Silk Fibroin-Based Materials for Catalyst Immobilization
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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. -
The Classification of Esterases: an Important Gene Family Involved in Insecticide Resistance - a Review
Mem Inst Oswaldo Cruz, Rio de Janeiro, Vol. 107(4): 437-449, June 2012 437 The classification of esterases: an important gene family involved in insecticide resistance - A Review Isabela Reis Montella1,2, Renata Schama1,2,3/+, Denise Valle1,2,3 1Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21040-900 Rio de Janeiro, RJ, Brasil 2Instituto de Biologia do Exército, Rio de Janeiro, RJ, Brasil 3Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brasil The use of chemical insecticides continues to play a major role in the control of disease vector populations, which is leading to the global dissemination of insecticide resistance. A greater capacity to detoxify insecticides, due to an increase in the expression or activity of three major enzyme families, also known as metabolic resistance, is one major resistance mechanisms. The esterase family of enzymes hydrolyse ester bonds, which are present in a wide range of insecticides; therefore, these enzymes may be involved in resistance to the main chemicals employed in control programs. Historically, insecticide resistance has driven research on insect esterases and schemes for their classification. Currently, several different nomenclatures are used to describe the esterases of distinct species and a universal standard classification does not exist. The esterase gene family appears to be rapidly evolving and each insect species has a unique complement of detoxification genes with only a few orthologues across species. The examples listed in this review cover different aspects of their biochemical nature. However, they do not appear to contribute to reliably distinguish among the different resistance mechanisms. -
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). -
Supporting Information
Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus. -
Reduction of Pectinesterase Activity in a Commercial Enzyme Preparation
Journal of the Science of Food and Agriculture J Sci Food Agric 85:1613–1621 (2005) DOI: 10.1002/jsfa.2154 Reduction of pectinesterase activity in a commercial enzyme preparation by pulsed electric fields: comparison of inactivation kinetic models Joaquın´ Giner, Pascal Grouberman, Vicente Gimeno and Olga Martın´ ∗ Department of Food Technology, University of Lleida, CeRTA-UTPV, ETSEA, Avda Alcalde Rovira Roure 191, 25198-Lleida, Spain Abstract: The inactivation of pectinesterase (PE) in a commercial enzyme preparation (CEP) under high intensity pulsed electric fields (HIPEF) was studied. After desalting and water dilution of the raw CEP, samples were exposed to exponentially decay waveform pulses for up to 463 µs at electric field intensities ranging from 19 to 38 kV cm−1. Pulses were applied in monopolar mode. Experimental data were fitted to a first-order kinetic model as well as to models based on Fermi, Hulsheger¨ or Weibull equations to describe PE inactivation kinetics. Characteristic parameters for each model were calculated. Relationships between some of the parameters and process variables were obtained. The Weibull model yielded the best accuracy factor. The relationship between residual PE and input of electrical energy density was found to be that of exponential decay. 2005 Society of Chemical Industry Keywords: pulsed electric fields; kinetics; pectinesterase; model; inactivation INTRODUCTION It has become customary to use CEPs in fruit and Pectinesterase (PE; EC 3.1.1.11) is a pectic enzyme vegetable juice technology. Depending -
Discovery of an Alternate Metabolic Pathway for Urea Synthesis in Adult Aedes Aegypti Mosquitoes
Discovery of an alternate metabolic pathway for urea synthesis in adult Aedes aegypti mosquitoes Patricia Y. Scaraffia*†‡, Guanhong Tan§, Jun Isoe*†, Vicki H. Wysocki*§, Michael A. Wells*†, and Roger L. Miesfeld*† Departments of §Chemistry and *Biochemistry and Molecular Biophysics and †Center for Insect Science, University of Arizona, Tucson, AZ 85721-0088 Edited by Anthony A. James, University of California, Irvine, CA, and approved December 4, 2007 (received for review August 27, 2007) We demonstrate the presence of an alternate metabolic pathway We previously reported that mosquitoes dispose of toxic for urea synthesis in Aedes aegypti mosquitoes that converts uric ammonia through glutamine (Gln) and proline (Pro) synthesis, acid to urea via an amphibian-like uricolytic pathway. For these along with excretion of ammonia, uric acid, and urea (20). By studies, female mosquitoes were fed a sucrose solution containing using labeled isotopes and mass spectrometry techniques (21), 15 15 15 15 15 NH4Cl, [5- N]-glutamine, [ N]-proline, allantoin, or allantoic we have recently determined how the N from NH4Cl is acid. At 24 h after feeding, the feces were collected and analyzed incorporated into the amide side chain of Gln, and then into Pro, in a mass spectrometer. Specific enzyme inhibitors confirmed that in Ae. aegypti (22). In the present article we demonstrate that the 15 15 15 mosquitoes incorporate N from NH4Cl into [5- N]-glutamine nitrogen of the amide group of Gln contributes to uric acid and use the 15N of the amide group of glutamine to produce synthesis in mosquitoes and, surprisingly, that uric acid can be 15 labeled uric acid. -
Catalytic, Theoretical, and Biological Investigation of an Enzyme Mimic Model
Turkish Journal of Chemistry Turk J Chem (2021) 45: 1270-1278 http://journals.tubitak.gov.tr/chem/ © TÜBİTAK Research Article doi:10.3906/kim-2104-51 Catalytic, theoretical, and biological investigation of an enzyme mimic model Gülcihan GÜLSEREN* Department of Molecular Biology and Genetics, Faculty of Agriculture and Natural Sciences, Konya Food and Agriculture University, Turkey Received: 20.04.2021 Accepted/Published Online: 12.06.2021 Final Version: 27.08.2021 Abstract: Artificial catalyst studies were always stayed at the kinetics investigation level, in this work bioactivity of designed catalyst were shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications. The development of artificial enzymes is a continuous quest for the development of tailored catalysts with improved activity and stability. Understanding the catalytic mechanism is a replaceable step for catalytic studies and artificial enzyme mimics provide an alternative way for catalysis and a better understanding of catalytic pathways at the same time. Here we designed an artificial catalyst model by decorating peptide nanofibers with a covalently conjugated catalytic triad sequence. Owing to the self-assembling nature of the peptide amphiphiles, multiple action units can be presented on the surface for enhanced catalytic performance. The designed catalyst has shown an enzyme-like kinetics profile with a significant substrate affinity. The cooperative action in between catalytic triad amino acids has shown improved catalytic activity in comparison to only the histidine-containing control group. Histidine is an irreplaceable contributor to catalytic action and this is an additional reason for control group selection. This new method based on the self-assembly of covalently conjugated action units offers a new platform for enzyme investigations and their further applications. -
Francisella Tularensis 6/06 Tularemia Is a Commonly Acquired Laboratory Colony Morphology Infection; All Work on Suspect F
Francisella tularensis 6/06 Tularemia is a commonly acquired laboratory Colony Morphology infection; all work on suspect F. tularensis cultures .Aerobic, fastidious, requires cysteine for growth should be performed at minimum under BSL2 .Grows poorly on Blood Agar (BA) conditions with BSL3 practices. .Chocolate Agar (CA): tiny, grey-white, opaque A colonies, 1-2 mm ≥48hr B .Cysteine Heart Agar (CHA): greenish-blue colonies, 2-4 mm ≥48h .Colonies are butyrous and smooth Gram Stain .Tiny, 0.2–0.7 μm pleomorphic, poorly stained gram-negative coccobacilli .Mostly single cells Growth on BA (A) 48 h, (B) 72 h Biochemical/Test Reactions .Oxidase: Negative A B .Catalase: Weak positive .Urease: Negative Additional Information .Can be misidentified as: Haemophilus influenzae, Actinobacillus spp. by automated ID systems .Infective Dose: 10 colony forming units Biosafety Level 3 agent (once Francisella tularensis is . Growth on CA (A) 48 h, (B) 72 h suspected, work should only be done in a certified Class II Biosafety Cabinet) .Transmission: Inhalation, insect bite, contact with tissues or bodily fluids of infected animals .Contagious: No Acceptable Specimen Types .Tissue biopsy .Whole blood: 5-10 ml blood in EDTA, and/or Inoculated blood culture bottle Swab of lesion in transport media . Gram stain Sentinel Laboratory Rule-Out of Francisella tularensis Oxidase Little to no growth on BA >48 h Small, grey-white opaque colonies on CA after ≥48 h at 35/37ºC Positive Weak Negative Positive Catalase Tiny, pleomorphic, faintly stained, gram-negative coccobacilli (red, round, and random) Perform all additional work in a certified Class II Positive Biosafety Cabinet Weak Negative Positive *Oxidase: Negative Urease *Catalase: Weak positive *Urease: Negative *Oxidase, Catalase, and Urease: Appearances of test results are not agent-specific. -
Extended Spectrum Β-Lactamases and Class C Β
F1000Research 2020, 9:774 Last updated: 01 APR 2021 RESEARCH ARTICLE Extended spectrum β-lactamases and class C β-lactamases gene frequency in Pseudomonas aeruginosa isolated from various clinical specimens in Khartoum State, Sudan: a cross sectional study [version 1; peer review: 1 not approved] Dina N. Abdelrahman 1,2, Aya A. Taha2, Mazar M. Dafaallah2, Alaa Abdelgafoor Mohammed3, Abdel Rahim M. El Hussein 1, Ahmed I. Hashim 2, Yousif F. Hamedelnil2, Hisham N. Altayb 4 1Department of Virology, Central Laboratory, Khartoum, Sudan 2Department of Microbiology, College of Medical Laboratory Sciences, Sudan University of Science and Technology, Khartoum, Sudan 3Department of Pharmaceutical Biotechnology, College of Pharmacy, Ahfad University for Women, Omdurman, Khartoum, Sudan 4Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia v1 First published: 27 Jul 2020, 9:774 Open Peer Review https://doi.org/10.12688/f1000research.24818.1 Second version: 15 Sep 2020, 9:774 https://doi.org/10.12688/f1000research.24818.2 Reviewer Status Latest published: 01 Apr 2021, 9:774 https://doi.org/10.12688/f1000research.24818.3 Invited Reviewers 1 2 Abstract Background: Pseudomonas aeruginosa is a pathogenic bacterium, version 3 causing nosocomial infections with intrinsic and acquired resistance (revision) mechanisms to a large group of antibiotics, including β-lactams. This 01 Apr 2021 study aimed to determine the susceptibility pattern to selected antibiotics and to index the first reported β-lactamases gene version 2 (extended spectrum β-lactamases (ESBLs) genes and class C β- (revision) report report lactamases genes) frequency in Ps. aeruginosa in Khartoum State, 15 Sep 2020 Sudan. Methods: 121 Ps. -
Download Product Insert (PDF)
PRODUCT INFORMATION Lysophospholipase D Polyclonal Antibody Item No. 10005375 Overview and Properties Contents: This vial contains 500 µl of peptide affinity-purified antibody. Synonyms: Autotaxin, ENPP2, lysoPLD Immunogen: Peptide from the C-terminal region of rat LysoPLD Species Reactivity: (+) Human, mouse, and rat; other species not tested Form: Liquid Storage: -20°C (as supplied) Stability: ≥1 year Storage Buffer: TBS, pH 7.4, with 50% glycerol, 0.1%l BSA, and 0.02% sodium azide Host: Rabbit Applications: Immunocytochemistry (ICC), Immunohistochemistry (IHC), and Western blot (WB); the recommended starting dilution for ICC is 1:500, 1:80 for IHC, and 1:200 for WB. Other applications were not tested, therefore optimal working concentration/dilution should be determined empirically. Images 1 · · · · · · · 104 kDa · · · · · · · 60 kDa Lane 1: Human cerebella supernatant (40 µg) Immunohistochemistry analysis of formalin-fixed, paraffin-embedded (FFPE) human cerebellum ǎssue aer heat-induced anǎgen retrieval in pH 6.0 citrate buffer. Aer incubaǎon with Lysophospholipase D Polyclonal Anǎbody (Item No. 10005375) at a 1:80 diluǎon, slides were incubated with bioǎnylated secondary anǎbody, followed by alkaline phosphatase-strepavidin and chromogen (DAB). WARNING CAYMAN CHEMICAL THIS PRODUCT IS FOR RESEARCH ONLY - NOT FOR HUMAN OR VETERINARY DIAGNOSTIC OR THERAPEUTIC USE. 1180 EAST ELLSWORTH RD SAFETY DATA ANN ARBOR, MI 48108 · USA This material should be considered hazardous until further information becomes available. Do not ingest, inhale, get in eyes, on skin, or on clothing. Wash thoroughly after handling. Before use, the user must review the complete Safety Data Sheet, which has been sent via email to your institution. PHONE: [800] 364-9897 WARRANTY AND LIMITATION OF REMEDY [734] 971-3335 Buyer agrees to purchase the material subject to Cayman’s Terms and Conditions. -
(12) United States Patent (10) Patent No.: US 9.422,609 B2 Teichberg (45) Date of Patent: Aug
USOO9422609B2 (12) United States Patent (10) Patent No.: US 9.422,609 B2 Teichberg (45) Date of Patent: Aug. 23, 2016 (54) METHODS, COMPOSITIONS AND DEVICES (58) Field of Classification Search FOR MANTAINING CHEMICAL BALANCE CPC ........................ C02F 1/725; C12Y 305/01005 OF CHLORINATED WATER USPC ........................... 210/754; 435/195, 227 231 See application file for complete search history. (75) Inventor: Vivian I. Teichberg, Savyon (IL) (56) References Cited (73) Assignees: Mia Levite, Savyon (IL); Yaar Teichberg, Savyon (IL); Nof Lyle U.S. PATENT DOCUMENTS Teichberg, Savyon (IL) 4,793,935 A * 12/1988 Stillman ............... CO2F 1.5236 21Of727 (*) Notice: Subject to any disclaimer, the term of this 6,673,582 B2 * 1/2004 McTavish ..................... 435/122 patent is extended or adjusted under 35 U.S.C. 154(b) by 1044 days. (Continued) (21) Appl. No.: 12/225.18O FOREIGN PATENT DOCUMENTS y x- - - 9 AU 41971 5, 1979 (22) PCT Filed: Mar. 14, 2007 GB 2025919 1, 1980 (86). PCT No.: PCT/L2007/OOO336 (Continued) S 371 (c)(1) OTHER PUBLICATIONS (2), (4) Date: Sep. 16, 2008 Examiner's Report Dated Oct. 6, 2010 From the Australian Govern (87) PCT Pub. No.: WO2007/107.981 ment, IP Australia Re. Application No. 2007228391. (Continued) PCT Pub. Date: Sep. 27, 2007 (65) Prior Publication Data Primary Examiner — Peter Keyworth (74) Attorney, Agent, or Firm — Browdy and Neimark, US 201OfO270228A1 Oct. 28, 2010 PLLC Related U.S. Application Data (57) ABSTRACT (60) Provisional application No. 60/783,028, filed on Mar. A composition-of-matter for use in water treatment, com 17, 2006.