Modifications in Phospholipase D Activity and Isoform Expression
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Ribonuclease A: Disulfide Bonds, Conformational Stability, and Cytotoxicity
Ribonuclease A: Disulfide Bonds, Conformational Stability, and Cytotoxicity by Tony A. Klink A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biochemistry) at the UNIVERSITY OF WISCONSIN-MADISON 2()()() r OJ A dissertation entitled Ribonuclease A: Disulfide Bonds, Conformational Stability and Cytotoxicity submitted to the Graduate School of the University of Wisconsin-Madison in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Tony Anthony Klink Date of Final Oral Examination: August 4, 2000 Month & Year Degree to be awarded: December May August 2000 • * * * * * * • * * • * • • • • • * • • • * • • • • • • • • • • • • • * * • * • * * * • * • * • • • • • • * App oval Signature. f Dissertation Readers: Signature, Dean of Graduate School ---..., v.C~vJ,1A. 5. lJ,~k;at 1 Abstract Disulfide bonds between the side chains of cysteine residues are the only common cross links in proteins. Bovine pancreatic ribonuclease A (RNase A) is a 124-residue enzyme that contains four interweaving disulfide bonds (Cys26-Cys84, Cys40-Cys95, Cys58-CysllO, and Cys65-Cys72) and catalyzes the cleavage of RNA. The contribution of each disulfide bond to the confonnational stability and catalytic activity of RNase A was detennined using variants in which each cystine was replaced independently with a pair of alanine residues. Of the four disulfide bonds, the Cys40-Cys95 and Cys65-Cys72 cross-links are the least important to confonnational stability. Removing these disulfide bonds leads to RNase A variants that have Tm values below that of the wild-type enzyme but above physiological temperature. Unlike wild-type RNase A. G88R RNase A is toxic to cancer cells. To investigate the relationship between conformational stability and cytotoxicity, the C40AlC95A and C65A1C72A variants were made in the G88R background. -
Supplemental Figure 1. Vimentin
Double mutant specific genes Transcript gene_assignment Gene Symbol RefSeq FDR Fold- FDR Fold- FDR Fold- ID (single vs. Change (double Change (double Change wt) (single vs. wt) (double vs. single) (double vs. wt) vs. wt) vs. single) 10485013 BC085239 // 1110051M20Rik // RIKEN cDNA 1110051M20 gene // 2 E1 // 228356 /// NM 1110051M20Ri BC085239 0.164013 -1.38517 0.0345128 -2.24228 0.154535 -1.61877 k 10358717 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 /// BC 1700025G04Rik NM_197990 0.142593 -1.37878 0.0212926 -3.13385 0.093068 -2.27291 10358713 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 1700025G04Rik NM_197990 0.0655213 -1.71563 0.0222468 -2.32498 0.166843 -1.35517 10481312 NM_027283 // 1700026L06Rik // RIKEN cDNA 1700026L06 gene // 2 A3 // 69987 /// EN 1700026L06Rik NM_027283 0.0503754 -1.46385 0.0140999 -2.19537 0.0825609 -1.49972 10351465 BC150846 // 1700084C01Rik // RIKEN cDNA 1700084C01 gene // 1 H3 // 78465 /// NM_ 1700084C01Rik BC150846 0.107391 -1.5916 0.0385418 -2.05801 0.295457 -1.29305 10569654 AK007416 // 1810010D01Rik // RIKEN cDNA 1810010D01 gene // 7 F5 // 381935 /// XR 1810010D01Rik AK007416 0.145576 1.69432 0.0476957 2.51662 0.288571 1.48533 10508883 NM_001083916 // 1810019J16Rik // RIKEN cDNA 1810019J16 gene // 4 D2.3 // 69073 / 1810019J16Rik NM_001083916 0.0533206 1.57139 0.0145433 2.56417 0.0836674 1.63179 10585282 ENSMUST00000050829 // 2010007H06Rik // RIKEN cDNA 2010007H06 gene // --- // 6984 2010007H06Rik ENSMUST00000050829 0.129914 -1.71998 0.0434862 -2.51672 -
Novel Allosteric Modulators of the M1 Muscarinic Acetylcholine Receptor Provide New Insights Into M1-Dependent Synaptic Plasticity and Receptor Signaling
Novel allosteric modulators of the M1 muscarinic acetylcholine receptor provide new insights into M1-dependent synaptic plasticity and receptor signaling By Sean P Moran Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Neuroscience December 14, 2019 Nashville, Tennessee Approved: Sachin Patel M.D., Ph.D. Colleen Niswender, Ph.D. Danny Winder, Ph.D. P. Jeffrey Conn, Ph.D. ACKNOWLEDGMENTS Throughout my scientific career, there have been many people instrumental in my scientific journey. I would first like to thank Jeff Conn for providing a very supportive research atmosphere, for always making me laugh, for his insight and constructive criticism in our one-on-one meetings and for occasionally getting my name correct. I would also like to thank my thesis committee of Sachin Patel, Colleen Niswender and Danny Winder for their unwavering support during my time here at Vanderbilt. Additionally, I have very much enjoyed collaborating with Jerri Rook on many projects and would like to thank her for her sage behavioral pharmacology advice over the years. Also, thanks to the many members of the VCNDD including: Zixiu, Craig, Jon Dickerson, Dan Foster, Max, Nicole, Mark and Carrie who provided intellectual contributions, technical training or research support throughout my graduate career. Thank you to the many other members of the VCNDD, past and present, that have contributed to my various projects over the years. Thanks to the better half of Shames (James). I will our miss our long winded, highly pedantic and semantic discussions that occasionally touched on pharmacology topics…and thanks for making me not homeless. -
Determination of Pk, Values of the Histidine Side
Protein Science (1997), 6:1937-1944. Cambridge University Press. Printed in the USA Copyright 0 1997 The Protein Society Determination of pK, values of the histidine side chains of phosphatidylinositol-specific phospholipase C from Bacillus cereus by NMR spectroscopy and site-directed mutagenesis TUN LIU, MARGRET RYAN, FREDERICK W. DAHLQUIST, AND 0. HAYES GRIFFITH Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, Oregon 97403 (RECEIVEDDecember 4, 1996: ACCEPTEDMay 19, 1997) Abstract Two active site histidine residues have been implicated in the catalysis of phosphatidylinositol-specific phospholipase C (PI-PLC). In this report, we present the first study of the pK,, values of histidines of a PI-PLC. All six histidines of Bacillus cereus PI-PLC were studied by 2D NMR spectroscopy and site-directed mutagenesis. The protein was selec- tively labeled with '3C"-histidine. A series of 'H-I3C HSQC NMR spectra were acquired over a pH range of 4.0-9.0. Five of the six histidines have been individually substituted with alanine to aid the resonance assignments in the NMR spectra. Overall, the remaining histidines in the mutants show little chemical shift changes in the 'H-"C HSQC spectra, indicating that the alanine substitution has no effect on the tertiary structure of the protein. H32A and H82A mutants are inactive enzymes, while H92A and H61A are fully active, and H81A retains about 15% of the wild-type activity. The active site histidines, His32 and His82, display pK,, values of 7.6 and 6.9, respectively. His92 and His227 exhibit pK, values of 5.4 and 6.9. -
Families and the Structural Relatedness Among Globular Proteins
Protein Science (1993), 2, 884-899. Cambridge University Press. Printed in the USA. Copyright 0 1993 The Protein Society -~~ ~~~~ ~ Families and the structural relatedness among globular proteins DAVID P. YEE AND KEN A. DILL Department of Pharmaceutical Chemistry, University of California, San Francisco, California94143-1204 (RECEIVEDJanuary 6, 1993; REVISEDMANUSCRIPT RECEIVED February 18, 1993) Abstract Protein structures come in families. Are families “closely knit” or “loosely knit” entities? We describe a mea- sure of relatedness among polymer conformations. Based on weighted distance maps, this measure differs from existing measures mainly in two respects: (1) it is computationally fast, and (2) it can compare any two proteins, regardless of their relative chain lengths or degree of similarity. It does not require finding relative alignments. The measure is used here to determine the dissimilarities between all 12,403 possible pairs of 158 diverse protein structures from the Brookhaven Protein Data Bank (PDB). Combined with minimal spanning trees and hier- archical clustering methods,this measure is used to define structural families. It is also useful for rapidly searching a dataset of protein structures for specific substructural motifs.By using an analogy to distributions of Euclid- ean distances, we find that protein families are not tightly knit entities. Keywords: protein family; relatedness; structural comparison; substructure searches Pioneering work over the past 20 years has shown that positions after superposition. RMS is a useful distance proteins fall into families of related structures (Levitt & metric for comparingstructures that arenearly identical: Chothia, 1976; Richardson, 1981; Richardson & Richard- for example, when refining or comparing structures ob- son, 1989; Chothia & Finkelstein, 1990). -
Role of Phospholipases in Adrenal Steroidogenesis
229 1 W B BOLLAG Phospholipases in adrenal 229:1 R29–R41 Review steroidogenesis Role of phospholipases in adrenal steroidogenesis Wendy B Bollag Correspondence should be addressed Charlie Norwood VA Medical Center, One Freedom Way, Augusta, GA, USA to W B Bollag Department of Physiology, Medical College of Georgia, Augusta University (formerly Georgia Regents Email University), Augusta, GA, USA [email protected] Abstract Phospholipases are lipid-metabolizing enzymes that hydrolyze phospholipids. In some Key Words cases, their activity results in remodeling of lipids and/or allows the synthesis of other f adrenal cortex lipids. In other cases, however, and of interest to the topic of adrenal steroidogenesis, f angiotensin phospholipases produce second messengers that modify the function of a cell. In this f intracellular signaling review, the enzymatic reactions, products, and effectors of three phospholipases, f phospholipids phospholipase C, phospholipase D, and phospholipase A2, are discussed. Although f signal transduction much data have been obtained concerning the role of phospholipases C and D in regulating adrenal steroid hormone production, there are still many gaps in our knowledge. Furthermore, little is known about the involvement of phospholipase A2, Endocrinology perhaps, in part, because this enzyme comprises a large family of related enzymes of that are differentially regulated and with different functions. This review presents the evidence supporting the role of each of these phospholipases in steroidogenesis in the Journal Journal of Endocrinology adrenal cortex. (2016) 229, R1–R13 Introduction associated GTP-binding protein exchanges a bound GDP for a GTP. The G protein with GTP bound can then Phospholipids serve a structural function in the cell in that activate the enzyme, phospholipase C (PLC), that cleaves they form the lipid bilayer that maintains cell integrity. -
Structures, Functions, and Mechanisms of Filament Forming Enzymes: a Renaissance of Enzyme Filamentation
Structures, Functions, and Mechanisms of Filament Forming Enzymes: A Renaissance of Enzyme Filamentation A Review By Chad K. Park & Nancy C. Horton Department of Molecular and Cellular Biology University of Arizona Tucson, AZ 85721 N. C. Horton ([email protected], ORCID: 0000-0003-2710-8284) C. K. Park ([email protected], ORCID: 0000-0003-1089-9091) Keywords: Enzyme, Regulation, DNA binding, Nuclease, Run-On Oligomerization, self-association 1 Abstract Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI system are also highlighted. 2 Contents INTRODUCTION…………………………………………………………..4 STRUCTURALLY CHARACTERIZED ENZYME FILAMENTS…….5 Acetyl CoA Carboxylase (ACC)……………………………………………………………………5 Phosphofructokinase (PFK)……………………………………………………………………….6 -
Purification and Characterization of Cutinase from Venturia Inaequalis
Physiology and Biochemistry Purification and Characterization of Cutinase from Venturia inaequalis Wolfram K611er and Diana M. Parker Assistant professor and research assistant, Department of Plant Pathology, Cornell University, New York State Agricultural Experiment Station, Geneva 14456. We thank Professor A. L. Jones for the isolates of Venturia inaequalis, Mr. Robert W. Ennis, Jr. for his help in cutin preparation, and Comstock Foods, Alton, NY, for the apple peels. Accepted for publication 16 August 1988. ABSTRACT K61ler, W., and Parker, D. M. 1989. Purification and characterization of cutinase from Venturia inaequalis. Phytopathology 79:278-283. Venturia inaequalis was grown in a culture medium containing purified cutinase from V. inaequalisis optimal at a pH of 6 and thus different from apple cutin as the sole carbon source. After 8 wk of growth an esterase was the alkaline pH-optimum reported for other purified cutinases. The isolated from the culture fluid and purified to apparent homogeneity. The hydrolysis of the model esterp-nitrophenyl butyrate was less affected by the enzyme hydrolyzed tritiated cutin and thus was identified as cutinase. The pH. The esterase activity was strongly inhibited by diisopropyl purified cutinase is a glycoprotein with a molecular mass of 21-23 kg/ mol, fluorophosphate, and the phosphorylation of one serine was sufficient for as determined by various procedures. Remarkable structural features are a complete inhibition. Thus, cutinase from V. inaequalis belongs to the class high content of glycine, a high content of nonpolar amino acids, two of serine hydrolases, a characterisitic shared with other fungal cutinases. disulfide bridges, and a high degree of hydrophobicity. -
Ribonuclease A: Exploring the Function of the Active-Site Lysine
Ribonuclease A: Exploring the Function of the Active-Site Lysine Residue in Catalysis and Inhibition By June M. Messmore A dissertation submitted in partial fulfillment of the degree of Doctor of Philosophy (Biochemistry) UNIVERSITY OF WISCONSIN-MADISON 1999 A dissertation entitled Ribonuclease A: Exploring the Function of the Active-Site Lysine Residue in Catalysis and Inhibition submitted to the Graduate School of the University of Wisconsin-Madison Jp'part.i~l f~lfillment of ~~ereq~ire~~nt$ for the degree of Doctor·of Philosophy by June M. Messmore Degree to be awarded: December 19_ May 19_ August 19~ th May 28 , 1999 Date of Examination . ~ r:i~ b lli{\~~ Dean. Graduate School 1 Ribonuclease A: Exploring the Function of an Active-Site Lysine in Catalysis and Inhibition June M. Messmore Under the supervision of Professor Ronald T. Raines at the University of Wisconsin-Madison ABSTRACT Structural analyses had suggested that the active-site lysine residue of RNase A (Lys41) may interact preferentially with the transition state for covalent bond cleavage, thus facilitating catalysis. Site-directed mutagenesis and chemical modification were combined (1) to probe the role of Lys41 in catalysis, (2) to provide a chemical on/off switch for RNase A activity in in vitro applications, and (3) to probe the analogy ofuridine 2',3'-cyclic vanadate to the catalytic transition state. In addition to studying inhibition by the uridine vanadate, inhibition by a polyvanadate species was also characterized. Results indicate the importance of positive charge and the donation of a single hydrogen bond in catalysis. Chemical modification can reversibly modulate the activity of ribonuclease by a factor of 30,000. -
Hypoxic Regulation of the 6-Phosphofructo-2-Kinase/Fructose
FEBS Letters 554 (2003) 264^270 FEBS 27797 CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier -Hypoxic Publisher Connector regulation of the 6-phosphofructo-2-kinase/fructose-2,6- bisphosphatase gene family (PFKFB-1^4) expression in vivo Oleksandr Minchenkoa;b, Iryna Opentanovaa, Jaime Carob;Ã aDepartment of Molecular Biology, Institute of Biochemistry, National Academy of Science of Ukraine, Kyiv 01601, Ukraine bCardeza Foundation for Hematologic Research, Department of Medicine, Je¡erson Medical College of Thomas Je¡erson University, Curtis Bldg. 810, 1015 Walnut Street, Philadelphia, PA 19107, USA Received 12 May 2003; revised 10 September 2003; accepted 6 October 2003 First published online 21October 2003 Edited by Vladimir Skulachev 1. Introduction Abstract When oxygen becomes limiting, cells shift primarily to a glycolytic mode for generation of energy. A key regulator of glycolytic £ux is fructose-2,6-bisphosphate (F-2,6-BP), a po- The ability to respond to hypoxia is an essential evolution- tent allosteric regulator of 6-phosphofructo-1-kinase (PFK-1). ary adaptation in higher vertebrates. Hypoxia could be caused The levels of F-2,6-BP are maintained by a family of bifunc- by a generalized reduction in oxygen delivery, such as in alti- tional enzymes, 6-phosphofructo-2-kinase/fructose-2,6-bisphos- tude and pulmonary diseases, or by disruption in the local phatase (PFKFBor PFK-2), which have both kinase and phos- blood supply, such as in ischemic disorders. Important in phatase activities. Each member of the enzyme family is the adaptations to hypoxia is the activation of genes that characterized by their phosphatase:kinase activity ratio (K:B) ameliorate or compensate for the oxygen de¢cit. -
1H HR-MAS and Genomic Analysis of Human Tumor Biopsies Discriminate Between High and Low Grade Astrocytomas Valeria Righi A,B,C, Jose M
Research Article Received: 16 April 2008, Revised: 22 January 2009, Accepted: 22 January 2009, Published online in Wiley InterScience: 2009 (www.interscience.wiley.com) DOI:10.1002/nbm.1377 1H HR-MAS and genomic analysis of human tumor biopsies discriminate between high and low grade astrocytomas Valeria Righi a,b,c, Jose M. Rodad, Jose´ Pazd, Adele Muccib, Vitaliano Tugnolic, Gemma Rodriguez-Tarduchya, Laura Barriose, Luisa Schenettib, Sebastia´n Cerda´na* and Marı´a L. Garcı´a-Martı´na,y We investigate the profile of choline metabolites and the expression of the genes of the Kennedy pathway in biopsies of human gliomas (n ¼ 23) using 1H High Resolution Magic Angle Spinning (HR-MAS, 11.7 Tesla, 277 K, 4000 Hz) and individual genetic assays. 1H HR-MAS spectra allowed the resolution and relative quantification by the LCModel of the resonances from choline (Cho), phosphocholine (PC) and glycerophosphorylcholine (GPC), the three main components of the combined tCho peak observed in gliomas by in vivo 1H NMR spectroscopy. All glioma biopsies depicted a prominent tCho peak. However, the relative contributions of Cho, PC, and GPC to tCho were different for low and high grade gliomas. Whereas GPC is the main component in low grade gliomas, the high grade gliomas show a dominant contribution of PC. This circumstance allowed the discrimination of high and low grade gliomas by 1H HR-MAS, a result that could not be obtained using the tCho/Cr ratio commonly used by in vivo 1H NMR spectroscopy. The expression of the genes involved in choline metabolism has been investigated in the same biopsies. -
Cyclic Phosphatidic Acid: an Endogenous Antagonist of Pparγ
Central Journal of Endocrinology, Diabetes & Obesity Editorial Corresponding author Tamotsu Tsukahara, Department of Hematology and Immunology, Kanazawa Medical University, 1-1 Cyclic Phosphatidic Acid: An Daigaku, Uchinada, Ishikawa 920-0293, Japan, E-mail: [email protected] Submitted: 25 August 2013 Endogenous Antagonist of Accepted: 26 August 2013 Published: 29 August 2013 PPARg Copyright © 2013 Tsukahara et al. Tamotsu Tsukahara1*, Yoshikazu Matsuda2, Hisao Haniu3 and Kimiko Murakami- Murofushi4 OPEN ACCESS 1Department of Hematology and Immunology, Kanazawa Medical University, Japan 2Clinical Pharmacology Educational Center, Nihon Pharmaceutical University, Japan 3Department of Orthopaedic Surgery, Shinshu University School of Medicine, Japan 4Endowed Research Division of Human Welfare Sciences, Ochanomizu University, Japan Lysophospholipids (LPLs) have long been recognized as phosphatidylcholine (PC) to generate choline and bioactive membrane phospholipid metabolites. LPLs are small bioactive lipid, has been implicated in signal transduction, membrane lipid molecules that are characterized by a single carbon 10]. There are two chain and a polar head group. LPLs have been implicated in a PLD isoenzymes, PLD1 and PLD2, which are expressed in a number of pathological states and human diseases. LPLs include varietytrafficking, of tissues and cytoskeletal and cells [ 11reorganization]. We labeled [ cultured cells with lysophosphatidic acid (LPA), alkyl-glycerol phosphate (AGP), [32P]-orthophosphate for 30 min and compared that to [32P]- sphingoshine-1-phosphate, and cyclic phosphatidic acid (cPA). labeled cPA from vehicle control cells using two-dimensional thin In recent years, cPA has been reported to be a target for many layer chromatography. Furthermore, we used CHO cells stably diseases, including obesity [1], atherosclerosis [2], cancer [3], expressing PLD1 or PLD2 or catalytically inactive forms of PLD1 and pain [4].