Computational Genome and Pathway Analysis of Halophilic Archaea
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Quantum Effects in Radical B12 Enzymes
Quantum Effects in Adenosylcobalamin-dependent Enzymes by M. Hossein Khalilian Boroujeni B.Sc., Chemistry, Razi University, 2014 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE in THE COLLEGE OF GRADUATE STUDIES (Chemistry) THE UNIVERSITY OF BRITISH COLUMBIA (Okanagan) April 2019 © M. Hossein Khalilian Boroujeni, 2019 The following individuals certify that they have read, and recommend to the College of Graduate Studies for acceptance, a thesis/dissertation entitled: Quantum Effects in Adenosylcobalamin-dependent Enzymes submitted by M. Hossein Khalilian Boroujeni in partial fulfillment of the requirements for the degree of Master of Science Examining Committee: Gino A. DiLabio, I. K. Barber School of Arts & Sciences Supervisor W. Stephen McNeil, I. K. Barber School of Arts & Sciences Supervisory Committee Member Kirsten Wolthers, I. K. Barber School of Arts & Sciences Supervisory Committee Member Michael Deyholos, I. K. Barber School of Arts & Sciences University Examiner ii Abstract The ability of radical enzymes to maintain tight control over the high reactive radical intermediates generated in their active sites is not completely understood. In this thesis, we report on a strategy that radical (B12-dependent) enzymes appear to exploit in order to manipulate and control the reactivity of one of their radical intermediate (5'-deoxyadenosyl radical) contained in the active site. The results of quantum mechanical calculations suggest that these enzymes utilize the little known quantum Coulombic effect (QCE), which causes the radical to acquire an electronic structure that contradicts the Aufbau Principle. This effect causes the energy of the singly-occupied molecular orbital (SOMO) of the radical to be well below that of the highest-occupied molecular orbital (HOMO), which renders the radical less reactive. -
In Situ Detection of Protein Interactions for Recombinant Therapeutic Enzymes
In situ detection of protein interactions for recombinant therapeutic enzymes Mojtaba Samoudi1, Chih-Chung Kuo1, Caressa Robinson1, Km Shams-Ud-Doha2, Song-Min Schinn1, Stefan Kol3, Linus Weiss4, Sara Petersen Bjørn5, Bjørn Voldborg5, Alexandre Rosa Campos2, and Nathan Lewis6 1University of California San Diego 2Sanford Burnham Prebys Medical Discovery Institute 3Technical University of Denmark 4Eberhard Karls University T¨ubingen 5DTU Biosustain 6University of California, San Diego May 15, 2020 Abstract Despite their therapeutic potential, many protein drugs remain inaccessible to patients since they are difficult to secrete. Each recombinant protein has unique physicochemical properties and requires different machinery for proper folding, assembly, and post-translational modifications (PTMs). Here we aimed to identify the machinery supporting recombinant protein secretion by measuring the protein-protein interaction (PPI) networks of four different recombinant proteins (SERPINA1, SERPINC1, SERPING1 and SeAP) with various PTMs and structural motifs using the proximity-dependent biotin identification (BioID) method. We identified PPIs associated with specific features of the secreted proteins using a Bayesian statistical model, and found proteins involved in protein folding, disulfide bond formation and N-glycosylation were positively correlated with the corresponding features of the four model proteins. Among others, oxidative folding enzymes showed the strongest association with disulfide bond formation, supporting their critical roles in proper folding and maintaining the ER stability. Knock down of ERP44, a measured interactor with the highest fold change, led to the decreased secretion of SERPINC1, which relies on its extensive disulfide bonds. Proximity-dependent labeling successfully identified the transient interactions supporting synthesis of secreted recombinant proteins and refined our understanding of key molecular mechanisms of the secretory pathway during recombinant protein production. -
Anaerobic Radical Enzymes for Biotechnology
ChemBioEng Reviews Anaerobic radical enzymes for biotechnology Journal: ChemBioEng Reviews Manuscript ID cben.201800003.R1 Wiley - Manuscript type:For Review Peer Review Date Submitted by the Author: n/a Complete List of Authors: Jäger, Christof; University of Nottingham, Chemical and Environmental Engineering Croft, Anna; University of Nottingham, Chemical and Environmental Engineering Keywords: Radicals, Enzymes, Catalysis, Biotechnology, Anaerobic reactions Wiley-VCH Page 1 of 61 ChemBioEng Reviews 1 2 3 Christof M. Jäger* and Anna K. Croft* 4 5 6 7 8 9 Anaerobic radical enzymes for biotechnology 10 11 12 13 AUTHORS: Dr Christof Martin Jäger* and Dr Anna Kristina Croft* 14 15 16 ADDRESS: Department of Chemical and Environmental Engineering, University of 17 18 Nottingham, Nottingham, NG7 2RD, United Kingdom. [email protected], 19 For Peer Review 20 21 [email protected] 22 23 24 ABSTRACT: 25 26 27 28 Enzymes that proceed through radical intermediates have a rich chemistry that includes 29 30 functionalisation of otherwise unreactive carbon atoms, carbon-skeleton rearrangements, 31 32 aromatic reductions, and unusual eliminations. Especially under anaerobic conditions, 33 34 organisms have developed a wide range of approaches for managing these transformations 35 36 that can be exploited to generate new biological routes towards both bulk and specialty 37 38 39 chemicals. These routes are often either much more direct or allow access to molecules that 40 41 are inaccessible through standard (bio)chemical approaches. This review gives an overview 42 43 of some of the key enzymes in this area: benzoyl-CoA reductases (that effect the enzymatic 44 45 Birch reduction), ketyl radical dehydratases, coenzyme B12-dependant enzymes, glycyl 46 47 radical enzymes, and radical SAM (AdoMet radical) enzymes. -
(10) Patent No.: US 8119385 B2
US008119385B2 (12) United States Patent (10) Patent No.: US 8,119,385 B2 Mathur et al. (45) Date of Patent: Feb. 21, 2012 (54) NUCLEICACIDS AND PROTEINS AND (52) U.S. Cl. ........................................ 435/212:530/350 METHODS FOR MAKING AND USING THEMI (58) Field of Classification Search ........................ None (75) Inventors: Eric J. Mathur, San Diego, CA (US); See application file for complete search history. Cathy Chang, San Diego, CA (US) (56) References Cited (73) Assignee: BP Corporation North America Inc., Houston, TX (US) OTHER PUBLICATIONS c Mount, Bioinformatics, Cold Spring Harbor Press, Cold Spring Har (*) Notice: Subject to any disclaimer, the term of this bor New York, 2001, pp. 382-393.* patent is extended or adjusted under 35 Spencer et al., “Whole-Genome Sequence Variation among Multiple U.S.C. 154(b) by 689 days. Isolates of Pseudomonas aeruginosa” J. Bacteriol. (2003) 185: 1316 1325. (21) Appl. No.: 11/817,403 Database Sequence GenBank Accession No. BZ569932 Dec. 17. 1-1. 2002. (22) PCT Fled: Mar. 3, 2006 Omiecinski et al., “Epoxide Hydrolase-Polymorphism and role in (86). PCT No.: PCT/US2OO6/OOT642 toxicology” Toxicol. Lett. (2000) 1.12: 365-370. S371 (c)(1), * cited by examiner (2), (4) Date: May 7, 2008 Primary Examiner — James Martinell (87) PCT Pub. No.: WO2006/096527 (74) Attorney, Agent, or Firm — Kalim S. Fuzail PCT Pub. Date: Sep. 14, 2006 (57) ABSTRACT (65) Prior Publication Data The invention provides polypeptides, including enzymes, structural proteins and binding proteins, polynucleotides US 201O/OO11456A1 Jan. 14, 2010 encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. -
Microbial Biochemistry, 2Nd Edition
Microbial Biochemistry . G.N. Cohen Microbial Biochemistry Second Edition Prof. G.N. Cohen Institut Pasteur rue du Docteur Roux 28 75724 Paris France [email protected] ISBN 978-90-481-9436-0 e-ISBN 978-90-481-9437-7 DOI 10.1007/978-90-481-9437-7 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2010938472 # Springer Science+Business Media B.V. 2011 No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Foreword This book originates from almost 60 years of living in the company of micro- organisms, mainly with Escherichia coli. My scientific life has taken place almost exclusively at the Institut Pasteur in Paris, where many concepts of modern molecular biology were born or developed. The present work emphasizes the interest of microbial physiology, biochemistry and genetics. It takes into account the considerable advances which have been made in the field in the last 30 years by the introduction of gene cloning and sequencing and by the exponential development of physical methods such as X-ray crystallog- raphy of proteins. The younger generation of biochemists is legitimately interested in the problems raised by differentiation and development in higher organisms, and also in neuros- ciences. -
Distinct C-Terminal Amino Acid Sequence Motifs Serve As the Targeting Signals for Outer Mitochondrial Membrane and Plastid Outer Envelope TA Proteins
Distinct C-terminal Amino Acid Sequence Motifs Serve as the Targeting Signals for Outer Mitochondrial Membrane and Plastid Outer Envelope TA Proteins by Howard James Teresinski A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Molecular and cellular Biology Guelph, Ontario, Canada © Howard James Teresinski, January, 2015 ABSTRACT Distinct C-terminal amino acid sequence motifs serve as the targeting signals for outer mitochondrial membrane and plastid outer envelope TA proteins Howard James Teresinski Advisor: University of Guelph, 2014 Dr. Robert T. Mullen Tail-anchored (TA) proteins are a unique class of functionally diverse membrane proteins that are defined by their single C-terminal transmembrane domain and their ability to insert post-translationally into specific organelles in an Ncytosol-CIMS orientation. While in recent years considerable progress has been made towards understanding the biogenesis of TA proteins in yeast and mammals, relatively little is known about how these proteins are properly partitioned within plant cells, mostly because so few plant TA proteins have been identified. Here we show the results of experiments aimed at cataloguing, in silico, all of the TA outer mitochondrial membrane and plastid outer envelope proteins in Arabidopsis and then identifying and characterising distinct, C-terminal targeting motifs responsible for the proper sorting of at least a subset of these proteins. Collectively, the results of this thesis provide important insight into the molecular mechanisms that underlie the biogenesis of TA proteins in plant cells. Acknowledgments I would first and foremost like to thank my MSc advisor Dr. -
And Multiple Conformations Kinase 4 Structures Reveal Novel Features Cutting Edge: IL-1 Receptor-Associated
Cutting Edge: IL-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features and Multiple Conformations This information is current as Andreas Kuglstatter, Armando G. Villaseñor, David Shaw, of September 23, 2021. Simon W. Lee, Stan Tsing, Linghao Niu, Kyung W. Song, Jim W. Barnett and Michelle F. Browner J Immunol 2007; 178:2641-2645; ; doi: 10.4049/jimmunol.178.5.2641 http://www.jimmunol.org/content/178/5/2641 Downloaded from References This article cites 23 articles, 5 of which you can access for free at: http://www.jimmunol.org/content/178/5/2641.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication by guest on September 23, 2021 *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2007 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. THE JOURNAL OF IMMUNOLOGY CUTTING EDGE Cutting Edge: IL-1 Receptor-Associated Kinase 4 Structures Reveal Novel Features and Multiple Conformations Andreas Kuglstatter,1 Armando G. Villasen˜or, David Shaw, Simon W. -
Downloaded for Personal Non-Commercial Research Or Study, Without Prior Permission Or Charge
https://theses.gla.ac.uk/ Theses Digitisation: https://www.gla.ac.uk/myglasgow/research/enlighten/theses/digitisation/ This is a digitised version of the original print thesis. Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Anion And Cation Binding In Proteins James David Watson Submitted for the degree of Doctor of Philosophy The University of Glasgow Faculty of IBLS September 2002 ProQuest Number: 10390636 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 10390636 Published by ProQuest LLO (2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLO. ProQuest LLO. 789 East Eisenhower Parkway P.Q. -
O O2 Enzymes Available from Sigma Enzymes Available from Sigma
COO 2.7.1.15 Ribokinase OXIDOREDUCTASES CONH2 COO 2.7.1.16 Ribulokinase 1.1.1.1 Alcohol dehydrogenase BLOOD GROUP + O O + O O 1.1.1.3 Homoserine dehydrogenase HYALURONIC ACID DERMATAN ALGINATES O-ANTIGENS STARCH GLYCOGEN CH COO N COO 2.7.1.17 Xylulokinase P GLYCOPROTEINS SUBSTANCES 2 OH N + COO 1.1.1.8 Glycerol-3-phosphate dehydrogenase Ribose -O - P - O - P - O- Adenosine(P) Ribose - O - P - O - P - O -Adenosine NICOTINATE 2.7.1.19 Phosphoribulokinase GANGLIOSIDES PEPTIDO- CH OH CH OH N 1 + COO 1.1.1.9 D-Xylulose reductase 2 2 NH .2.1 2.7.1.24 Dephospho-CoA kinase O CHITIN CHONDROITIN PECTIN INULIN CELLULOSE O O NH O O O O Ribose- P 2.4 N N RP 1.1.1.10 l-Xylulose reductase MUCINS GLYCAN 6.3.5.1 2.7.7.18 2.7.1.25 Adenylylsulfate kinase CH2OH HO Indoleacetate Indoxyl + 1.1.1.14 l-Iditol dehydrogenase L O O O Desamino-NAD Nicotinate- Quinolinate- A 2.7.1.28 Triokinase O O 1.1.1.132 HO (Auxin) NAD(P) 6.3.1.5 2.4.2.19 1.1.1.19 Glucuronate reductase CHOH - 2.4.1.68 CH3 OH OH OH nucleotide 2.7.1.30 Glycerol kinase Y - COO nucleotide 2.7.1.31 Glycerate kinase 1.1.1.21 Aldehyde reductase AcNH CHOH COO 6.3.2.7-10 2.4.1.69 O 1.2.3.7 2.4.2.19 R OPPT OH OH + 1.1.1.22 UDPglucose dehydrogenase 2.4.99.7 HO O OPPU HO 2.7.1.32 Choline kinase S CH2OH 6.3.2.13 OH OPPU CH HO CH2CH(NH3)COO HO CH CH NH HO CH2CH2NHCOCH3 CH O CH CH NHCOCH COO 1.1.1.23 Histidinol dehydrogenase OPC 2.4.1.17 3 2.4.1.29 CH CHO 2 2 2 3 2 2 3 O 2.7.1.33 Pantothenate kinase CH3CH NHAC OH OH OH LACTOSE 2 COO 1.1.1.25 Shikimate dehydrogenase A HO HO OPPG CH OH 2.7.1.34 Pantetheine kinase UDP- TDP-Rhamnose 2 NH NH NH NH N M 2.7.1.36 Mevalonate kinase 1.1.1.27 Lactate dehydrogenase HO COO- GDP- 2.4.1.21 O NH NH 4.1.1.28 2.3.1.5 2.1.1.4 1.1.1.29 Glycerate dehydrogenase C UDP-N-Ac-Muramate Iduronate OH 2.4.1.1 2.4.1.11 HO 5-Hydroxy- 5-Hydroxytryptamine N-Acetyl-serotonin N-Acetyl-5-O-methyl-serotonin Quinolinate 2.7.1.39 Homoserine kinase Mannuronate CH3 etc. -
12) United States Patent (10
US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S. -
Pump Ena1 Is a Yeast Epsin-Specific Cargo Requiring Its Ubiquitylation and Phosphorylation Sites for Internalization Arpita Sen1,*,§, Wen-Chieh Hsieh1,‡,§, Claudia B
© 2020. Published by The Company of Biologists Ltd | Journal of Cell Science (2020) 133, jcs245415. doi:10.1242/jcs.245415 RESEARCH ARTICLE The Na+ pump Ena1 is a yeast epsin-specific cargo requiring its ubiquitylation and phosphorylation sites for internalization Arpita Sen1,*,§, Wen-Chieh Hsieh1,‡,§, Claudia B. Hanna1, Chuan-Chih Hsu2, McKeith Pearson II1, W. Andy Tao2 and R. Claudio Aguilar1,¶ ABSTRACT Since Ub constitutes the main trafficking signal in Saccharomyces cerevisiae It is well known that in addition to its classical role in protein turnover, (reviewed in Lauwers et al., 2010), ubiquitylation is required for a variety of membrane protein sorting studies in yeast have been instrumental in advancing our events. However, and despite substantial progress in the field, a long- understanding of the mechanisms operating in Ub-mediated standing question remains: given that all ubiquitin units are identical, sorting. For example, it has been clearly established that budding how do different elements of the sorting machinery recognize their yeast utilizes the E3 ubiquitin ligase Rsp5 to promote cargo specific cargoes? Our results indicate that the yeast Na+ pump Ena1 ubiquitylation relevant to endocytosis and other vesicle trafficking is an epsin (Ent1 and Ent2 in yeast)-specific cargo and that its events (Belgareh-Touze et al., 2008; Lauwers et al., 2010). Indeed, internalization requires K1090, which likely undergoes Art3-dependent Rsp5-mediated ubiquitylation is required for the internalization of ubiquitylation. In addition, an Ena1 serine and threonine (ST)-rich cargoes such as the pheromone receptor Ste2 (Dunn and Hicke, patch, proposed to be targeted for phosphorylation by casein 2001; Hicke and Riezman, 1996), the uracil transporter Fur4 (Galan kinases, was also required for its uptake. -
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii
POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii http://rcin.org.pl WSKAZÓWKI DLA AUTORÓW Kwartalnik „Postępy Biochemii” publikuje artykuły monograficzne omawiające wąskie tematy, oraz artykuły przeglądowe referujące szersze zagadnienia z biochemii i nauk pokrewnych. Artykuły pierwszego typu winny w sposób syntetyczny omawiać wybrany temat na podstawie możliwie pełnego piśmiennictwa z kilku ostatnich lat, a artykuły drugiego typu na podstawie piśmiennictwa z ostatnich dwu lat. Objętość takich artykułów nie powinna przekraczać 25 stron maszynopisu (nie licząc ilustracji i piśmiennictwa). Kwartalnik publikuje także artykuły typu minireviews, do 10 stron maszynopisu, z dziedziny zainteresowań autora, opracowane na podstawie najnow szego piśmiennictwa, wystarczającego dla zilustrowania problemu. Ponadto kwartalnik publikuje krótkie noty, do 5 stron maszynopisu, informujące o nowych, interesujących osiągnięciach biochemii i nauk pokrewnych, oraz noty przybliżające historię badań w zakresie różnych dziedzin biochemii. Przekazanie artykułu do Redakcji jest równoznaczne z oświadczeniem, że nadesłana praca nie była i nie będzie publikowana w innym czasopiśmie, jeżeli zostanie ogłoszona w „Postępach Biochemii”. Autorzy artykułu odpowiadają za prawidłowość i ścisłość podanych informacji. Autorów obowiązuje korekta autorska. Koszty zmian tekstu w korekcie (poza poprawieniem błędów drukarskich) ponoszą autorzy. Artykuły honoruje się według obowiązujących stawek. Autorzy otrzymują bezpłatnie 25 odbitek swego artykułu; zamówienia na dodatkowe odbitki (płatne) należy zgłosić pisemnie odsyłając pracę po korekcie autorskiej. Redakcja prosi autorów o przestrzeganie następujących wskazówek: Forma maszynopisu: maszynopis pracy i wszelkie załączniki należy nadsyłać w dwu egzem plarzach. Maszynopis powinien być napisany jednostronnie, z podwójną interlinią, z marginesem ok. 4 cm po lewej i ok. 1 cm po prawej stronie; nie może zawierać więcej niż 60 znaków w jednym wierszu nie więcej niż 30 wierszy na stronie zgodnie z Normą Polską.