Activity-Based Protein Profiling
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Bran Serine Hydrolases Achintya Kumar Dolui1,2, Arun Kumar Vijayakumar2,3, Ram Rajasekharan1,2,4 & Panneerselvam Vijayaraj1,2*
www.nature.com/scientificreports OPEN Activity‑based protein profling of rice (Oryza sativa L.) bran serine hydrolases Achintya Kumar Dolui1,2, Arun Kumar Vijayakumar2,3, Ram Rajasekharan1,2,4 & Panneerselvam Vijayaraj1,2* Rice bran is an underutilized agricultural by‑product with economic importance. The unique phytochemicals and fatty acid compositions of bran have been targeted for nutraceutical development. The endogenous lipases and hydrolases are responsible for the rapid deterioration of rice bran. Hence, we attempted to provide the frst comprehensive profling of active serine hydrolases (SHs) present in rice bran proteome by activity‑based protein profling (ABPP) strategy. The active site‑directed fuorophosphonate probe (rhodamine and biotin‑conjugated) was used for the detection and identifcation of active SHs. ABPP revealed 55 uncharacterized active‑SHs and are representing fve diferent known enzyme families. Based on motif and domain analyses, one of the uncharacterized and miss annotated SHs (Os12Ssp, storage protein) was selected for biochemical characterization by overexpressing in yeast. The purifed recombinant protein authenticated the serine protease activity in time and protein‑dependent studies. Os12Ssp exhibited the maximum activity at a pH between 7.0 and 8.0. The protease activity was inhibited by the covalent serine protease inhibitor, which suggests that the ABPP approach is indeed reliable than the sequence‑based annotations. Collectively, the comprehensive knowledge generated from this study would be useful in expanding the current understanding of rice bran SHs and paves the way for better utilization/ stabilization of rice bran. Rice (Oryza sativa) is one of the major staple foods for almost half the world’s population, especially in Asia 1. -
An ER Stress/Defective Unfolded Protein Response Model Richard T
ORIGINAL RESEARCH Ethanol Induced Disordering of Pancreatic Acinar Cell Endoplasmic Reticulum: An ER Stress/Defective Unfolded Protein Response Model Richard T. Waldron,1,2 Hsin-Yuan Su,1 Honit Piplani,1 Joseph Capri,3 Whitaker Cohn,3 Julian P. Whitelegge,3 Kym F. Faull,3 Sugunadevi Sakkiah,1 Ravinder Abrol,1 Wei Yang,1 Bo Zhou,1 Michael R. Freeman,1,2 Stephen J. Pandol,1,2 and Aurelia Lugea1,2 1Department of Medicine, Cedars Sinai Medical Center, Los Angeles, California; 2Department of Medicine, or 3Psychiatry and Biobehavioral Sciences, University of California Los Angeles David Geffen School of Medicine, Los Angeles, California Pancreatic acinar cells Pancreatic acinar cells - no pathology - - Pathology - Ethanol feeding ER sXBP1 Pdi, Grp78… (adaptive UPR) aggregates Proper folding and secretion • disordered ER of proteins processed in the • impaired redox folding endoplasmic reticulum (ER) • ER protein aggregation • secretory defects SUMMARY METHODS: Wild-type and Xbp1þ/- mice were fed control and ethanol diets, then tissues were homogenized and fraction- Heavy alcohol consumption is associated with pancreas ated. ER proteins were labeled with a cysteine-reactive probe, damage, but light drinking shows the opposite effects, isotope-coded affinity tag to obtain a novel pancreatic redox ER reinforcing proteostasis through the unfolded protein proteome. Specific labeling of active serine hydrolases in ER with response orchestrated by X-box binding protein 1. Here, fluorophosphonate desthiobiotin also was characterized pro- ethanol-induced changes in endoplasmic reticulum protein teomically. Protein structural perturbation by redox changes redox and structure/function emerge from an unfolded was evaluated further in molecular dynamic simulations. protein response–deficient genetic model. -
Catalysis by Acetylcholinesterase
Proc. Nat. Acad. Sci. USA Vol. 72, No. 10, pp. 3834-38, October 1975 Biochemistry Catalysis by acetylcholinesterase: Evidence that the rate-limiting step for acylation with certain substrates precedes general acid-base catalysis (enzyme mechanism/diffusion control/induced-fit conformational change/pH dependence/deuterium oxide isotope effects) TERRONE L. ROSENBERRY Departments of Biochemistry and Neurology, College of Physicians and Surgeons, Columbia University, New York, N.Y. 10032 Communicated by David Nachmansohn, June 9,1975 ABSTRACT Inferences about the catalytic mechanism of The proposed intermediates include the initial Michaelis acetylcholinesterase (acetyicholine hydrolase, EC 3.1.1.7) are complex E-RX and the acyl enzyme ER, for which evidence frequently made on the basis of a presumed analogy with has long been obtained (5, 6, 1). The pH dependence of sub- chymotrypsin, EC 3.4.21.1. Although both enzymes are serine hydrolases, several differences in the steady-state kinetic strate hydrolysis for chymotrypsin and other serine hydro- properties of the two have been observed. In this report par- lases suggests general acid-base catalysis by a group in the ticujar attention is focused on the second-order reaction con- free enzyme with a pKai of 6 to 7. Furthermore, Hammett stant, kcat/KapD While the reported pH dependence and deu- relationships with positive rho values are found with chymo- terium oxide isotope effect associated with this parameter trypsin both for deacylation (7) and acylation (8) reactions for chymotrypsin are generally consistent with simple mod- and indicate rate-limiting general base catalysis. Deacyla- els involving rate-limiting general acid-base catalysis, this study finds a more complicated situation with acetylcholi- tion rates are typically reduced in deuterium oxide by fac- nesterase. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
HMGB1 in Health and Disease R
Donald and Barbara Zucker School of Medicine Journal Articles Academic Works 2014 HMGB1 in health and disease R. Kang R. C. Chen Q. H. Zhang W. Hou S. Wu See next page for additional authors Follow this and additional works at: https://academicworks.medicine.hofstra.edu/articles Part of the Emergency Medicine Commons Recommended Citation Kang R, Chen R, Zhang Q, Hou W, Wu S, Fan X, Yan Z, Sun X, Wang H, Tang D, . HMGB1 in health and disease. 2014 Jan 01; 40():Article 533 [ p.]. Available from: https://academicworks.medicine.hofstra.edu/articles/533. Free full text article. This Article is brought to you for free and open access by Donald and Barbara Zucker School of Medicine Academic Works. It has been accepted for inclusion in Journal Articles by an authorized administrator of Donald and Barbara Zucker School of Medicine Academic Works. Authors R. Kang, R. C. Chen, Q. H. Zhang, W. Hou, S. Wu, X. G. Fan, Z. W. Yan, X. F. Sun, H. C. Wang, D. L. Tang, and +8 additional authors This article is available at Donald and Barbara Zucker School of Medicine Academic Works: https://academicworks.medicine.hofstra.edu/articles/533 NIH Public Access Author Manuscript Mol Aspects Med. Author manuscript; available in PMC 2015 December 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Aspects Med. 2014 December ; 0: 1–116. doi:10.1016/j.mam.2014.05.001. HMGB1 in Health and Disease Rui Kang1,*, Ruochan Chen1, Qiuhong Zhang1, Wen Hou1, Sha Wu1, Lizhi Cao2, Jin Huang3, Yan Yu2, Xue-gong Fan4, Zhengwen Yan1,5, Xiaofang Sun6, Haichao Wang7, Qingde Wang1, Allan Tsung1, Timothy R. -
The Role of Caspase-2 in Regulating Cell Fate
cells Review The Role of Caspase-2 in Regulating Cell Fate Vasanthy Vigneswara and Zubair Ahmed * Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; [email protected] * Correspondence: [email protected] Received: 15 April 2020; Accepted: 12 May 2020; Published: 19 May 2020 Abstract: Caspase-2 is the most evolutionarily conserved member of the mammalian caspase family and has been implicated in both apoptotic and non-apoptotic signaling pathways, including tumor suppression, cell cycle regulation, and DNA repair. A myriad of signaling molecules is associated with the tight regulation of caspase-2 to mediate multiple cellular processes far beyond apoptotic cell death. This review provides a comprehensive overview of the literature pertaining to possible sophisticated molecular mechanisms underlying the multifaceted process of caspase-2 activation and to highlight its interplay between factors that promote or suppress apoptosis in a complicated regulatory network that determines the fate of a cell from its birth and throughout its life. Keywords: caspase-2; procaspase; apoptosis; splice variants; activation; intrinsic; extrinsic; neurons 1. Introduction Apoptosis, or programmed cell death (PCD), plays a pivotal role during embryonic development through to adulthood in multi-cellular organisms to eliminate excessive and potentially compromised cells under physiological conditions to maintain cellular homeostasis [1]. However, dysregulation of the apoptotic signaling pathway is implicated in a variety of pathological conditions. For example, excessive apoptosis can lead to neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease, whilst insufficient apoptosis results in cancer and autoimmune disorders [2,3]. Apoptosis is mediated by two well-known classical signaling pathways, namely the extrinsic or death receptor-dependent pathway and the intrinsic or mitochondria-dependent pathway. -
Caspase-7 Expanded Function and Intrinsic Expression Level Underlies Strain-Specific Brain Phenotype of Caspase-3-Null Mice
The Journal of Neuroscience, November 3, 2004 • 24(44):9977–9984 • 9977 Development/Plasticity/Repair Caspase-7 Expanded Function and Intrinsic Expression Level Underlies Strain-Specific Brain Phenotype of Caspase-3-Null Mice Caroline Houde,1 Kathleen G. Banks,2 Nathalie Coulombe,3 Dita Rasper,3 Erich Grimm,3 Sophie Roy,1,4 Elizabeth M. Simpson,2 and Donald W. Nicholson1,4 1Biochemistry Department, McGill University, Montreal, Quebec H3G 1Y6, Canada, 2Centre for Molecular Medicine and Therapeutics, British Columbia Institute for Children’s and Women’s Health, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada, 3Merck Frosst Canada and Company, Pointe-Claire–Dorval, Quebec H9R 4P8, Canada, and 4Merck Research Laboratories, San Diego, California 92121 Caspase-3-deficient mice of the 129S1/SvImJ (129) strain show severe brain development defects resulting in brain overgrowth and perinatal lethality, whereas on the C57BL/6J (B6) background, these mice develop normally. We therefore sought to identify the strain- Ϫ Ϫ dependent ameliorating gene. We biochemically isolated caspase-7 from B6-caspase-3-null (Casp3 / ) tissues as being the enzyme with caspase-3-like properties and capability of performing a caspase-3 surrogate function, apoptotic DNA fragmentation. Moreover, we show that, in contrast to the human enzymes, mouse caspase-7 is as efficient as caspase-3 at cleaving and thus inactivating ICAD (inhibitor of caspase-activated DNase), the inhibitor of apoptotic DNA fragmentation. Low levels of caspase-7 expression and activation correlate with Ϫ Ϫ Ϫ Ϫ lack of DNA fragmentation in 129-Casp3 / apoptotic precursor neurons, whereas B6-Casp3 / cells, which can fragment their DNA, show higher levels of caspase-7 expression and activation. -
The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z
REVIEW pubs.acs.org/CR The Metabolic Serine Hydrolases and Their Functions in Mammalian Physiology and Disease Jonathan Z. Long* and Benjamin F. Cravatt* The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States CONTENTS 2.4. Other Phospholipases 6034 1. Introduction 6023 2.4.1. LIPG (Endothelial Lipase) 6034 2. Small-Molecule Hydrolases 6023 2.4.2. PLA1A (Phosphatidylserine-Specific 2.1. Intracellular Neutral Lipases 6023 PLA1) 6035 2.1.1. LIPE (Hormone-Sensitive Lipase) 6024 2.4.3. LIPH and LIPI (Phosphatidic Acid-Specific 2.1.2. PNPLA2 (Adipose Triglyceride Lipase) 6024 PLA1R and β) 6035 2.1.3. MGLL (Monoacylglycerol Lipase) 6025 2.4.4. PLB1 (Phospholipase B) 6035 2.1.4. DAGLA and DAGLB (Diacylglycerol Lipase 2.4.5. DDHD1 and DDHD2 (DDHD Domain R and β) 6026 Containing 1 and 2) 6035 2.1.5. CES3 (Carboxylesterase 3) 6026 2.4.6. ABHD4 (Alpha/Beta Hydrolase Domain 2.1.6. AADACL1 (Arylacetamide Deacetylase-like 1) 6026 Containing 4) 6036 2.1.7. ABHD6 (Alpha/Beta Hydrolase Domain 2.5. Small-Molecule Amidases 6036 Containing 6) 6027 2.5.1. FAAH and FAAH2 (Fatty Acid Amide 2.1.8. ABHD12 (Alpha/Beta Hydrolase Domain Hydrolase and FAAH2) 6036 Containing 12) 6027 2.5.2. AFMID (Arylformamidase) 6037 2.2. Extracellular Neutral Lipases 6027 2.6. Acyl-CoA Hydrolases 6037 2.2.1. PNLIP (Pancreatic Lipase) 6028 2.6.1. FASN (Fatty Acid Synthase) 6037 2.2.2. PNLIPRP1 and PNLIPR2 (Pancreatic 2.6.2. -
Caspase-6 Induces 7A6 Antigen Localization to Mitochondria During FAS-Induced Apoptosis of Jurkat Cells HIROAKI SUITA, TAKAHISA SHINOMIYA and YUKITOSHI NAGAHARA
ANTICANCER RESEARCH 37 : 1697-1704 (2017) doi:10.21873/anticanres.11501 Caspase-6 Induces 7A6 Antigen Localization to Mitochondria During FAS-induced Apoptosis of Jurkat Cells HIROAKI SUITA, TAKAHISA SHINOMIYA and YUKITOSHI NAGAHARA Division of Life Science and Engineering, School of Science and Engineering, Tokyo Denki University, Hatoyama, Japan Abstract. Background: Mitochondria are central to caspases (caspase-8 and -9) that activate effector caspases (1). apoptosis. However, apoptosis progression involving Caspases are constructed of a pro-domain, a large subunit, and mitochondria is not fully understood. A factor involved in a small subunit. Upon caspase activation, cleavage of the mitochondria-mediated apoptosis is 7A6 antigen. 7A6 caspase occurs. Caspase-6 and -7, which are effector caspases, localizes to mitochondria from the cytosol during apoptosis, each have a large subunit that is 20 kDa (p20) and a small which seems to involve ‘effector’ caspases. In this study, we subunit that is 10 kDa (p10), but caspase-3, which is also an investigated the precise role of effector caspases in 7A6 effector caspase, has a large subunit of 17 kDa and a small localization to mitochondria during apoptosis. Materials and subunit of 12 kDa (p12) (2-4). Moreover, the large and small Methods: Human T-cell lymphoma Jurkat cells were treated subunits of caspase-6 and -7 are connected by a linker, but with an antibody against FAS. 7A6 localization was analyzed caspase-3 does not have a linker (Figure 1). The difference by confocal laser scanning microscopy and flow cytometry. between effector and initiator caspases is that the pro-domain Caspases activation was determined by western blot of an initiator caspase is long and that the pro-domain of an analysis. -
Executioner Caspase-3 and Caspase-7 Are Functionally Distinct Proteases
Executioner caspase-3 and caspase-7 are functionally distinct proteases John G. Walsh, Sean P. Cullen, Clare Sheridan, Alexander U. Luthi,¨ Christopher Gerner*, and Seamus J. Martin† Molecular Cell Biology Laboratory, Department of Genetics, The Smurfit Institute, Trinity College, Dublin 2, Ireland Edited by Doug R. Green, St. Jude Children’s Research Hospital, Memphis, TN, and accepted by the Editorial Board July 8, 2008 (received for review August 15, 2007) Members of the caspase family of cysteine proteases play central CASP-3 and CASP-7 on the B6 background die immediately roles in coordinating the stereotypical events that occur during after birth because of defective heart development (9). The latter apoptosis. Because the major executioner caspases, caspase-3 and result suggests that there may be a degree of functional com- caspase-7, exhibit almost indistinguishable activity toward certain pensation in operation between caspase-3 and caspase-7, synthetic peptide substrates, this has led to the widespread view whereas the knockout phenotypes observed on the 129 back- that these proteases occupy functionally redundant roles within ground suggest that caspase-3 and caspase-7 serve distinct roles. the cell death machinery. However, the distinct phenotypes of mice However, a major problem in interpreting these data is that the deficient in either of these caspases, as well as mice deficient in relative expression levels of caspase-3 and caspase-7 may vary both, is at odds with this view. These distinct phenotypes could be dramatically between mouse strains, as well as within particular related to differences in the relative expression levels of caspase-3 tissues. -
Serine Hydrolases Involved in Lipid Metabolism in P
Article The Antimalarial Natural Product Salinipostin A Identifies Essential a/b Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites Graphical Abstract Authors Euna Yoo, Christopher J. Schulze, Barbara H. Stokes, ..., Eranthie Weerapana, David A. Fidock, Matthew Bogyo Correspondence [email protected] In Brief Using a probe analog of the antimalarial natural product Sal A, Yoo et al. identify its targets as multiple essential serine hydrolases, including a homolog of human monoacylglycerol lipase. Because parasites were unable to generate robust in vitro resistance to Sal A, these enzymes represent promising targets for antimalarial drugs. Highlights d Semi-synthesis of an affinity analog of the antimalarial natural product Sal A d Identification of serine hydrolases as the primary targets of Sal A in P. falciparum d Sal A covalently binds to and inhibits a MAGL-like protein in P. falciparum d Parasites are unable to generate strong in vitro resistance to Sal A Yoo et al., 2020, Cell Chemical Biology 27, 143–157 February 20, 2020 ª 2020 Elsevier Ltd. https://doi.org/10.1016/j.chembiol.2020.01.001 Cell Chemical Biology Article The Antimalarial Natural Product Salinipostin A Identifies Essential a/b Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites Euna Yoo,1,11 Christopher J. Schulze,1,11 Barbara H. Stokes,2 Ouma Onguka,1 Tomas Yeo,2 Sachel Mok,2 Nina F. Gnadig,€ 2 Yani Zhou,3 Kenji Kurita,4 Ian T. Foe,1 Stephanie M. Terrell,1,5 Michael J. Boucher,6,7 Piotr Cieplak,8 Krittikorn Kumpornsin,9 Marcus C.S. Lee,9 Roger G. -
Contribution of Calpain and Caspases to Cell Death in Cultured Monkey RPE Cells
Biochemistry and Molecular Biology Contribution of Calpain and Caspases to Cell Death in Cultured Monkey RPE Cells Emi Nakajima,1,2 Katherine B. Hammond,1,2 Masayuki Hirata,1,2 Thomas R. Shearer,2 and Mitsuyoshi Azuma1,2 1Senju Laboratory of Ocular Sciences, Senju Pharmaceutical Corporation Limited, Portland, Oregon, United States 2Department of Integrative Biosciences, Oregon Health & Science University, Portland, Oregon, United States Correspondence: Mitsuyoshi Azuma, PURPOSE. AMD is the leading cause of human vision loss after 65 years of age. Several Senju Pharmaceutical Corporation mechanisms have been proposed: (1) age-related failure of the choroidal vasculature leads to Limited, 4640 SW Macadam Avenue, loss of RPE; (2) RPE dysfunctions due to accumulation of phagocytized, but unreleased A2E Suite 200C, Portland, OR 97239, (N-retinylidene-N-retinylethanolamine); (3) zinc deficiency activation of calpain and caspase USA; proteases, leading to cell death. The purpose of the present study is to compare activation of [email protected]. calpain and caspase in monkey RPE cells cultured under hypoxia or with A2E. Submitted: June 1, 2017 Accepted: September 19, 2017 METHODS. Monkey primary RPE cells were cultured under hypoxic conditions in a Gaspak pouch or cultured with synthetic A2E. Immunoblotting was used to detect activation of Citation: Nakajima E, Hammond KB, calpain and caspase. Calpain inhibitor, SNJ-1945, and pan-caspase inhibitor, z-VAD-fmk, were Hirata M, Shearer TR, Azuma M. Contribution of calpain and caspases used to confirm activation of the proteases. to cell death in cultured monkey RPE RESULTS. (1) Hypoxia and A2E each decreased viability of RPE cells in a time-dependent cells.