Arginine Kinase Expression in Crab Gill 2397
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Arginine Kinase: a Crystallographic Investigation of Essential Substrate Structure Shawn A
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2006 Arginine Kinase: A Crystallographic Investigation of Essential Substrate Structure Shawn A. (Shawn Adam) Clark Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES ARGININE KINASE; A CRYSTALLOGRAPHIC INVESTIGATION OF ESSENTIAL SUBSTRATE STRUCTURE BY SHAWN A. CLARK A Dissertation submitted to the Department of Chemistry and Biochemistry In partial fulfillment of the requirements for the Degree of Doctor of Philosophy Degree Awarded: Fall Semester, 2006 The members of committee approve the dissertation of Shawn A. Clark defended on 11/2/2006 __________________ Michael Chapman Professor Co-Directing Dissertation __________________ Tim Logan Professor Co-Directing Dissertation __________________ Ross Ellington Outside Committee Member __________________ Al Stiegman Committee Member _________________ Tim Cross Committee Member Approved: ________________________________________ Naresh Dalal, Department Chair, Department of Chemistry & Biochemistry The Office of Graduate Studies has verified and approved the above named committee members. ii ACKNOWLEDGEMENTS The voyage through academic maturity is full of numerous challenges that present themselves at many levels: physically, mentally, and emotionally. These hurdles can only be overcome with dedication, guidance, patience and above all support. It is for these reasons that I would like to express my sincerest and deepest admiration and love for my family; my wife Bobbi, and my two children Allexis and Brytney. Their encouragement, sacrifice, patience, loving support, and inquisitive nature have been the pillar of my strength, the beacon of my determination, and the spark of my intuition. -
(12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin Et Al
US 20100317005A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2010/0317005 A1 Hardin et al. (43) Pub. Date: Dec. 16, 2010 (54) MODIFIED NUCLEOTIDES AND METHODS (22) Filed: Mar. 15, 2010 FOR MAKING AND USE SAME Related U.S. Application Data (63) Continuation of application No. 11/007,794, filed on Dec. 8, 2004, now abandoned, which is a continuation (75) Inventors: Susan H. Hardin, College Station, in-part of application No. 09/901,782, filed on Jul. 9, TX (US); Hongyi Wang, Pearland, 2001. TX (US); Brent A. Mulder, (60) Provisional application No. 60/527,909, filed on Dec. Sugarland, TX (US); Nathan K. 8, 2003, provisional application No. 60/216,594, filed Agnew, Richmond, TX (US); on Jul. 7, 2000. Tommie L. Lincecum, JR., Publication Classification Houston, TX (US) (51) Int. Cl. CI2O I/68 (2006.01) Correspondence Address: (52) U.S. Cl. ............................................................ 435/6 LIFE TECHNOLOGES CORPORATION (57) ABSTRACT CFO INTELLEVATE Labeled nucleotide triphosphates are disclosed having a label P.O. BOX S2OSO bonded to the gamma phosphate of the nucleotide triphos MINNEAPOLIS, MN 55402 (US) phate. Methods for using the gamma phosphate labeled nucleotide are also disclosed where the gamma phosphate labeled nucleotide are used to attach the labeled gamma phos (73) Assignees: LIFE TECHNOLOGIES phate in a catalyzed (enzyme or man-made catalyst) reaction to a target biomolecule or to exchange a phosphate on a target CORPORATION, Carlsbad, CA biomolecule with a labeled gamme phosphate. Preferred tar (US); VISIGEN get biomolecules are DNAs, RNAs, DNA/RNAs, PNA, BIOTECHNOLOGIES, INC. polypeptide (e.g., proteins enzymes, protein, assemblages, etc.), Sugars and polysaccharides or mixed biomolecules hav ing two or more of DNAs, RNAs, DNA/RNAs, polypeptide, (21) Appl. -
Lombricine Kinase Structure and Substrate Specificity: a Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D
Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2007 Lombricine Kinase Structure and Substrate Specificity: A Paradigm for Elucidation of Substrate Specificity in Phosphagen Kinases D. Jeffrey. Bush Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES LOMBRICINE KINASE STRUCTURE AND SUBSTRATE SPECIFICITY: A PARADIGM FOR ELUCIDATION OF SUBSTRATE SPECIFICITY IN PHOSPHAGEN KINASES By D. JEFFREY BUSH A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Spring Semester, 2007 The members of the Committee approve the Dissertation of D. Jeffrey Bush defended on February 20, 2007. Michael S. Chapman Professor Co-Directing Dissertation John Dorsey Professor Co-Directing Dissertation W. Ross Ellington Outside Committee Member Michael Blaber Committee Member Approved: ____________________________________________ Joseph Schlenoff, Department Chair, Department of Chemistry & Biochemistry ____________________________________________ Joseph Travis, Dean, College of Arts & Sciences The Office of Graduate Studies has verified and approved the above named committee members. ii To the late Clifford M. Bush, who with statements such as “A heterogeneous compound of two or more substances whose ray through certain limits is confined to a specific area…” fostered a strong interest of the author in science at a very young age, if only just to know more about what he spoke. iii ACKNOWLEDGEMENTS I wish to first convey my sincere gratitude to my parents, Donald and Roberta for raising me in the nurture and admonition of the Almighty God. -
Acidophilic Green Algal Genome Provides Insights Into Adaptation to an Acidic Environment
Acidophilic green algal genome provides insights into adaptation to an acidic environment Shunsuke Hirookaa,b,1, Yuu Hirosec, Yu Kanesakib,d, Sumio Higuchie, Takayuki Fujiwaraa,b,f, Ryo Onumaa, Atsuko Eraa,b, Ryudo Ohbayashia, Akihiro Uzukaa,f, Hisayoshi Nozakig, Hirofumi Yoshikawab,h, and Shin-ya Miyagishimaa,b,f,1 aDepartment of Cell Genetics, National Institute of Genetics, Shizuoka 411-8540, Japan; bCore Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan; cDepartment of Environmental and Life Sciences, Toyohashi University of Technology, Aichi 441-8580, Japan; dNODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan; eResearch Group for Aquatic Plants Restoration in Lake Nojiri, Nojiriko Museum, Nagano 389-1303, Japan; fDepartment of Genetics, Graduate University for Advanced Studies, Shizuoka 411-8540, Japan; gDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan; and hDepartment of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan Edited by Krishna K. Niyogi, Howard Hughes Medical Institute, University of California, Berkeley, CA, and approved August 16, 2017 (received for review April 28, 2017) Some microalgae are adapted to extremely acidic environments in pumps that biotransform arsenic and archaeal ATPases, which which toxic metals are present at high levels. However, little is known probably contribute to the algal heat tolerance (8). In addition, the about how acidophilic algae evolved from their respective neutrophilic reduction in the number of genes encoding voltage-gated ion ancestors by adapting to particular acidic environments. To gain channels and the expansion of chloride channel and chloride car- insights into this issue, we determined the draft genome sequence rier/channel families in the genome has probably contributed to the of the acidophilic green alga Chlamydomonas eustigma and per- algal acid tolerance (8). -
Conserved Phosphoryl Transfer Mechanisms Within Kinase Families
Kenyon et al. BMC Research Notes 2012, 5:131 http://www.biomedcentral.com/1756-0500/5/131 RESEARCHARTICLE Open Access Conserved phosphoryl transfer mechanisms within kinase families and the role of the C8 proton of ATP in the activation of phosphoryl transfer Colin P Kenyon*, Robyn L Roth, Chris W van der Westhuyzen and Christopher J Parkinson Abstract Background: The kinome is made up of a large number of functionally diverse enzymes, with the classification indicating very little about the extent of the conserved kinetic mechanisms associated with phosphoryl transfer. It has been demonstrated that C8-H of ATP plays a critical role in the activity of a range of kinase and synthetase enzymes. Results: A number of conserved mechanisms within the prescribed kinase fold families have been identified directly utilizing the C8-H of ATP in the initiation of phosphoryl transfer. These mechanisms are based on structurally conserved amino acid residues that are within hydrogen bonding distance of a co-crystallized nucleotide. On the basis of these conserved mechanisms, the role of the nucleotide C8-H in initiating the formation of a pentavalent intermediate between the g-phosphate of the ATP and the substrate nucleophile is defined. All reactions can be clustered into two mechanisms by which the C8-H is induced to be labile via the coordination of a backbone carbonyl to C6-NH2 of the adenyl moiety, namely a “push” mechanism, and a “pull” mechanism, based on the protonation of N7. Associated with the “push” mechanism and “pull” mechanisms are a series of proton transfer cascades, initiated from C8-H, via the tri-phosphate backbone, culminating in the formation of the pentavalent transition state between the g-phosphate of the ATP and the substrate nucleophile. -
Natural Products Containing 'Rare'
molecules Review Natural Products Containing ‘Rare’ Organophosphorus Functional Groups Janusz J. Petkowski 1,* , William Bains 2 and Sara Seager 1,3,4 1 Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA; [email protected] 2 Rufus Scientific, 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK; [email protected] 3 Department of Physics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA 4 Department of Aeronautics and Astronautics, Massachusetts Institute of Technology, 77 Mass. Ave., Cambridge, MA 02139, USA * Correspondence: [email protected] Received: 21 January 2019; Accepted: 22 February 2019; Published: 28 February 2019 Abstract: Phosphorous-containing molecules are essential constituents of all living cells. While the phosphate functional group is very common in small molecule natural products, nucleic acids, and as chemical modification in protein and peptides, phosphorous can form P–N (phosphoramidate), P–S (phosphorothioate), and P–C (e.g., phosphonate and phosphinate) linkages. While rare, these moieties play critical roles in many processes and in all forms of life. In this review we thoroughly categorize P–N, P–S, and P–C natural organophosphorus compounds. Information on biological source, biological activity, and biosynthesis is included, if known. This review also summarizes the role of phosphorylation on unusual amino acids in proteins (N- and S-phosphorylation) and reviews the natural phosphorothioate (P–S) and phosphoramidate (P–N) modifications of DNA and nucleotides with an emphasis on their role in the metabolism of the cell. We challenge the commonly held notion that nonphosphate organophosphorus functional groups are an oddity of biochemistry, with no central role in the metabolism of the cell. -
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. -
The Incidence and Functional Relevance of Intrinsic Disorder in Enzymes and the Protein Data Bank Shelly Deforte University of South Florida, [email protected]
University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 6-27-2016 Intrinsic Disorder Where You Least Expect It: The Incidence and Functional Relevance of Intrinsic Disorder in Enzymes and the Protein Data Bank Shelly Deforte University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Bioinformatics Commons, Medicine and Health Sciences Commons, and the Molecular Biology Commons Scholar Commons Citation Deforte, Shelly, "Intrinsic Disorder Where You Least Expect It: The ncI idence and Functional Relevance of Intrinsic Disorder in Enzymes and the Protein Data Bank" (2016). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6219 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Intrinsic Disorder Where You Least Expect It: The Incidence and Functional Relevance of Intrinsic Disorder in Enzymes and the Protein Data Bank by Shelly DeForte A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Molecular Medicine College of Medicine University of South Florida Major Professor: Vladimir Uversky, Ph.D. Yu Chen, Ph.D. Robert Deschenes, Ph.D. Sandy Westerheide, Ph.D. Bin Xue, Ph.D. Date of Approval: June 14, 2016 Keywords: intrinsically disordered protein, x-ray crystallography, structural biology, enzyme function Copyright © 2016, Shelly DeForte Table of Contents List of Tables ................................................................................................ iv List of Figures ............................................................................................... -
(12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur Et Al
US 2012026.6329A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0266329 A1 Mathur et al. (43) Pub. Date: Oct. 18, 2012 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/10 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/24 (2006.01) CI2N 9/02 (2006.01) (75) Inventors: Eric J. Mathur, Carlsbad, CA CI2N 9/06 (2006.01) (US); Cathy Chang, San Marcos, CI2P 2L/02 (2006.01) CA (US) CI2O I/04 (2006.01) CI2N 9/96 (2006.01) (73) Assignee: BP Corporation North America CI2N 5/82 (2006.01) Inc., Houston, TX (US) CI2N 15/53 (2006.01) CI2N IS/54 (2006.01) CI2N 15/57 2006.O1 (22) Filed: Feb. 20, 2012 CI2N IS/60 308: Related U.S. Application Data EN f :08: (62) Division of application No. 1 1/817,403, filed on May AOIH 5/00 (2006.01) 7, 2008, now Pat. No. 8,119,385, filed as application AOIH 5/10 (2006.01) No. PCT/US2006/007642 on Mar. 3, 2006. C07K I4/00 (2006.01) CI2N IS/II (2006.01) (60) Provisional application No. 60/658,984, filed on Mar. AOIH I/06 (2006.01) 4, 2005. CI2N 15/63 (2006.01) Publication Classification (52) U.S. Cl. ................... 800/293; 435/320.1; 435/252.3: 435/325; 435/254.11: 435/254.2:435/348; (51) Int. Cl. 435/419; 435/195; 435/196; 435/198: 435/233; CI2N 15/52 (2006.01) 435/201:435/232; 435/208; 435/227; 435/193; CI2N 15/85 (2006.01) 435/200; 435/189: 435/191: 435/69.1; 435/34; CI2N 5/86 (2006.01) 435/188:536/23.2; 435/468; 800/298; 800/320; CI2N 15/867 (2006.01) 800/317.2: 800/317.4: 800/320.3: 800/306; CI2N 5/864 (2006.01) 800/312 800/320.2: 800/317.3; 800/322; CI2N 5/8 (2006.01) 800/320.1; 530/350, 536/23.1: 800/278; 800/294 CI2N I/2 (2006.01) CI2N 5/10 (2006.01) (57) ABSTRACT CI2N L/15 (2006.01) CI2N I/19 (2006.01) The invention provides polypeptides, including enzymes, CI2N 9/14 (2006.01) structural proteins and binding proteins, polynucleotides CI2N 9/16 (2006.01) encoding these polypeptides, and methods of making and CI2N 9/20 (2006.01) using these polynucleotides and polypeptides. -
All Enzymes in BRENDA™ the Comprehensive Enzyme Information System
All enzymes in BRENDA™ The Comprehensive Enzyme Information System http://www.brenda-enzymes.org/index.php4?page=information/all_enzymes.php4 1.1.1.1 alcohol dehydrogenase 1.1.1.B1 D-arabitol-phosphate dehydrogenase 1.1.1.2 alcohol dehydrogenase (NADP+) 1.1.1.B3 (S)-specific secondary alcohol dehydrogenase 1.1.1.3 homoserine dehydrogenase 1.1.1.B4 (R)-specific secondary alcohol dehydrogenase 1.1.1.4 (R,R)-butanediol dehydrogenase 1.1.1.5 acetoin dehydrogenase 1.1.1.B5 NADP-retinol dehydrogenase 1.1.1.6 glycerol dehydrogenase 1.1.1.7 propanediol-phosphate dehydrogenase 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+) 1.1.1.9 D-xylulose reductase 1.1.1.10 L-xylulose reductase 1.1.1.11 D-arabinitol 4-dehydrogenase 1.1.1.12 L-arabinitol 4-dehydrogenase 1.1.1.13 L-arabinitol 2-dehydrogenase 1.1.1.14 L-iditol 2-dehydrogenase 1.1.1.15 D-iditol 2-dehydrogenase 1.1.1.16 galactitol 2-dehydrogenase 1.1.1.17 mannitol-1-phosphate 5-dehydrogenase 1.1.1.18 inositol 2-dehydrogenase 1.1.1.19 glucuronate reductase 1.1.1.20 glucuronolactone reductase 1.1.1.21 aldehyde reductase 1.1.1.22 UDP-glucose 6-dehydrogenase 1.1.1.23 histidinol dehydrogenase 1.1.1.24 quinate dehydrogenase 1.1.1.25 shikimate dehydrogenase 1.1.1.26 glyoxylate reductase 1.1.1.27 L-lactate dehydrogenase 1.1.1.28 D-lactate dehydrogenase 1.1.1.29 glycerate dehydrogenase 1.1.1.30 3-hydroxybutyrate dehydrogenase 1.1.1.31 3-hydroxyisobutyrate dehydrogenase 1.1.1.32 mevaldate reductase 1.1.1.33 mevaldate reductase (NADPH) 1.1.1.34 hydroxymethylglutaryl-CoA reductase (NADPH) 1.1.1.35 3-hydroxyacyl-CoA -
(12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur Et Al
US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015 (54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006. -
BMC Structural Biology Biomed Central
BMC Structural Biology BioMed Central Research article Open Access A comprehensive update of the sequence and structure classification of kinases Sara Cheek2, Krzysztof Ginalski2,3, Hong Zhang2 and Nick V Grishin*1,2 Address: 1Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA, 2Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA and 3Bioinformatics Laboratory, Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland Email: Sara Cheek - [email protected]; Krzysztof Ginalski - [email protected]; Hong Zhang - [email protected]; Nick V Grishin* - [email protected] * Corresponding author Published: 16 March 2005 Received: 11 January 2005 Accepted: 16 March 2005 BMC Structural Biology 2005, 5:6 doi:10.1186/1472-6807-5-6 This article is available from: http://www.biomedcentral.com/1472-6807/5/6 © 2005 Cheek et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results: The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years.