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Takahashi S, Yue G, Miyagi R, Kiwamu S. Production of recombinant intact and N-terminal truncated lipoxygenase isozyme III expressed in Saccharomyces cerevisiae and its influence on glutenin polypeptides. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100195. [PMID: 38327512 PMCID: PMC10847848 DOI: 10.1016/j.fochms.2024.100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/09/2024]
Abstract
This study investigated the effects of wheat lipoxygenase isozyme III (LOX III) and its truncated form, Mini-LOX III, on flour dough properties using yeast-expressed recombinant enzymes and hypothesized their potential to enhance cereal-based food quality. These enzymes actively catalyze linoleic acid, which is crucial for dough formation. The addition of recombinant LOX III and Mini-LOX III to wheat flour significantly changed glutenin protein composition. An increase in the amount of soluble glutenin and a shift in polypeptide distribution were observed, marked by a decrease in the high-molecular-weight regions and an increase in the low-molecular-weight regions. This result reflects the role of enzymes in altering the hydrophobicity of glutenin surfaces, thereby affecting the protein solubility and dough properties. Thus, recombinant LOX III and Mini-LOX III offer new avenues for enhancing the texture and quality of cereal-based foods, providing valuable insights into the role of wheat LOX in flour processing and its potential industrial applications.
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Affiliation(s)
- Shunsuke Takahashi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan
| | - Gao Yue
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan
| | - Reina Miyagi
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan
| | - Shiiba Kiwamu
- Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Ishizaka, Hatoyama-cho, Hiki-gun, Saitama 350-0394, Japan
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2
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Oliw EH. Thirty years with three-dimensional structures of lipoxygenases. Arch Biochem Biophys 2024; 752:109874. [PMID: 38145834 DOI: 10.1016/j.abb.2023.109874] [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: 09/29/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/27/2023]
Abstract
The X-ray crystal structures of soybean lipoxygenase (LOX) and rabbit 15-LOX were reported in the 1990s. Subsequent 3D structures demonstrated a conserved U-like shape of the substrate cavities as reviewed here. The 8-LOX:arachidonic acid (AA) complex showed AA bound to the substrate cavity carboxylate-out with C10 at 3.4 Å from the iron metal center. A recent cryo-electron microscopy (EM) analysis of the 12-LOX:AA complex illustrated AA in the same position as in the 8-LOX:AA complex. The 15- and 12-LOX complexes with isoenzyme-specific inhibitors/substrate mimics confirmed the U-fold. 5-LOX oxidizes AA to leukotriene A4, the first step in biosynthesis of mediators of asthma. The X-ray structure showed that the entrance to the substrate cavity was closed to AA by Phe and Tyr residues of a partly unfolded α2-helix. Recent X-ray analysis revealed that soaking with inhibitors shifted the short α2-helix to a long and continuous, which opened the substrate cavity. The α2-helix also adopted two conformations in 15-LOX. 12-LOX dimers consisted of one closed and one open subunit with an elongated α2-helix. 13C-ENDOR-MD computations of the 9-MnLOX:linoleate complex showed carboxylate-out position with C11 placed 3.4 ± 0.1 Å from the catalytic water. 3D structures have provided a solid ground for future research.
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Affiliation(s)
- Ernst H Oliw
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, SE 751 24, Uppsala, Sweden.
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3
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Lavrentaki V, Kousaxidis A, Theodosis-Nobelos P, Papagiouvannis G, Koutsopoulos K, Nicolaou I. Design, synthesis, and pharmacological evaluation of indazole carboxamides of N-substituted pyrrole derivatives as soybean lipoxygenase inhibitors. Mol Divers 2023:10.1007/s11030-023-10775-8. [PMID: 38145424 DOI: 10.1007/s11030-023-10775-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023]
Abstract
In this paper, we attempted to develop a novel class of compounds against lipoxygenase, a key enzyme in the biosynthesis of leukotrienes implicated in a series of inflammatory diseases. Given the absence of appropriate human 5-lipoxygenase crystallographic data, solved soybean lipoxygenase-1 and -3 structures were used as a template to generate an accurate pharmacophore model which was further used for virtual screening purposes. Eight compounds (1-8) have been derived from the in-house library consisting of N-substituted pyrroles conjugated with 5- or 6-indazole moieties through a carboxamide linker. This study led to the discovery of hit molecule 8 bearing a naphthyl group with the IC50 value of 22 μM according to soybean lipoxygenase in vitro assay. Isosteric replacement of naphthyl ring with quinoline moieties and reduction of carbonyl carboxamide group resulted in compounds 9-12 and 13, respectively. Compound 12 demonstrated the most promising enzyme inhibition. In addition, compounds 8 and 12 were found to reduce the carrageenan-induced paw edema in vivo by 52.6 and 49.8%, respectively. In view of the encouraging outcomes concerning their notable in vitro and in vivo anti-inflammatory activities, compounds 8 and 12 could be further optimized for the discovery of novel 5-lipoxygenase inhibitors in future. A structure-based 3D pharmacophore model was used in the virtual screening of in-house library to discover novel potential 5-lipoxygenase inhibitors.
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Affiliation(s)
- Vasiliki Lavrentaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Antonios Kousaxidis
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Georgios Papagiouvannis
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036, Nicosia, Cyprus
| | | | - Ioannis Nicolaou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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Ramírez-Flores CJ, Erazo Flores BJ, Tibabuzo Perdomo AM, Barnes KL, Wilson SK, Mendoza Cavazos C, Knoll LJ. A Toxoplasma gondii lipoxygenase-like enzyme is necessary for virulence and changes localization associated with the host immune response. mBio 2023; 14:e0127923. [PMID: 37646522 PMCID: PMC10653942 DOI: 10.1128/mbio.01279-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/12/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Lipoxygenases (LOXs) are enzymes that catalyze the deoxygenation of polyunsaturated fatty acids such as linoleic and arachidonic acid. These modifications create signaling molecules that are best characterized for modulating the immune response. Deletion of the first lipoxygenase-like enzyme characterized for Toxoplasma gondii (TgLOXL1) generated a less virulent strain, and infected mice showed a decreased immune response. This virulence defect was dependent on the mouse cytokine interferon gamma IFNγ. TgLOXL1 changes location from inside the parasite in tissue culture conditions to vesicular structures within the host immune cells during mouse infection. These results suggest that TgLOXL1 plays a role in the modification of the host immune response in mice.
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Affiliation(s)
- Carlos J. Ramírez-Flores
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Billy Joel Erazo Flores
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrés M. Tibabuzo Perdomo
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katie L. Barnes
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sarah K. Wilson
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Carolina Mendoza Cavazos
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Laura J. Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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5
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Sharanya CS, Abhithaj J, Arun KG, Eeda KR, Bhat V, Variyar EJ, Sabu A, Haridas M. Lipoxygenase inhibitory synthetic derivatives of methyl gallate regulate gene expressions of COX-2 and cytokines to reduce animal model arthritis. Sci Rep 2023; 13:10644. [PMID: 37391468 PMCID: PMC10313808 DOI: 10.1038/s41598-023-37613-z] [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: 11/04/2022] [Accepted: 06/24/2023] [Indexed: 07/02/2023] Open
Abstract
Mammalian lipoxygenases (LOXs) are involved in the biosynthesis of mediators of anaphylactic reactions and have been implicated in cell maturation, the pathogenesis of bronchial asthma, atherosclerosis, rheumatoid arthritis, cardiovascular diseases, Alzheimer's disease and osteoporosis. Hence LOX inhibition in chronic conditions can lead to reducing the disease progression, which can be a good target for treating these diseases. The present study deals with designing methyl gallate derivatives and their anti-inflammatory effect by in silico, in vitro and in vivo methods. Designed derivatives were docked against LOX enzyme, and molecular dynamic simulations were carried out. Following the synthesis of derivatives, in vitro LOX inhibition assay, enzyme kinetics and fluorescence quenching studies were performed. One of the derivatives of methyl gallate (MGSD 1) was demonstrated as an anti-inflammatory agent for the treatment of rheumatoid arthritis in the animal model. Amelioration of Freund's complete adjuvant (FCA)-induced arthritis by methyl gallate and its derivative with a concentration of 10-40 mg.kg-1 has been assessed in vivo in a 28-day-long study. TNF-α and COX-2 gene expression were also studied. Methyl gallate synthetic derivatives (MGSDs) inhibited LOX with an IC50 of 100 nM, 304 nM, and 226 nM for MGSD 1, MGSD 2, and MGSD 3, respectively. Fluorescence quenching methods also prove their binding characteristics, and 200 ns simulations studies showed that the RMSDs for the entire complex were less than 2.8 Å. The in vivo results showed that methyl gallate was required approximately five times diclofenac for the same level of effect, and the synthesised (MGSD 1) compound required only approximately 1/12 of diclofenac for the same level of effect in in-vivo studies. The preeminent expression of COX-2 and TNF-α genes was significantly decreased after the treatment of the methyl gallate derivative. Hence, the in vivo results showed that the referenced synthetic derivative might have more arthritis-reducing properties than the parent compound methyl gallate and is more potent than the standard drug diclofenac, with no apparent induced toxicity.
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Affiliation(s)
- C S Sharanya
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India
- Transdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - J Abhithaj
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India
| | - K G Arun
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India
| | - Koti Reddy Eeda
- Department of Chemistry, Vignan Foundation for Science Technology and Research, Vignan University (Deemed to be University), Vadlamudi, Guntur, Andhra Pradesh, 522 213, India
| | - Vignesh Bhat
- Department of Chemistry, Mangalore University, Mangalagangothri, Karnataka, 574 199, India
| | - E J Variyar
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India
| | - A Sabu
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India
| | - M Haridas
- Department of Biotechnology and Microbiology and IUCB, Dr Janaki Ammal Campus, Kannur University, Palayad, Thalassery, Kannur, Kerala, 670661, India.
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Functional Characterization of Novel Bony Fish Lipoxygenase Isoforms and Their Possible Involvement in Inflammation. Int J Mol Sci 2022; 23:ijms232416026. [PMID: 36555666 PMCID: PMC9787790 DOI: 10.3390/ijms232416026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/10/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Eicosanoids and related compounds are pleiotropic lipid mediators, which are biosynthesized in mammals via three distinct metabolic pathways (cyclooxygenase pathway, lipoxygenase pathway, epoxygenase pathway). These mediators have been implicated in the pathogenesis of inflammatory diseases and drugs interfering with eicosanoid signaling are currently available as antiphlogistics. Eicosanoid biosynthesis has well been explored in mammals including men, but much less detailed information is currently available on eicosanoid biosynthesis in other vertebrates including bony fish. There are a few reports in the literature describing the expression of arachidonic acid lipoxygenases (ALOX isoforms) in several bony fish species but except for two zebrafish ALOX-isoforms (zfALOX1 and zfALOX2) bony fish eicosanoid biosynthesizing enzymes have not been characterized. To fill this gap and to explore the possible roles of ALOX15 orthologs in bony fish inflammation we cloned and expressed putative ALOX15 orthologs from three different bony fish species (N. furzeri, P. nyererei, S. formosus) as recombinant N-terminal his-tag fusion proteins and characterized the corresponding enzymes with respect to their catalytic properties (temperature-dependence, activation energy, pH-dependence, substrate affinity and substrate specificity with different polyenoic fatty acids). Furthermore, we identified the chemical structure of the dominant oxygenation products formed by the recombinant enzymes from different free fatty acids and from more complex lipid substrates. Taken together, our data indicate that functional ALOX isoforms occur in bony fish but that their catalytic properties are different from those of mammalian enzymes. The possible roles of these ALOX-isoforms in bony fish inflammation are discussed.
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7
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Perry SC, van Hoorebeke C, Sorrentino J, Bautista L, Akinkugbe O, Conrad WS, Rutz N, Holman TR. Structural basis for altered positional specificity of 15-lipoxygenase-1 with 5S-HETE and 7S-HDHA and the implications for the biosynthesis of resolvin E4. Arch Biochem Biophys 2022; 727:109317. [PMID: 35709965 DOI: 10.1016/j.abb.2022.109317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023]
Abstract
Human 15-lipoxygenases (LOX) are critical enzymes in the inflammatory process, producing various pro-resolution molecules, such as lipoxins and resolvins, but the exact role each of the two 15-LOXs in these biosynthetic pathways remains elusive. Previously, it was observed that h15-LOX-1 reacted with 5S-HETE in a non-canonical manner, producing primarily the 5S,12S-diHETE product. To determine the active site constraints of h15-LOX-1 in achieving this reactivity, amino acids involved in the fatty acid binding were investigated. It was observed that R402L did not have a large effect on 5S-HETE catalysis, but F414 appeared to π-π stack with 5S-HETE, as seen with AA binding, indicating an aromatic interaction between a double bond of 5S-HETE and F414. Decreasing the size of F352 and I417 shifted oxygenation of 5S-HETE to C12, while increasing the size of these residues reversed the positional specificity of 5S-HETE to C15. Mutants at these locations demonstrated a similar effect with 7S-HDHA as the substrate, indicating that the depth of the active site regulates product specificity for both substrates. Together, these data indicate that of the three regions proposed to control positional specificity, π-π stacking and active site cavity depth are the primary determinants of positional specificity with 5S-HETE and h15-LOX-1. Finally, the altered reactivity of h15-LOX-1 was also observed with 5S-HEPE, producing 5S,12S-diHEPE instead of 5S,15S-diHEPE (aka resolvin E4 (RvE4). However, h15-LOX-2 efficiently produces 5S,15S-diHEPE from 5S-HEPE. This result is important with respect to the biosynthesis of the RvE4 since it obscures which LOX isozyme is involved in its biosynthesis. Future work detailing the expression levels of the lipoxygenase isoforms in immune cells and selective inhibition during the inflammatory response will be required for a comprehensive understanding of RvE4 biosynthesis.
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Affiliation(s)
- Steven C Perry
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | | | - James Sorrentino
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Leslie Bautista
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Oluwayomi Akinkugbe
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - William S Conrad
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Natalie Rutz
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, USA.
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8
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Sardar A, Abid OUR, Daud S, Ali Shah B, Shahid W, Ashraf M, fatima M, ezzine S, Wadood A, Shareef A, Al-Ghulikah HA, Alissa SA. Identification of novel diclofenac acid and naproxen bearing hydrazones as 15-LOX inhibitors: Design, Synthesis, In vitro evaluation, cytotoxicity, and In silico studies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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9
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Nikolaiczyk V, Kirschning A, Díaz E. Lipoxygenase‐catalysed co‐oxidation for sustained production of oxyfunctionalized terpenoids. FLAVOUR FRAG J 2022. [DOI: 10.1002/ffj.3700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vanessa Nikolaiczyk
- Institute of Organic Chemistry Leibniz University Hannover Hannover Germany
- Symrise AG Holzminden Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry Leibniz University Hannover Hannover Germany
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10
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Kong X, Li Y, Liu X. A review of thermosensitive antinutritional factors in plant-based foods. J Food Biochem 2022; 46:e14199. [PMID: 35502149 DOI: 10.1111/jfbc.14199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022]
Abstract
Legumes and cereals account for the vast proportion of people's daily intake of plant-based foods. Meanwhile, a large number of antinutritional factors in legumes and cereals hinder the body absorption of nutrients and reduce the nutritional value of food. In this paper, the antinutritional effects, determination, and passivation methods of thermosensitive antinutritional factors such as trypsin inhibitors, urease, lipoxygenase, and lectin were reviewed to provide theoretical help to reduce antinutritional factors in food and improve the utilization rate of plant-based food nutrition. Since trypsin inhibitors and lectin have been more extensively studied and reviewed previously, the review mainly focused on urease and lipoxygenase. This review summarized the information of thermosensitive antinutritional factors, trypsin inhibitors, urease, lipoxygenase, and lectin, in cereals and legumes. The antinutritional effects, and physical and chemical properties of trypsin inhibitors, urease, lipoxygenase, and lectin were introduced. At the same time, the research methods for the detection and inactivation of these four antinutritional factors were also summarized in the order of research conducted time. The rapid determination and inactivation of antinutrients will be the focus of attention for the food industry in the future to improve the nutritional value of food. Exploring what structural changes could passivation technologies bring to antinutritional factors will provide a theoretical basis for further understanding the mechanisms of antinutritional factor inactivation. PRACTICAL APPLICATIONS: Antinutritional factors in plant-based foods hinder the absorption of nutrients and reduce the nutritional value of the food. Among them, thermosensitive antinutritional factors, such as trypsin inhibitors, urease, lipoxygenase, and lectins, have a high proportion among the antinutritional factors. In this paper, we investigate thermosensitive antinutritional factors from three perspectives: the antinutritional effect of thermosensitive antinutritional factors, determination, and passivation methods. The current passivation methods for thermosensitive antinutritional factors revolve around biological, physical, and chemical aspects, and their elimination mechanisms still need further research, especially at the protein structure level. Reducing the level of antinutritional factors in the future food industry while controlling the loss of other nutrients in food is a goal that needs to be balanced. This paper reviews the antinutritional effects of thermosensitive antinutritional factors and passivation methods, expecting to provide new research ideas to improve the nutrient utilization of food.
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Affiliation(s)
- Xin Kong
- College of Food and Health, National Soybean Processing Industry Technology Innovation Center, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - You Li
- College of Food and Health, National Soybean Processing Industry Technology Innovation Center, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Xinqi Liu
- College of Food and Health, National Soybean Processing Industry Technology Innovation Center, Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
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11
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Roberts DE, Benton AM, Fabian-Bayola C, Spuches AM, Offenbacher AR. Thermodynamic and biophysical study of fatty acid effector binding to soybean lipoxygenase: implications for allostery driven by helix α2 dynamics. FEBS Lett 2022; 596:350-359. [PMID: 34997975 DOI: 10.1002/1873-3468.14275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 11/10/2022]
Abstract
Previous comparative kinetic isotope effects have inferred an allosteric site for fatty acids and their derivatives that modulates substrate selectivity in 15-lipoxygenases. Hydrogen-deuterium exchange also previously revealed regionally defined enhanced protein flexibility, centred at helix α2 - a gate to the substrate entrance. Direct evidence for allosteric binding and a complete understanding of its mechanism remains elusive. In this study, we examine the binding thermodynamics of the fatty acid mimic, oleyl sulfate (OS), with the monomeric model plant 15-LOX, soybean lipoxygenase (SLO), using isothermal titration calorimetry. Dynamic light scattering and differential scanning calorimetry rule out OS-induced oligomerization or structural changes. These data provide evidence that the fatty acid allosteric regulation of SLO is controlled by the dynamics of helix α2.
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Affiliation(s)
| | - Amy M Benton
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | | | - Anne M Spuches
- Department of Chemistry, East Carolina University, Greenville, NC, USA
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12
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Chang L, Wu S, Tian L. Methyl jasmonate elicits distinctive hydrolyzable tannin, flavonoid, and phyto-oxylipin responses in pomegranate (Punica granatum L.) leaves. PLANTA 2021; 254:89. [PMID: 34586513 PMCID: PMC8481150 DOI: 10.1007/s00425-021-03735-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Transcriptome and biochemical analyses suggested that, while suppression of multiple flavonoids and anthocyanins occurs at least partially at the transcriptional level, increased biosynthesis of non-jasmonate phyto-oxylipins is likely controlled non-transcriptionally. Methyl jasmonate (MeJA) produced in plants can mediate their response to environmental stresses. Exogenous application of MeJA has also shown to activate signaling pathways and induce phytoalexin accumulation in many plant species. To understand how pomegranate plants respond biochemically to environmental stresses, metabolite analysis was conducted in pomegranate leaves subjected to MeJA application and revealed unique changes in hydrolyzable tannins, flavonoids, and phyto-oxylipins. Additionally, transcriptome and real-time qPCR analyses of mock- and MeJA-treated pomegranate leaves identified differentially expressed metabolic genes and transcription factors that are potentially involved in the control of hydrolyzable tannin, flavonoid, and phyto-oxylipin pathways. Molecular, biochemical, and bioinformatic characterization of the only lipoxygenase with sustained, MeJA-induced expression showed that it is capable of oxidizing polyunsaturated fatty acids, though not located in the subcellular compartment where non-jasmonate (non-JA) phyto-oxylipins were produced. These results collectively suggested that while the broad suppression of flavonoids and anthocyanins is at least partially controlled at the transcriptional level, the induced biosynthesis of non-JA phyto-oxylipins is likely not regulated transcriptionally. Overall, a better understanding of how pomegranate leaves respond to environmental stresses will not only promote plant health and productivity, but also have an impact on human health as fruits produced by pomegranate plants are a rich source of nutritional compounds.
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Affiliation(s)
- Lijing Chang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Sheng Wu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Li Tian
- Department of Plant Sciences, Mail Stop 3, University of California, Davis, CA, 95616, USA.
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13
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Synthesis, reactivity, and DFT studies of a series of non-heme alkoxoiron(III) complexes as models for lipoxygenase. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Guan X, Zhong X, Lu Y, Du X, Jia R, Li H, Zhang M. Changes of Soybean Protein during Tofu Processing. Foods 2021; 10:1594. [PMID: 34359464 PMCID: PMC8306988 DOI: 10.3390/foods10071594] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Tofu has a long history of use and is rich in high-quality plant protein; however, its production process is relatively complicated. The tofu production process includes soybean pretreatment, soaking, grinding, boiling, pulping, pressing, and packing. Every step in this process has an impact on the soy protein and, ultimately, affects the quality of the tofu. Furthermore, soy protein gel is the basis for the formation of soy curd. This review summarizes the series of changes in the composition and structure of soy protein that occur during the processing of tofu (specifically, during the pressing, preservation, and packaging steps) and the effects of soybean varieties, storage conditions, soybean milk pretreatment, and coagulant types on the structure of soybean protein and the quality of tofu. Finally, we highlight the advantages and limitations of current research and provide directions for future research in tofu production. This review is aimed at providing a reference for research into and improvement of the production of tofu.
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Affiliation(s)
- Xiangfei Guan
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China;
| | - Xuequn Zhong
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
| | - Yuhao Lu
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
| | - Xin Du
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
| | - Rui Jia
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
| | - Hansheng Li
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 102488, China;
| | - Minlian Zhang
- Department of Chemical Engineering, Institute of Biochemical Engineering, Tsinghua University, Beijing 100084, China; (X.G.); (X.Z.); (Y.L.); (X.D.); (R.J.)
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15
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CENGİZ S, CAVAS L. Can soybean lipoxygenases be real models for mammalian lipoxygenases? A bioinformatics approach. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2020. [DOI: 10.18596/jotcsa.785109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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16
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The Molecular and Functional Characterization of the Durum Wheat Lipoxygenase TdLOX2 Suggests Its Role in Hyperosmotic Stress Response. PLANTS 2020; 9:plants9091233. [PMID: 32962020 PMCID: PMC7570197 DOI: 10.3390/plants9091233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 11/17/2022]
Abstract
In plants, lipoxygenases (LOXs) are involved in various processes, such as growth, development, and response to stress cues. In the present study, the expression pattern of six durum wheat LOX-encoding genes (TdLpx-B1.1, TdLpx-B1.2, TdLpx-A2, TdLpx-B2, TdLpx-A3 and TdLpx-B3) under hyperosmotic stress was investigated. With osmotic (0.42 M mannitol) and salt (0.21 M NaCl) stress imposed at the early stages of seedling growth, a strong induction of the TdLpx-A2 gene expression in the shoots paralleled an equally strong increase in the LOX activity. Enhanced levels of malondialdehyde (MDA) and increased rates of superoxide anion generation were also observed as a result of the stress imposition. Sequence analysis of the TdLOX2 encoded by the TdLpx-A2 gene revealed that it belonged to the type-1 9-LOX group. When overexpressed in E. coli, TdLOX2 exhibited normal enzyme activity, high sensitivity to specific LOX inhibitors, with 76% and 99% inhibition by salicylhydroxamic and propyl gallate, respectively, and a preference for linoleic acid as substrate, which was converted exclusively to its corresponding 13-hydroperoxide. This unexpected positional specificity could be related to the unusual TV/K motif that in TdLOX2 replaces the canonical TV/R motif of 9-LOXs. Treatment of seedlings with propyl gallate strongly suppressed the increase in LOX activity induced by the hyperosmotic stress; the MDA accumulation was also reduced but less markedly, whereas the rate of superoxide anion generation was even more increased. Overall, our findings suggest that the up-regulation of the TdLpx-A2 gene is a component of the durum wheat response to hyperosmotic stress and that TdLOX2 may act by counteracting the excessive generation of harmful reactive oxygen species responsible for the oxidative damages that occur in plants under stress.
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17
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Mohapatra SB, Manoj N. A conserved π-helix plays a key role in thermoadaptation of catalysis in the glycoside hydrolase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140523. [PMID: 32853774 DOI: 10.1016/j.bbapap.2020.140523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 01/21/2023]
Abstract
Here, we characterize the role of a π-helix in the molecular mechanisms underlying thermoadaptation in the glycoside hydrolase family 4 (GH4). The interspersed π-helix present in a subgroup is evolutionarily related to a conserved α-helix in other orthologs by a single residue insertion/deletion event. The insertional residue, Phe407, in a hyperthermophilic α-glucuronidase, makes specific interactions across the inter-subunit interface. In order to establish the sequence-structure-stability implications of the π-helix, the wild-type and the deletion variant (Δ407) were characterized. The variant showed a significant lowering of melting temperature and optimum temperature for the highest activity. Crystal structures of the proteins show a transformation of the π-helix to a continuous α-helix in the variant, identical to that in orthologs lacking this insertion. Thermodynamic parameters were determined from stability curves representing the temperature dependence of unfolding free energy. Though the proteins display maximum stabilities at similar temperatures, a higher melting temperature in the wild-type is achieved by a combination of higher enthalpy and lower heat capacity of unfolding. Comparisons of the structural changes, and the activity and thermodynamic profiles allow us to infer that specific non-covalent interactions, and the existence of residual structure in the unfolded state, are crucial determinants of its thermostability. These features permit the enzyme to balance the preservation of structure at a higher temperature with the thermodynamic stability required for optimum catalysis.
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Affiliation(s)
- Samar Bhallabha Mohapatra
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Narayanan Manoj
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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18
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Offenbacher AR, Holman TR. Fatty Acid Allosteric Regulation of C-H Activation in Plant and Animal Lipoxygenases. Molecules 2020; 25:molecules25153374. [PMID: 32722330 PMCID: PMC7436259 DOI: 10.3390/molecules25153374] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Lipoxygenases (LOXs) catalyze the (per) oxidation of fatty acids that serve as important mediators for cell signaling and inflammation. These reactions are initiated by a C-H activation step that is allosterically regulated in plant and animal enzymes. LOXs from higher eukaryotes are equipped with an N-terminal PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain that has been implicated to bind to small molecule allosteric effectors, which in turn modulate substrate specificity and the rate-limiting steps of catalysis. Herein, the kinetic and structural evidence that describes the allosteric regulation of plant and animal lipoxygenase chemistry by fatty acids and their derivatives are summarized.
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Affiliation(s)
- Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
- Correspondence:
| | - Theodore R. Holman
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA;
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19
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Alaei L, Izadi Z, Jafari S, Jahanshahi F, Jaymand M, Mohammadi P, Paray BA, Hasan A, Falahati M, Varnamkhasti BS, Saboury AA, Moosavi-Nejad Z, Sheikh-Hosseini M, Derakhshankhah H. Irreversible thermal inactivation and conformational lock of alpha glucosidase. J Biomol Struct Dyn 2020; 39:3256-3262. [DOI: 10.1080/07391102.2020.1762742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Loghman Alaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Biology and Biotechnology, Faculty of Sciences, University of Kurdistan, Sanandaj, Iran
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Zistmavad Pharmed Co, Tehran, Iran
| | - Samira Jafari
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Zistmavad Pharmed Co, Tehran, Iran
| | - Fatemeh Jahanshahi
- Student research committee, Faculty of Medicine, Iran University of Medical Science, Tehran, Iran
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pantea Mohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Bilal Ahamad Paray
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Mojtaba Falahati
- Department of Nanotechnology, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Behrang Shiri Varnamkhasti
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Zistmavad Pharmed Co, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Zahra Moosavi-Nejad
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Mehrnaz Sheikh-Hosseini
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Zistmavad Pharmed Co, Tehran, Iran
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20
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Miller KR, Paretsky JD, Follmer AH, Heinisch T, Mittra K, Gul S, Kim IS, Fuller FD, Batyuk A, Sutherlin KD, Brewster AS, Bhowmick A, Sauter NK, Kern J, Yano J, Green MT, Ward TR, Borovik AS. Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Inorg Chem 2020; 59:6000-6009. [PMID: 32309932 PMCID: PMC7219546 DOI: 10.1021/acs.inorgchem.9b03791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.
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Affiliation(s)
- Kelsey R. Miller
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Jonathan D. Paretsky
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Alec H. Follmer
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Michael T. Green
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - A. S. Borovik
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
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21
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Offenbacher AR, Sharma A, Doan PE, Klinman JP, Hoffman BM. The Soybean Lipoxygenase-Substrate Complex: Correlation between the Properties of Tunneling-Ready States and ENDOR-Detected Structures of Ground States. Biochemistry 2020; 59:901-910. [PMID: 32022556 PMCID: PMC7188194 DOI: 10.1021/acs.biochem.9b00861] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hydrogen tunneling in enzymatic C-H activation requires a dynamical sampling among ground-state enzyme-substrate (E-S) conformations, which transiently generates a tunneling-ready state (TRS). The TRS is characterized by a hydrogen donor-acceptor distance (DAD) of 2.7 Å, ∼0.5 Å shorter than the dominant DAD of optimized ground states. Recently, a high-resolution, 13C electron-nuclear double-resonance (ENDOR) approach was developed to characterize the ground-state structure of the complex of the linoleic acid (LA) substrate with soybean lipoxygenase (SLO). The resulting enzyme-substrate model revealed two ground-state conformers with different distances between the target C11 of LA and the catalytically active cofactor [Fe(III)-OH]: the active conformer "a", with a van der Waals DAD of 3.1 Å between C11 and metal-bound hydroxide, and an inactive conformer "b", with a distance that is almost 1 Å longer. Herein, the structure of the E-S complex is examined for a series of six variants in which subtle structural modifications of SLO have been introduced either at a hydrophobic side chain near the bound substrate or at a remote residue within a protein network whose flexibility influences hydrogen transfer. A remarkable correlation is found between the ENDOR-derived population of the active ground-state conformer a and the kinetically derived differential enthalpic barrier for D versus H transfer, ΔEa, with the latter increasing as the fraction of conformer a decreases. As proposed, ΔEa provides a "ruler" for the DAD within the TRS. ENDOR measurements further corroborate the previous identification of a dynamical network coupling the buried active site of SLO to the surface. This study shows that subtle imperfections within the initial ground-state structures of E-S complexes are accompanied by compromised geometries at the TRS.
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Affiliation(s)
- Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
- Department of Chemistry and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
| | - Peter E. Doan
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
| | - Judith P. Klinman
- Department of Chemistry and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 602084
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22
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Mishra VK, Mishra S. Flipped regiospecificity in L434F mutant of 8-lipoxygenase. Phys Chem Chem Phys 2020; 22:16013-16022. [DOI: 10.1039/d0cp02351e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Conformational change of Phe434 controls regio- and stereospecificity of L434F lipoxygenase catalysis.
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Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
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23
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Stolterfoht H, Rinnofner C, Winkler M, Pichler H. Recombinant Lipoxygenases and Hydroperoxide Lyases for the Synthesis of Green Leaf Volatiles. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13367-13392. [PMID: 31591878 DOI: 10.1021/acs.jafc.9b02690] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Green leaf volatiles (GLVs) are mainly C6- and in rare cases also C9-aldehydes, -alcohols, and -esters, which are released by plants in response to biotic or abiotic stresses. These compounds are named for their characteristic smell reminiscent of freshly mowed grass. This review focuses on GLVs and the two major pathway enzymes responsible for their formation: lipoxygenases (LOXs) and fatty acid hydroperoxide lyases (HPLs). LOXs catalyze the peroxidation of unsaturated fatty acids, such as linoleic and α-linolenic acids. Hydroperoxy fatty acids are further converted by HPLs into aldehydes and oxo-acids. In many industrial applications, plant extracts have been used as LOX and HPL sources. However, these processes are limited by low enzyme concentration, stability, and specificity. Alternatively, recombinant enzymes can be used as biocatalysts for GLV synthesis. The increasing number of well-characterized enzymes efficiently expressed by microbial hosts will foster the development of innovative biocatalytic processes for GLV production.
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Affiliation(s)
- Holly Stolterfoht
- Austrian Centre of Industrial Biotechnology , Petersgasse 14 , 8010 Graz , Austria
| | - Claudia Rinnofner
- Austrian Centre of Industrial Biotechnology , Petersgasse 14 , 8010 Graz , Austria
- bisy e.U. , Wetzawinkel 20 , 8200 Hofstaetten , Austria
| | - Margit Winkler
- Austrian Centre of Industrial Biotechnology , Petersgasse 14 , 8010 Graz , Austria
- Institute of Molecular Biotechnology , TU Graz, NAWI Graz, BioTechMed Graz , Petersgasse 14 , 8010 Graz , Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology , Petersgasse 14 , 8010 Graz , Austria
- Institute of Molecular Biotechnology , TU Graz, NAWI Graz, BioTechMed Graz , Petersgasse 14 , 8010 Graz , Austria
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24
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Gaffney BJ. EPR Spectroscopic Studies of Lipoxygenases. Chem Asian J 2019; 15:42-50. [PMID: 31782616 DOI: 10.1002/asia.201901461] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/27/2019] [Indexed: 11/11/2022]
Abstract
Polyunsaturated fatty acids are sources of diverse natural, and chemically designed products. The enzyme lipoxygenase selectively oxidizes fatty acid acyl chains using controlled free radical chemistry; the products are regio- and stereo-chemically unique hydroperoxides. A conserved structural fold of ≈600 amino acids harbors a long and narrow substrate channel and a well-shielded catalytic iron. Oxygen, a co-substrate, is blocked from the active site until a hydrogen atom is abstracted from substrate bis-allylic carbon, in a non-heme iron redox cycle. EPR spectroscopy of ferric intermediates in lipoxygenase catalysis reveals changes in the metal coordination and leads to a proposal on the nature of the reactive intermediate. Remarkably, free radicals are so well controlled in lipoxygenase chemistry that spin label technology can be applied as well. The current level of understanding of steps in lipoxygenase catalysis, from the EPR perspective, will be reviewed.
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Affiliation(s)
- Betty J Gaffney
- Biological Science, Florida State University, Tallahassee, FL, 32306, USA
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25
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Bioinformatics Analysis of the Lipoxygenase Gene Family in Radish ( Raphanus sativus) and Functional Characterization in Response to Abiotic and Biotic Stresses. Int J Mol Sci 2019; 20:ijms20236095. [PMID: 31816887 PMCID: PMC6928601 DOI: 10.3390/ijms20236095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022] Open
Abstract
Lipoxygenases (LOXs) are non-heme iron-containing dioxygenases involved in many developmental and stress-responsive processes in plants. However, little is known about the radish LOX gene family members and their functions in response to biotic and abiotic stresses. In this study, we completed a genome-wide analysis and expression profiling of RsLOX genes under abiotic and biotic stress conditions. We identified 11 RsLOX genes, which encoded conserved domains, and classified them in 9-LOX and 13-LOX categories according to their phylogenetic relationships. The characteristic structural features of 9-LOX and 13-LOX genes and the encoded protein domains as well as their evolution are presented herein. A qRT-PCR analysis of RsLOX expression levels in the roots under simulated drought, salinity, heat, and cold stresses, as well as in response to a Plasmodiophora brassicae infection, revealed three tandem-clustered RsLOX genes that are involved in responses to various environmental stresses via the jasmonic acid pathway. Our findings provide insights into the evolution and potential biological roles of RsLOXs related to the adaptation of radish to stress conditions.
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26
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Sanfilippo C, Paterna A, Biondi DM, Patti A. Lyophilized extracts from vegetable flours as valuable alternatives to purified oxygenases for the synthesis of oxylipins. Bioorg Chem 2019; 93:103325. [PMID: 31586707 DOI: 10.1016/j.bioorg.2019.103325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 12/31/2022]
Abstract
In this work, the whole aqueous extracts of soybean flour and oat flour have been used as valuable alternatives to purified oxygenase enzymes for the preparation of oxylipins derived from (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoic acid (EPA). The lipoxygenase activity in the aqueous extracts of soybean (Glycine max. L.) flour was monitored with linoleic acid as substrate and compared with the commercially available purified enzyme (LOX-1). Oat flour extracts (Avena sativa L.) were evaluated for their peroxygenase activity by comparing different enzyme preparations in the epoxidation of methyl oleate. It was found that lyophilization of the aqueous extracts from these vegetable flours offers advantages in terms of enzyme stability, reproducibility and applicability to preparative organic synthesis. The lyophilized enzyme preparations were tested for the oxyfunctionalization of EPA and the formed products were isolated in satisfactory yields. In the presence of lyophilized extract from soybean, EPA gave 15S-hydroxy-(5Z,8Z,11Z,13E,17Z)-eicosapentaenoic acid in enantiopure form as exclusive product. Peroxygenase from oat flour was less selective and catalyzed the formation of different epoxides of EPA. However, the biocatalyzed epoxidation of EPA under controlled conditions allowed to obtain optically active (17R,18S)-epoxy-(5Z,8Z,11Z,14Z)-eicosatetraenoic acid (65% ee) as the main monoepoxide, among the five possible ones.
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Affiliation(s)
- Claudia Sanfilippo
- CNR - Istituto di Chimica Biomolecolare, Via Paolo Gaifami 18, I-95126 Catania, Italy
| | - Angela Paterna
- CNR - Istituto di Chimica Biomolecolare, Via Paolo Gaifami 18, I-95126 Catania, Italy
| | - Daniela M Biondi
- CNR - Istituto di Chimica Biomolecolare, Via Paolo Gaifami 18, I-95126 Catania, Italy
| | - Angela Patti
- CNR - Istituto di Chimica Biomolecolare, Via Paolo Gaifami 18, I-95126 Catania, Italy.
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27
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Hu S, Offenbacher AR, Lu ED, Klinman JP. Comparative kinetic isotope effects on first- and second-order rate constants of soybean lipoxygenase variants uncover a substrate-binding network. J Biol Chem 2019; 294:18069-18076. [PMID: 31624150 PMCID: PMC6885649 DOI: 10.1074/jbc.ra119.010826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/14/2019] [Indexed: 01/08/2023] Open
Abstract
Lipoxygenases are widespread enzymes found in virtually all eukaryotes, including fungi, and, more recently, in prokaryotes. These enzymes act on long-chain polyunsaturated fatty acid substrates (C18 to C20), raising questions regarding how the substrate threads its way from solvent to the active site. Herein, we report a comparison of the temperature dependence of isotope effects on first- and second-order rate constants among single-site variants of the prototypic plant enzyme soybean lipoxygenase-1 substituted at amino acid residues inferred to impact substrate binding. We created 10 protein variants including four amino acid positions, Val-750, Ile-552, Ile-839, and Trp-500, located within a previously proposed substrate portal. The conversion of these bulky hydrophobic side chains to smaller side chains is concluded to increase the mobility of flanking helices, giving rise to increased off rates for substrate dissociation from the enzyme. In this manner, we identified a specific "binding network" that can regulate movement of the substrate from the solvent to the active site. Taken together with our previous findings on C-H and O2 activation of soybean lipoxygenase-1, these results support the emergence of multiple complementary networks within a single protein scaffold that modulate different steps along the enzymatic reaction coordinate.
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Affiliation(s)
- Shenshen Hu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Adam R Offenbacher
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720; Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Edbert D Lu
- Department of Chemistry, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, California 94720; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720.
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Mishra VK, Mishra S. Origin of Regio- and Stereospecific Catalysis by 8-Lipoxygenase. J Phys Chem B 2019; 123:10605-10621. [PMID: 31775504 DOI: 10.1021/acs.jpcb.9b07917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Vipin Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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29
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Biocatalytic Synthesis of Natural Green Leaf Volatiles Using the Lipoxygenase Metabolic Pathway. Catalysts 2019. [DOI: 10.3390/catal9100873] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
In higher plants, the lipoxygenase enzymatic pathway combined actions of several enzymes to convert lipid substrates into signaling and defense molecules called phytooxylipins including short chain volatile aldehydes, alcohols, and esters, known as green leaf volatiles (GLVs). GLVs are synthesized from C18:2 and C18:3 fatty acids that are oxygenated by lipoxygenase (LOX) to form corresponding hydroperoxides, then the action of hydroperoxide lyase (HPL) produces C6 or C9 aldehydes that can undergo isomerization, dehydrogenation, and esterification. GLVs are commonly used as flavors to confer a fresh green odor of vegetable to perfumes, cosmetics, and food products. Given the increasing demand in these natural flavors, biocatalytic processes using the LOX pathway reactions constitute an interesting application. Vegetable oils, chosen for their lipid profile are converted in natural GLVs with high added value. This review describes the enzymatic reactions of GLVs biosynthesis in the plant, as well as the structural and functional properties of the enzymes involved. The various stages of the biocatalytic production processes are approached from the lipid substrate to the corresponding aldehyde or alcoholic aromas, as well as the biotechnological improvements to enhance the production potential of the enzymatic catalysts.
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30
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Zaragoza JPT, Nguy A, Minnetian N, Deng Z, Iavarone AT, Offenbacher AR, Klinman JP. Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase. J Phys Chem B 2019; 123:8662-8674. [PMID: 31580070 PMCID: PMC6944211 DOI: 10.1021/acs.jpcb.9b07228] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Å inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced "protein quakes" as the origin of enthalpic barriers in catalysis.
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Affiliation(s)
- Jan Paulo T. Zaragoza
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Andy Nguy
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Natalie Minnetian
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Zhenyu Deng
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Anthony T. Iavarone
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Adam R. Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858
| | - Judith P. Klinman
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California 94720, United States
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31
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Hershelman D, Kahler KM, Price MJ, Lu I, Fu Y, Plumeri PA, Karaisz F, Bassett NF, Findeis PM, Clapp CH. Oxygenation reactions catalyzed by the F557V mutant of soybean lipoxygenase-1: Evidence for two orientations of substrate binding. Arch Biochem Biophys 2019; 674:108082. [PMID: 31473191 DOI: 10.1016/j.abb.2019.108082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 01/18/2023]
Abstract
Plant lipoxygenases oxygenate linoleic acid to produce 13(S)-hydroperoxy-9Z,11E-octadecadienoic acid (13(S)-HPOD) or 9-hydroperoxy-10E,12Z-octadecadienoic acid (9(S)-HPOD). The manner in which these enzymes bind substrates and the mechanisms by which they control regiospecificity are uncertain. Hornung et al. (Proc. Natl. Acad. Sci. USA96 (1999) 4192-4197) have identified an important residue, corresponding to phe-557 in soybean lipoxygenase-1 (SBLO-1). These authors proposed that large residues in this position favored binding of linoleate with the carboxylate group near the surface of the enzyme (tail-first binding), resulting in formation of 13(S)-HPOD. They also proposed that smaller residues in this position facilitate binding of linoleate in a head-first manner with its carboxylate group interacting with a conserved arginine residue (arg-707 in SBLO-1), which leads to 9(S)-HPOD. In the present work, we have tested these proposals on SBLO-1. The F557V mutant produced 33% 9-HPOD (S:R = 87:13) from linoleic acid at pH 7.5, compared with 8% for the wild-type enzyme and 12% with the F557V,R707L double mutant. Experiments with 11(S)-deuteriolinoleic acid indicated that the 9(S)-HPOD produced by the F557V mutant involves removal of hydrogen from the pro-R position on C-11 of linoleic acid, as expected if 9(S)-HPOD results from binding in an orientation that is inverted relative to that leading to 13(S)-HPOD. The product distributions obtained by oxygenation of 10Z,13Z-nonadecadienoic acid and arachidonic acid by the F557V mutant support the hypothesis that ω6 oxygenation results from tail-first binding and ω10 oxygenation from head-first binding. The results demonstrate that the regiospecificity of SBLO-1 can be altered by a mutation that facilitates an alternative mode of substrate binding and adds to the body of evidence that 13(S)-HPOD arises from tail-first binding.
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Affiliation(s)
| | - Kirsten M Kahler
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Morgan J Price
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Iris Lu
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Yuhan Fu
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | | | - Fred Karaisz
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | | | - Peter M Findeis
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA
| | - Charles H Clapp
- Department of Chemistry, Bucknell University, Lewisburg, PA, USA.
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32
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Structural changes associated with the inactivation of lipoxygenase by pulsed light. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.108332] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Sinha S, Doble M, Manju SL. 5-Lipoxygenase as a drug target: A review on trends in inhibitors structural design, SAR and mechanism based approach. Bioorg Med Chem 2019; 27:3745-3759. [PMID: 31331653 DOI: 10.1016/j.bmc.2019.06.040] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 01/22/2023]
Abstract
The most common inflammatory disease of the airways is asthma among children affecting around 235 million people worldwide. 5-Lipoxygenase (5-LOX) is a crucial enzyme which helps in the conversion of arachidonic acid (AA) to leukotrienes (LTs), the lipid mediators. It is associated with several inflammation related disorders such as asthma, allergy, and atherosclerosis. Therefore, it is considered as a promising target against inflammation and asthma. Currently, the only drug against 5-LOX which is available is Zileuton, while a few inhibitors are in clinical trial stages such as Atreleuton and Setileuton. So, there is a dire requirement in the area of progress of novel 5-LOX inhibitors which necessitates an understanding of their structure activity relationship and mode of action. In this review, novel 5-LOX inhibitors reported so far, their structural design, SAR and developmental strategies along with clinical updates are discussed over the last two decades.
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Affiliation(s)
- Shweta Sinha
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India; Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Tamil Nadu 600036, India
| | - Mukesh Doble
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology, Madras, Tamil Nadu 600036, India.
| | - S L Manju
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
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Wegeberg C, Browne WR, McKenzie CJ. cis Donor Influence on O–O Bond Lability in Iron(III) Hydroperoxo Complexes: Oxidation Catalysis and Ligand Transformation. Inorg Chem 2019; 58:8983-8994. [DOI: 10.1021/acs.inorgchem.9b00247] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christina Wegeberg
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Wesley R. Browne
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christine J. McKenzie
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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35
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Pakhomova S, Boeglin WE, Neau DB, Bartlett SG, Brash AR, Newcomer ME. An ensemble of lipoxygenase structures reveals novel conformations of the Fe coordination sphere. Protein Sci 2019; 28:920-927. [PMID: 30861228 PMCID: PMC6459989 DOI: 10.1002/pro.3602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 01/07/2023]
Abstract
The regio- and stereo-specific oxygenation of polyunsaturated fatty acids is catalyzed by lipoxygenases (LOX); both Fe and Mn forms of the enzyme have been described. Structural elements of the Fe and Mn coordination spheres and the helical catalytic domain in which the metal center resides are highly conserved. However, animal, plant, and microbial LOX each have distinct features. We report five crystal structures of a LOX from the fungal plant pathogen Fusarium graminearum. This LOX displays a novel amino terminal extension that provides a wrapping domain for dimerization. Moreover, this extension appears to interfere with the iron coordination sphere, as the typical LOX configuration is not observed at the catalytic metal when the enzyme is dimeric. Instead novel tetra-, penta-, and hexa-coordinate Fe2+ ligations are apparent. In contrast, a monomeric structure indicates that with repositioning of the amino terminal segment, the enzyme can assume a productive conformation with the canonical Fe2+ coordination sphere.
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Affiliation(s)
- Svetlana Pakhomova
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - William E. Boeglin
- Department of Pharmacology VanderbiltUniversity School of MedicineNashvilleTennessee, 37232
| | - David B. Neau
- Northeastern Collaborative Access Team, Argonne National LaboratoryCornell UniversityArgonneIllinois
| | - Sue G. Bartlett
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
| | - Alan R. Brash
- Department of Pharmacology VanderbiltUniversity School of MedicineNashvilleTennessee, 37232
| | - Marcia E. Newcomer
- Department of Biological SciencesLouisiana State UniversityBaton RougeLouisiana
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36
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Thürich J, Meichsner D, Furch ACU, Pfalz J, Krüger T, Kniemeyer O, Brakhage A, Oelmüller R. Arabidopsis thaliana responds to colonisation of Piriformospora indica by secretion of symbiosis-specific proteins. PLoS One 2018; 13:e0209658. [PMID: 30589877 PMCID: PMC6307754 DOI: 10.1371/journal.pone.0209658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 12/10/2018] [Indexed: 11/24/2022] Open
Abstract
Plants interact with a wide variety of fungi in a mutualistic, parasitic or neutral way. The associations formed depend on the exchange of nutrients and signalling molecules between the partners. This includes a diverse set of protein classes involved in defence, nutrient uptake or establishing a symbiotic relationship. Here, we have analysed the secretomes of the mutualistic, root-endophytic fungus Piriformospora indica and Arabidopsis thaliana when cultivated alone or in a co-culture. More than one hundred proteins were identified as differentially secreted, including proteins associated with growth, development, abiotic and biotic stress response and mucilage. While some of the proteins have been associated before to be involved in plant-microbial interaction, other proteins are newly described in this context. One plant protein found in the co-culture is PLAT1 (Polycystin, Lipoxygenase, Alpha-toxin and Triacylglycerol lipase). PLAT1 has not been associated with plant-fungal-interaction and is known to play a role in abiotic stress responses. In colonised roots PLAT1 shows an altered gene expression in a stage specific manner and plat1 knock-out plants are colonised stronger. It co-localises with Brassicaceae-specific endoplasmic reticulum bodies (ER-bodies) which are involved in the formation of the defence compound scopolin. We observed degraded ER-bodies in infected Arabidopsis roots and a change in the scopolin level in response to the presence of the fungus.
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Affiliation(s)
- Johannes Thürich
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Doreen Meichsner
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Alexandra C. U. Furch
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jeannette Pfalz
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Thomas Krüger
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany
| | - Olaf Kniemeyer
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany
| | - Axel Brakhage
- Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
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Goloshchapova K, Stehling S, Heydeck D, Blum M, Kuhn H. Functional characterization of a novel arachidonic acid 12S-lipoxygenase in the halotolerant bacterium Myxococcus fulvus exhibiting complex social living patterns. Microbiologyopen 2018; 8:e00775. [PMID: 30560563 PMCID: PMC6612559 DOI: 10.1002/mbo3.775] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 01/24/2023] Open
Abstract
Lipoxygenases are lipid peroxidizing enzymes, which frequently occur in higher plants and mammals. These enzymes are also expressed in lower multicellular organisms but here they are not widely distributed. In bacteria, lipoxygenases rarely occur and evaluation of the currently available bacterial genomes suggested that <0.5% of all sequenced bacterial species carry putative lipoxygenase genes. We recently rescreened the public bacterial genome databases for lipoxygenase-like sequences and identified two novel lipoxygenase isoforms (MF-LOX1 and MF-LOX2) in the halotolerant Myxococcus fulvus. Both enzymes share a low degree of amino acid conservation with well-characterized eukaryotic lipoxygenase isoforms but they involve the catalytically essential iron cluster. Here, we cloned the MF-LOX1 cDNA, expressed the corresponding enzyme as N-terminal hexa-his-tag fusion protein, purified the recombinant enzyme to electrophoretic homogeneity, and characterized it with respect to its protein-chemical and enzymatic properties. We found that M. fulvus expresses a catalytically active intracellular lipoxygenase that converts arachidonic acid and other polyunsaturated fatty acids enantioselectively to the corresponding n-9 hydroperoxy derivatives. The enzyme prefers C20 - and C22 -polyenoic fatty acids but does not exhibit significant membrane oxygenase activity. The possible biological relevance of MF-LOX1 will be discussed in the context of the suggested concepts of other bacterial lipoxygenases.
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Affiliation(s)
- Kateryna Goloshchapova
- Institute of BiochemistryCharité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Sabine Stehling
- Institute of BiochemistryCharité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Dagmar Heydeck
- Institute of BiochemistryCharité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | | | - Hartmut Kuhn
- Institute of BiochemistryCharité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
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Li P, Soudackov AV, Hammes-Schiffer S. Impact of Mutations on the Binding Pocket of Soybean Lipoxygenase: Implications for Proton-Coupled Electron Transfer. J Phys Chem Lett 2018; 9:6444-6449. [PMID: 30359035 PMCID: PMC6402330 DOI: 10.1021/acs.jpclett.8b02945] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Soybean lipoxygenase catalyzes a proton-coupled electron transfer (PCET) reaction and serves as a prototype for hydrogen tunneling in enzymes due to the unusually high kinetic isotope effect and significant modulation of the rate constant and kinetic isotope effect by mutation. Herein these experimental observations are interpreted in the context of changes to the substrate binding pocket in microsecond molecular dynamics simulations of wild-type and mutant soybean lipoxygenase. The binding pocket exhibits an hourglass shape with residues L546 and L754 bracketing the bottleneck, positioning the linoleic acid substrate for PCET. Mutation of I553 to less bulky residues slightly increases the width of the bottleneck and the volume of the binding pocket. Mutating L546 or L754 to a smaller residue also enlarges this width and volume, and mutating both has an even more dramatic effect. This analysis illustrates how mutation of the substrate binding pocket can be used as a strategy to tune the kinetics.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Alexander V. Soudackov
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520
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39
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Sankaralingam M, Lee YM, Karmalkar DG, Nam W, Fukuzumi S. A Mononuclear Non-heme Manganese(III)–Aqua Complex as a New Active Oxidant in Hydrogen Atom Transfer Reactions. J Am Chem Soc 2018; 140:12695-12699. [DOI: 10.1021/jacs.8b07772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Deepika G. Karmalkar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Faculty of Science and Engineering, Meijo University, Nagoya, Aichi 468-8502, Japan
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40
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Sugio A, Østergaard LH, Matsui K, Takagi S. Characterization of two fungal lipoxygenases expressed in Aspergillus oryzae. J Biosci Bioeng 2018; 126:436-444. [PMID: 29805113 DOI: 10.1016/j.jbiosc.2018.04.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/20/2018] [Accepted: 04/06/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Akiko Sugio
- Novozymes Japan Ltd., CB-6 MTG, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan
| | | | - Kenji Matsui
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, Yamaguchi 753-8515, Japan
| | - Shinobu Takagi
- Novozymes Japan Ltd., CB-6 MTG, 1-3 Nakase, Mihama-ku, Chiba 261-8501, Japan.
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Clapp CH, Pachuski J, Bassett NF, Bishop KA, Carter G, Young M, Young T, Fu Y. N-linoleoylamino acids as chiral probes of substrate binding by soybean lipoxygenase-1. Bioorg Chem 2018; 78:170-177. [PMID: 29573638 DOI: 10.1016/j.bioorg.2018.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 02/25/2018] [Accepted: 03/07/2018] [Indexed: 12/30/2022]
Abstract
Lipoxygenases catalyze the oxygenation of polyunsaturated fatty acids and their derivatives to produce conjugated diene hydroperoxides. Soybean lipoxygenase-1 (SBLO-1) has been the subject of intensive structural and mechanistic study, but the manner in which this enzyme binds substrates is uncertain. Previous studies suggest that the fatty acyl group of the substrate binds in an internal cavity near the catalytic iron with the polar end at the surface of the protein or perhaps external to the protein. To test this model, we have investigated two pairs of enantiomeric N-linoleoylamino acids as substrates for SBLO-1. If the amino acid moiety binds external to the protein, the kinetics and product distribution should show little or no sensitivity to the stereochemical configuration of the amino acid moiety. Consistent with this expectation, N-linoleoyl-l-valine (LLV) and N-linoleoyl-d-valine (LDV) are both good substrates with kcat/Km values that are equal within error and about 40% higher than kcat/Km for linoleic acid. Experiments with N-linoleoyl-l-tryptophan (LLT) and N-linoleoyl-d-tryptophan (LDT) were complicated by the low critical micelle concentrations (CMC = 6-8 μM) of these substances. Below the CMC, LDT is a better substrate by a factor of 2.7. The rates of oxygenation of LDT and LLT continue to rise above the CMC, with modest stereoselectivity in favor of the d enantiomer. With all of the substrates tested, the major product is the 13(S)-hydroperoxide, and the distribution of minor products is not appreciably affected by the configuration of the amino acid moiety. The absence of stereoselectivity with LLV and LDV, the modest magnitude of the stereoselectivity with LLT and LDT, and the ability micellar forms of LLT and LDT to increase the concentration of available substrate are all consistent with the hypothesis that the amino acid moiety binds largely external to SBLO-1 and interacts with it only weakly.
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Affiliation(s)
- Charles H Clapp
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States.
| | - Justin Pachuski
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Natasha F Bassett
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Kathleen A Bishop
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Gillian Carter
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Megan Young
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Thomas Young
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
| | - Yuhan Fu
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, United States
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Tsolaki E, Eleftheriou P, Kartsev V, Geronikaki A, Saxena AK. Application of Docking Analysis in the Prediction and Biological Evaluation of the Lipoxygenase Inhibitory Action of Thiazolyl Derivatives of Mycophenolic Acid. Molecules 2018; 23:E1621. [PMID: 29970872 PMCID: PMC6099768 DOI: 10.3390/molecules23071621] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/21/2018] [Accepted: 06/27/2018] [Indexed: 12/25/2022] Open
Abstract
5-LOX inhibition is among the desired characteristics of anti-inflammatory drugs, while 15-LOX has also been considered as a drug target. Similarity in inhibition behavior between soybean LOX-1 and human 5-LOX has been observed and soybean LOX (sLOX) type 1b has been used for the evaluation of LOX inhibition in drug screening for years. After prediction of LOX inhibition by PASS and docking as well as toxicity by PROTOX and ToxPredict sixteen (E)-N-(thiazol-2-yl)-6-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydroisobenzofuran-5-yl)-4-methylhex-4-enamide derivatives with lengths varying from about 15⁻20 Å were evaluated in vitro for LOX inhibitory action using the soybean lipoxygenase sLOX 1b. Docking analysis was performed using soybean LOX L-1 (1YGE), soybean LOX-3 (1JNQ), human 5-LOX (3O8Y and 3V99) and mammalian 15-LOX (1LOX) structures. Different dimensions of target center and docking boxes and a cavity prediction algorithm were used. The compounds exhibited inhibitory action between 2.5 μΜ and 165 μΜ. Substituents with an electronegative atom at two-bond proximity to position 4 of the thiazole led to enhanced activity. Docking results indicated that the LOX structures 1JNQ, 3V99 and 1LOX can effectively be used for estimation of LOX inhibition and amino acid interactions of these compounds.
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Affiliation(s)
- Evangelia Tsolaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Phaedra Eleftheriou
- Department of Medical Laboratories, School of Health and Care Professions, Alexander Technological Educational Institute of Thessaloniki, 54700 Thessaloniki, Greece.
| | | | - Athina Geronikaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Anil K Saxena
- Division of Medicinal & Process Chemistry, Central Drug Research Institute, 226031 Lucknow, India.
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C. S. S, K. G. A, V. V, A. S, M. H. Designing of enzyme inhibitors based on active site specificity: lessons from methyl gallate and its lipoxygenase inhibitory profile. J Recept Signal Transduct Res 2018; 38:256-265. [DOI: 10.1080/10799893.2018.1478856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Sharanya C. S.
- Inter University Centre for Bioscience and Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Palayad, India
| | - Arun K. G.
- Inter University Centre for Bioscience and Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Palayad, India
| | - Vijaytha V.
- Inter University Centre for Bioscience and Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Palayad, India
| | - Sabu A.
- Inter University Centre for Bioscience and Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Palayad, India
| | - Haridas M.
- Inter University Centre for Bioscience and Department of Biotechnology & Microbiology, Kannur University, Thalassery Campus, Palayad, India
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Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Characterizing metal-binding sites in proteins with X-ray crystallography. Nat Protoc 2018; 13:1062-1090. [PMID: 29674755 PMCID: PMC6235626 DOI: 10.1038/nprot.2018.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
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Gilbert NC, Neau DB, Newcomer ME. Expression of an 8R-Lipoxygenase From the Coral Plexaura homomalla. Methods Enzymol 2018; 605:33-49. [PMID: 29909831 DOI: 10.1016/bs.mie.2018.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods are presented for the use of the coral 8R-lipoxygenase from the Caribbean sea whip coral Plexaura homomalla as a model enzyme for structural studies of animal lipoxygenases. The 8R-lipoxygenase is remarkably stable and can be stored at 4°C for 3 months with virtually no loss of activity. In addition, an engineered "pseudo wild-type" enzyme is soluble in the absence of detergents, which helps facilitate the preparation of enzyme:substrate complexes.
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Affiliation(s)
| | - David B Neau
- Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, IL, United States
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In vitro study of iron coordination properties, anti-inflammatory potential, and cytotoxic effects of N-salicylidene and N-vanillidene anil Schiff bases. CHEMICAL PAPERS 2018. [DOI: 10.1007/s11696-018-0419-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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ElBordiny HS, El-Miligy MM, Kassab SE, Daabees H, Mohamed Ali WA, Abdelhamid Mohamed El-Hawash S. Design, synthesis, biological evaluation and docking studies of new 3-(4,5-dihydro-1H-pyrazol/isoxazol-5-yl)-2-phenyl-1H-indole derivatives as potent antioxidants and 15-lipoxygenase inhibitors. Eur J Med Chem 2018; 145:594-605. [PMID: 29339254 DOI: 10.1016/j.ejmech.2018.01.026] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
New candidates of 3-(4,5-dihydro-1H-pyrazol/isoxazol-5-yl)-2-phenyl-1H-indole derivatives (4-7) were designed combining the pyrazoline/isoxazoline heterocycles and 2-phenylindole to explore its potential as 15-lipoxygenase (15-LOX) inhibitors. The design of the new derivatives was based on utilizing the antioxidant properties of pyrazoline, 2-phenylindole and the good 15-LOX inhibition properties of indolylpyrazoline. The derivatives were synthesized adopting simple and laboratory friendly reaction conditions to give the target compounds in quantitative yields. The resulting indolylpyrazolines/isoxazolines were evaluated as antioxidants against 2,2-diphenyl-1-picrylhydrazyl (DPPH), nitric oxide (NO) and superoxide dismutase (SOD); indolylpyrazoline (4b) was the most potent antioxidant against SOD assay (IC50 = 1.78 μM) to be superior to ascorbic by 2 folds. Consistently, (4b) was the most potent inhibitor when tested against Soybean 15-LOX (IC50 = 3.84 μM) excelling quercetin as standard inhibitor by 1.8 folds. Some of the new derivatives were docked into the active binding site of human 15-LOX (PDB entry 4NRE) emphasizing the most potent derivative (4b) and the least potent one (4c). Docking solutions of compounds (4b), (4c), (5b) and (6c) revealed that (4b) was the only compound that got stabilized into the catalytic pocket of enzyme by π-cation interaction with the catalytic Fe+ and formation of one hydrogen bond with Ile 676 amino acid. Other derivatives including the least potent one variably got stabilized into the active binding pocket by π-cation interaction with the catalytic Fe+ but failed to form hydrogen bond with Ile 676. For the future optimization of the generated inhibitors, (i) antioxidant activity against SOD, (ii) the inhibitor stabilization by π-cation interaction with the catalytic Fe+3 and (iii) formation of hydrogen bond with Ile 676 should be regarded.
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Affiliation(s)
- Haydi Saher ElBordiny
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt
| | - Mostafa Mahmoud El-Miligy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21526, Egypt
| | - Shaymaa Emam Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt.
| | - Hoda Daabees
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt
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Fenzl V, Schönberger ØL. Improved Method for Measuring Lipoxygenase Activity in Barley and Malt. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2017.1402583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Viktoria Fenzl
- Temporarily at the Department of Chemistry (Organic Chemistry), Technical University of Munich, Garching, Germany
| | - Øyvind L. Schönberger
- Temporarily at the Department of Chemistry (Organic Chemistry), Technical University of Munich, Garching, Germany
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Offenbacher AR, Iavarone AT, Klinman JP. Hydrogen-deuterium exchange reveals long-range dynamical allostery in soybean lipoxygenase. J Biol Chem 2018; 293:1138-1148. [PMID: 29191828 PMCID: PMC5787793 DOI: 10.1074/jbc.m117.817197] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/28/2017] [Indexed: 11/06/2022] Open
Abstract
In lipoxygenases, the topologically conserved C-terminal domain catalyzes the oxidation of polyunsaturated fatty acids, generating an assortment of biologically relevant signaling mediators. Plant and animal lipoxygenases also contain a 100-150-amino acid N-terminal C2-like domain that has been implicated in interactions with isolated fatty acids and at the phospholipid bilayer. These interactions may lead to increased substrate availability and contribute to the regulation of active-site catalysis. Because of a lack of structural information, a molecular understanding of this lipid-protein interaction remains unresolved. Herein, we employed hydrogen-deuterium exchange MS (HDXMS) to spatially resolve changes in protein conformation upon interaction of soybean lipoxygenase with a fatty acid surrogate, oleyl sulfate (OS), previously shown to act at a site separate from the substrate-binding site. Specific, OS-induced conformational changes are detected both at the N-terminal domain and within the substrate portal nearly 30 Å away. Combining previously measured kinetic properties in the presence of OS with its impact on the Kd for linoleic acid substrate binding, we conclude that OS binding brings about an increase in rate constants for both the ingress and egress of substrate. We discuss the role of OS-induced changes in protein flexibility in the context of changes in the mechanism of substrate acquisition.
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Affiliation(s)
- Adam R Offenbacher
- From the Department of Chemistry, California Institute for Quantitative Biosciences (QB3), and
| | - Anthony T Iavarone
- From the Department of Chemistry, California Institute for Quantitative Biosciences (QB3), and
| | - Judith P Klinman
- From the Department of Chemistry, California Institute for Quantitative Biosciences (QB3), and
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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50
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Teng L, Han W, Fan X, Xu D, Zhang X, Dittami SM, Ye N. Evolution and Expansion of the Prokaryote-Like Lipoxygenase Family in the Brown Alga Saccharina japonica. FRONTIERS IN PLANT SCIENCE 2017; 8:2018. [PMID: 29234336 PMCID: PMC5712309 DOI: 10.3389/fpls.2017.02018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/13/2017] [Indexed: 05/07/2023]
Abstract
Lipoxygenase (LOX) plays important roles in fatty acid oxidation and lipid mediator biosynthesis. In this study, we give first insights into brown algal LOX evolution. Whole genome searches revealed four, three, and eleven LOXs in Ectocarpus siliculosus, Cladosiphon okamuranus, and Saccharina japonica, respectively. In phylogenetic analyses, LOXs from brown algae form a robust clade with those from prokaryotes, suggesting an ancestral origin and slow evolution. Brown algal LOXs were divided into two clades, C1 and C2 in a phylogenetic tree. Compared to the two species of Ectocarpales, LOX gene expansion occurred in the kelp S. japonica through tandem duplication and segmental duplication. Selection pressure analysis showed that LOX genes in brown algae have undergone strong purifying selection, while the selective constraint in the C2 clade was more relaxed than that in the C1 clade. Furthermore, within each clade, LOXs of S. japonica evolved under more relaxed selection constraints than E. siliculosus and C. okamuranus. Structural modeling showed that unlike LOXs of plants and animals, which contain a β barrel in the N-terminal part of the protein, LOXs in brown algae fold into a single domain. Analysis of previously published transcriptomic data showed that LOXs in E. siliculosus are responsive to hyposaline, hypersaline, oxidative, and copper stresses. Moreover, clear divergence of expression patterns was observed among different life stages, as well as between duplicate gene pairs. In E. siliculosus, all four LOXs are male-biased in immature gametophytes, and mature gametophytes showed significantly higher LOX mRNA levels than immature gametophytes and sporophytes. In S. japonica, however, our RNA-Seq data showed that most LOXs are highly expressed in sporophytes. Even the most recently duplicated gene pairs showed divergent expression patterns, suggesting that functional divergence has likely occurred since LOX genes duplicated, which potentially contributes to the production of various oxylipins in brown algae.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Simon M. Dittami
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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