for Health Research (IIS-Aragon), Zaragoza 50009, Spain; Biomedical Research Networking Center in Digestive and Hepatic Diseases (CIBERehd), Madrid, Spain; Fundacion ARAID, Government of Aragon, Zaragoza 50018, Spain
| | - Víctor Polo
- Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Química Física, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (Joint Units: BIFI-IQFR and GBsC-CSIC), Universidad de Zaragoza, 50018 Zaragoza, Spain.
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10
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Binding of ferredoxin NADP + oxidoreductase (FNR) to plant photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:689-698. [PMID: 31336103 DOI: 10.1016/j.bbabio.2019.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/11/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022]
Abstract
The binding of FNR to PSI has been postulated long ago, however, a clear evidence is still missing. In this work, using isothermal titration calorimetry (ITC), we found that FNR binds to photosystem I with its light harvesting complex I (PSI-LHCI) from C. reinhardtii with a 1:1 stoichiometry, a Kd of ~0.8 μM and ∆H of -20.7 kcal/mol. Titrations at different temperatures were used to determine the heat capacity change, ∆CP, of the binding, through which the size of the interface area between the proteins was assessed as ~3000 Å2. In a different set of ITC experiments, introduction of various sucrose concentrations was used to estimate that ~95 water molecules are released to the solvent. These observations support the notion of a binding site shared by few of the photosystem I - light harvesting complex I (PSI-LHCI) subunits in addition to PsaE. Based on these results, a hypothetical model was built for the binding site of FNR at PSI, using known crystallographic structures of: cyanobacterial PSI in complex with ferredoxin (Fd), plant PSI-LHCI and Fd:FNR complex from cyanobacteria. FNR binding site location is proposed to be at the foot of the stromal ridge and above the inner LHCI belt. It is expected to form contacts with PsaE, PsaB, PsaF and at least one of the LHCI. In addition, a ~4.5-fold increased affinity between FNR and PSI-LHCI under crowded 1 M sucrose environment led us to conclude that in C. reinhardtii FNR also functions as a subunit of PSI-LHCI.
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11
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Sebastián M, Velázquez-Campoy A, Medina M. The RFK catalytic cycle of the pathogen Streptococcus pneumoniae shows species-specific features in prokaryotic FMN synthesis. J Enzyme Inhib Med Chem 2018; 33:842-849. [PMID: 29693467 PMCID: PMC6010069 DOI: 10.1080/14756366.2018.1461857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023] Open
Abstract
Emergence of multidrug-resistant bacteria forces us to explore new therapeutic strategies, and proteins involved in key metabolic pathways are promising anti-bacterial targets. Bifunctional flavin-adenine dinucleotide (FAD) synthetases (FADS) are prokaryotic enzymes that synthesise the flavin mononucleotide (FMN) and FAD cofactors. The FADS from the human pathogen Streptococcus pneumoniae (SpnFADS)-causative agent of pneumonia in humans - shows relevant catalytic dissimilarities compared to other FADSs. Here, by integrating thermodynamic and kinetic data, we present a global description of the riboflavin kinase activity of SpnFADS, as well as of the inhibition mechanisms regulating this activity. Our data shed light on biophysical determinants that modulate species-specific conformational changes leading to catalytically competent conformations, as well as binding rates and affinities of substrates versus products. This knowledge paves the way for the development of tools - that taking advantage of the regulatory dissimilarities during FMN biosynthesis in different species - might be used in the discovery of specific anti-pneumococcal drugs.
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Affiliation(s)
- María Sebastián
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
- Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Facultad de Ciencias, Departamento de Bioquímica y Biología Molecular y Celular, and Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC and BIFI-CSIC Joint Units), Universidad de Zaragoza, Zaragoza, Spain
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12
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Marco P, Kozuleva M, Eilenberg H, Mazor Y, Gimeson P, Kanygin A, Redding K, Weiner I, Yacoby I. Binding of ferredoxin to algal photosystem I involves a single binding site and is composed of two thermodynamically distinct events. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:234-243. [DOI: 10.1016/j.bbabio.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
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13
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Lamazares E, Vega S, Ferreira P, Medina M, Galano-Frutos JJ, Martínez-Júlvez M, Velázquez-Campoy A, Sancho J. Direct examination of the relevance for folding, binding and electron transfer of a conserved protein folding intermediate. Phys Chem Chem Phys 2018; 19:19021-19031. [PMID: 28702545 DOI: 10.1039/c7cp02606d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Near the minimum free energy basin of proteins where the native ensemble resides, partly unfolded conformations of slightly higher energy can be significantly populated under native conditions. It has been speculated that they play roles in molecular recognition and catalysis, but they might represent contemporary features of the evolutionary process without functional relevance. Obtaining conclusive evidence on these alternatives is difficult because it requires comparing the performance of a given protein when populating and when not populating one such intermediate, in otherwise identical conditions. Wild type apoflavodoxin populates under native conditions a partly unfolded conformation (10% of molecules) whose unstructured region includes the binding sites for the FMN cofactor and for redox partner proteins. We recently engineered a thermostable variant where the intermediate is no longer detectable. Using the wild type and variant, we assess the relevance of the intermediate comparing folding kinetics, cofactor binding kinetics, cofactor affinity, X-ray structure, intrinsic dynamics, redox potential of the apoflavodoxin-cofactor complex (Fld), its affinity for partner protein FNR, and electron transfer rate within the Fld/FNR physiological complex. Our data strongly suggest the intermediate state, conserved in long-chain apoflavodoxins, is not required for the correct assembly of flavodoxin nor does it contribute to shape its electron transfer properties. This analysis can be applied to evaluate other native basin intermediates.
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Affiliation(s)
- Emilio Lamazares
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain
| | - Patricia Ferreira
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Milagros Medina
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Juan J Galano-Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Fundación ARAID, Gobierno de Aragón, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Units: BIFI-IQFR (CSIC) and GBsC-CSIC, Universidad de Zaragoza, Zaragoza, Spain and Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain and Aragon Health Research Institute (IIS Aragón), Universidad de Zaragoza, Zaragoza, Spain.
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14
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Hirasawa M, Solis J, Vaidyanathan N, Srivastava AP, Wynn RM, Sutton RB, Knaff DB. Identification of the ferredoxin interaction sites on ferredoxin-dependent glutamate synthase from Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2017; 134:317-328. [PMID: 28975508 DOI: 10.1007/s11120-017-0446-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
Based on in silico docking methods, five amino acids in glutamate synthase (Gln-467, His-1144, Asn-1147, Arg-1162, and Trp-676) likely constitute key binding residues in the interface of a glutamate synthase:ferredoxin complex. Although all interfacial mutants studied showed the ability to form a complex under low ionic strength, these docking mutations showed significantly less ferredoxin-dependent activities, while still retaining enzymatic activity. Furthermore, isothermal titration calorimetry showed a possible 1:2 molar ratio between the wild-type glutamate synthase and ferredoxin. However, each of our interfacial mutants showed only a 1:1 complex with ferredoxin, suggesting that the mutations directly affect the glutamate synthase:ferredoxin heterodimer interface.
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Affiliation(s)
- Masakazu Hirasawa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
| | - Jacaranda Solis
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Immunology and Molecular Microbiology, Texas Tech University Health Science Center, Lubbock, TX, 79430-6591, USA
| | - Nanditha Vaidyanathan
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
- Depuy Synthes Companies, 1302 Wrights Lane East, West Chester, PA, 19380, USA
| | - Anurag P Srivastava
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Illinoi, 60064, USA
| | - R Max Wynn
- Departments of Internal Medicine and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390-9038, USA.
| | - Roger B Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech Health Science Center, Lubbock, TX, 79430-6551, USA
| | - David B Knaff
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409-1061, USA
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, 79409-3132, USA
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15
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Mulo P, Medina M. Interaction and electron transfer between ferredoxin-NADP + oxidoreductase and its partners: structural, functional, and physiological implications. PHOTOSYNTHESIS RESEARCH 2017; 134:265-280. [PMID: 28361449 DOI: 10.1007/s11120-017-0372-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/20/2017] [Indexed: 05/25/2023]
Abstract
Ferredoxin-NADP+ reductase (FNR) catalyzes the last step of linear electron transfer in photosynthetic light reactions. The FAD cofactor of FNR accepts two electrons from two independent reduced ferredoxin molecules (Fd) in two sequential steps, first producing neutral semiquinone and then the fully anionic reduced, or hydroquinone, form of the enzyme (FNRhq). FNRhq transfers then both electrons in a single hydride transfer step to NADP+. We are presenting the recent progress in studies focusing on Fd:FNR interaction and subsequent electron transfer processes as well as on interaction of FNR with NADP+/H followed by hydride transfer, both from the structural and functional point of views. We also present the current knowledge about the physiological role(s) of various FNR isoforms present in the chloroplasts of higher plants and the functional impact of subchloroplastic location of FNR. Moreover, open questions and current challenges about the structure, function, and physiology of FNR are discussed.
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Affiliation(s)
- Paula Mulo
- Molecular Plant Biology, University of Turku, 20520, Turku, Finland
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, 50009, Zaragoza, Spain.
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16
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Sebastián M, Serrano A, Velázquez-Campoy A, Medina M. Kinetics and thermodynamics of the protein-ligand interactions in the riboflavin kinase activity of the FAD synthetase from Corynebacterium ammoniagenes. Sci Rep 2017; 7:7281. [PMID: 28779158 PMCID: PMC5544777 DOI: 10.1038/s41598-017-07875-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/04/2017] [Indexed: 01/20/2023] Open
Abstract
Enzymes known as bifunctional and bimodular prokaryotic type-I FAD synthetase (FADS) exhibit ATP:riboflavin kinase (RFK) and FMN:ATP adenylyltransferase (FMNAT) activities in their C-terminal and N-terminal modules, respectively, and produce flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). These act as cofactors of a plethora of flavoproteins in all organisms. Therefore, regulation of their production maintains the cellular flavoproteome homeostasis. Here, we focus on regulation of the FMN synthesis in Corynebacterium ammoniagenes (Ca) by the inhibition of its RFK activity by substrates and products of the reaction. We use a truncated CaFADS variant consisting in the isolated C-terminal RFK module, whose RFK activity is similar to that of the full-length enzyme. Inhibition of the RFK activity by the RF substrate is independent of the FMNAT module, and FMN production, in addition to being inhibited by an excess of RF, is also inhibited by both of the reaction products. Pre-steady-state kinetic and thermodynamic studies reveal key aspects to the substrates induced fit to produce the catalytically competent complex. Among them, the role of Mg2+ in the concerted allocation of substrates for catalysis and the ensemble of non-competent complexes that contribute to the regulated inhibition of the RFK activity are particularly relevant.
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Affiliation(s)
- María Sebastián
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain
| | - Ana Serrano
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, Madrid, Spain
| | - Adrián Velázquez-Campoy
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.,ARAID Foundation, Diputación General de Aragón, Zaragoza, Spain.,Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain
| | - Milagros Medina
- Department of Biochemistry and Molecular and Cellular Biology, Faculty of Sciences, and Institute of Biocomputation and Physics of Complex Systems (Joint Units: BIFI-IQFR and GBsC-CSIC), University of Zaragoza, Zaragoza, Spain.
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17
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Tapia-Rojo R, Marcuello C, Lostao A, Gómez-Moreno C, J Mazo J, Falo F. A physical picture for mechanical dissociation of biological complexes: from forces to free energies. Phys Chem Chem Phys 2017; 19:4567-4575. [PMID: 28124058 DOI: 10.1039/c6cp07508h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Single-molecule force spectroscopy is a powerful technique based on the application of controlled forces to macromolecules. In order to relate the measured response of the molecule to its equilibrium and dynamic properties, a suitable physical picture of the involved process is necessary. In this work, we introduce a plausible model for mechanical unbinding of some molecular complexes, based on a novel free energy profile. We combine two standard theoretical frameworks for analyzing force spectroscopy experiments on two protein:protein complexes, obtaining key magnitudes of the underlying free energy profile, which are only understood within the mentioned model. Additionally, we carry out detailed stochastic dynamics simulations to prove the validity of the analysis protocol and the reliability of the free energy profile. Remarkably, we can compare directly the obtained unbinding free energies with the previously known bulk binding free energies, bridging the gap between bulk and single molecule techniques.
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Affiliation(s)
- Rafael Tapia-Rojo
- Instituto de Biocomputación y Física de Sistemas Complejos and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain.
| | - Carlos Marcuello
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, 50018 Zaragoza, Spain and Fundación INA, 50018 Zaragoza, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, 50018 Zaragoza, Spain and Fundación INA, 50018 Zaragoza, Spain and Fundación ARAID, 50018 Zaragoza, Spain
| | - Carlos Gómez-Moreno
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, 50018 Zaragoza, Spain and Fundación INA, 50018 Zaragoza, Spain
| | - Juan J Mazo
- Instituto de Ciencia de Materiales de Aragón and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Fernando Falo
- Instituto de Biocomputación y Física de Sistemas Complejos and Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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18
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Kozuleva M, Goss T, Twachtmann M, Rudi K, Trapka J, Selinski J, Ivanov B, Garapati P, Steinhoff HJ, Hase T, Scheibe R, Klare JP, Hanke GT. Ferredoxin:NADP(H) Oxidoreductase Abundance and Location Influences Redox Poise and Stress Tolerance. PLANT PHYSIOLOGY 2016; 172:1480-1493. [PMID: 27634426 PMCID: PMC5100767 DOI: 10.1104/pp.16.01084] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/13/2016] [Indexed: 05/20/2023]
Abstract
In linear photosynthetic electron transport, ferredoxin:NADP(H) oxidoreductase (FNR) transfers electrons from ferredoxin (Fd) to NADP+ Both NADPH and reduced Fd (Fdred) are required for reductive assimilation and light/dark activation/deactivation of enzymes. FNR is therefore a hub, connecting photosynthetic electron transport to chloroplast redox metabolism. A correlation between FNR content and tolerance to oxidative stress is well established, although the precise mechanism remains unclear. We investigated the impact of altered FNR content and localization on electron transport and superoxide radical evolution in isolated thylakoids, and probed resulting changes in redox homeostasis, expression of oxidative stress markers, and tolerance to high light in planta. Our data indicate that the ratio of Fdred to FNR is critical, with either too much or too little FNR potentially leading to increased superoxide production, and perception of oxidative stress at the level of gene transcription. In FNR overexpressing plants, which show more NADP(H) and glutathione pools, improved tolerance to high-light stress indicates that disturbance of chloroplast redox poise and increased free radical generation may help "prime" the plant and induce protective mechanisms. In fnr1 knock-outs, the NADP(H) and glutathione pools are more oxidized relative to the wild type, and the photoprotective effect is absent despite perception of oxidative stress at the level of gene transcription.
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Affiliation(s)
- Marina Kozuleva
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Tatjana Goss
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Manuel Twachtmann
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Katherina Rudi
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Jennifer Trapka
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Jennifer Selinski
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Boris Ivanov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Prashanth Garapati
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Heinz-Juergen Steinhoff
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Toshiharu Hase
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Renate Scheibe
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Johann P Klare
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.)
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
| | - Guy T Hanke
- Institute of Basic Biological Problems, Russian Academy of Sciences, Puschino, 142290 Russia (M.K., B.I.);
- Department of Plant Physiology (T.G., M.T., J.T., J.S., P.G., R.S., G.T.H.) and Department of Biophysics (K.R., H.-J.S., J.P.K.), Osnabrück University, Osnabrück 49076, Germany;
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan (T.H.); and
- School of Biochemistry and Chemistry, Queen Mary University of London, London E1 4NS, United Kingdom (G.T.H.)
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19
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On the link between conformational changes, ligand binding and heat capacity. Biochim Biophys Acta Gen Subj 2016; 1860:868-878. [DOI: 10.1016/j.bbagen.2015.10.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/09/2015] [Accepted: 10/10/2015] [Indexed: 10/22/2022]
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Marcuello C, de Miguel R, Martínez-Júlvez M, Gómez-Moreno C, Lostao A. Mechanostability of the Single-Electron-Transfer Complexes of Anabaena Ferredoxin-NADP(+) Reductase. Chemphyschem 2015; 16:3161-9. [PMID: 26248023 DOI: 10.1002/cphc.201500534] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 01/24/2023]
Abstract
The complexes formed between the flavoenzyme ferredoxin-NADP(+) reductase (FNR; NADP(+) =nicotinamide adenine dinucleotide phosphate) and its redox protein partners, ferredoxin (Fd) and flavodoxin (Fld), have been analysed by using dynamic force spectroscopy through AFM. A strategy is developed to immobilise proteins on a substrate and AFM tip to optimise the recognition ability. The differences in the recognition efficiency regarding a random attachment procedure, together with nanomechanical results, show two binding models for these systems. The interaction of the reductase with the natural electron donor, Fd, is threefold stronger and its lifetime is longer and more specific than that with the substitute under iron-deficient conditions, Fld. The higher bond probability and two possible dissociation pathways in Fld binding to FNR are probably due to the nature of this complex, which is closer to a dynamic ensemble model. This is in contrast with the one-step dissociation kinetics that has been observed and a specific interaction described for the FNR:Fd complex.
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Affiliation(s)
- Carlos Marcuello
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain
| | - Rocío de Miguel
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain
| | - Marta Martínez-Júlvez
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Facultad de Ciencias, C/Pedro Cerbuna, 12, 50009, Zaragoza, Spain
| | - Carlos Gómez-Moreno
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Facultad de Ciencias, C/Pedro Cerbuna, 12, 50009, Zaragoza, Spain
| | - Anabel Lostao
- Laboratorio de Microscopías Avanzadas, Instituto de Nanociencia de Aragón, Universidad de Zaragoza, C/Mariano Esquillor, s/n. Ed. I+D+i, 50018, Zaragoza, Spain. .,Fundación ARAID, C/María de Luna, 11. Ed. CEEI Aragón, 50018, Zaragoza, Spain.
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A theoretical multiscale treatment of protein-protein electron transfer: The ferredoxin/ferredoxin-NADP(+) reductase and flavodoxin/ferredoxin-NADP(+) reductase systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1530-8. [PMID: 26385068 DOI: 10.1016/j.bbabio.2015.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/10/2015] [Accepted: 09/14/2015] [Indexed: 11/21/2022]
Abstract
In the photosynthetic electron transfer (ET) chain, two electrons transfer from photosystem I to the flavin-dependent ferredoxin-NADP(+) reductase (FNR) via two sequential independent ferredoxin (Fd) electron carriers. In some algae and cyanobacteria (as Anabaena), under low iron conditions, flavodoxin (Fld) replaces Fd as single electron carrier. Extensive mutational studies have characterized the protein-protein interaction in FNR/Fd and FNR/Fld complexes. Interestingly, even though Fd and Fld share the interaction site on FNR, individual residues on FNR do not participate to the same extent in the interaction with each of the protein partners, pointing to different electron transfer mechanisms. Despite of extensive mutational studies, only FNR/Fd X-ray structures from Anabaena and maize have been solved; structural data for FNR/Fld remains elusive. Here, we present a multiscale modelling approach including coarse-grained and all-atom protein-protein docking, the QM/MM e-Pathway analysis and electronic coupling calculations, allowing for a molecular and electronic comprehensive analysis of the ET process in both complexes. Our results, consistent with experimental mutational data, reveal the ET in FNR/Fd proceeding through a bridge-mediated mechanism in a dominant protein-protein complex, where transfer of the electron is facilitated by Fd loop-residues 40-49. In FNR/Fld, however, we observe a direct transfer between redox cofactors and less complex specificity than in Fd; more than one orientation in the encounter complex can be efficient in ET.
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Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
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Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
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23
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Kinoshita M, Kim JY, Kume S, Sakakibara Y, Sugiki T, Kojima C, Kurisu G, Ikegami T, Hase T, Kimata-Ariga Y, Lee YH. Physicochemical nature of interfaces controlling ferredoxin NADP(+) reductase activity through its interprotein interactions with ferredoxin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1200-11. [PMID: 26087388 DOI: 10.1016/j.bbabio.2015.05.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Although acidic residues of ferredoxin (Fd) are known to be essential for activities of various Fd-dependent enzymes, including ferredoxin NADP(+) reductase (FNR) and sulfite reductase (SiR), through electrostatic interactions with basic residues of partner enzymes, non-electrostatic contributions such as hydrophobic forces remain largely unknown. We herein demonstrated that intermolecular hydrophobic and charge-charge interactions between Fd and enzymes were both critical for enzymatic activity. Systematic site-directed mutagenesis, which altered physicochemical properties of residues on the interfaces of Fd for FNR /SiR, revealed various changes in activities of both enzymes. The replacement of serine 43 of Fd to a hydrophobic residue (S43W) and charged residue (S43D) increased and decreased FNR activity, respectively, while S43W showed significantly lower SiR activity without affecting SiR activity by S43D, suggesting that hydrophobic and electrostatic interprotein forces affected FNR activity. Enzyme kinetics revealed that changes in FNR activity by mutating Fd correlated with Km, but not with kcat or activation energy, indicating that interprotein interactions determined FNR activity. Calorimetry-based binding thermodynamics between Fd and FNR showed different binding modes of FNR to wild-type, S43W, or S43D, which were controlled by enthalpy and entropy, as shown by the driving force plot. Residue-based NMR spectroscopy of (15)N FNR with Fds also revealed distinct binding modes of each complex based on different directions of NMR peak shifts with similar overall chemical shift differences. We proposed that subtle adjustments in both hydrophobic and electrostatic forces were critical for enzymatic activity, and these results may be applicable to protein-based electron transfer systems.
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Affiliation(s)
- Misaki Kinoshita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Ju Yaen Kim
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Satoshi Kume
- Cellular Function Imaging Team, Division of Bio-function Dynamics Imaging, RIKEN Center for Life Science Technologies, Kobe, Hyogo 650-0047, Japan
| | - Yukiko Sakakibara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Chojiro Kojima
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Toshiharu Hase
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Yoko Kimata-Ariga
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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24
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Lehtimäki N, Koskela MM, Dahlström KM, Pakula E, Lintala M, Scholz M, Hippler M, Hanke GT, Rokka A, Battchikova N, Salminen TA, Mulo P. Posttranslational modifications of FERREDOXIN-NADP+ OXIDOREDUCTASE in Arabidopsis chloroplasts. PLANT PHYSIOLOGY 2014; 166:1764-76. [PMID: 25301888 PMCID: PMC4256869 DOI: 10.1104/pp.114.249094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rapid responses of chloroplast metabolism and adjustments to photosynthetic machinery are of utmost importance for plants' survival in a fluctuating environment. These changes may be achieved through posttranslational modifications of proteins, which are known to affect the activity, interactions, and localization of proteins. Recent studies have accumulated evidence about the crucial role of a multitude of modifications, including acetylation, methylation, and glycosylation, in the regulation of chloroplast proteins. Both of the Arabidopsis (Arabidopsis thaliana) leaf-type FERREDOXIN-NADP(+) OXIDOREDUCTASE (FNR) isoforms, the key enzymes linking the light reactions of photosynthesis to carbon assimilation, exist as two distinct forms with different isoelectric points. We show that both AtFNR isoforms contain multiple alternative amino termini and undergo light-responsive addition of an acetyl group to the α-amino group of the amino-terminal amino acid of proteins, which causes the change in isoelectric point. Both isoforms were also found to contain acetylation of a conserved lysine residue near the active site, while no evidence for in vivo phosphorylation or glycosylation was detected. The dynamic, multilayer regulation of AtFNR exemplifies the complex regulatory network systems controlling chloroplast proteins by a range of posttranslational modifications, which continues to emerge as a novel area within photosynthesis research.
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Affiliation(s)
- Nina Lehtimäki
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Minna M Koskela
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Käthe M Dahlström
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Eveliina Pakula
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Minna Lintala
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Martin Scholz
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Michael Hippler
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Guy T Hanke
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Anne Rokka
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Natalia Battchikova
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Tiina A Salminen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
| | - Paula Mulo
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland (N.L., M.M.K., E.P., M.L., N.B., P.M.);Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, FI-20520 Turku, Finland (K.M.D., T.A.S.);Institute of Plant Biology and Biotechnology, Faculty of Biology, Westfälische Wilhelms-Universität Münster, DE-48143 Muenster, Germany (M.S., M.H.);Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076 Osnabruck, Germany (G.T.H.); andTurku Centre for Biotechnology, FI-20520 Turku, Finland (A.R.)
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25
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Bernal-Bayard P, Ojeda V, Hervás M, Cejudo FJ, Navarro JA, Velázquez-Campoy A, Pérez-Ruiz JM. Molecular recognition in the interaction of chloroplast 2-Cys peroxiredoxin with NADPH-thioredoxin reductase C (NTRC) and thioredoxinx. FEBS Lett 2014; 588:4342-7. [DOI: 10.1016/j.febslet.2014.09.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/25/2014] [Accepted: 09/25/2014] [Indexed: 12/30/2022]
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26
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Ferreira P, Martínez-Júlvez M, Medina M. Electron transferases. Methods Mol Biol 2014; 1146:79-94. [PMID: 24764089 DOI: 10.1007/978-1-4939-0452-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The flavin isoalloxazine ring in electron transferases functions in a redox capacity, being able to take up electrons from a donor to subsequently deliver them to an acceptor. The main characteristics of these flavoproteins, including their unique ability to mediate obligatory processes of two-electron transfers with those involving single-electron transfer, are here described. To illustrate the versatility of these proteins, the acquired knowledge of the function of the two electron transferases involved in the cyanobacterial photosynthetic electron transfer from photosystem I to NADP(+) is presented. Many aspects of their biochemistry and biophysics have been extensively characterized using site-directed mutagenesis, steady-state and transient kinetics, spectroscopy, calorimetry, X-ray crystallography, electron paramagnetic resonance, and computational methods.
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Affiliation(s)
- Patricia Ferreira
- Department of Biochemistry and Molecular and Cellular Biology, Institute for Biocomputation and Physics of Complex Systems, Zaragoza, Spain
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27
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Bortolotti A, Sánchez-Azqueta A, Maya CM, Velázquez-Campoy A, Hermoso JA, Medina M, Cortez N. The C-terminal extension of bacterial flavodoxin-reductases: involvement in the hydride transfer mechanism from the coenzyme. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:33-43. [PMID: 24016470 DOI: 10.1016/j.bbabio.2013.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022]
Abstract
To study the role of the mobile C-terminal extension present in bacterial class of plant type NADP(H):ferredoxin reductases during catalysis, we generated a series of mutants of the Rhodobacter capsulatus enzyme (RcFPR). Deletion of the six C-terminal amino acids beyond alanine 266 was combined with the replacement A266Y, emulating the structure present in plastidic versions of this flavoenzyme. Analysis of absorbance and fluorescence spectra suggests that deletion does not modify the general geometry of FAD itself, but increases exposure of the flavin to the solvent, prevents a productive geometry of FAD:NADP(H) complex and decreases the protein thermal stability. Although the replacement A266Y partially coats the isoalloxazine from solvent and slightly restores protein stability, this single change does not allow formation of active charge-transfer complexes commonly present in the wild-type FPR, probably due to restraints of C-terminus pliability. A proton exchange process is deduced from ITC measurements during coenzyme binding. All studied RcFPR variants display higher affinity for NADP(+) than wild-type, evidencing the contribution of the C-terminus in tempering a non-productive strong (rigid) interaction with the coenzyme. The decreased catalytic rate parameters confirm that the hydride transfer from NADPH to the flavin ring is considerably hampered in the mutants. Although the involvement of the C-terminal extension from bacterial FPRs in stabilizing overall folding and bent-FAD geometry has been stated, the most relevant contributions to catalysis are modulation of coenzyme entrance and affinity, promotion of the optimal geometry of an active complex and supply of a proton acceptor acting during coenzyme binding.
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Affiliation(s)
- Ana Bortolotti
- Instituto de Biología Molecular y Celular de Rosario, Universidad Nacional de Rosario & CONICET, Rosario, Argentina
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28
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Hanke G, Mulo P. Plant type ferredoxins and ferredoxin-dependent metabolism. PLANT, CELL & ENVIRONMENT 2013; 36:1071-1084. [PMID: 23190083 DOI: 10.1111/pce.12046] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 05/24/2023]
Abstract
Ferredoxin (Fd) is a small [2Fe-2S] cluster-containing protein found in all organisms performing oxygenic photosynthesis. Fd is the first soluble acceptor of electrons on the stromal side of the chloroplast electron transport chain, and as such is pivotal to determining the distribution of these electrons to different metabolic reactions. In chloroplasts, the principle sink for electrons is in the production of NADPH, which is mostly consumed during the assimilation of CO2 . In addition to this primary function in photosynthesis, Fds are also involved in a number of other essential metabolic reactions, including biosynthesis of chlorophyll, phytochrome and fatty acids, several steps in the assimilation of sulphur and nitrogen, as well as redox signalling and maintenance of redox balance via the thioredoxin system and Halliwell-Asada cycle. This makes Fds crucial determinants of the electron transfer between the thylakoid membrane and a variety of soluble enzymes dependent on these electrons. In this article, we will first describe the current knowledge on the structure and function of the various Fd isoforms present in chloroplasts of higher plants and then discuss the processes involved in oxidation of Fd, introducing the corresponding enzymes and discussing what is known about their relative interaction with Fd.
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Affiliation(s)
- Guy Hanke
- Plant Physiology, Faculty of Biology and Chemistry, University of Osnabrück, DE-49076, Osnabrück, Germany
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29
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Yeom J, Park W. Biochemical characterization of ferredoxin-NADP(+) reductase interaction with flavodoxin in Pseudomonas putida. BMB Rep 2012; 45:476-81. [PMID: 22917033 DOI: 10.5483/bmbrep.2012.45.8.071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Flavodoxin (Fld) has been demonstrated to bind to ferredoxin- NADP(+) reductase A (FprA) in Pseudomonas putida. Two residues (Phe(256), Lys(259)) of FprA are likely to be important for interacting with Fld based on homology modeling. Sitedirected mutagenesis and pH-dependent enzyme kinetics were performed to further examine the role of these residues. The catalytic efficiencies of FprA-Ala(259) and FprA-Asp(259) proteins were two-fold lower than those of the wild-type FprA. Homology modeling also strongly suggested that these two residues are important for electron transfer. Thermodynamic properties such as entropy, enthalpy, and heat capacity changes of FprA-Ala(259) and FprA-Asp(259) were examined by isothermal titration calorimetry. We demonstrated, for the first time, that Phe(256) and Lys(259) are critical residues for the interaction between FprA and Fld. Van der Waals interactions and hydrogen bonding were also more important than ionic interactions for forming the FprA-Fld complex.
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Affiliation(s)
- Jinki Yeom
- Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Korea
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González B, Garrido F, Ortega R, Martínez-Júlvez M, Revilla-Guarinos A, Pérez-Pertejo Y, Velázquez-Campoy A, Sanz-Aparicio J, Pajares MA. NADP+ binding to the regulatory subunit of methionine adenosyltransferase II increases intersubunit binding affinity in the hetero-trimer. PLoS One 2012. [PMID: 23189196 PMCID: PMC3506619 DOI: 10.1371/journal.pone.0050329] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mammalian methionine adenosyltransferase II (MAT II) is the only hetero-oligomer in this family of enzymes that synthesize S-adenosylmethionine using methionine and ATP as substrates. Binding of regulatory β subunits and catalytic α2 dimers is known to increase the affinity for methionine, although scarce additional information about this interaction is available. This work reports the use of recombinant α2 and β subunits to produce oligomers showing kinetic parameters comparable to MAT II purified from several tissues. According to isothermal titration calorimetry data and densitometric scanning of the stained hetero-oligomer bands on denatured gels, the composition of these oligomers is that of a hetero-trimer with α2 dimers associated to single β subunits. Additionally, the regulatory subunit is able to bind NADP(+) with a 1:1 stoichiometry, the cofactor enhancing β to α2-dimer binding affinity. Mutants lacking residues involved in NADP(+) binding and N-terminal truncations of the β subunit were able to oligomerize with α2-dimers, although the kinetic properties appeared altered. These data together suggest a role for both parts of the sequence in the regulatory role exerted by the β subunit on catalysis. Moreover, preparation of a structural model for the hetero-oligomer, using the available crystal data, allowed prediction of the regions involved in β to α2-dimer interaction. Finally, the implications that the presence of different N-terminals in the β subunit could have on MAT II behavior are discussed in light of the recent identification of several splicing forms of this subunit in hepatoma cells.
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Affiliation(s)
- Beatriz González
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - Francisco Garrido
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Madrid, Spain
| | - Rebeca Ortega
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - Marta Martínez-Júlvez
- Departmento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Complejos, Unidad Asociada IQFR-BIFI, Mariano Esquillor s/n, Edificio I+D, Campus Rio Ebro, Zaragoza, Spain
| | | | - Yolanda Pérez-Pertejo
- Departamento de Farmacología y Toxicología (INTOXCAL), Universidad de León, Campus de Vegazana s/n, León, Spain
| | - Adrián Velázquez-Campoy
- Departmento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Complejos, Unidad Asociada IQFR-BIFI, Mariano Esquillor s/n, Edificio I+D, Campus Rio Ebro, Zaragoza, Spain
- Fundacion ARAID, Diputación General de Aragón, Zaragoza, Spain
| | - Julia Sanz-Aparicio
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano” (CSIC), Madrid, Spain
| | - María A. Pajares
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Madrid, Spain
- Molecular Hepatology Group, IdiPAZ, Madrid, Spain
- * E-mail:
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Martinez-Julvez M, Abian O, Vega S, Medina M, Velazquez-Campoy A. Studying the allosteric energy cycle by isothermal titration calorimetry. Methods Mol Biol 2012; 796:53-70. [PMID: 22052485 DOI: 10.1007/978-1-61779-334-9_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Isothermal titration calorimetry (ITC) is a powerful biophysical technique which allows a complete thermodynamic characterization of protein interactions with other molecules. The possibility of dissecting the Gibbs energy of interaction into its enthalpic and entropic contributions, as well as the detailed additional information experimentally accessible on the intermolecular interactions (stoichiometry, cooperativity, heat capacity changes, and coupled equilibria), make ITC a suitable technique for studying allosteric interactions in proteins. Two experimental methodologies for the characterization of allosteric heterotropic ligand interactions by ITC are described in this chapter, illustrated with two proteins with markedly different structural and functional features: a photosynthetic electron transfer protein and a drug target viral protease.
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Affiliation(s)
- Marta Martinez-Julvez
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain.
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32
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Lee YH, Ikegami T, Standley DM, Sakurai K, Hase T, Goto Y. Binding Energetics of Ferredoxin-NADP+ Reductase with Ferredoxin and Its Relation to Function. Chembiochem 2011; 12:2062-70. [DOI: 10.1002/cbic.201100189] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Indexed: 11/10/2022]
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The transient catalytically competent coenzyme allocation into the active site of Anabaena ferredoxin NADP+ -reductase. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 41:117-28. [PMID: 21538059 DOI: 10.1007/s00249-011-0704-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
Ferredoxin-NADP(+) reductase (FNR) catalyses the electron transfer from ferredoxin to NADP(+) via its flavin FAD cofactor. A molecular dynamics theoretical approach is applied here to visualise the transient catalytically competent interaction of Anabaena FNR with its coenzyme, NADP(+). The particular role of some of the residues identified as key in binding and accommodating the 2'P-AMP moiety of the coenzyme is confirmed in molecular terms. Simulations also indicate that the architecture of the active site precisely contributes to the orientation of the N5 of the FAD isoalloxazine ring and the C4 of the coenzyme nicotinamide ring in the conformation of the catalytically competent hydride transfer complex and, therefore, contributes to the efficiency of the process. In particular, the side chain of the C-terminal Y303 in Anabaena FNR appears key to providing the optimum geometry by reducing the stacking probability between the isoalloxazine and nicotinamide rings, thus providing the required co-linearity and distance among the N5 of the flavin cofactor, the C4 of the coenzyme nicotinamide and the hydride that has to be transferred between them. All these factors are highly related to the reaction efficiency, mechanism and reversibility of the process.
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Falconer RJ, Collins BM. Survey of the year 2009: applications of isothermal titration calorimetry. J Mol Recognit 2010; 24:1-16. [DOI: 10.1002/jmr.1073] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Pulido NO, Salcedo G, Pérez-Hernández G, José-Núñez C, Velázquez-Campoy A, García-Hernández E. Energetic effects of magnesium in the recognition of adenosine nucleotides by the F(1)-ATPase beta subunit. Biochemistry 2010; 49:5258-68. [PMID: 20518490 DOI: 10.1021/bi1006767] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Nucleotide-induced conformational changes of the catalytic beta subunits play a crucial role in the rotary mechanism of F(1)-ATPase. To gain insights into the energetic bases that govern the recognition of nucleotides by the isolated beta subunit from thermophilic Bacillus PS3 (Tbeta), the binding of this monomer to Mg(II)-free and Mg(II)-bound adenosine nucleotides was characterized using high-precision isothermal titration calorimetry. The interactions of Mg(II) with free ATP or ADP were also measured calorimetrically. A model that considers simultaneously the interactions of Tbeta with Mg.ATP or with ATP and in which ATP is able to bind two Mg(II) atoms sequentially was used to determine the formation parameters of the Tbeta-Mg.ATP complex from calorimetric data. This analysis yielded significantly different DeltaH(b) and DeltaS(b) values in relation to those obtained using a single-binding site model, while DeltaG(b) was almost unchanged. Published calorimetric data for the titration of Tbeta with Mg.ADP [Perez-Hernandez, G., et al. (2002) Arch. Biochem. Biophys. 408, 177-183] were reanalyzed with the ternary model to determine the corresponding true binding parameters. Interactions of Tbeta with Mg.ATP, ATP, Mg.ADP, or ADP were enthalpically driven. Larger differences in thermodynamic properties were observed between Tbeta-Mg.ATP and Tbeta-ATP complexes than between Tbeta-Mg.ADP and Tbeta-ADP complexes or between Tbeta-Mg.ATP and Tbeta-Mg.ADP complexes. These binding data, in conjunction with those for the association of Mg(II) with free nucleotides, allowed for a determination of the energetic effects of the metal ion on the recognition of adenosine nucleotides by Tbeta [i.e., Tbeta.AT(D)P + Mg(II) right harpoon over left harpoon Tbeta.AT(D)P-Mg]. Because of a more favorable binding enthalpy, Mg(II) is recognized more avidly by the Tbeta.ATP complex, indicating better stereochemical complementarity than in the Tbeta.ADP complex. Furthermore, a structural-energetic analysis suggests that Tbeta adopts a more closed conformation when it is bound to Mg.ATP than to ATP or Mg.ADP, in agreement with recently published NMR data [Yagi, H., et al. (2009) J. Biol. Chem. 284, 2374-2382]. Using published binding data, a similar analysis of Mg(II) energetic effects was performed for the free energy change of F(1) catalytic sites, in the framework of bi- or tri-site binding models.
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Affiliation(s)
- Nancy O Pulido
- Instituto de Quimica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Mexico
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Analysis of cooperativity by isothermal titration calorimetry. Int J Mol Sci 2009; 10:3457-77. [PMID: 20111687 PMCID: PMC2812830 DOI: 10.3390/ijms10083457] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 07/28/2009] [Accepted: 07/31/2009] [Indexed: 11/25/2022] Open
Abstract
Cooperative binding pervades Nature. This review discusses the use of isothermal titration calorimetry (ITC) in the identification and characterisation of cooperativity in biological interactions. ITC has broad scope in the analysis of cooperativity as it determines binding stiochiometries, affinities and thermodynamic parameters, including enthalpy and entropy in a single experiment. Examples from the literature are used to demonstrate the applicability of ITC in the characterisation of cooperative systems.
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