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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms. Structure 2024; 32:1184-1196.e4. [PMID: 38729161 PMCID: PMC11316656 DOI: 10.1016/j.str.2024.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also a promiscuous integrin that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands remains unclear. We have characterized the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, a stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms and that the active αMI-domain has a preference for motifs containing both positively and negatively charged amino acids.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | - Tatiana P Ugarova
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA.
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2
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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of Integrin Mac-1 Binds the Cytokine Pleiotrophin Using Multiple Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578455. [PMID: 38352421 PMCID: PMC10862807 DOI: 10.1101/2024.02.01.578455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an important adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also the most promiscuous member of the integrin family that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands is not clear. We have determined the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a cationic protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of the active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms, and suggest that active αMI-domain prefers acidic amino acids in zwitterionic motifs.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | | | | | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
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3
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Osborne MJ, Sulekha A, Culjkovic-Kraljacic B, Gasiorek J, Ruediger E, Jolicouer E, Marinier A, Assouline S, Borden KLB. Medicinal Chemistry and NMR Driven Discovery of Novel UDP-glucuronosyltransferase 1A Inhibitors That Overcome Therapeutic Resistance in Cells. J Mol Biol 2024; 436:168378. [PMID: 38043731 PMCID: PMC10841659 DOI: 10.1016/j.jmb.2023.168378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
The UDP glucuronosyltransferases (UGT) deactivate many therapeutics via glucuronidation while being required for clearance of normal metabolites and xenobiotics. There are 19 UGT enzymes categorized into UGT1A and UGT2B families based on sequence conservation. This presents a challenge in terms of targeting specific UGTs to overcome drug resistance without eliciting overt toxicity. Here, we identified for the first time that UGT1A4 is highly elevated in acute myeloid leukemia (AML) patients and its reduction corresponded to objective clinical responses. To develop inhibitors to UGT1A4, we leveraged previous NMR-based fragment screening data against the C-terminal domain of UGT1A (UGT1A-C). NMR and medicinal chemistry strategies identified novel chemical matter based on fragment compounds with the capacity to bind ∼20 fold more tightly to UGT1A-C (Kd ∼ 600 μM vs ∼30 μM). Some compounds differentially inhibited UGT1A4 versus UGT1A1 enzyme activity and restored drug sensitivity in resistant human cancer cells. NMR-based NOE experiments revealed these novel compounds recognised a region distal to the catalytic site suggestive of allosteric regulation. This binding region is poorly conserved between UGT1A and UGT2B C-terminal sequences, which otherwise exhibit high similarity. Consistently, these compounds did not bind to the C-terminal domain of UGT2B7 nor a triple mutant of UGT1A-C replaced with UGT2B7 residues in this region. Overall, we discovered a site on UGTs that can be leveraged to differentially target UGT1As and UGT2Bs, identified UGT1A4 as a therapeutic target, and found new chemical matter that binds the UGT1A C-terminus, inhibits glucuronidation and restores drug sensitivity.
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Affiliation(s)
- Michael J Osborne
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Anamika Sulekha
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Jadwiga Gasiorek
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
| | - Edward Ruediger
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Eric Jolicouer
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Anne Marinier
- Drug Discovery Unit, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Quebec, Canada
| | - Sarit Assouline
- Jewish General Hospital and McGill University, 3755 Cote Ste Catherine, Montreal, Quebec H3T1E2, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer and Department of Pathology and Cell Biology, University of Montreal, Montreal, Quebec, Canada
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4
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. J Biol Chem 2023; 299:105380. [PMID: 37866629 PMCID: PMC10694664 DOI: 10.1016/j.jbc.2023.105380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 09/30/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Mitochondrial fission protein 1 (Fis1) and dynamin-related protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in Saccharomyces cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 (KD = 12-68 μM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss-of-function and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A), demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae. These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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Affiliation(s)
- Kelsey A Nolden
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Megan C Harwig
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - R Blake Hill
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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5
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Nolden KA, Harwig MC, Hill RB. Human Fis1 directly interacts with Drp1 in an evolutionarily conserved manner to promote mitochondrial fission. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539292. [PMID: 37205551 PMCID: PMC10187221 DOI: 10.1101/2023.05.03.539292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mitochondrial Fission Protein 1 (Fis1) and Dynamin Related Protein 1 (Drp1) are the only two proteins evolutionarily conserved for mitochondrial fission, and directly interact in S. cerevisiae to facilitate membrane scission. However, it remains unclear if a direct interaction is conserved in higher eukaryotes as other Drp1 recruiters, not present in yeast, are known. Using NMR, differential scanning fluorimetry, and microscale thermophoresis, we determined that human Fis1 directly interacts with human Drp1 ( K D = 12-68 µM), and appears to prevent Drp1 assembly, but not GTP hydrolysis. Similar to yeast, the Fis1-Drp1 interaction appears governed by two structural features of Fis1: its N-terminal arm and a conserved surface. Alanine scanning mutagenesis of the arm identified both loss- and gain-of-function alleles with mitochondrial morphologies ranging from highly elongated (N6A) to highly fragmented (E7A) demonstrating a profound ability of Fis1 to govern morphology in human cells. An integrated analysis identified a conserved Fis1 residue, Y76, that upon substitution to alanine, but not phenylalanine, also caused highly fragmented mitochondria. The similar phenotypic effects of the E7A and Y76A substitutions, along with NMR data, support that intramolecular interactions occur between the arm and a conserved surface on Fis1 to promote Drp1-mediated fission as in S. cerevisiae . These findings indicate that some aspects of Drp1-mediated fission in humans derive from direct Fis1-Drp1 interactions that are conserved across eukaryotes.
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Costanzi E, Coletti A, Zambelli B, Macchiarulo A, Bellanda M, Battistutta R. Calmodulin binds to the STAS domain of SLC26A5 prestin with a calcium-dependent, one-lobe, binding mode. J Struct Biol 2021; 213:107714. [PMID: 33667636 DOI: 10.1016/j.jsb.2021.107714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/14/2021] [Accepted: 02/25/2021] [Indexed: 10/22/2022]
Abstract
SLC26A5 transporter prestin is fundamental for the higher hearing sensitivity and frequency selectivity of mammals. Prestin is a voltage-dependent transporter found in the cochlear outer hair cells responsible for their electromotility. Intracellular chloride binding is considered essential for voltage sensitivity and electromotility. Prestin is composed by a transmembrane domain and by a cytosolic domain called STAS. There is evidence of a calcium/calmodulin regulation of prestin mediated by the STAS domain. Using different biophysical techniques, namely SEC, CD, ITC, MST, NMR and SAXS, here we demonstrate and characterize the direct interaction between calmodulin and prestin STAS. We show that the interaction is calcium-dependent and that involves residues at the N-terminal end of the "variable loop". This is an intrinsically disordered insertion typical of the STAS domains of the SLC26 family of transporters whose function is still unclear. We derive a low-resolution model of the STAS/CaM complex, where only one lobe of calmodulin is engaged in the interaction, and build a model for the entire dimeric prestin in complex with CaM, which can use the unoccupied lobe to interact with other regions of prestin or with other regulatory proteins. We show that also a non-mammalian STAS can interact with calmodulin via the variable loop. These data start to shed light on the regulatory role of the STAS variable loop of prestin.
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Affiliation(s)
- Elisa Costanzi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Alice Coletti
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy; Department of Pharmacy, University of Chieti-Pescara, via dei Vestini 31, 66100 Chieti, Italy
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, viale Fanin 40, 40127 Bologna, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, via del Liceo 1, 06123 Perugia, Italy
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
| | - Roberto Battistutta
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy.
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Ye Y, Fulcher YG, Sliman DJ, Day MT, Schroeder MJ, Koppisetti RK, Bates PD, Thelen JJ, Van Doren SR. The BADC and BCCP subunits of chloroplast acetyl-CoA carboxylase sense the pH changes of the light-dark cycle. J Biol Chem 2020; 295:9901-9916. [PMID: 32467229 PMCID: PMC7380191 DOI: 10.1074/jbc.ra120.012877] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/26/2020] [Indexed: 01/20/2023] Open
Abstract
Acetyl-CoA carboxylase (ACCase) catalyzes the first committed step in the de novo synthesis of fatty acids. The multisubunit ACCase in the chloroplast is activated by a shift to pH 8 upon light adaptation and is inhibited by a shift to pH 7 upon dark adaptation. Here, titrations with the purified ACCase biotin attachment domain-containing (BADC) and biotin carboxyl carrier protein (BCCP) subunits from Arabidopsis indicated that they can competently and independently bind biotin carboxylase (BC) but differ in responses to pH changes representing those in the plastid stroma during light or dark conditions. At pH 7 in phosphate buffer, BADC1 and BADC2 gain an advantage over BCCP1 and BCCP2 in affinity for BC. At pH 8 in KCl solution, however, BCCP1 and BCCP2 had more than 10-fold higher affinity for BC than did BADC1. The pH-modulated shifts in BC preferences for BCCP and BADC partners suggest they contribute to light-dependent regulation of heteromeric ACCase. Using NMR spectroscopy, we found evidence for increased intrinsic disorder of the BADC and BCCP subunits at pH 7. We propose that this intrinsic disorder potentially promotes fast association with BC through a "fly-casting mechanism." We hypothesize that the pH effects on the BADC and BCCP subunits attenuate ACCase activity by night and enhance it by day. Consistent with this hypothesis, Arabidopsis badc1 badc3 mutant lines grown in a light-dark cycle synthesized more fatty acids in their seeds. In summary, our findings provide evidence that the BADC and BCCP subunits function as pH sensors required for light-dependent switching of heteromeric ACCase activity.
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Affiliation(s)
- Yajin Ye
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Yan G Fulcher
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - David J Sliman
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Mizani T Day
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Mark J Schroeder
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Rama K Koppisetti
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Philip D Bates
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - Jay J Thelen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Steven R Van Doren
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, USA
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8
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Brinson RG, Arbogast LW, Marino JP, Delaglio F. Best Practices in Utilization of 2D-NMR Spectral Data as the Input for Chemometric Analysis in Biopharmaceutical Applications. J Chem Inf Model 2020; 60:2339-2355. [DOI: 10.1021/acs.jcim.0c00081] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Robert G. Brinson
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, The University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Luke W. Arbogast
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, The University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - John P. Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, The University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Frank Delaglio
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology, The University of Maryland, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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9
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Namanja AT, Xu J, Wu H, Sun Q, Upadhyay AK, Sun C, Van Doren SR, Petros AM. NMR-based fragment screening and lead discovery accelerated by principal component analysis. JOURNAL OF BIOMOLECULAR NMR 2019; 73:675-685. [PMID: 31541395 DOI: 10.1007/s10858-019-00279-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Protein-based NMR spectroscopy has proven to be a very robust method for finding fragment leads to protein targets. However, one limitation of protein-based NMR is that the data acquisition and analysis can be time consuming. In order to streamline the scoring of protein-based NMR fragment screening data and the determination of ligand affinities using 2D NMR experiments we have developed a data analysis workflow based on principal component analysis (PCA) within the TREND NMR Pro software package. We illustrate this using four different proteins and sets of ligands which interact with these proteins over a range of affinities. Also, these PCA-based methods can be successfully applied even to systems where ligand binding to target proteins is in intermediate or even slow exchange on the NMR time scale. Finally, these methods will work for scoring of fragment binding data using protein spectra that are either highly overlapped or lower in resolution.
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Affiliation(s)
- Andrew T Namanja
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Jia Xu
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
| | - Haihong Wu
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Qi Sun
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Anup K Upadhyay
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Chaohong Sun
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA
| | - Steven R Van Doren
- Biochemistry Department, University of Missouri, 117 Schweitzer Hall, Columbia, MO, 65211, USA.
| | - Andrew M Petros
- Research & Development, AbbVie, 1 North Waukegan Road, North Chicago, IL, 60064, USA.
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10
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Zhou P, Hu O, Fu H, Ouyang L, Gong X, Meng P, Wang Z, Dai M, Guo X, Wang Y. UPLC-Q-TOF/MS-based untargeted metabolomics coupled with chemometrics approach for Tieguanyin tea with seasonal and year variations. Food Chem 2019; 283:73-82. [PMID: 30722928 DOI: 10.1016/j.foodchem.2019.01.050] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 12/05/2018] [Accepted: 01/05/2019] [Indexed: 12/20/2022]
Abstract
The taste and aroma quality of Tieguanyin tea fluctuate seasonally and yearly. However, the compounds responsible for the seasonal and year variations of metabolic pattern and its sensory quality are far from clear. 60 Tieguanyin tea samples harvested in different years and seasons were analyzed by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) and chemometrics. Principal component analysis (PCA) explained 33.2% of the total variance, while orthogonal projection to latent structures discriminate analysis (OPLS-DA) can obtain potential metabolites with better discrimination, and with R2X and Q2 of cross-validation as 0.974 and 0.937, respectively. Subsequently, heat map analysis (HCA) visualized relationships between Tieguanyin teas with these significantly different potential metabolites by Mann-Whitney U test (p < 0.05). Furthermore, the best discriminate metabolites contributing to different sensory qualities were revealed by stepwise liner discrimination analysis (SLDA) with 100% accuracy rate. The present strategy also exhibited great potential for untargeted metabolomics of other foods.
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Affiliation(s)
- Peng Zhou
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China; China National Quality Supervision and Testing Center for Processed Food (FuZhou), Fujian Inspection and Research Institute for Product Quality, Fuzhou 350002, PR China
| | - Ou Hu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Haiyan Fu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, PR China.
| | - Liqun Ouyang
- China National Quality Supervision and Testing Center for Processed Food (FuZhou), Fujian Inspection and Research Institute for Product Quality, Fuzhou 350002, PR China
| | - Xuedong Gong
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Peng Meng
- China National Quality Supervision and Testing Center for Processed Food (FuZhou), Fujian Inspection and Research Institute for Product Quality, Fuzhou 350002, PR China
| | - Zheng Wang
- China National Quality Supervision and Testing Center for Processed Food (FuZhou), Fujian Inspection and Research Institute for Product Quality, Fuzhou 350002, PR China
| | - Ming Dai
- China National Quality Supervision and Testing Center for Processed Food (FuZhou), Fujian Inspection and Research Institute for Product Quality, Fuzhou 350002, PR China
| | - Xiaoming Guo
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan 430074, PR China
| | - Ying Wang
- School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China.
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11
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Mi W, Zhang Y, Lyu J, Wang X, Tong Q, Peng D, Xue Y, Tencer AH, Wen H, Li W, Kutateladze TG, Shi X. The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation. Nat Commun 2018; 9:3759. [PMID: 30217978 PMCID: PMC6138639 DOI: 10.1038/s41467-018-06247-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/15/2018] [Indexed: 01/05/2023] Open
Abstract
Recognition of histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Most reader modules target specific post-translational modifications on histones. Here, we report the identification of a reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-two-A-containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain, indicating a specific recognition of H3 versus other histones. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC-dependent promoter histone H3K9 acetylation and target gene expression. Overall, our study identifies the ZZ domain of ZZZ3 as a histone H3 reader that is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation. Histones are recognized by epigenetic readers, which play essential roles in regulation of chromatin and transcription. Here the authors provide evidence that the ZZ-type zinc finger domain of ZZZ3 functions as a reader of histone H3, which is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.
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Affiliation(s)
- Wenyi Mi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Jie Lyu
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Danni Peng
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Yongming Xue
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Adam H Tencer
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA. .,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA.
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12
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13
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Combination of 1H nuclear magnetic resonance spectroscopy and principal component analysis to evaluate the lipid fluidity of flutamide-encapsulated lipid nanoemulsions. Anal Bioanal Chem 2018; 410:5033-5042. [DOI: 10.1007/s00216-018-1154-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 10/14/2022]
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Comparison of common components analysis with principal components analysis and independent components analysis: Application to SPME-GC-MS volatolomic signatures. Talanta 2018; 178:854-863. [DOI: 10.1016/j.talanta.2017.10.025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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Stiers KM, Beamer LJ. Assessment and Impacts of Phosphorylation on Protein Flexibility of the α-d-Phosphohexomutases. Methods Enzymol 2018; 607:241-267. [DOI: 10.1016/bs.mie.2018.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Affinities and Comparisons of Enzyme States by Principal Component Analysis of NMR Spectra, Automated using TREND Software. Methods Enzymol 2018; 607:217-240. [DOI: 10.1016/bs.mie.2018.05.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Multiple Ligand-Bound States of a Phosphohexomutase Revealed by Principal Component Analysis of NMR Peak Shifts. Sci Rep 2017; 7:5343. [PMID: 28706231 PMCID: PMC5509744 DOI: 10.1038/s41598-017-05557-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/31/2017] [Indexed: 11/08/2022] Open
Abstract
Enzymes sample multiple conformations during their catalytic cycles. Chemical shifts from Nuclear Magnetic Resonance (NMR) are hypersensitive to conformational changes and ensembles in solution. Phosphomannomutase/phosphoglucomutase (PMM/PGM) is a ubiquitous four-domain enzyme that catalyzes phosphoryl transfer across phosphohexose substrates. We compared states the enzyme visits during its catalytic cycle. Collective responses of Pseudomonas PMM/PGM to phosphosugar substrates and inhibitor were assessed using NMR-detected titrations. Affinities were estimated from binding isotherms obtained by principal component analysis (PCA). Relationships among phosphosugar-enzyme associations emerge from PCA comparisons of the titrations. COordiNated Chemical Shifts bEhavior (CONCISE) analysis provides novel discrimination of three ligand-bound states of PMM/PGM harboring a mutation that suppresses activity. Enzyme phosphorylation and phosphosugar binding appear to drive the open dephosphorylated enzyme to the free phosphorylated state, and on toward ligand-closed states. Domain 4 appears central to collective responses to substrate and inhibitor binding. Hydrogen exchange reveals that binding of a substrate analogue enhances folding stability of the domains to a uniform level, establishing a globally unified structure. CONCISE and PCA of NMR spectra have discovered novel states of a well-studied enzyme and appear ready to discriminate other enzyme and ligand binding states.
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Xu J, Van Doren SR. Tracking Equilibrium and Nonequilibrium Shifts in Data with TREND. Biophys J 2017; 112:224-233. [PMID: 28122211 DOI: 10.1016/j.bpj.2016.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/21/2016] [Accepted: 12/09/2016] [Indexed: 11/16/2022] Open
Abstract
Principal component analysis (PCA) discovers patterns in multivariate data that include spectra, microscopy, and other biophysical measurements. Direct application of PCA to crowded spectra, images, and movies (without selecting peaks or features) was shown recently to identify their equilibrium or temporal changes. To enable the community to utilize these capabilities with a wide range of measurements, we have developed multiplatform software named TREND to Track Equilibrium and Nonequilibrium population shifts among two-dimensional Data frames. TREND can also carry this out by independent component analysis. We highlight a few examples of finding concurrent processes. TREND extracts dual phases of binding to two sites directly from the NMR spectra of the titrations. In a cardiac movie from magnetic resonance imaging, TREND resolves principal components (PCs) representing breathing and the cardiac cycle. TREND can also reconstruct the series of measurements from selected PCs, as illustrated for a biphasic, NMR-detected titration and the cardiac MRI movie. Fidelity of reconstruction of series of NMR spectra or images requires more PCs than needed to plot the largest population shifts. TREND reads spectra from many spectroscopies in the most common formats (JCAMP-DX and NMR) and multiple movie formats. The TREND package thus provides convenient tools to resolve the processes recorded by diverse biophysical methods.
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Affiliation(s)
- Jia Xu
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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Abstract
Heparan sulfate proteoglycans activate the matrix metalloproteinase-7 zymogen (proMMP-7) and recruit it in order to shed proteins from cell surfaces. This occurs in uterine and mammary epithelia, bacterial killing, lung healing, and tumor cell signaling. Basic tracks on proMMP-7 recognize polyanionic heparin, according to nuclear magnetic resonance and mutations disruptive of maturation. Contacts and proximity measurements guided docking of a heparin octasaccharide to proMMP-7. The reducing end fits into a basic pocket in the pro-domain while the chain continues toward the catalytic domain. Another oligosaccharide traverses a basic swath remote on the catalytic domain and inserts its reducing end into a slot formed with the basic C terminus. This latter association appears to support allosteric acceleration of proteolysis. The modes of binding account for extended, heterogeneous assemblies of proMMP-7 with heparinoids during maturation and for bridging to pro-α-defensins and proteoglycans. These associations support proteolytic release of activities at epithelial cell surfaces.
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