Encyclopedia of Metalloproteins

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springer.com Springer Reference Kretsinger, R.H., Uversky, V.N., Permyakov, E.A. (Eds.) Encyclopedia of Metalloproteins Covers various aspects of metalloprotein/ metalloproteomics, dealing with the different issues related to the intracellular and extracellular metal- binding proteins, including their structures, properties and functions Exhaustively reviews all catalytically and biologically crucial metal ions and to find at least one interacting protein for other metal ions Provides a key resource for advanced undergraduate and graduate students, researchers, instructors, and professors interested in protein-science, biochemistry, cell biology, and genetics Springer In biochemistry, a metalloprotein is a generic term for a protein that contains a metal cofactor. 2013, LVII, 2574 p. 1108 The metal may be an isolated ion or may be coordinated with a nonprotein organic compound, 1st illus., 777 illus. in color. In 4 such as the porphyrin found in hemoproteins. In some cases, the metal is co-coordinated with edition volumes, not available a side chain of the protein and an inorganic nonmetallic ion. This kind of protein-metal- separately. nonmetal structure is seen in iron-sulfur clusters Metalloproteins deals with all aspects related to the intracellular and extracellular metal-binding proteins, including their structures, Printed book properties and functions. The biological roles of metal cations and metal-binding proteins are Hardcover endless. They are involved in all crucial cellular activities. Many pathological conditions are related to the problematic metal metabolism. Research in metalloprotein-related topics is Printed book therefore rapidly growing, and different aspects of metal-binding proteins progressively enter Hardcover curricula at Universities and even at the High School level on occasion. However, no key ISBN 978-1-4614-1532-9 resource providing basic, but comprehensible knowledge on this rapidly expanding field exists. $ 949,99 The Encyclopedia of Metalloproteins aims to bridge this gap, and will attempt to cover various Available aspects of metalloprotein/metalloproteomics and will deal with the different issues related to Discount group the intracellular and extracellular metal-binding proteins, including their structures, properties Professional Books (2) and functions. Product category Encyclop(a)edia Order online at springer.com/booksellers Springer Nature Customer Service Center LLC Other renditions 233 Spring Street E-reference work New York, NY 10013 ISBN 978-1-4614-1533-6 USA Book with Online Access T: +1-800-SPRINGER NATURE ISBN 978-1-4614-1534-3 (777-4643) or 212-460-1500 [email protected] Prices and other details are subject to change without notice. All errors and omissions excepted. Americas: Tax will be added where applicable. Canadian residents please add PST, QST or GST. Please add $5.00 for shipping one book and $ 1.00 for each additional book. Outside the US and Canada add $ 10.00 for first book, $5.00 for each additional book. If an order cannot be fulfilled within 90 days, payment will be refunded upon request. Prices are payable in US currency or its equivalent. ISBN 978-1-4614-1532-9 / BIC: PSB / SPRINGER NATURE: SCL14005 Part of .

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How Do Bacterial Cells Ensure That Metalloproteins Get the Correct Metal?
REVIEWS How do bacterial cells ensure that metalloproteins get the correct metal? Kevin J. Waldron and Nigel J. Robinson Abstract | Protein metal-coordination sites are richly varied and exquisitely attuned to their inorganic partners, yet many metalloproteins still select the wrong metals when presented with mixtures of elements. Cells have evolved elaborate mechanisms to scavenge for sufficient metal atoms to meet their needs and to adjust their needs to match supply. Metal sensors, transporters and stores have often been discovered as metal-resistance determinants, but it is emerging that they perform a broader role in microbial physiology: they allow cells to overcome inadequate protein metal affinities to populate large numbers of metalloproteins with the right metals. It has been estimated that one-quarter to one-third of all Both monovalent (cuprous) copper, which is expected proteins require metals, although the exploitation of ele- to predominate in a reducing cytosol, and trivalent ments varies from cell to cell and has probably altered over (ferric) iron, which is expected to predominate in an the aeons to match geochemistry1–3 (BOX 1). The propor- oxidizing periplasm, are also highly competitive, as are tions have been inferred from the numbers of homologues several non-essential metals, such as cadmium, mercury of known metalloproteins, and other deduced metal- and silver6 (BOX 2). How can a cell simultaneously contain binding motifs, encoded within sequenced genomes. A some proteins that require copper or zinc and others that large experimental estimate was generated using native require uncompetitive metals, such as magnesium or polyacrylamide-gel electrophoresis of extracts from iron- manganese? In a most simplistic model in which pro- rich Ferroplasma acidiphilum followed by the detection of teins pick elements from a cytosol in which all divalent metal in protein spots using inductively coupled plasma metals are present and abundant, all proteins would bind mass spectrometry4.
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Characterization of Triggerable Quinones for the Development Of
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2011 Characterization of Triggerable Quinones for the Development of Enzyme-Responsive Liposomes Maria Fabiana Mendoza Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Chemistry Commons Recommended Citation Mendoza, Maria Fabiana, "Characterization of Triggerable Quinones for the Development of Enzyme-Responsive Liposomes" (2011). LSU Doctoral Dissertations. 1173. https://digitalcommons.lsu.edu/gradschool_dissertations/1173 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. CHARACTERIZATION OF TRIGGERABLE QUINONES FOR THE DEVELOPMENT OF ENZYME-RESPONSIVE LIPOSOMES A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the Requirements for the degree of Doctor of Philosophy In The Department of Chemistry by Maria Fabiana Mendoza B.S., Missouri Baptist University, 2005 May 2012 DEDICATION This dissertation is dedicated to my loving grandmother: Mabel Cerri Burgantis de Mendoza And to My Mom, Ibis Elizabeth Paris Bargas My Dad, Hector Eduardo Mendoza Cerri My Brother, Facundo Horacio Jesus Mendoza Paris My Brother, Jose Hector Mendoza Paris My Partner, Dayna Tatiana Pastorino Martinez ii ACKNOWLEDGMENTS I would like to thank my advisor, Dr. Robin L. McCarley, for his extraordinarily guidance and support through all these years in graduate school. I still remember my visit to LSU and how from the moment I interacted with his graduate students and met him I knew that I would like to be a part of his group.
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Electron Transfer Precedes ATP Hydrolysis During Nitrogenase Catalysis
Electron transfer precedes ATP hydrolysis during nitrogenase catalysis Simon Duvala,1, Karamatullah Danyala,1, Sudipta Shawa, Anna K. Lytlea, Dennis R. Deanb, Brian M. Hoffmanc, Edwin Antonya,2, and Lance C. Seefeldta,2 aDepartment of Chemistry and Biochemistry, Utah State University, Logan, UT 84322; bDepartment of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061; and cDepartment of Chemistry, Northwestern University, Evanston, IL 60208 Edited by Harry B. Gray, California Institute of Technology, Pasadena, CA, and approved August 28, 2013 (received for review June 12, 2013) 2+ The biological reduction of N2 to NH3 catalyzed by Mo-dependent an oxidized [4Fe–4S] cluster in the Fe protein (12). This second − nitrogenase requires at least eight rounds of a complex cycle of step is fast, having a rate constant greater than 1,700 s 1 (12). events associated with ATP-driven electron transfer (ET) from the Transfer of one electron from the Fe protein to an αβ-unit of Fe protein to the catalytic MoFe protein, with each ET coupled to MoFe protein is known to be coupled to the hydrolysis of the the hydrolysis of two ATP molecules. Although steps within this two ATP molecules bound to the Fe protein, yielding two ADP cycle have been studied for decades, the nature of the coupling and two Pi (2). Following the hydrolysis reaction, the two between ATP hydrolysis and ET, in particular the order of ET and phosphates (Pi) are released from the protein complex with −1 ATP hydrolysis, has been elusive. Here, we have measured ﬁrst- a ﬁrst-order rate constant (kPi)of22s at 23 °C (13).
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WO 2017/062311 Al 13 April 2017 (13.04.2017) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2017/062311 Al 13 April 2017 (13.04.2017) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, A61P 39/00 (2006.01) A23L 33/175 (2016.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, A23L 33/13 (201 6.01) A61K 36/48 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, PCT/US20 16/055 173 MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (22) International Filing Date: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 3 October 2016 (03. 10.2016) SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, (25) Filing Language: English ZW. (26) Publication Language: English (84) Designated States (unless otherwise indicated, for every (30) Priority Data: kind of regional protection available): ARIPO (BW, GH, 62/238,338 7 October 201 5 (07. 10.2015) US GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, (72) Inventor; and TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant : HUIZENGA, Joel [US/US]; 354 Gravilla DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, Street, La Jolla, California 92037 (US).
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1 Characterization of Metalloproteins by High-Throughput X-Ray
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Characterization of Metalloproteins by High-Throughput X-ray Absorption Spectroscopy Wuxian Shi1,*, Marco Punta2, Jen Bohon1, J. Michael Sauder3, Rhijuta D’Mello1, Mike Sullivan1, John Toomey1, Don Abel1, Marco Lippi4, Andrea Passerini5, Paolo Frasconi4, Stephen K. Burley3, Burkhard Rost2,6 and Mark R. Chance1 1 New York SGX Research Center for Structural Genomics (NYSGXRC), Case Western Reserve University, Center for Proteomics and Bioinformatics, Case Center for Synchrotron Biosciences, Upton, NY 11973 USA. 2 TUM Munich, Informatik, Bioinformatik, Institute for Advanced Studies, Germany. 3 New York SGX Research Center for Structural Genomics (NYSGXRC), Eli Lilly and Company, Lilly Biotechnology Center, 10300 Campus Point Drive, Suite 200, San Diego, CA 92121 USA. 4 Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze, Italy 5 Dipartimento di Ingegneria e Scienza dell’Informazione, Università degli Studi di Trento, Italy. 6 New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA. *Corresponding author: Professor Wuxian Shi, contact [email protected] Key words: metalloproteomics, structural genomics, metalloprotein, homology modeling, metal binding site, transition metal. Running title: Characterization of Metalloproteins by HT-XAS 1 Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract: High-Throughput X-ray Absorption Spectroscopy was used to measure transition metal content based on quantitative detection of X-ray fluorescence signals for 3879 purified proteins from several hundred different protein families generated by the New York SGX Research Center for Structural Genomics.
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University of Groningen Exploring the Cofactor-Binding and Biocatalytic
University of Groningen Exploring the cofactor-binding and biocatalytic properties of flavin-containing enzymes Kopacz, Malgorzata IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2014 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Kopacz, M. (2014). Exploring the cofactor-binding and biocatalytic properties of flavin-containing enzymes. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date: 29-09-2021 Exploring the cofactor-binding and biocatalytic properties of flavin-containing enzymes Małgorzata M. Kopacz The research described in this thesis was carried out in the research group Molecular Enzymology of the Groningen Biomolecular Sciences and Biotechnology Institute (GBB), according to the requirements of the Graduate School of Science, Faculty of Mathematics and Natural Sciences.
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Observing 3-Hydroxyanthranilate-3,4-Dioxygenase in Action Through a Crystalline Lens
Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens Yifan Wanga,1, Kathy Fange Liub,1, Yu Yanga, Ian Davisa, and Aimin Liua,2 aDepartment of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249; and bDepartment of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 Edited by John T. Groves, Princeton University, Princeton, NJ, and approved July 7, 2020 (received for review March 20, 2020) The synthesis of quinolinic acid from tryptophan is a critical step in the shared in these two pathways (Scheme 1). HAO from all sources de novo biosynthesis of nicotinamide adenine dinucleotide (NAD+)in presents in a homodimeric form, and each subunit consists of a mammals. Herein, the nonheme iron-based 3-hydroxyanthranilate-3,4- Cupin structural fold (12, 13). The catalytic machinery is orches- dioxygenase responsible for quinolinic acid production was studied by trated by a nonheme iron ion coordinated by a 2-His-1-Glu facial performing time-resolved in crystallo reactions monitored by UV-vis triad (14), which is located in the center of a Cupin domain. Some microspectroscopy, electron paramagnetic resonance (EPR) spectros- bacterial HAOs contain a noncatalytic, rubredoxin-like site on the copy, and X-ray crystallography. Seven catalytic intermediates were protein surface for iron acquisition and storage (15). In the solu- kinetically and structurally resolved in the crystalline state, and each tion state, HAO is an efficient catalyst with a reported turnover − accompanies protein conformational changes at the active site. Among rate of 25 s 1 (12, 16).
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Metalloprotein Entatic Control of Ligand-Metal Bonds Quantified by Ultrafast X-Ray Spectroscopy
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Science Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 November 29. Published in final edited form as: Science. 2017 June 23; 356(6344): 1276–1280. doi:10.1126/science.aam6203. Metalloprotein entatic control of ligand-metal bonds quantified by ultrafast x-ray spectroscopy Michael W. Mara1,2,*, Ryan G. Hadt1,†, Marco Eli Reinhard3, Thomas Kroll2,4, Hyeongtaek Lim1,2, Robert W. Hartsock3, Roberto Alonso-Mori4, Matthieu Chollet4, James M. Glownia4, Silke Nelson4, Dimosthenis Sokaras2,4, Kristjan Kunnus3, Keith O. Hodgson1,2, Britt Hedman2, Uwe Bergmann3,4, Kelly J. Gaffney2,3, and Edward I. Solomon1,2,‡ 1Department of Chemistry, Stanford University, Stanford, CA 94305, USA 2Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA 3PULSE Institute, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305, USA 4Linac Coherent Light Source, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA Abstract The multifunctional protein cytochrome c (cyt c) plays key roles in electron transport and apoptosis, switching function by modulating bonding between a heme iron and the sulfur in a methionine residue. This Fe–S(Met) bond is too weak to persist in the absence of protein constraints. We ruptured the bond in ferrous cyt c using an optical laser pulse and monitored the bond reformation within the protein active site using ultrafast x-ray pulses from an x-ray free- electron laser, determining that the Fe–S(Met) bond enthalpy is ~4 kcal/mol stronger than in the absence of protein constraints.
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Analysis of the Structural Consensus of the Zinc Coordination Centers of Metalloprotein Structures ⁎ Kirti Patel, Anil Kumar, Susheel Durani
Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures ⁎ Kirti Patel, Anil Kumar, Susheel Durani Department of Chemistry, Indian Institute of Technology Bombay, Mumbai-400076, India Abstract In a recent sequence-analysis study it was concluded that up to 10% of the human proteome could be comprised of zinc proteins, quite varied in the functional spread. The native structures of only few of the proteins are actually established. The elucidation of rest of the sequences of not just human but even other actively investigated genomes may benefit from knowledge of the structural consensus of the zinc-binding centers of the currently known zinc proteins. Nearly four hundred X-ray and NMR structures in the database of zinc–protein structures available as of April 2007 were investigated for geometry and conformation in the zinc-binding centers; separately for the structural and catalytic proteins and individually in the zinc centers coordinated to three and four amino-acid ligands. Enhanced cysteine involvement in agreement with the observation in human proteome has been detected in contrast with previous reports. Deviations from ideal coordination geometries are detected, possible underlying reasons are investigated, and correlations of geometry and conformation in zinc-coordination centers with protein function are established, providing possible benchmarks for putative zinc-binding patterns of the burgeoning genome data. Keywords: Metalloprotein; Zinc–protein; Zinc binding pattern; Zinc coordination; Structural zinc-center; Catalytic zinc-center 1. Introduction processes, like, transcription, translation, and metabolism [3–8]. Based on homology based searches of human genome, Andreini The second most abundant transition element in biological et al.
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University of California, San Diego
UNIVERSITY OF CALIFORNIA, SAN DIEGO Design and Characterization of an Allosteric Metalloprotein Assembly A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry by Lewis Anthony Churchfield Committee in charge: Professor F. Akif Tezcan, Chair Professor Michael D. Burkart Professor Neal K. Devaraj Professor Tracy M. Handel Professor Valerie A. Schmidt 2018 Copyright Lewis Anthony Churchfield, 2018 All rights reserved. Signature Page This Dissertation of Lewis Anthony Churchfield is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2018 iii EPIGRAPH Epigraph Sometimes science is more art than science. Dr. Rick Sanchez iv TABLE OF CONTENTS Table of Contents Signature Page ................................................................................................................... iii Epigraph ............................................................................................................................. iv Table of Contents ................................................................................................................ v List of Abbreviations ........................................................................................................ vii List of Figures .................................................................................................................... ix List of Tables ..................................................................................................................
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Design of Metalloproteins for Catalysis and Bioimaging
Syracuse University SURFACE Syracuse University Honors Program Capstone Syracuse University Honors Program Capstone Projects Projects Spring 5-1-2013 Design of Metalloproteins for Catalysis and Bioimaging Krystyna Zhezherya Follow this and additional works at: https://surface.syr.edu/honors_capstone Part of the Biochemistry Commons Recommended Citation Zhezherya, Krystyna, "Design of Metalloproteins for Catalysis and Bioimaging" (2013). Syracuse University Honors Program Capstone Projects. 75. https://surface.syr.edu/honors_capstone/75 This Honors Capstone Project is brought to you for free and open access by the Syracuse University Honors Program Capstone Projects at SURFACE. It has been accepted for inclusion in Syracuse University Honors Program Capstone Projects by an authorized administrator of SURFACE. For more information, please contact [email protected]. Introduction: Metalloprotein s Metalloproteins are a versatile class of biological molecules containing a protein and a metal ion cofactor. It is estimated that 25-50% of all proteins coordinate at least one metal ion .1 Often, the metal cofactor is necessary for metalloprotein function, which can incl ude involvement in signal transduction pathways, transport of metal ions within cells, and carrying out enzymatic roles in a multitude of biochemical reactions .2,3 Proteins provide a fairl y limited number of options for size and geometry for the metal coor dination sphere . Nevertheless, some metalloproteins are highly specific for metal ions, while others can bind a wide array of metals. An example of a non- specific metalloprotein is metallothionein, MT, which is a protein that contains ~30% cysteine residue s, whose thiol groups are capable of coordinating metals commonly Figure 1. ααα-domain of human found in the body including zinc, selenium, metallothionein -3, MT-3 and copper as well as xenobiotic metals The featured MT domain is shown coordinating four including arseni c, silver, cadmium, and cadmium ions, illustrated as 4 blue spheres; PDB ID 2FJ4 mercury.
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QM/MM Molecular Dynamics Studies of Metal Binding Proteins
Biomolecules 2014, 4, 616-645; doi:10.3390/biom4030616 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review QM/MM Molecular Dynamics Studies of Metal Binding Proteins Pietro Vidossich 1,2 and Alessandra Magistrato 3,* 1 Department of Chemistry, Autonomous University of Barcelona, 08193 Cerdanyola del Vallés, Spain; E-Mail: [email protected] 2 German Research School for Simulation Sciences, D-52425 Jülich, Germany 3 CNR-IOM-Democritos National Simulation Center c/o, International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34165 Trieste, Italy * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +39-040-3787-529; Fax: +39-040-3787-528. Received: 18 March 2014; in revised form: 5 June 2014 / Accepted: 6 June 2014 / Published: 8 July 2014 Abstract: Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals.
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