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Mori T, Teramoto T, Kakuta Y. Crystal structure of activating sulfotransferase SgdX2 involved in biosynthesis of secondary metabolite sungeidine. Biochem Biophys Res Commun 2024; 711:149891. [PMID: 38621346 DOI: 10.1016/j.bbrc.2024.149891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Microorganisms synthesize a plethora of complex secondary metabolites, many of which are beneficial to human health, such as anticancer agents and antibiotics. Among these, the Sungeidines are a distinct class of secondary metabolites known for their bulky and intricate structures. They are produced by a specific biosynthetic gene cluster within the genome of the soil-dwelling actinomycete Micromonospora sp. MD118. A notable enzyme in the Sungeidine biosynthetic pathway is the activating sulfotransferase SgdX2. In this pathway, SgdX2 mediates a key sulfation step, after which the product undergoes spontaneous dehydration to yield a Sungeidine compound. To delineate the structural basis for SgdX2's substrate recognition and catalytic action, we have determined the crystal structure of SgdX2 in complex with its sulfate donor product, 3'-phosphoadenosine 5'-phosphate (PAP), at a resolution of 1.6 Å. Although SgdX2 presents a compact overall structure, its core elements are conserved among other activating sulfotransferases. Our structural analysis reveals a unique substrate-binding pocket that accommodates bulky, complex substrates, suggesting a specialized adaptation for Sungeidine synthesis. Moreover, we have constructed a substrate docking model that provides insights into the molecular interactions between SgdX2 and Sungeidine F, enhancing our understanding of the enzyme's specificity and catalytic mechanism. The model supports a general acid-base catalysis mechanism, akin to other sulfotransferases, and underscores the minor role of disordered regions in substrate recognition. This integrative study of crystallography and computational modeling advances our knowledge of microbial secondary metabolite biosynthesis and may facilitate the development of novel biotechnological applications.
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Affiliation(s)
- Takahiro Mori
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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2
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Brewer A, Sathe G, Pflug BE, Clarke RG, Macartney TJ, Sapkota GP. Mapping the substrate landscape of protein phosphatase 2A catalytic subunit PPP2CA. iScience 2024; 27:109302. [PMID: 38450154 PMCID: PMC10915630 DOI: 10.1016/j.isci.2024.109302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/18/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Protein phosphatase 2A (PP2A) is an essential Ser/Thr phosphatase. The PP2A holoenzyme complex comprises a scaffolding (A), regulatory (B), and catalytic (C) subunit, with PPP2CA being the principal catalytic subunit. The full scope of PP2A substrates in cells remains to be defined. To address this, we employed dTAG proteolysis-targeting chimeras to efficiently and selectively degrade dTAG-PPP2CA in homozygous knock-in HEK293 cells. Unbiased global phospho-proteomics identified 2,204 proteins with significantly increased phosphorylation upon dTAG-PPP2CA degradation, implicating them as potential PPP2CA substrates. A vast majority of these are novel. Bioinformatic analyses revealed involvement of the potential PPP2CA substrates in spliceosome function, cell cycle, RNA transport, and ubiquitin-mediated proteolysis. We identify a pSP/pTP motif as a predominant target for PPP2CA and confirm some of our phospho-proteomic data with immunoblotting. We provide an in-depth atlas of potential PPP2CA substrates and establish targeted degradation as a robust tool to unveil phosphatase substrates in cells.
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Affiliation(s)
- Abigail Brewer
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gajanan Sathe
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Billie E. Pflug
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rosemary G. Clarke
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas J. Macartney
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Gopal P. Sapkota
- Medical Research Council (MRC) Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Cai J, Nielsen MW, Kalogeropoulos K, auf dem Keller U, van der Plas MJ. Peptidomic analysis of endogenous and bacterial protease activity in human plasma and wound fluids. iScience 2024; 27:109005. [PMID: 38333691 PMCID: PMC10850760 DOI: 10.1016/j.isci.2024.109005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Endogenous and bacterial proteases play important roles in wound healing and infection. Analysis of alterations in the low-molecular-weight peptidome by individual enzymes could therefore provide insight into proteolytic events occurring in wounds and may aid in the discovery of biomarkers. Using liquid chromatography with tandem mass spectrometry, we characterized the peptidome of plasma and acute wound fluids digested ex vivo with human (neutrophil elastase and cathepsin G) and bacterial proteases (Pseudomonas aeruginosa LasB and Staphyloccocus aureus V8). We identified over 100 protein targets for each enzyme and characterized enzyme specific peptides and cleavage patterns. Moreover, we found unique peptide regions in V8 digested samples that were also present in dressing extracts from S. aureus infected wounds. Finally, the work indicates that peptidomic analysis of qualitative differences of proteolytic activity of individual enzymes may aid in the discovery of potential diagnostic biomarkers for wound healing status.
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Affiliation(s)
- Jun Cai
- LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Maike W. Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | | | - Ulrich auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Mariena J.A. van der Plas
- LEO Foundation Center for Cutaneous Drug Delivery, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
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Genodepa J, Zeng C, Militz TA, Southgate PC. Responses of digestive enzyme profiles in newly-hatched (Zoea I) larvae of the mud crab Scylla serrata to intermittent food availability and food deprivation. Comp Biochem Physiol B Biochem Mol Biol 2024; 269:110906. [PMID: 37816451 DOI: 10.1016/j.cbpb.2023.110906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023]
Abstract
Activities (mU larva-1) of enzymes critical to digestion were examined to better understand how newly-hatched (Zoea I) larvae of the mud crab Scylla serrata respond to intermittent food availability and food deprivation. Specifically, this study examined the activities of trypsin-like proteases, nonspecific esterases, and α-amylase across three experiments that simulated scenarios in which larvae hatch and experience rearing conditions where food was either: (1) continuously available or unavailable; (2) initially unavailable, but subsequently available; or (3) initially available, but subsequently unavailable. Results showed that food availability exerts a significant influence on enzyme profiles in newly-hatched larvae, with nutritional history influencing their response to food deprivation. When food was unavailable from hatch, there was no significant change in larval enzyme activities between 6 and 78 h post-hatch. If food became available at any point during this period, however, newly-hatched larvae were capable of rapidly (within 12-24 h) adjusting enzyme activities in response. Furthermore, a short (36 h) period of food availability appears sufficient to permit continuous substrate utilization during subsequent food deprivation of equivalent duration. Such flexibility is an important physiological strategy allowing newly-hatched larvae of S. serrata to adapt and thrive in challenging tropical oceanic environments and provides a basis for optimizing protocols for hatchery production of this species.
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Affiliation(s)
- Jerome Genodepa
- Centre for Sustainable Tropical Fisheries Aquaculture (CSTFA) / College of Sciences and Engineering, James Cook University, Townsville, QLD 4811, Queensland, Australia
| | - Chaoshu Zeng
- Centre for Sustainable Tropical Fisheries Aquaculture (CSTFA) / College of Sciences and Engineering, James Cook University, Townsville, QLD 4811, Queensland, Australia
| | - Thane A Militz
- Australian Centre for Pacific Islands Research (ACPIR) / School of Science, Technology & Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Queensland, Australia
| | - Paul C Southgate
- Australian Centre for Pacific Islands Research (ACPIR) / School of Science, Technology & Engineering, University of the Sunshine Coast, Sippy Downs, QLD 4556, Queensland, Australia.
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Szulc NA, Piechota M, Biriczová L, Thapa P, Pokrzywa W. Lysine deserts and cullin-RING ligase receptors: Navigating untrodden paths in proteostasis. iScience 2023; 26:108344. [PMID: 38026164 PMCID: PMC10665810 DOI: 10.1016/j.isci.2023.108344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/15/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) governs the degradation of proteins by ubiquitinating their lysine residues. Our study focuses on lysine deserts - regions in proteins conspicuously low in lysine residues - in averting ubiquitin-dependent proteolysis. We spotlight the prevalence of lysine deserts among bacteria leveraging the pupylation-dependent proteasomal degradation, and in the UPS of eukaryotes. To further scrutinize this phenomenon, we focused on human receptors VHL and SOCS1 to ascertain if lysine deserts could limit their ubiquitination within the cullin-RING ligase (CRL) complex. Our data indicate that the wild-type and lysine-free variants of VHL and SOCS1 maintain consistent turnover rates, unaltered by CRL-mediated ubiquitination, hinting at a protective mechanism facilitated by lysine deserts. Nonetheless, we noted their ubiquitination at non-lysine sites, alluding to alternative regulation by the UPS. Our research underscores the role of lysine deserts in limiting CRL-mediated ubiquitin tagging while promoting non-lysine ubiquitination, thereby advancing our understanding of proteostasis.
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Affiliation(s)
- Natalia A. Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Małgorzata Piechota
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Lilla Biriczová
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Pankaj Thapa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Str., 02-109 Warsaw, Poland
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Zangelmi E, Ruffolo F, Dinhof T, Gerdol M, Malatesta M, Chin JP, Rivetti C, Secchi A, Pallitsch K, Peracchi A. Deciphering the role of recurrent FAD-dependent enzymes in bacterial phosphonate catabolism. iScience 2023; 26:108108. [PMID: 37876809 PMCID: PMC10590968 DOI: 10.1016/j.isci.2023.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/30/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Phosphonates-compounds containing a direct C-P bond-represent an important source of phosphorus in some environments. The most common natural phosphonate is 2-aminoethylphosphonate (AEP). Many bacteria can break AEP down through specialized "hydrolytic" pathways, which start with the conversion of AEP into phosphonoacetaldehyde (PAA), catalyzed by the transaminase PhnW. However, the substrate scope of these pathways is very narrow, as PhnW cannot process other common AEP-related phosphonates, notably N-methyl AEP (M1AEP). Here, we describe a heterogeneous group of FAD-dependent oxidoreductases that efficiently oxidize M1AEP to directly generate PAA, thus expanding the versatility and usefulness of the hydrolytic AEP degradation pathways. Furthermore, some of these enzymes can also efficiently oxidize plain AEP. By doing so, they surrogate the role of PhnW in organisms that do not possess the transaminase and create novel versions of the AEP degradation pathways in which PAA is generated solely by oxidative deamination.
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Affiliation(s)
- Erika Zangelmi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Francesca Ruffolo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Tamara Dinhof
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, 1090 Vienna, Austria
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Jason P. Chin
- School of Biological Sciences and Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL Belfast, UK
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Katharina Pallitsch
- Institute of Organic Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Alessio Peracchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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Yue C, Zhang C, Zhang R, Yuan J. Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis. iScience 2023; 26:107950. [PMID: 37817931 PMCID: PMC10561060 DOI: 10.1016/j.isci.2023.107950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/25/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Bacteria perform chemotactic adaptation by sequential modification of multiple modifiable sites on chemoreceptors through stochastic action of tethered adaptation enzymes (CheR and CheB). To study the molecular kinetics of this process, we measured the response to different concentrations of MeAsp for the Tar-only Escherichia coli strain. We found a strong dependence of the methylation rate on the methylation level and established a new mechanism of adaptation kinetics due to tethered particle motion of the methylation enzyme CheR. Experiments with various lengths of the C-terminal flexible chain in the Tar receptor further validated this mechanism. The tethered particle motion resulted in a CheR concentration gradient that ensures encounter-rate matching of the sequential modifiable sites. An analytical model of multisite catalytic reaction showed that this enables robustness of methylation to fluctuations in receptor activity or cell-to-cell variations in the expression of adaptation enzymes and reduces the variation in methylation level among individual receptors.
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Affiliation(s)
- Caijuan Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chi Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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8
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Fan Z, Liu Z, Zhang N, Wei W, Cheng K, Sun H, Hao Q. Identification of SIRT3 as an eraser of H4K16la. iScience 2023; 26:107757. [PMID: 37720100 PMCID: PMC10504495 DOI: 10.1016/j.isci.2023.107757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/24/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023] Open
Abstract
Lysine lactylation (Kla) is a novel histone post-translational modification discovered in late 2019. Later, HDAC1-3, were identified as the robust Kla erasers. While the Sirtuin family proteins showed weak eraser activities toward Kla, as reported. However, the catalytic mechanisms and physiological functions of HDACs and Sirtuins are not identical. In this study, we observed that SIRT3 exhibits a higher eraser activity against the H4K16la site than the other human Sirtuins. Crystal structures revealed the detailed binding mechanisms between lactyl-lysine peptides and SIRT3. Furthermore, a chemical probe, p-H4K16laAlk, was developed to capture potential Kla erasers from cell lysates. SIRT3 was captured by this probe and detected via proteomic analysis. And another chemical probe, p-H4K16la-NBD, was developed to detect the eraser-Kla delactylation processes directly via fluorescence indication. Our findings and chemical probes provide new directions for further investigating Kla and its roles in gene transcription regulation.
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Affiliation(s)
- Zhuming Fan
- Institute of High Energy Physics, CAS, Beijing 100000, China
- Spallation Neutron Source Science Center, CAS, Dongguan, Guangdong 523000, China
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Zhiyang Liu
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Nan Zhang
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Wenyu Wei
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Ke Cheng
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, Hong Kong, China
| | - Quan Hao
- Institute of High Energy Physics, CAS, Beijing 100000, China
- Spallation Neutron Source Science Center, CAS, Dongguan, Guangdong 523000, China
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
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9
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Iwamoto Y, Saito S, Teramoto T, Maruyama-Nakashita A, Kakuta Y. Crystal structure of Arabidopsis thaliana sulfotransferase SOT16 involved in glucosinolate biosynthesis. Biochem Biophys Res Commun 2023; 677:149-154. [PMID: 37586213 DOI: 10.1016/j.bbrc.2023.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Glucosinolates (GSLs), a class of secondary metabolites found in Brassicaceae plants, play important roles in plant defense and contribute distinct flavors and aromas when used as food ingredients. Following tissue damage, GSLs undergo enzymatic hydrolysis to release bioactive volatile compounds. Understanding GSL biosynthesis and enzyme involvement is crucial for improving crop quality and advancing agriculture. Plant sulfotransferases (SOTs) play a key role in the final step of GSL biosynthesis by transferring sulfate groups to the precursor molecules. In the present study, we investigated the enzymatic reaction mechanism and broad substrate specificity of Arabidopsis thaliana sulfotransferase AtSOT16, which is involved in GSL biosynthesis, using crystal structure analysis. Our analysis revealed the specific catalytic residues involved in the sulfate transfer reaction and supported the hypothesis of a concerted acid-base catalytic mechanism. Furthermore, the docking models showed a strong correlation between the substrates with high predicted binding affinities and those experimentally reported to exhibit high activity. These findings provide valuable insights into the enzymatic reaction mechanisms and substrate specificity of GSL biosynthesis. The information obtained in this study may contribute to the development of novel strategies for manipulating GSL synthesis pathways in Brassica plants and has potential agricultural applications.
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Affiliation(s)
- Yuka Iwamoto
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan
| | - Seira Saito
- Kyushu University Future Creators in Science Project (QFC-SP), Japan; Meizen High School, Fukuoka, 830-0022, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan.
| | - Akiko Maruyama-Nakashita
- Laboratory of Plant Nutrition, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Kyushu University Future Creators in Science Project (QFC-SP), Japan.
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10
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Vriens E, De Ruysscher D, Weir ANM, Dekimpe S, Steurs G, Shemy A, Persoons L, Santos AR, Williams C, Daelemans D, Crump MP, Voet A, De Borggraeve W, Lescrinier E, Masschelein J. Polyketide Synthase-Mediated O-Methyloxime Formation in the Biosynthesis of the Oximidine Anticancer Agents. Angew Chem Int Ed Engl 2023; 62:e202304476. [PMID: 37218580 DOI: 10.1002/anie.202304476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H+ -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.
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Affiliation(s)
- Eveline Vriens
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Dries De Ruysscher
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Angus N M Weir
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Sofie Dekimpe
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
| | - Gert Steurs
- Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Ahmed Shemy
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Leentje Persoons
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | | | | | - Dirk Daelemans
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Arnout Voet
- Laboratory for Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Wim De Borggraeve
- Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, 3001, Heverlee, Belgium
| | - Eveline Lescrinier
- Laboratory for Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Joleen Masschelein
- Laboratory for Biomolecular Discovery and Engineering, Department of Biology, KU Leuven, 3001, Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, 3001, Heverlee, Belgium
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11
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023; 688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.
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Affiliation(s)
- Michael C Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, United States.
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12
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Meyer JM, Boeglin WE, Brash AR. Recombinant PNPLA1 catalyzes the synthesis of acylceramides and acyl acids with selective incorporation of linoleic acid. J Lipid Res 2023; 64:100379. [PMID: 37087101 PMCID: PMC10209018 DOI: 10.1016/j.jlr.2023.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/24/2023] Open
Abstract
Loss-of-function mutations in patatin-like phospholipase domain-containing protein 1 (PNPLA1) cause autosomal recessive congenital ichthyosis, and altered PNPLA1 activity is implicated in the pathogenesis of atopic dermatitis and other common skin diseases. To examine the hypothesis that PNPLA1 catalyzes the synthesis of acylceramides and acyl acids, we expressed and partially purified a soluble, truncated form of PNPLA1 in Escherichia coli, (PNPLA1trun) along with the related protein PNPLA2 (ATGL, adipose triglyceride lipase) and coactivator CGI-58. Liposomal substrates were incubated with recombinant enzymes for 0.5-24 h and products analyzed by HPLC-UV and LC-MS. Using trilinolein or dilinolein substrates, PNPLA1trun, like ATGLtrun, catalyzed lipolysis and acyltransferase reactions with 2-30% conversion into linoleic acid, monolinolein, and trilinolein. CGI-58 enhanced ATGL-catalyzed lipolysis as previously reported, but transacylase activity was not enhanced with ATGL or PNPLA1. In matching the proposed activity in vivo, PNPLA1 catalyzed acyl transfer from trilinolein and dilinolein donors to omega-hydroxy ceramide, omega-hydroxy glucosylceramide, and omega-hydroxy acid acceptors to form acylceramide, glucosyl-acylceramide, and acyl acid, respectively, albeit with only ∼0.05% conversion of the substrates. Notably, in experiments comparing dilinolein vs. diolein acyl donors, PNPLA1 transferred linoleate with 3:1 selectivity over oleate into acylceramide. These results support the role for PNPLA1 in the synthesis of acylceramides and acyl acids in epidermis and suggest that the enrichment of these lipids with linoleic acid could result from the substrate selectivity of PNPLA1.
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Affiliation(s)
- Jason M Meyer
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN, USA; Dermatology Service, Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA.
| | - William E Boeglin
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Alan R Brash
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
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13
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Petri YD, Gutierrez CS, Raines RT. Chemoselective Caging of Carboxyl Groups for On-Demand Protein Activation with Small Molecules. Angew Chem Int Ed Engl 2023; 62:e202215614. [PMID: 36964973 PMCID: PMC10243506 DOI: 10.1002/anie.202215614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Tools for on-demand protein activation enable impactful gain-of-function studies in biological settings. Thus far, however, proteins have been chemically caged at primarily Lys, Tyr, and Sec, typically through the genetic encoding of unnatural amino acids. Herein, we report that the preferential reactivity of diazo compounds with protonated acids can be used to expand this toolbox to solvent-accessible carboxyl groups with an elevated pKa value. As a model protein, we employed lysozyme (Lyz), which has an active-site Glu35 residue with a pKa value of 6.2. A diazo compound with a bioorthogonal self-immolative handle esterified Glu35 selectively, inactivating Lyz. The hydrolytic activity of the caged Lyz on bacterial cell walls was restored with two small-molecule triggers. The decaging was more efficient by small molecules than by esterases. This simple chemical strategy was also applied to a hemeprotein and an aspartyl protease, setting the stage for broad applicability.
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Affiliation(s)
- Yana D. Petri
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Clair S. Gutierrez
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
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14
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Perbal B, Perbal M, Perbal A. Cooperation is the key: the CCN biological system as a gate to high complex protein superfamilies' signaling. J Cell Commun Signal 2023:10.1007/s12079-023-00749-8. [PMID: 37166690 DOI: 10.1007/s12079-023-00749-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Cellular signaling is generally understood as the support of communication between contiguous cells belonging to the same tissue or cells being far apart of each other, at a molecular scale, when the message emitted by the transmitters is traveling in liquid or solid matter to reach recipient targets. Subcellular signaling is also important to ensure the proper cell constitution and functioning. However cell signaling is mostly used in the first understanding, to describe how the message sent from one point to another one, will reach a target where it will be interpreted. The Cellular Communication Network (CCN) factors (Perbal et al. 2018) constitute a family of biological regulators thought to be responsible for signaling pathways coordination (Perbal 2018). Indeed, these proteins interact with a diverse group of cell receptors, such as integrins, low density lipoprotein receptors, heparan sulfate proteoglycan receptors (HSPG), and the immunoglobulin superfamily expressed exclusively in the nervous system, or with soluble factors such as bone morphogenetic proteins (BMPS) and other growth factors such as vascular endothelial growth factor, fibroblastic growth factor, and transforming growth factor (TGFbeta). Starting from the recapitulation of basic concepts in enzymology and protein-ligands interactions, we consider, in this manuscript, interpretations of the mechanistic interactions that have been put forward to explain the diversity of CCN proteins biological activities. We suggest that the cross-talks between superfamilies of proteins under the control of CCNs might play a central role in the coordination of developmental signaling pathways.
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Affiliation(s)
| | - Matthieu Perbal
- M2 Probabilités et Modèles Aléatoires, Sorbonne Université, Paris, France
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15
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Ge YD, Guo YT, Jiang LL, Wang HH, Hou SL, Su FZ. Enzymatic Characterization and Coenzyme Specificity Conversion of a Novel Dimeric Malate Dehydrogenase from Bacillus subtilis. Protein J 2023; 42:14-23. [PMID: 36534341 PMCID: PMC9761052 DOI: 10.1007/s10930-022-10087-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Malate is an important material to various industrials and clinical applications. Bacillus subtilis is a widely used biocatalyst tool for chemical production. However, the specific enzymatic properties of malate dehydrogenase from Bacillus subtilis (BsMDH) remain largely unknown. In the present study, BsMDH was cloned, recombinantly expressed and purified to test its enzymatic properties. The molecular weight of single unit of BsMDH was 34,869.7 Da. Matrix-Assisted Laser-Desorption Ionization-Time-of-Flight Mass Spectrometry and gel filtration analysis indicated that the recombinant BsMDH could form dimers. The kcat/Km values of oxaloacetate and NADH were higher than those of malate and NAD+, respectively, indicating a better catalysis in the direction of malate synthesis than the reverse. Furthermore, six BsMDH mutants were constructed with the substitution of amino acids at the coenzyme binding site. Among them, BsMDH-T7 showed a greatly higher affinity and catalysis efficiency to NADPH than NADH with the degree of alteration of 2039, suggesting the shift of the coenzyme dependence from NADH to NADPH. In addition, BsMDH-T7 showed a relatively lower Km value, but a higher kcat and kcat/Km than NADPH-dependent MDHs from Thermus flavus and Corynebacterium glutamicum. Overall, these results indicated that BsMDH and BsMDH-T7 mutant might be promising enzymes for malate production.
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Affiliation(s)
- Ya-Dong Ge
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China.
| | - Yi-Tian Guo
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China
| | - Lu-Lu Jiang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China
| | - Hui-Hui Wang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China
| | - Shao-Lin Hou
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China
| | - Feng-Zhi Su
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, People's Republic of China
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16
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Adelakun N, Parrish J, Chu N. Analyzing protein posttranslational modifications using enzyme-catalyzed expressed protein ligation. Methods Enzymol 2023; 682:319-350. [PMID: 36948706 DOI: 10.1016/bs.mie.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Expressed protein ligation (EPL) allows for the attachment of a synthetic peptide into the N- or C-terminus of a recombinant protein fragment to generate a site-specifically modified protein with substantial yields for biochemical and biophysical studies. In this method, multiple posttranslational modifications (PTMs) can be incorporated into a synthetic peptide containing an N-terminal Cysteine, which selectively reacts with a protein C-terminal thioester to afford an amide bond formation. However, the requirement of a Cysteine at the ligation site can limit EPL's potential applications. Here, we describe a method called enzyme-catalyzed EPL, which uses subtiligase to ligate protein thioesters with Cysteine-free peptides. The procedure includes generating protein C-terminal thioester and peptide, performing the enzymatic EPL reaction, and purifying the protein ligation product. We exemplify this method by generating phospholipid phosphatase PTEN with site-specific phosphorylations installed onto its C-terminal tail for biochemical assays.
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Affiliation(s)
- Niyi Adelakun
- Department of Cancer Biology and Genetics, the Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Jordan Parrish
- Department of Cancer Biology and Genetics, the Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Nam Chu
- Department of Cancer Biology and Genetics, the Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States.
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17
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Abstract
Assays for measuring enzyme activity can be useful tools for proteomics applications. Enzyme testing can be performed to validate an experimental system prior to a difference gel electrophoresis (DIGE) proteomic experiment and can also be utilized as an integral part of multifaceted experiment in conjunction with DIGE. Data from enzyme tests can be used to corroborate results of DIGE proteomic experiments where an enzyme or enzymes are demonstrated by DIGE to be differentially expressed. Enzyme testing can also be utilized to support data from DIGE experiments that demonstrate metabolic changes in a biological system. The different types of enzyme assays that can be performed in conjunction with DIGE experiments are reviewed alongside a discussion of experimental approaches for designing enzyme assays.
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Affiliation(s)
- Andrew Dowd
- Croda Europe Limited, Daresbury, Cheshire, UK.
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18
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Arnal G, Attia MA, Asohan J, Lei Z, Golisch B, Brumer H. A Low-Volume, Parallel Copper-Bicinchoninic Acid (BCA) Assay for Glycoside Hydrolases. Methods Mol Biol 2023; 2657:3-14. [PMID: 37149519 DOI: 10.1007/978-1-0716-3151-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The quantitation of liberated reducing sugars by the copper-bicinchoninic acid (BCA) assay provides a highly sensitive method for the measurement of glycoside hydrolase (GH) activity, particularly on soluble polysaccharide substrates. Here we describe a straightforward method adapted to low-volume polymerase chain reaction (PCR) tubes that enables the rapid, parallel determination of GH kinetics in applications ranging from initial activity screening and assay optimization to precise Michaelis-Menten analysis.
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Affiliation(s)
- Gregory Arnal
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mohamed A Attia
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Jathavan Asohan
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Zhenhuan Lei
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Benedikt Golisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
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19
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Abstract
Enzyme activity assay methods can be used to corroborate the results generated by difference gel electrophoresis (DIGE) proteomic experiments. Two assay methods were chosen to demonstrate how this can be achieved. Assays for determining the activity of superoxide dismutase and NADH dehydrogenase are outlined in detail in this chapter. These methods were chosen as examples because they are frequently used in conjunction with DIGE proteomics.
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Affiliation(s)
- Andrew Dowd
- Croda Europe Limited, Daresbury, Cheshire, UK.
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20
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Kumar M, Bandi CK, Chundawat SPS. High-throughput screening of glycosynthases using azido sugars for oligosaccharides synthesis. Methods Enzymol 2023; 682:211-245. [PMID: 36948703 DOI: 10.1016/bs.mie.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Glycosynthases are mutant glycosyl hydrolases that can synthesize glycosidic bonds between acceptor glycone/aglycone groups and activated donor sugars with suitable leaving groups (e.g., azido, fluoro). However, it has been challenging to rapidly detect glycosynthase reaction products involving azido sugars as donor sugars. This has limited our ability to apply rational engineering and directed evolution methods to rapidly screen for improved glycosynthases that are capable of synthesizing bespoke glycans. Here, we outline our recently developed screening methodologies for rapidly detecting glycosynthase activity using a model fucosynthase enzyme engineered to be active on fucosyl azide as donor sugar. We created a diverse library of fucosynthase mutants using semi-random and random error prone mutagenesis and then identified improved fucosynthase mutants with desired activity using two distinct screening methods developed by our group to detect glycosynthase activity (i.e., by detecting azide formed upon completion of fucosynthase reaction); (a) pCyn-GFP regulon method, and (b) Click chemistry method. Finally, we provide some proof-of-concept results illustrating the utility of both these screening methods to rapidly detect products of glycosynthase reactions involving azido sugars as donor groups.
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Affiliation(s)
- Mohit Kumar
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Chandra Kanth Bandi
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Shishir P S Chundawat
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, United States.
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21
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Rohweder PJ, Jiang Z, Hurysz BM, O'Donoghue AJ, Craik CS. Multiplex substrate profiling by mass spectrometry for proteases. Methods Enzymol 2022; 682:375-411. [PMID: 36948708 PMCID: PMC10201391 DOI: 10.1016/bs.mie.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Proteolysis is a central regulator of many biological pathways and the study of proteases has had a significant impact on our understanding of both native biology and disease. Proteases are key regulators of infectious disease and misregulated proteolysis in humans contributes to a variety of maladies, including cardiovascular disease, neurodegeneration, inflammatory diseases, and cancer. Central to understanding a protease's biological role, is characterizing its substrate specificity. This chapter will facilitate the characterization of individual proteases and complex, heterogeneous proteolytic mixtures and provide examples of the breadth of applications that leverage the characterization of misregulated proteolysis. Here we present the protocol of Multiplex Substrate Profiling by Mass Spectrometry (MSP-MS), a functional assay that quantitatively characterizes proteolysis using a synthetic library of physiochemically diverse, model peptide substrates, and mass spectrometry. We present a detailed protocol as well as examples of the use of MSP-MS for the study of disease states, for the development of diagnostic and prognostic tests, for the generation of tool compounds, and for the development of protease-targeted drugs.
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Affiliation(s)
- Peter J Rohweder
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States
| | - Brianna M Hurysz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, United States.
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States.
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22
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Vogel U, Beerens K, Desmet T. A colorimetric assay for the screening and kinetic analysis of nucleotide sugar 4,6-dehydratases. Anal Biochem 2022; 655:114870. [PMID: 36027972 DOI: 10.1016/j.ab.2022.114870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/22/2022]
Abstract
Nucleotide sugar 4,6-dehydratases belong to the Short-chain Dehydrogenase/Reductase (SDR) superfamily and catalyze the conversion of an NDP-hexose to an NDP-4-keto-6-deoxy hexose, a key step in the biosynthesis of a plethora of deoxy and amino sugars. Here, we present a colorimetric assay for the detection of their reaction products (NDP-4-keto-6-deoxy hexoses) using concentrated sulfuric acid and an ethanolic resorcinol solution. Under these conditions, the keto-function of the dehydratase product reacts specifically with resorcinol to form an orange-red or pink complex for NDP-glucose/GDP-mannose and UDP-N-acetylglucosamine, respectively, with an absorption maximum at 510 nm. The presented assay allows reliable product detection at low concentrations and can be applied in microtiter plates. It thus allows the determination of kinetic enzyme parameters like the optimal temperature, pH, Vmax, KM and kcat, as well as the miniaturization for screening purposes with crude cell extracts. As such, this detection assay opens new possibilities for the characterization and screening of these dehydratases in 96-well plates for different research goals.
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23
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Datsomor AK, Gillard G, Jin Y, Olsen RE, Sandve SR. Molecular Regulation of Biosynthesis of Long Chain Polyunsaturated Fatty Acids in Atlantic Salmon. Mar Biotechnol (NY) 2022; 24:661-670. [PMID: 35907166 PMCID: PMC9385821 DOI: 10.1007/s10126-022-10144-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Salmon is a rich source of health-promoting omega-3 long chain polyunsaturated fatty acids (n-3 LC-PUFA), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3). The LC-PUFA biosynthetic pathway in Atlantic salmon is one of the most studied compared to other teleosts. This has largely been due to the massive replacement of LC-PUFA-rich ingredients in aquafeeds with terrestrial plant oils devoid of these essential fatty acids (EFA) which ultimately pushed dietary content towards the minimal requirement of EFA. The practice would also reduce tissue content of n-3 LC-PUFA compromising the nutritional value of salmon to the human consumer. These necessitated detailed studies of endogenous biosynthetic capability as a contributor to these EFA. This review seeks to provide a comprehensive and concise overview of the current knowledge about the molecular genetics of PUFA biosynthesis in Atlantic salmon, highlighting the enzymology and nutritional regulation as well as transcriptional control networks. Furthermore, we discuss the impact of genome duplication on the complexity of salmon LC-PUFA pathway and highlight probable implications on endogenous biosynthetic capabilities. Finally, we have also compiled and made available a large RNAseq dataset from 316 salmon liver samples together with an R-script visualization resource to aid in explorative and hypothesis-driven research into salmon lipid metabolism.
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Affiliation(s)
- Alex K. Datsomor
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Gareth Gillard
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Yang Jin
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Rolf E. Olsen
- Institute of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Simen R. Sandve
- Center for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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24
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Unterlander N, Mats L, McGary LC, Gordon HOW, Bozzo GG. Kaempferol rhamnoside catabolism in rosette leaves of senescing Arabidopsis and postharvest stored radish. Planta 2022; 256:36. [PMID: 35816223 DOI: 10.1007/s00425-022-03949-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Flavonol rhamnosides including kaempferitrin (i.e., kaempferol 3-O-α-rhamnoside-7-O-α-rhamnoside) occur throughout the plant kingdom. Mechanisms governing flavonol rhamnoside biosynthesis are established, whereas degradative processes occurring in plants are relatively unknown. Here, we investigated the catabolic events affecting kaempferitrin status in the rosette leaves of Arabidopsis thaliana L. Heynh. (Arabidopsis) and Raphanus sativus L. (radish), respectively, in response to developmental senescence and postharvest handling. On a per plant basis, losses of several kaempferol rhamnosides including kaempferitrin were apparent in senescing leaves of Arabidopsis during development and postharvest radish stored at 5 °C. Conversely, small pools of kaempferol 7-O-α-rhamnoside (K7R), kaempferol 3-O-α-rhamnoside (K3R), and kaempferol built up in senescing leaves of both species. Evidence is provided for ⍺-rhamnosidase activities targeting the 7-O-α-rhamnoside of kaempferitrin and K7R in rosette leaves of both species. An HPLC analysis of in vitro assays of clarified leaf extracts prepared from developing Arabidopsis and postharvest radish determined that these metabolic shifts were coincident with respective 237% and 645% increases in kaempferitrin 7-O-⍺-rhamnosidase activity. Lower activity rates were apparent when these ⍺-rhamnosidase assays were performed with K7R. A radish ⍺-rhamnosidase containing peak eluting from a DEAE-Sepharose Fast Flow column hydrolyzed various 7-O-rhamnosylated flavonols, as well as kaempferol 3-O-β-glucoside. Together it is apparent that the catabolism of 7-O-α-rhamnosylated kaempferol metabolites in senescing plant leaves is associated with a flavonol 7-O-α-rhamnoside-utilizing α-rhamnosidase.
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Affiliation(s)
- Nicole Unterlander
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Lili Mats
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, N1G 5C9, Canada
| | - Laura C McGary
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Harley O W Gordon
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Gale G Bozzo
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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25
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Smith JL, Madrigal Harrison I, Bingman C, Buller AR. Investigation of β-substitution activity of O-acetylserine sulfhydrolase from Citrullus vulgaris. Chembiochem 2022; 23:e202200157. [PMID: 35476889 PMCID: PMC9401013 DOI: 10.1002/cbic.202200157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/24/2022] [Indexed: 11/17/2022]
Abstract
Pyridoxal‐5’‐phosphate (PLP)‐dependent enzymes have garnered interest for their ability to synthesize non‐standard amino acids (nsAAs). One such class of enzymes, O‐acetylserine sulfhydrylases (OASSs), catalyzes the final step in the biosynthesis of l‐cysteine. Here, we examine the β‐substitution capability of the OASS from Citrullus vulgaris (CvOASS), a putative l‐mimosine synthase. While the previously reported mimosine synthase activity was not reproducible in our hands, we successfully identified non‐native reactivity with a variety of O‐nucleophiles. Optimization of reaction conditions for carboxylate and phenolate substrates led to distinct conditions that were leveraged for the preparative‐scale synthesis of nsAAs. We further show this enzyme is capable of C−C bond formation through a β‐alkylation reaction with an activated nitroalkane. To facilitate understanding of this enzyme, we determined the crystal structure of the enzyme bound to PLP as the internal aldimine at 1.55 Å, revealing key features of the active site and providing information that may guide subsequent development of CvOASS as a practical biocatalyst.
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Affiliation(s)
| | | | - Craig Bingman
- University of Wisconsin-Madison, Biochemistry, UNITED STATES
| | - Andrew Richard Buller
- University of Wisconsin Madison, Chemistry, 1101 University Ave, 53706, Madison, UNITED STATES
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26
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Sun P, Li X, Dilokpimol A, Henrissat B, de Vries RP, Kabel MA, Mäkelä MR. Fungal glycoside hydrolase family 44 xyloglucanases are restricted to the phylum Basidiomycota and show a distinct xyloglucan cleavage pattern. iScience 2022; 25:103666. [PMID: 35028537 PMCID: PMC8741620 DOI: 10.1016/j.isci.2021.103666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/23/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022] Open
Abstract
Xyloglucan is a prominent matrix heteropolysaccharide binding to cellulose microfibrils in primary plant cell walls. Hence, the hydrolysis of xyloglucan facilitates the overall lignocellulosic biomass degradation. Xyloglucanases (XEGs) are key enzymes classified in several glycoside hydrolase (GH) families. So far, family GH44 has been shown to contain bacterial XEGs only. Detailed genome analysis revealed GH44 members in fungal species from the phylum Basidiomycota, but not in other fungi, which we hypothesized to also be XEGs. Two GH44 enzymes from Dichomitus squalens and Pleurotus ostreatus were heterologously produced and characterized. They exhibited XEG activity and displayed a hydrolytic cleavage pattern different from that observed in fungal XEGs from other GH families. Specifically, the fungal GH44 XEGs were not hindered by substitution of neighboring glucosyl units and generated various "XXXG-type," "GXXX(G)-type," and "XXX-type" oligosaccharides. Overall, these fungal GH44 XEGs represent a novel class of enzymes for plant biomass conversion and valorization.
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Affiliation(s)
- Peicheng Sun
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Xinxin Li
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Adiphol Dilokpimol
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Bernard Henrissat
- DTU Bioengineering, Technical University of Denmark, Søltofts Plads, 2800 Kongens Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Mirjam A Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, the Netherlands
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00790 Helsinki, Finland
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Davis I, Geng J, Liu A. Metalloenzymes involved in carotenoid biosynthesis in plants. Methods Enzymol 2022; 671:207-222. [PMID: 35878978 PMCID: PMC9315058 DOI: 10.1016/bs.mie.2022.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Carotenoids are a family of pigment compounds, a subset of which are precursors for vitamin A biosynthesis. These pigments are derived from isopentenyl pyrophosphate (IPP), with geranylgeranyl diphosphate being the first metabolite unique to carotenoid biosynthesis in plants, algae, fungi, some bacteria, and arthropods. This chapter highlights the metal-dependent enzymes involved in synthesizing carotenoids in plants and the current state of knowledge of their cofactors and mechanisms. Emphasis is given to spectroscopic methods used to characterize metal centers. The recently discovered heme-dependent isomerase Z-ISO is presented as a case study in how to interrogate a metalloenzyme. Use of UV-vis, electron paramagnetic resonance, and magnetic circular dichroism spectroscopies of a metal center at various oxidation states and with external small molecule probes (CN-, CO, and NO) can provide information about the nature of the metal center, the identity of its ligands, and its mechanism of action. Z-ISO is a histidine/cysteine ligated heme-dependent enzyme that is only active in the ferrous state and possesses redox-linked ligand switching. The choice and design of experiments are discussed as well as the conclusions that can be drawn.
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Affiliation(s)
- Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States.
| | - Jiafeng Geng
- Department of Chemistry, Emory University, Atlanta, GA, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, United States.
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Malhotra M, Kalluri A, Kumar CV. Nanoarmored Multi-Enzyme Cascade Catalysis. Methods Mol Biol 2022; 2487:205-225. [PMID: 35687239 DOI: 10.1007/978-1-0716-2269-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This chapter reports a single-step preparation of nanoarmored bi-enzyme systems assembled on 1-D and 2-D nanomaterials, with glucose oxidase and peroxidase enzymes as model systems for cascade bio-catalysis. This is a simple and facile method to both exfoliate the bulk 1D (carbon nanotubes, CNT) and 2D nanomaterials (α-Zirconium phosphate, α-ZrP) and bind the enzymes in a single step. Exfoliation of the bulk material enhances the accessible surface area of the materials for the enzyme binding, and it also boosts the diffusion of reagents from the bulk phase to the active sites of the bio-catalysts. For example, a mixture of horseradish peroxidase, glucose oxidase, and bovine serum albumin (BSA) were adsorbed on the surfaces of the α-ZrP nanoplates or carbon nanotubes (CNT) as the bulk materials are exfoliated simultaneously, in a one-step process. The resulting bio-catalysts were thoroughly characterized by powder X-ray diffraction, electron microscopy, biochemical and biophysical methods, while enzyme activity studies proved successful binding of enzymes with retention of activities or even enhancements in their specific activities. For example, GOx/HRP/BSA/CNT displayed 6 times the activity of a mixture of GOx/HRP/BSA, under otherwise identical conditions. Similarly, GOx/HRP/BSA/ZrP had 3.5 times the activity of the corresponding mixture of GOx/HRP/BSA, in the absence of the nanoplates. These robust nano-dispersions worked extraordinarily well as active bio-catalysts. These two kinds of fabricated biocatalyst dispersions are also highly stable.
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Affiliation(s)
- Mansi Malhotra
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Ankarao Kalluri
- Department of Material Science, University of Connecticut, Storrs, CT, USA
| | - Challa Vijaya Kumar
- Department of Chemistry, University of Connecticut, Storrs, CT, USA.
- Department of Material Science, University of Connecticut, Storrs, CT, USA.
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
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Abstract
Hepatitis B virus (HBV) is a hepatotropic, partially double-stranded DNA virus that replicates by reverse transcription and is a major cause of chronic liver disease and hepatocellular carcinoma. Reverse transcription is catalyzed by the four-domain multifunctional HBV polymerase (P) protein that has protein-priming, RNA- and DNA-dependent DNA synthesis (i.e., reverse transcriptase), and ribonuclease H activities. P also likely promotes the three strand transfers that occur during reverse transcription, and it may participate in immune evasion by HBV. Reverse transcription is primed by a tyrosine residue in the amino-terminal domain of P, and P remains covalently attached to the product DNA throughout reverse transcription. The reverse transcriptase activity of P is the target for the nucleos(t)ide analog drugs that dominate HBV treatment, and P is the target of ongoing efforts to develop new drugs against both the reverse transcriptase and ribonuclease H activities. Despite the unusual reverse transcription pathway catalyzed by P and the importance of P to HBV therapy, understanding the enzymology and structure of HBV P severely lags that of the retroviral reverse transcriptases due to substantial technical challenges to studying the enzyme. Obtaining a better understanding of P will broaden our appreciation of the diversity among reverse transcribing elements in nature, and will help improve treatment for people chronically infected with HBV.
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Affiliation(s)
- Daniel N Clark
- Department of Microbiology, Weber State University, Ogden, UT, United States
| | - Razia Tajwar
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States
| | - Jianming Hu
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - John E Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, Saint Louis, MO, United States.
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Kitakaze K, Tsuboi K, Tsuda M, Takenouchi Y, Ishimaru H, Okamoto Y. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. J Lipid Res 2021; 62:100141. [PMID: 34673020 PMCID: PMC8591415 DOI: 10.1016/j.jlr.2021.100141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
Lysophosphatidic acid (LPA) is a lipid mediator that regulates various processes, including cell migration and cancer progression. Autotaxin (ATX) is a lysophospholipase D-type exoenzyme that produces extracellular LPA. In contrast, glycerophosphodiesterase (GDE) family members GDE4 and GDE7 are intracellular lysophospholipases D that form LPA, depending on Mg2+ and Ca2+, respectively. Since no fluorescent substrate for these GDEs has been reported, in the present study, we examined whether a fluorescent ATX substrate, FS-3, could be applied to study GDE activity. We found that the membrane fractions of human GDE4- and GDE7-overexpressing human embryonic kidney 293T cells hydrolyzed FS-3 in a manner almost exclusively dependent on Mg2+ and Ca2+, respectively. Using these assay systems, we found that several ATX inhibitors, including α-bromomethylene phosphonate analog of LPA and 3-carbacyclic phosphatidic acid, also potently inhibited GDE4 and GDE7 activities. In contrast, the ATX inhibitor S32826 hardly inhibited these activities. Furthermore, FS-3 was hydrolyzed in a Mg2+-dependent manner by the membrane fraction of human prostate cancer LNCaP cells that express GDE4 endogenously but not by those of GDE4-deficient LNCaP cells. Similar Ca2+-dependent GDE7 activity was observed in human breast cancer MCF-7 cells but not in GDE7-deficient MCF-7 cells. Finally, our assay system could selectively measure GDE4 and GDE7 activities in a mixture of the membrane fractions of GDE4- and GDE7-overexpressing human embryonic kidney 293T cells in the presence of S32826. These findings allow high-throughput assays of GDE4 and GDE7 activities, which could lead to the development of selective inhibitors and stimulators as well as a better understanding of the biological roles of these enzymes.
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Affiliation(s)
- Keisuke Kitakaze
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan.
| | - Kazuhito Tsuboi
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan.
| | - Maho Tsuda
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Yasuhiro Takenouchi
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Hironobu Ishimaru
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Yasuo Okamoto
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
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Saganuwan SA. Application of modified Michaelis - Menten equations for determination of enzyme inducing and inhibiting drugs. BMC Pharmacol Toxicol 2021; 22:57. [PMID: 34635182 PMCID: PMC8507113 DOI: 10.1186/s40360-021-00521-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pharmacokinetics (PK) is the process of absorption, distribution, metabolism and elimination (ADME) of drugs. Some drugs undergo zero-order kinetics (ethyl alcohol), first order kinetics (piroxicam) and mixed order kinetics (ascorbic acid). Drugs that undergo Michaelis-Menten metabolism are characterized by either increased or decreased metabolism constant (Km) and maximum velocity (Vmax) of enzyme reaction. Hence literatures were searched with a view to translating in vitro-in vivo enzyme kinetics to pharmacokinetic/pharmacodynamic parameters for determination of enzyme inducing and inhibiting drugs, in order to achieve optimal clinical efficacy and safety. METHODS A narrative review of retrospective secondary data on drugs, their metabolites, Vmax and Km, generated in the laboratory and clinical environments was adopted, using inclusion and exclusion criteria. Key word search strategy was applied, to assess databases of published articles on enzyme inducing and inhibiting drugs, that obey Michaelis-Menten kinetics. In vitro and in vivo kinetic parameters, such as concentration of substrate, rate of endogenous substrate production, cellular metabolic rate, initial velocity of metabolism, intrinsic clearance, percent saturation and unsaturation of the enzyme substrate, were calculated using original and modified formulas. Years and numbers of searched publications, types of equations and their applications were recorded. RESULTS A total of fifty-six formulas both established and modified were applied in the present study. Findings have shown that theophylline, voriconazole, phenytoin, thiopental, fluorouracil, thyamine and thymidine are enzyme inducers whereas, mibefradil, metronidazole, isoniazid and puromicin are enzyme inhibitors. They are metabolized and eliminated according to Michaelis-Menten principle. The order could be mixed but may change to zero or first order, depending on drug concentration, frequency and route of drug administration. CONCLUSION Hence, pharmacokinetic-pharmacodynamic translation can be optimally achieved by incorporating, newly modified Michaelis-Menten equations into pharmacokinetic formulas for clinical efficacy and safety of the enzyme inducing and inhibiting therapeutic agents used in laboratory and clinical settings.
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Affiliation(s)
- Saganuwan Alhaji Saganuwan
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, Federal University of Agriculture, P.M.B.2373, Makurdi, Benue State, Nigeria.
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Jolly RD, Hunter SA, Alley MR, King BM, Lau AA, Trim PJ, Snel MF, Hemsley KM. MUCOPOLYSACCHARIDOSIS II (MPS II) IN A FREE-LIVING KAKA (NESTOR MERIDIONALIS) IN NEW ZEALAND. J Wildl Dis 2021; 57:884-90. [PMID: 34424960 DOI: 10.7589/JWD-D-20-00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/18/2021] [Indexed: 11/20/2022]
Abstract
A lysosomal storage disease, identified as a mucopolysaccharidosis (MPS), was diagnosed in a free-living Kaka (Nestor meridionalis), an endemic New Zealand parrot, which exhibited weakness, incoordination, and seizures. Histopathology showed typical colloid-like cytoplasmic inclusions in Purkinje cells and many other neurons throughout the brain. Electron microscopy revealed that storage bodies contained a variety of linear, curved, or circular membranous profiles and electron-dense bodies. Because the bird came from a small isolated population of Kaka in the northern South Island, a genetic cause was deemed likely. Tandem mass spectrometry revealed increased levels of heparan sulfate-derived disaccharides in the brain and liver compared with tissues from controls. Enzymatic assays documented low levels of iduronate-2-sulfatase activity, which causes a lysosomal storage disorder called MPS type II or Hunter syndrome. A captive breeding program is currently in progress, and the possibility of detecting carriers of this disorder warrants further investigation.
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Tsai WC, Gilbert NC, Ohler A, Armstrong M, Perry S, Kalyanaraman C, Yasgar A, Rai G, Simeonov A, Jadhav A, Standley M, Lee HW, Crews P, Iavarone AT, Jacobson MP, Neau DB, Offenbacher AR, Newcomer M, Holman TR. Kinetic and structural investigations of novel inhibitors of human epithelial 15-lipoxygenase-2. Bioorg Med Chem 2021; 46:116349. [PMID: 34500187 DOI: 10.1016/j.bmc.2021.116349] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 11/16/2022]
Abstract
Human epithelial 15-lipoxygenase-2 (h15-LOX-2, ALOX15B) is expressed in many tissues and has been implicated in atherosclerosis, cystic fibrosis and ferroptosis. However, there are few reported potent/selective inhibitors that are active ex vivo. In the current work, we report newly discovered molecules that are more potent and structurally distinct from our previous inhibitors, MLS000545091 and MLS000536924 (Jameson et al, PLoS One, 2014, 9, e104094), in that they contain a central imidazole ring, which is substituted at the 1-position with a phenyl moiety and with a benzylthio moiety at the 2-position. The initial three molecules were mixed-type, non-reductive inhibitors, with IC50 values of 0.34 ± 0.05 μM for MLS000327069, 0.53 ± 0.04 μM for MLS000327186 and 0.87 ± 0.06 μM for MLS000327206 and greater than 50-fold selectivity versus h5-LOX, h12-LOX, h15-LOX-1, COX-1 and COX-2. A small set of focused analogs was synthesized to demonstrate the validity of the hits. In addition, a binding model was developed for the three imidazole inhibitors based on computational docking and a co-structure of h15-LOX-2 with MLS000536924. Hydrogen/deuterium exchange (HDX) results indicate a similar binding mode between MLS000536924 and MLS000327069, however, the latter restricts protein motion of helix-α2 more, consistent with its greater potency. Given these results, we designed, docked, and synthesized novel inhibitors of the imidazole scaffold and confirmed our binding mode hypothesis. Importantly, four of the five inhibitors mentioned above are active in an h15-LOX-2/HEK293 cell assay and thus they could be important tool compounds in gaining a better understanding of h15-LOX-2's role in human biology. As such, a suite of similar pharmacophores that target h15-LOX-2 both in vitro and ex vivo are presented in the hope of developing them as therapeutic agents.
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Affiliation(s)
- Wan-Chen Tsai
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Nathan C Gilbert
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Amanda Ohler
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Michelle Armstrong
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Steven Perry
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Chakrapani Kalyanaraman
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, CA 94158, United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Melissa Standley
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Phillip Crews
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Anthony T Iavarone
- Department of Chemistry and California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA 94720, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, CA 94158, United States
| | - David B Neau
- Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, IL, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, NC 27858, United States
| | - Marcia Newcomer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, United States
| | - Theodore R Holman
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States.
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Trubitsina LI, Abdullatypov AV, Larionova AP, Trubitsin IV, Alferov SV, Ponamoreva ON, Leontievsky AA. Expression of thermophilic two-domain laccase from Catenuloplanes japonicus in Escherichia coli and its activity against triarylmethane and azo dyes. PeerJ 2021; 9:e11646. [PMID: 34221729 PMCID: PMC8236229 DOI: 10.7717/peerj.11646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/29/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Two-domain laccases are copper-containing oxidases found in bacteria in the beginning of 2000ths. Two-domain laccases are known for their thermal stability, wide substrate specificity and, the most important of all, their resistance to so-called «strong inhibitors» of classical fungal laccases (azides, fluorides). Low redox potential was found to be specific for all the two-domain laccases, due to which these enzymes lost the researchers' interest as potentially applicable for various biotechnological purposes, such as bioremediation. Searching, obtaining and studying the properties of novel two-domain laccases will help to obtain an enzyme with high redox-potential allowing its practical application. METHODS A gene encoding two-domain laccase was identified in Catenuloplanes japonicus genome, cloned and expressed in an Echerichia coli strain. The protein was purified to homogeneity by immobilized metal ion affinity chromatography. Its molecular properties were studied using electrophoresis in native and denaturing conditions. Physico-chemical properties, kinetic characteristics, substrate specificity and decolorization ability of laccase towards triphenylmethane dyes were measured spectrophotometrically. RESULTS A novel two-domain recombinant laccase CjSL appeared to be a multimer with a subunit molecular mass of 37 kDa. It oxidized a wide range of phenolic substrates (ferulic acid, caffeic acid, hydroquinone, catechol, etc.) at alkaline pH, while oxidizing of non phenolic substrates (K4[Fe(CN)6], ABTS) was optimal at acidic pH. The UV-visible absorption spectrum of the purified enzyme was specific for all two-domain laccases with peak of absorption at 600 nm and shoulder at 340 nm. The pH optima of CjSL for oxidation of ABTS and 2, 6-DMP substrates were 3.6 and 9.2 respectively. The temperature optimum was 70 °C. The enzyme was most stable in neutral-alkaline conditions. CjSL retained 53% activity after pre-incubation at 90 °C for 60 min. The enzyme retained 26% activity even after 60 min of boiling. The effects of NaF, NaN3, NaCl, EDTA and 1,10-phenanthroline on enzymatic activity were investigated. Only 1,10-phenanthroline reduced laccase activity under both acidic and alkaline conditions. Laccase was able to decolorize triphenylmethane dyes and azo-dyes. ABTS and syringaldehyde were effective mediators for decolorization. The efficacy of dye decolorization depended on pH of the reaction medium.
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Affiliation(s)
- Liubov Igorevna Trubitsina
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences – A Separate Subdivision of PSCBR RAS (IBPM RAS), Pushchino, Moscow Region, Russian Federation
| | - Azat Vadimovich Abdullatypov
- Institute of Basic Biological Problems of the Russian Academy of Sciences – A Separate Subdivision of PSCBR RAS (IBBP RAS), Pushchino, Moscow Region, Russian Federation
| | - Anna Petrovna Larionova
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences – A Separate Subdivision of PSCBR RAS (IBPM RAS), Pushchino, Moscow Region, Russian Federation
- Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
| | - Ivan Vasilyevich Trubitsin
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences – A Separate Subdivision of PSCBR RAS (IBPM RAS), Pushchino, Moscow Region, Russian Federation
| | | | | | - Alexey Arkadyevich Leontievsky
- G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences – A Separate Subdivision of PSCBR RAS (IBPM RAS), Pushchino, Moscow Region, Russian Federation
- Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, Russian Federation
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Teramoto T, Nishio T, Kurogi K, Sakakibara Y, Kakuta Y. The crystal structure of mouse SULT2A8 reveals the mechanism of 7α-hydroxyl, bile acid sulfation. Biochem Biophys Res Commun 2021; 562:15-20. [PMID: 34030040 DOI: 10.1016/j.bbrc.2021.04.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Bile acids play essential roles in facilitating the intestinal absorption of lipophilic nutrients as well as regulation of glucose, lipid, and energy homeostasis via activation of some receptors. Bile acids are cytotoxic, and consequently their concentrations are tightly controlled. A critical pathway for bile acid elimination and detoxification is sulfation. The pattern of bile acid sulfation differs by species. Sulfation preferentially occurs at the 3α-OH of bile acids in humans, but at the 7α-OH in mice. A recent study identified mouse cytosolic sulfotransferase 2A8 (mSULT2A8) as the major hepatic 7α-hydroxyl bile acid-sulfating enzyme. To elucidate the 7α-OH specific sulfation mechanism of mSULT2A8, instead of 3α-OH specific sulfation in humans, we determined a crystal structure of mSULT2A8 in complex with cholic acid, a major bile acid, and 3'-phosphoadenosine-5'-phosphate, the sulfate donor product. Our study shows that bile acid-binding mode of mSULT2A8 and how the enzyme holds the 7α-OH group of bile acids at the catalytic center, revealing that the mechanism underlying 7α-OH specific sulfation. The structure shows the substrate binds to mSULT2A8 in an orientation perpendicular to that of human 3α-hydroxyl bile acid-sulfotransferase (hSULT2A1). The structure of the complex provides new insight into species different bile acid metabolism.
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Affiliation(s)
- Takamasa Teramoto
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Takeaki Nishio
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Katsuhisa Kurogi
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Yoshimitsu Kakuta
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan.
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Gault S, Cockell CS. Perchlorate Salts Exert a Dominant, Deleterious Effect on the Structure, Stability, and Activity of α-Chymotrypsin. Astrobiology 2021; 21:405-412. [PMID: 33784200 DOI: 10.1089/ast.2020.2223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The presence of perchlorate ions on Mars raises the question of how these ions influence the biochemistry of any contaminant life introduced into the martian environment, or what selection pressures perchlorate ions exert on any environment that contains these ions, such as the Atacama Desert. In this study, we investigated the structure, stability, and enzyme activity of the model enzyme α-chymotrypsin in the presence of five Mars relevant salts, MgSO4, MgCl2, Mg(ClO4)2, Ca(ClO4)2, and NaClO4. We found that all the perchlorate salts reduced the enzyme activity of α-chymotrypsin in a concentration-dependent manner, with Mg(ClO4)2 and Ca(ClO4)2 having the greatest effect. This observation extends to our structural studies, which show that 1 M Mg(ClO4)2 and Ca(ClO4)2 greatly alter the tertiary structural environment of α-chymotrypsin. We also found that all the perchlorate salts assayed reduced the melting temperature of α-chymotrypsin, whereas the sulfate and chloride salts were able to increase the protein melting temperature. We also demonstrated that a brine containing both perchlorate and sulfate ions exerts the same deleterious effects on α-chymotrypsin's melting temperature and enzyme activity as that of a perchlorate-only brine. This suggests that the perchlorate salts exert a dominant, deleterious effect on protein biochemistry. These results indicate that although perchlorate salts are beneficial to the presence of liquid water due to low eutectic points, they also hamper the habitability of their own environment. Life in such brines would, therefore, have to adapt its cellular machinery to the perchlorate ion's presence or find a way of excluding it from said machinery.
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Affiliation(s)
- Stewart Gault
- Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Charles S Cockell
- Centre for Astrobiology, SUPA School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
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Wloka C, Galenkamp NS, van der Heide NJ, Lucas FLR, Maglia G. Strategies for enzymological studies and measurements of biological molecules with the cytolysin A nanopore. Methods Enzymol 2021; 649:567-585. [PMID: 33712200 DOI: 10.1016/bs.mie.2021.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pore-forming toxins are used in a variety of biotechnological applications. Typically, individual membrane proteins are reconstituted in artificial lipid bilayers where they form water-filled nanoscale apertures (nanopores). When a voltage is applied, the ionic current passing through a nanopore can be used for example to sequence biopolymers, identify molecules, or to study chemical or enzymatic reactions at the single-molecule level. Here we present strategies for studying individual enzymes and measuring molecules, also in highly complex biological samples such as blood.
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Affiliation(s)
- Carsten Wloka
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Nicole S Galenkamp
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Nieck J van der Heide
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Florian L R Lucas
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences & Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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Fields PA. Reductionism in the study of enzyme adaptation. Comp Biochem Physiol B Biochem Mol Biol 2021; 254:110574. [PMID: 33600949 DOI: 10.1016/j.cbpb.2021.110574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 10/22/2022]
Abstract
One of the principal goals of comparative biology is the elucidation of mechanisms by which organisms adapt to different environments. The study of enzyme structure, function, and stability has contributed significantly to this effort, by revealing adaptation at a molecular level. Comparative biochemistry, including enzymology, necessarily pursues a reductionist approach in describing the function and structure of biomolecules, allowing more straightforward study of molecular systems by removing much of the complexity of their biological milieu. Although this reductionism has allowed a remarkable series of discoveries linking chemical processes to metabolism and to whole-organism function in the context of the environment, it also has the potential to mislead when careful consideration is not made of the simplifying assumptions inherent to such research. In this review, a brief history of the growth of enzymology, its reliance on a reductionist philosophy, and its contributions to our understanding of biological systems is given. Examples then are provided of research techniques, based on a reductionist approach, that have advanced our knowledge about enzyme adaptation to environmental stresses, including stability assays, enzyme kinetics, and the impact of solute composition on enzyme function. In each case, the benefits of the reductionist nature of the approach is emphasized, notable advances are described, but potential drawbacks due to inherent oversimplification of the study system are also identified.
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Affiliation(s)
- Peter A Fields
- Biology Department, Franklin & Marshall College, Lancaster, PA 17603, USA.
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Zhang Y, Dai Z, Zhang S, Yang X. The catalytic properties of Thermus thermophilus SG0.5JP17-16 laccase were regulated by the conformational dynamics of pocket loop 6. Biochim Biophys Acta Gen Subj 2021; 1865:129872. [PMID: 33588000 DOI: 10.1016/j.bbagen.2021.129872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Laccase is one member of the blue multicopper oxidase family. It can catalyze the oxidation of various substrates. The Thermus thermophilus SG0.5JP17-16 laccase (lacTT) is thermostable, pH-stable, and high tolerance to halides, and can decolorize the synthetic dyes. In lacTT, the function of the loop 6 constructing the substrate-binding pocket wasn't clear. METHODS The residues Asp394 and Asp396 located in loop 6, and were used to probe how the loop 6 influenced catalytic properties of the laccase. Site-directed mutagenesis was performed for two amino acids. Kinetic assay was utilized to characterize the catalytic efficiency of mutants. Mutants with different catalytic activities were used to decolorize the synthetic dyes to clarify the relationship between the catalytic efficiency and dye decolorization. Redox potential, structural and spectral analyses were performed to explain the differences in laccase activity between wild type and mutant enzymes. RESULTS D394M, D394E and D394R mutants with the lower laccase activity displayed a decreased decolorization efficiency, while D396A, D396M and D396E mutant enzymes with higher catalytic efficiency decolorized the synthetic dye more efficiently than the wild type enzyme. CONCLUSIONS The pocket loop 6 might experience a conformational dynamics. The D394 residue controlled this conformation change by amino acid interaction networks containing the D396 residue at the entrance of substrate channel. GENERAL SIGNIFICANCES These studies may provide clues to improve the activity of the laccase for the better use in industrial applications, and/or contribute to further understanding the mechanism of laccase oxidation on the substrate.
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Affiliation(s)
- Yi Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Zhuojun Dai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Shumin Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Xiaorong Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China.
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Angural S, Bala I, Kumar A, Kumar D, Jassal S, Gupta N. Bleach enhancement of mixed wood pulp by mixture of thermo-alkali-stable xylanase and mannanase derived through co-culturing of Alkalophilic Bacillus sp. NG-27 and Bacillus nealsonii PN-11. Heliyon 2021; 7:e05673. [PMID: 33553710 PMCID: PMC7855340 DOI: 10.1016/j.heliyon.2020.e05673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 04/23/2020] [Accepted: 12/03/2020] [Indexed: 02/01/2023] Open
Abstract
The Application of a combination of enzymes is the best alternative to reduce the use of chemicals in the paper industry. Bacillus sp. NG-27 and Bacillus nealsonii PN-11 are known to produce thermoalkali stable xylanse (X) and mannanase (M) respectively having potential for pulp biobleaching. The Present study, reports the production of a mixture of X + M by co-culturing of strains in SSF and standardizing its application for pulp biobleaching. Production of enzymes by co-cultivation in SSF was optimized by statistical methods. Substantial increase in the yield of enzymes; 3.61 fold of xylanase and 37.71 fold of mannanase was achieved. Application of enzyme cocktail for pulp biobleaching resulted in a 45.64% reduction of kappa number with 55 IU g-1odp of enzyme dose (xylanase:mannanase; 3:1) at pH 8.0 in 1h at 65 °C along with significant increase in brightness (11%) and whiteness (75%). The Same quality of paper as made up from chemical treated pulp can be made from enzyme-treated pulp with 30% less use of chlorine. Structural analysis of enzyme-treated pulp showed dissolution of hemicellulose as indicated by pores, cracks and increased roughness all over the surface. Cocktail of X + M produced economically in a single fermentation having all the requisite characteristics for pulp biobleaching is a highly suitable candidate for application in the pulp and paper industry.
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Affiliation(s)
- Steffy Angural
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Indu Bala
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Aditya Kumar
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Deepak Kumar
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sunena Jassal
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, India
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Grabowski GA, Antommaria AHM, Kolodny EH, Mistry PK. Gaucher disease: Basic and translational science needs for more complete therapy and management. Mol Genet Metab 2021; 132:59-75. [PMID: 33419694 PMCID: PMC8809485 DOI: 10.1016/j.ymgme.2020.12.291] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/15/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory A Grabowski
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, United States of America; Division of Human Genetics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Armand H M Antommaria
- Department of Pediatrics, University of Cincinnati College of Medicine, United States of America; Lee Ault Carter Chair of Pediatric Ethics, Cincinnati Children's Research Foundation, Cincinnati, OH, United States of America.
| | - Edwin H Kolodny
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States of America.
| | - Pramod K Mistry
- Departments of Medicine and Pediatrics, Yale School of Medicine, New Haven, CT, United States of America.
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Makoni NJ, Nichols MR. The intricate biophysical puzzle of caspase-1 activation. Arch Biochem Biophys 2021; 699:108753. [PMID: 33453207 DOI: 10.1016/j.abb.2021.108753] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
This review takes a closer look at the structural components of the molecules involved in the processes leading to caspase-1 activation. Interleukins 1β and 18 (IL-1β, IL-18) are well-known proinflammatory cytokines that are produced following cleavage of their respective precursor proteins by the cysteine protease caspase-1. Active caspase-1 is the final step of the NLRP3 inflammasome, a three-protein intracellular complex involved in inflammation and induction of pyroptosis (a proinflammatory cell-death process). NLRP3 activators facilitate assembly of the inflammasome complex and subsequent activation of caspase-1 by autoproteolysis. However, the definitive structural components of active caspase-1 are still unclear and new data add to the complexity of this process. This review outlines the historical and recent findings that provide supporting evidence for the structural aspects of caspase-1 autoproteolysis and activation.
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Affiliation(s)
- Nyasha J Makoni
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Michael R Nichols
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
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Johnstone MA, Nelson SJ, O'Leary C, Self WT. Exploring the selenium-over-sulfur substrate specificity and kinetics of a bacterial selenocysteine lyase. Biochimie 2021; 182:166-176. [PMID: 33444662 DOI: 10.1016/j.biochi.2021.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/15/2022]
Abstract
Selenium is a vital micronutrient in many organisms. While traces are required for microbial utilization, excess amounts are toxic; thus, selenium can be regarded as a biological double-edged sword. Selenium is chemically similar to the essential element sulfur, but curiously, evolution has selected the former over the latter for a subset of oxidoreductases. Enzymes involved in sulfur metabolism are less discriminate in terms of preventing selenium incorporation; however, its specific incorporation into selenoproteins reveals a highly discriminate process that is not completely understood. We have identified SclA, a NifS-like protein in the nosocomial pathogen, Enterococcus faecalis, and characterized its enzymatic activity and specificity for l-selenocysteine over l-cysteine. It is known that Asp-146 is required for selenocysteine specificity in the human selenocysteine lyase. Thus, using computational biology, we compared the bacterial and mammalian enzymes and identified His-100, an Asp-146 ortholog in SclA, and generated site-directed mutants in order to study the residue's potential role in the l-selenocysteine discrimination mechanism. The proteins were overexpressed, purified, and characterized for their biochemical properties. All mutants exhibited varying Michaelis-Menten behavior towards l-selenocysteine, but His-100 was not found to be essential for this activity. Additionally, l-cysteine acted as a competitive inhibitor of all enzymes with higher affinity than l-selenocysteine. Finally, we discovered that SclA exhibited low activity with l-cysteine as a poor substrate regardless of mutations. We conclude that His-100 is not required for l-selenocysteine specificity, underscoring the inherent differences in discriminatory mechanisms between bacterial NifS-like proteins and mammalian selenocysteine lyases.
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Affiliation(s)
- Michael A Johnstone
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Samantha J Nelson
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Christine O'Leary
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - William T Self
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA.
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Diaz-de-Quijano D, Stratman CN, Berger SA. DIY enzyme labelled fluorescence alcohol (ELFA) standard production protocol to quantify single-cell phosphatase activity (SCPA) of microplankton. Heliyon 2020; 6:e05582. [PMID: 33294708 DOI: 10.1016/j.heliyon.2020.e05582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/19/2020] [Accepted: 11/19/2020] [Indexed: 11/29/2022] Open
Abstract
Extracellular enzyme activities (EEA) are crucial components of microbial food web interactions and biogeochemical cycles in aquatic ecosystems. They also represent relevant biological traits in the ecophysiology of phytoplankton and other components of microbial plankton. To assess species-specific and (sub-)population-level characteristics of phytoplankton EEA at the single-cell level and close-to-in-situ conditions solely the enzyme labelled fluorescence (ELF)-based substrates have been used, because they become fluorescent and precipitate around the enzyme activity location upon enzymatic cleavage. However, the enzyme-labelled fluorescence alcohol (ELFA) standard is no longer commercially available, hence standard curves cannot be run anymore and single-cell phosphatase activity (SCPA) is no longer quantifiable. Therefore, we introduce a simple protocol for an ELFA standard do it yourself (DIY) production to enable quantifying microplankton SCPA again. This protocol is based on fluorescence measurements easily available to environmental enzyme activity laboratories, and it circumvents any need for chemical synthesis equipment and knowledge. The method is based on a controlled reaction of the ELF-phosphate (ELFP) substrate with commercially available alkaline phosphatase, which efficiently turns all the substrate into ELFA product. The ELFA product was dried out and dissolved again in dimethyl sulfoxide (DMSO) for storage. The ELFA concentration of that standard-to-be ELFA solution in DMSO was determined by linear regression between a low concentration dilution series of ELFA solution measured fluorimetrically and parallel measurements of a series of phosphatase-catalysed reactions at an overlapping ELFP concentration range. Finally, the fluorescence- and concentration-stable ELFA solution in DMSO with a known concentration constitutes the ELFA standard that is necessary to quantify bulk (fluorimeter) and single-cell (microscope and flow cytometer) phosphatase activity in microplankton.
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Song P, Wang ML, Zheng QY, Wang P, Zhu GP. Isocitrate dehydrogenase 1 from Acinetobacter baummanii (AbIDH1) enzymatic characterization and its regulation by phosphorylation. Biochimie 2020; 181:77-85. [PMID: 33290880 DOI: 10.1016/j.biochi.2020.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/22/2022]
Abstract
Acinetobacter baumannii encodes all enzymes required in the tricarboxylic acid (TCA) cycle and glyoxylate bypass except for isocitrate dehydrogenase kinase/phosphatase (IDHKP), which can phosphorylate isocitrate dehydrogenase (IDH) at a substrate-binding Ser site and control the carbon flux in enterobacteria, such as Escherichia coli. The potential kinase was not successfully pulled down from A. baumannii cell lyase; therefore, whether the IDH 1 from A. baumannii (AbIDH1) can be phosphorylated to regulate intracellular carbon flux has not been clarified. Herein, the AbIDH1 gene was cloned, the encoded protein was expressed and purified to homogeneity, and phosphorylation and enzyme kinetics were evaluated in vitro. Gel filtration and SDS-PAGE analyses showed that AbIDH1 is an 83.5 kDa homodimer in solution. The kinetics showed that AbIDH1 is a fully active NADP-dependent enzyme. The Michaelis constant Km is 46.6 (Mn2+) and 18.1 μM (Mg2+) for NADP+ and 50.5 (Mn2+) and 65.4 μM (Mg2+) for the substrate isocitrate. Phosphorylation experiments in vitro indicated that AbIDH1 is a substrate for E. coli IDHKP. The activity of AbIDH1 treated with E. coli IDHKP immediately decreased by 80% within 9 min. Mass spectrometry indicated that the conserved Ser113 of AbIDH1 is phosphorylated. Continuous phosphorylation-mimicking mutants (Ser113Glu and Ser113Asp) lack almost all enzymatic activity. Side-chain mutations at Ser113 (Ser113Thr, Ser113Ala, Ser113Gly and Ser113Tyr) remarkably reduce the enzymatic activity. Understanding the potential of AbIDH1 phosphorylation enables further investigations of the AbIDH1 physiological functions in A. baumannii.
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Affiliation(s)
- Ping Song
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, 241000, Anhui, China; College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, Anhui, China
| | - Meng-Li Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Qing-Yang Zheng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Guo-Ping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, 241000, Anhui, China.
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Yaari Z, Cheung JM, Baker HA, Frederiksen RS, Jena PV, Horoszko CP, Jiao F, Scheuring S, Luo M, Heller DA. Nanoreporter of an Enzymatic Suicide Inactivation Pathway. Nano Lett 2020; 20:7819-7827. [PMID: 33119310 PMCID: PMC8177003 DOI: 10.1021/acs.nanolett.0c01858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Enzymatic suicide inactivation, a route of permanent enzyme inhibition, is the mechanism of action for a wide array of pharmaceuticals. Here, we developed the first nanosensor that selectively reports the suicide inactivation pathway of an enzyme. The sensor is based on modulation of the near-infrared fluorescence of an enzyme-bound carbon nanotube. The nanosensor responded selectively to substrate-mediated suicide inactivation of the tyrosinase enzyme via bathochromic shifting of the nanotube emission wavelength. Mechanistic investigations revealed that singlet oxygen generated by the suicide inactivation pathway induced the response. We used the nanosensor to quantify the degree of enzymatic inactivation by measuring response rates to small molecule tyrosinase modulators. This work resulted in a new capability of interrogating a specific route of enzymatic death. Potential applications include drug screening and hit-validation for compounds that elicit or inhibit enzymatic inactivation and single-molecule measurements to assess population heterogeneity in enzyme activity.
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Affiliation(s)
- Zvi Yaari
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Justin M. Cheung
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Hanan A. Baker
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Rune S. Frederiksen
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Prakrit V. Jena
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Christopher, P. Horoszko
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Fang Jiao
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Simon Scheuring
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Anesthesiology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Minkui Luo
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
| | - Daniel A. Heller
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Physiology and Biophysics, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, United States
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Ásgeirsson B, Markússon S, Hlynsdóttir SS, Helland R, Hjörleifsson JG. X-ray crystal structure of Vibrio alkaline phosphatase with the non-competitive inhibitor cyclohexylamine. Biochem Biophys Rep 2020; 24:100830. [PMID: 33102813 PMCID: PMC7569297 DOI: 10.1016/j.bbrep.2020.100830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
Background Para-nitrophenyl phosphate, the common substrate for alkaline phosphatase (AP), is available as a cyclohexylamine salt. Here, we report that cyclohexylamine is a non-competitive inhibitor of APs. Methods Cyclohexylamine inhibited four different APs. Co-crystallization with the cold-active Vibrio AP (VAP) was performed and the structure solved. Results Inhibition of VAP fitted a non-competitive kinetic model (Km unchanged, Vmax reduced) with IC50 45.3 mM at the pH optimum 9.8, not sensitive to 0.5 M NaCl, and IC50 27.9 mM at pH 8.0, where the addition of 0.5 M NaCl altered the inhibition to the level observed at pH 9.8. APs from E. coli and calf intestines were less sensitive to cyclohexylamine, whereas an Antarctic bacterial AP was similar to VAP in this respect. X-ray crystallography at 2.3 Å showed two binding sites, one in the active site channel and another at the surface close to dimer interface. Antarctic bacterial AP and VAP have Trp274 in common in their active-sites, that takes part in binding cyclohexylamine. VAP variants W274A, W274K, and W274H gave IC50 values of 179 mM, 188 mM and 187 mM, respectively, at pH 9.8. Conclusions The binding of cyclohexylamine in locations at the dimeric interface and/or in the active site of APs may delay product release or reduce the rate of catalytic step(s) involving conformational changes and intersubunit communications. General significance Cyclohexylamine is a common chemical in industries and used as a counterion in substrates for alkaline phosphatase, a clinically important and common enzyme in the biosphere. Cyclohexylamine inhibits alkaline phosphatase activity non-competitively. X-ray structure was solved that shows cyclohexylamine bound to alkaline phosphatase at two sites. Alkaline phosphatases from four different organisms bind cyclohexylamine with varying affinity.
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Affiliation(s)
- Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Sigurbjörn Markússon
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Sigríður S Hlynsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ronny Helland
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT - the Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Jens G Hjörleifsson
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
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Moidu NA, A Rahman NS, Syafruddin SE, Low TY, Mohtar MA. Secretion of pro-oncogenic AGR2 protein in cancer. Heliyon 2020; 6:e05000. [PMID: 33005802 PMCID: PMC7519367 DOI: 10.1016/j.heliyon.2020.e05000] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Anterior gradient-2 (AGR2) protein mediates the formation, breakage and isomerization of disulphide bonds during protein maturation in the endoplasmic reticulum (ER) and contributes to the homoeostasis of the secretory pathway. AGR2 promotes tumour development and metastasis and its elevated expression is almost completely restricted to malignant tumours. Interestingly, this supposedly ER-resident protein can be localised to other compartments of cancer cells and can also be secreted into the extracellular milieu. There are emerging evidences that describe the gain-of-function activities of the extracellular AGR2, particularly in cancer development. Here, we reviewed studies detailing the expression, pathological and physiological roles associated with AGR2 and compared the duality of localization, intracellular and extracellular, with special emphasis on the later. We also discussed the possible mechanisms of AGR2 secretion as well as deliberating the functional impacts of AGR2 in cancer settings. Last, we deliberate the current therapeutic strategies and posit the potential use AGR2, as a prognosis and diagnosis marker in cancer.
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Affiliation(s)
- Nurshahirah Ashikin Moidu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras 56000 Kuala Lumpur, Malaysia
| | - Nisa Syakila A Rahman
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras 56000 Kuala Lumpur, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras 56000 Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras 56000 Kuala Lumpur, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Cheras 56000 Kuala Lumpur, Malaysia
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Roda S, Santiago G, Guallar V. Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes. Adv Protein Chem Struct Biol 2020; 122:1-31. [PMID: 32951809 DOI: 10.1016/bs.apcsb.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Lobo A, Liu Y, Song Y, Liu S, Zhang R, Liang H, Xin H. Effect of procyanidins on lipid metabolism and inflammation in rats exposed to alcohol and iron. Heliyon 2020; 6:e04847. [PMID: 32964156 PMCID: PMC7490533 DOI: 10.1016/j.heliyon.2020.e04847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/24/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023] Open
Abstract
Background Lifestyle involving uncontrolled alcohol consumption coupled regularly with red meat and other iron sources has detrimental effects on the liver, which in the long term, results in Alcoholic Liver Disease (ALD). Procyanidin has lately garnered increasing attention and has become the focus of research owing to its antioxidant properties. This study explores the anti-inflammatory effects of procyanidins, in preventing ALD, by analyzing the biological activities of the compound on liver injury caused by excessive alcohol and iron. Method Male SPF Wistar rats were placed in 4 groups; the control Group A (basic diet); the model Group B (excess alcohol 8–12 mL/kg/d and iron 1000 mg/kg diet); the low dose procyanidin Group C (model group diet plus 60 mg/kg/d of procyanidin); and the high dose procyanidin Group D (model group diet plus 120 mg/kg/d of procyanidin). Serum biochemical markers for liver damage were measured spectrophotometrically. The NFκB and IκB mRNA expression levels were determined using RT-PCR; the NFκB p65 and IκB protein expression levels were assessed via western blotting, while ELISA was used to detect serum inflammatory factors. Results The pathological score of the model Group B, low and high dose procyanidin Groups C and D were 6.58 ± 0.90,4.69 ± 0.70 and 2.00 ± 0.73, respectively (P < 0.05). The results showed that high alcohol and iron contents in the model group led to significant damage of liver structure, increased low-density lipoproteins (LDLs), steatosis, and increased levels of inflammatory cytokines. High amounts of procyanidins led to the preservation of the liver structure, production of high-density lipoproteins, and reduction in serum inflammatory cytokines while also significantly decreasing the expression levels of NFκB p65. Conclusion The results prove that procyanidins have hepatoprotective potential and could be effective in reversing histopathology, possibly by alleviating inflammation and improving lipid metabolism.
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Affiliation(s)
- Amara Lobo
- Department of Cardiology, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao 266071, China
| | - Ying Liu
- Basic Medical College, Qingdao University, 38 Deng Zhou Road, Qingdao 266021, China
| | - Yuqing Song
- Department of Cardiology, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao 266071, China
| | - Song Liu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao 266071, China
| | - Rui Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao 266071, China
| | - Hui Liang
- Department of Human Nutrition, College of Public Health, Qingdao University, 38 Deng Zhou Road, Qingdao 266021, China
| | - Hui Xin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, 16 Jiang Su Road, Qingdao 266071, China
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