Purification and Characterization of Cutinase from Venturia Inaequalis
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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. -
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). -
Kramers' Theory and the Dependence of Enzyme Dynamics on Trehalose
catalysts Review Kramers’ Theory and the Dependence of Enzyme Dynamics on Trehalose-Mediated Viscosity José G. Sampedro 1,* , Miguel A. Rivera-Moran 1 and Salvador Uribe-Carvajal 2 1 Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí C.P. 78290, Mexico; [email protected] 2 Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México C.P. 04510, Mexico; [email protected] * Correspondence: [email protected]fisica.uaslp.mx; Tel.: +52-(444)-8262-3200 (ext. 5715) Received: 29 April 2020; Accepted: 29 May 2020; Published: 11 June 2020 Abstract: The disaccharide trehalose is accumulated in the cytoplasm of some organisms in response to harsh environmental conditions. Trehalose biosynthesis and accumulation are important for the survival of such organisms by protecting the structure and function of proteins and membranes. Trehalose affects the dynamics of proteins and water molecules in the bulk and the protein hydration shell. Enzyme catalysis and other processes dependent on protein dynamics are affected by the viscosity generated by trehalose, as described by the Kramers’ theory of rate reactions. Enzyme/protein stabilization by trehalose against thermal inactivation/unfolding is also explained by the viscosity mediated hindering of the thermally generated structural dynamics, as described by Kramers’ theory. The analysis of the relationship of viscosity–protein dynamics, and its effects on enzyme/protein function and other processes (thermal inactivation and unfolding/folding), is the focus of the present work regarding the disaccharide trehalose as the viscosity generating solute. Finally, trehalose is widely used (alone or in combination with other compounds) in the stabilization of enzymes in the laboratory and in biotechnological applications; hence, considering the effect of viscosity on catalysis and stability of enzymes may help to improve the results of trehalose in its diverse uses/applications. -
Cutinase Structure, Function and Biocatalytic Applications
EJB Electronic Journal of Biotechnology ISSN: 0717-345 Vol.1 No.3, Issue of August 15, 1998. © 1998 by Universidad Católica de Valparaíso –- Chile Invited review paper/ Received 20 October, 1998. REVIEW ARTICLE Cutinase structure, function and biocatalytic applications Cristina M. L. Carvalho Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal Maria Raquel Aires-Barros Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal 1 Joaquim M. S. Cabral Centro de Engenharia Biológica e Química Instituto Superior Técnico 1000 Lisboa – Portugal Tel: + 351.1.8419065 Fax: + 351.1.8419062 E-mail: [email protected] http://www.ist.utl.pt/ This review analyses the role of cutinases in nature and Some microorganisms, including plant pathogens, have their potential biotechnological applications. The been shown to live on cutin as their sole carbon source cloning and expression of a fungal cutinase from (Purdy and Kolattukudy, 1975) and the production of Fusarium solani f. pisi, in Escherichia coli and extracellular cutinolytic enzymes has been presented (Purdy Saccharomyces cerevisiae hosts are described. The three and Kolattukudy, 1975; Lin and Kolattukudy, 1980). dimensional structure of this cutinase is also analysed Cutinases have been purified and characterized from and its function as a lipase discussed and compared with several different sources, mainly fungi (Purdy and other lipases. The biocatalytic applications of cutinase Kolattukudy, 1975 ; Lin and Kolattukudy, 1980; Petersen et are described taking into account the preparation of al., 1997; Dantzig et al., 1986; Murphy et al., 1996) and different cutinase forms and the media where the pollen (Petersen et al., 1997; Sebastian et al., 1987). -
Cutinases from Mycobacterium Tuberculosis
Identification of Residues Involved in Substrate Specificity and Cytotoxicity of Two Closely Related Cutinases from Mycobacterium tuberculosis Luc Dedieu, Carole Serveau-Avesque, Ste´phane Canaan* CNRS - Aix-Marseille Universite´ - Enzymologie Interfaciale et Physiologie de la Lipolyse - UMR 7282, Marseille, France Abstract The enzymes belonging to the cutinase family are serine enzymes active on a large panel of substrates such as cutin, triacylglycerols, and phospholipids. In the M. tuberculosis H37Rv genome, seven genes coding for cutinase-like proteins have been identified with strong immunogenic properties suggesting a potential role as vaccine candidates. Two of these enzymes which are secreted and highly homologous, possess distinct substrates specificities. Cfp21 is a lipase and Cut4 is a phospholipase A2, which has cytotoxic effects on macrophages. Structural overlay of their three-dimensional models allowed us to identify three areas involved in the substrate binding process and to shed light on this substrate specificity. By site-directed mutagenesis, residues present in these Cfp21 areas were replaced by residues occurring in Cut4 at the same location. Three mutants acquired phospholipase A1 and A2 activities and the lipase activities of two mutants were 3 and 15 fold greater than the Cfp21 wild type enzyme. In addition, contrary to mutants with enhanced lipase activity, mutants that acquired phospholipase B activities induced macrophage lysis as efficiently as Cut4 which emphasizes the relationship between apparent phospholipase A2 activity and cytotoxicity. Modification of areas involved in substrate specificity, generate recombinant enzymes with higher activity, which may be more immunogenic than the wild type enzymes and could therefore constitute promising candidates for antituberculous vaccine production. -
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 -
Letters to Nature
letters to nature Received 7 July; accepted 21 September 1998. 26. Tronrud, D. E. Conjugate-direction minimization: an improved method for the re®nement of macromolecules. Acta Crystallogr. A 48, 912±916 (1992). 1. Dalbey, R. E., Lively, M. O., Bron, S. & van Dijl, J. M. The chemistry and enzymology of the type 1 27. Wolfe, P. B., Wickner, W. & Goodman, J. M. Sequence of the leader peptidase gene of Escherichia coli signal peptidases. Protein Sci. 6, 1129±1138 (1997). and the orientation of leader peptidase in the bacterial envelope. J. Biol. Chem. 258, 12073±12080 2. Kuo, D. W. et al. Escherichia coli leader peptidase: production of an active form lacking a requirement (1983). for detergent and development of peptide substrates. Arch. Biochem. Biophys. 303, 274±280 (1993). 28. Kraulis, P.G. Molscript: a program to produce both detailed and schematic plots of protein structures. 3. Tschantz, W. R. et al. Characterization of a soluble, catalytically active form of Escherichia coli leader J. Appl. Crystallogr. 24, 946±950 (1991). peptidase: requirement of detergent or phospholipid for optimal activity. Biochemistry 34, 3935±3941 29. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and (1995). the thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281±296 (1991). 4. Allsop, A. E. et al.inAnti-Infectives, Recent Advances in Chemistry and Structure-Activity Relationships 30. Meritt, E. A. & Bacon, D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505± (eds Bently, P. H. & O'Hanlon, P. J.) 61±72 (R. Soc. Chem., Cambridge, 1997). -
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. -
Suppression of Cutinase Gene Expression in Isogenic Hypovirulent Strains Containing Double-Stranded Rnas D
MOLECULAR AND CELLULAR BIOLOGY, OCt. 1992, p. 4539-4544 Vol. 12, No. 10 0270-7306/92/104539-06$02.00/0 Copyright © 1992, American Society for Microbiology Cutinase in Cryphonectria parasitica, the Chestnut Blight Fungus: Suppression of Cutinase Gene Expression in Isogenic Hypovirulent Strains Containing Double-Stranded RNAs D. A. VARLEY,1 G. K. PODILA,1 AND S. T. HIREMATH2* Department ofBiological Sciences, Michigan Technological University, Houghton, Michigan 49931,' and Northeastern Forest Experiment Station, Delaware, Ohio 430152 Received 26 June 1992/Accepted 20 July 1992 Plant-pathogenic fungi produce cutinase, an enzyme required to degrade plant cuticles and facilitate penetration into the host. The absence of cutinase or a decrease in its production has been associated with a decrease in pathogenicity of the fungus. A set of isogenic strains of Cryphonectria parasitica, the chestnut blight fungus, was tested for the presence and amounts of cutinase activity. The virulent strain of C. parasitica produced and secreted significantly higher amounts of cutinase than the hypovirulent strains. Use of both nucleic acid and polyclonal antibody probes for cutinase from Fusarium solani f. sp. pisi showed that cutinase in C. parasitica is 25 kDa in size and is coded by a 1.1-kb mRNA. Both mRNA and protein were inducible by cutin hydrolysate, while hypovirlnence agents suppressed the level of mRNA and the enzyme. Since all the strains had the cutinase gene, the suppression of expression was due to the hypovirulence agents. The data presented are the first report indicating that hypovirulence agents in C. parasitica regulate a gene associated with pathogenicity in other plant-pathogenic fungi. -
Mycobacterial Lipolytic Enzymes: a Gold Mine for Tuberculosis Research Luc Dedieu, C
Mycobacterial lipolytic enzymes: A gold mine for tuberculosis research Luc Dedieu, C. Serveau-Avesque, L. Kremer, Stéphane Canaan To cite this version: Luc Dedieu, C. Serveau-Avesque, L. Kremer, Stéphane Canaan. Mycobacterial lipolytic en- zymes: A gold mine for tuberculosis research. Biochimie, Elsevier, 2013, 95 (1), pp.66-73. 10.1016/j.biochi.2012.07.008. hal-02646757 HAL Id: hal-02646757 https://hal.inrae.fr/hal-02646757 Submitted on 29 May 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - NonCommercial - NoDerivatives| 4.0 International License Version définitive du manuscrit publiée dans / Final version of the manuscript published in : Biochimie (2013), Vol. 95, p. 66-73, DOI: 10.1016/j.biochi.2012.07.008 Journal homepage : www.elsevier.com/locate/biochi ipt cr nus a Review m Mycobacterial lipolytic enzymes: A gold mine for tuberculosis research a a b,c a,* / Author L. Dedieu , C. Serveau-Avesque , L. Kremer , S. Canaan r a u CNRS UMR7282-Aix-Marseille Université e Enzymologie Interfaciale