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Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
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Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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2
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Laveglia V, Bazayeva M, Andreini C, Rosato A. Hunting down zinc(II)-binding sites in proteins with distance matrices. Bioinformatics 2023; 39:btad653. [PMID: 37878807 PMCID: PMC10630175 DOI: 10.1093/bioinformatics/btad653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
MOTIVATION In recent years, high-throughput sequencing technologies have made available the genome sequences of a huge variety of organisms. However, the functional annotation of the encoded proteins often still relies on low-throughput and costly experimental studies. Bioinformatics approaches offer a promising alternative to accelerate this process. In this work, we focus on the binding of zinc(II) ions, which is needed for 5%-10% of any organism's proteins to achieve their physiologically relevant form. RESULTS To implement a predictor of zinc(II)-binding sites in the 3D structures of proteins, we used a neural network, followed by a filter of the network output against the local structure of all known sites. The latter was implemented as a function comparing the distance matrices of the Cα and Cβ atoms of the sites. We called the resulting tool Master of Metals (MOM). The structural models for the entire proteome of an organism generated by AlphaFold can be used as input to our tool in order to achieve annotation at the whole organism level within a few hours. To demonstrate this, we applied MOM to the yeast proteome, obtaining a precision of about 76%, based on data for homologous proteins. AVAILABILITY AND IMPLEMENTATION Master of Metals has been implemented in Python and is available at https://github.com/cerm-cirmmp/Master-of-metals.
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Affiliation(s)
- Vincenzo Laveglia
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
| | - Milana Bazayeva
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Sesto Fiorentino 50019, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Sesto Fiorentino 50019, Italy
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3
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McGuinness KN, Klau GW, Morrison SM, Moore EK, Seipp J, Falkowski PG, Nanda V. Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution. ORIGINS LIFE EVOL B 2022; 52:263-275. [DOI: 10.1007/s11084-022-09630-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/03/2022] [Indexed: 11/17/2022]
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4
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Yang H, Kim J, Lee W, Lee J, Seo J. Electronic property of
alkoxo‐bridged
tetranuclear Fe(
II
) cluster and
CO
2
hydrogenation reactivity. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Hyoyi Yang
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Jihyun Kim
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Wonjung Lee
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
| | - Junseong Lee
- Department of Chemistry Chonnam National University Gwangju Republic of Korea
| | - Junhyeok Seo
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju Republic of Korea
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5
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Philpott CC, Jadhav S. The ins and outs of iron: Escorting iron through the mammalian cytosol. Free Radic Biol Med 2019; 133:112-117. [PMID: 30321701 DOI: 10.1016/j.freeradbiomed.2018.10.411] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 01/01/2023]
Abstract
Mammalian cells contain thousands of metalloproteins and have evolved sophisticated systems for ensuring that metal cofactors are correctly assembled and delivered to their proper destinations. Equally critical in this process are the strategies to avoid the insertion of the wrong metal cofactor into apo-proteins and to avoid the damage that redox-active metals can catalyze in the cellular milieu. Iron and zinc are the most abundant metal cofactors in cells and iron cofactors include heme, iron-sulfur clusters, and mono- and dinuclear iron centers. Systems for the intracellular trafficking of iron cofactors are being characterized. This review focuses on the trafficking of ferrous iron cofactors in the cytosol of mammalian cells, a process that involves specialized iron-binding proteins, termed iron chaperones, of the poly rC-binding protein family.
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Affiliation(s)
- Caroline C Philpott
- Genetics and Metabolism, Section Liver Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, United States.
| | - Shyamalagauri Jadhav
- Genetics and Metabolism, Section Liver Diseases Branch, NIDDK, National Institutes of Health, Bethesda, MD 20892, United States
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Trace Elements and Healthcare: A Bioinformatics Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1005:63-98. [PMID: 28916929 DOI: 10.1007/978-981-10-5717-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals. The relationship between individual elements and several diseases based on recent large-scale systematic studies such as genome-wide association studies and case-control studies is discussed. Lastly, developments of ionomics and its recent application in human health are also introduced.
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7
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Raanan H, Pike DH, Moore EK, Falkowski PG, Nanda V. Modular origins of biological electron transfer chains. Proc Natl Acad Sci U S A 2018; 115:1280-1285. [PMID: 29358375 PMCID: PMC5819401 DOI: 10.1073/pnas.1714225115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Oxidoreductases catalyze electron transfer reactions that ultimately provide the energy for life. A limited set of ancestral protein-metal modules are presumably the building blocks that evolved into this diverse protein family. However, the identity of these modules and their path to modern oxidoreductases is unknown. Using a comparative structural analysis approach, we identify a set of fundamental electron transfer modules that have evolved to form the extant oxidoreductases. Using transition metal-containing cofactors as fiducial markers, it is possible to cluster cofactor microenvironments into as few as four major modules: bacterial ferredoxin, cytochrome c, symerythrin, and plastocyanin-type folds. From structural alignments, it is challenging to ascertain whether modules evolved from a single common ancestor (homology) or arose by independent convergence on a limited set of structural forms (analogy). Additional insight into common origins is contained in the spatial adjacency network (SPAN), which is based on proximity of modules in oxidoreductases containing multiple cofactor electron transfer chains. Electron transfer chains within complex modern oxidoreductases likely evolved through repeated duplication and diversification of ancient modular units that arose in the Archean eon.
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Affiliation(s)
- Hagai Raanan
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854
| | - Douglas H Pike
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854
| | - Eli K Moore
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901;
- Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, NJ 08901
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854;
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854
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8
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Christenson ET, Gallegos AS, Banerjee A. In vitro reconstitution, functional dissection, and mutational analysis of metal ion transport by mitoferrin-1. J Biol Chem 2018; 293:3819-3828. [PMID: 29305420 DOI: 10.1074/jbc.m117.817478] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/21/2017] [Indexed: 01/01/2023] Open
Abstract
Iron is universally important to cellular metabolism, and mitoferrin-1 and -2 have been proposed to be the iron importers of mitochondria, the cell's assembly plant of heme and iron-sulfur clusters. These iron-containing prosthetic groups are critical for a host of physiological processes ranging from oxygen transport and energy consumption to maintaining protein structural integrity. Mitoferrin-1 (Mfrn1) belongs to the mitochondrial carrier (MC) family and is atypical given its putative metallic cargo; most MCs transport nucleotides, amino acids, or other small- to medium-size metabolites. Despite the clear importance of Mfrn1 in iron utilization, its transport activity has not been demonstrated unambiguously. To bridge this knowledge gap, we have purified recombinant Mfrn1 under non-denaturing conditions and probed its metal ion-binding and transport functions. Isothermal titration calorimetry indicates that Mfrn1 has micromolar affinity for Fe(II), Mn(II), Co(II), and Ni(II). Mfrn1 was incorporated into defined liposomes, and iron transport was reconstituted in vitro, demonstrating that Mfrn1 can transport iron. Mfrn1 can also transport manganese, cobalt, copper, and zinc but discriminates against nickel. Experiments with candidate ligands for cellular labile iron reveal that Mfrn1 transports free iron and not a chelated iron complex and selects against alkali divalent ions. Extensive mutagenesis identified multiple residues that are crucial for metal binding, transport activity, or both. There is a clear abundance of residues with side chains that can coordinate first-row transition metal ions, suggesting that these could form primary or auxiliary metal-binding sites during the transport process.
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Affiliation(s)
- Eric T Christenson
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Austin S Gallegos
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - Anirban Banerjee
- From the Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
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9
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Proteome scale identification, classification and structural analysis of iron-binding proteins in bread wheat. J Inorg Biochem 2017; 170:63-74. [DOI: 10.1016/j.jinorgbio.2017.02.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 01/23/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
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10
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Peroxiredoxin 1 (Prx1) is a dual-function enzyme by possessing Cys-independent catalase-like activity. Biochem J 2017; 474:1373-1394. [PMID: 28219939 PMCID: PMC5452528 DOI: 10.1042/bcj20160851] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 02/01/2023]
Abstract
Peroxiredoxin (Prx) was previously known as a Cys-dependent thioredoxin. However, we unexpectedly observed that Prx1 from the green spotted puffer fish Tetraodon nigroviridis (TnPrx1) was able to reduce H2O2 in a manner independent of Cys peroxidation and reductants. This study aimed to validate a novel function for Prx1, delineate the biochemical features and explore its antioxidant role in cells. We have confirmed that Prx1 from the puffer fish and humans truly possesses a catalase (CAT)-like activity that is independent of Cys residues and reductants, but dependent on iron. We have identified that the GVL motif was essential to the CAT-like activity of Prx1, but not to the Cys-dependent thioredoxin peroxidase (POX) activity, and generated mutants lacking POX and/or CAT-like activities for individual functional validation. We discovered that the TnPrx1 POX and CAT-like activities possessed different kinetic features in the reduction of H2O2. The overexpression of wild-type TnPrx1 and mutants differentially regulated the intracellular levels of reactive oxygen species (ROS) and the phosphorylation of p38 in HEK-293T cells treated with H2O2. Prx1 is a dual-function enzyme by acting as POX and CAT with varied affinities towards ROS. This study extends our knowledge on Prx1 and provides new opportunities to further study the biological roles of this family of antioxidants.
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11
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Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. Int J Mol Sci 2016; 17:ijms17050671. [PMID: 27153067 PMCID: PMC4881497 DOI: 10.3390/ijms17050671] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 04/18/2016] [Accepted: 04/28/2016] [Indexed: 12/12/2022] Open
Abstract
Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity.
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12
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Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D. Structural principles for computational and de novo design of 4Fe-4S metalloproteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1857:531-538. [PMID: 26449207 DOI: 10.1016/j.bbabio.2015.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/01/2015] [Indexed: 11/30/2022]
Abstract
Iron-sulfur centers in metalloproteins can access multiple oxidation states over a broad range of potentials, allowing them to participate in a variety of electron transfer reactions and serving as catalysts for high-energy redox processes. The nitrogenase FeMoCO cluster converts di-nitrogen to ammonia in an eight-electron transfer step. The 2(Fe4S4) containing bacterial ferredoxin is an evolutionarily ancient metalloprotein fold and is thought to be a primordial progenitor of extant oxidoreductases. Controlling chemical transformations mediated by iron-sulfur centers such as nitrogen fixation, hydrogen production as well as electron transfer reactions involved in photosynthesis are of tremendous importance for sustainable chemistry and energy production initiatives. As such, there is significant interest in the design of iron-sulfur proteins as minimal models to gain fundamental understanding of complex natural systems and as lead-molecules for industrial and energy applications. Herein, we discuss salient structural characteristics of natural iron-sulfur proteins and how they guide principles for design. Model structures of past designs are analyzed in the context of these principles and potential directions for enhanced designs are presented, and new areas of iron-sulfur protein design are proposed. This article is part of a Special issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, protein networks, edited by Ronald L. Koder and J.L Ross Anderson.
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Affiliation(s)
- Vikas Nanda
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
| | - Stefan Senn
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Douglas H Pike
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Agustina Rodriguez-Granillo
- Department of Biochemistry and Molecular Biology and the Center for Advanced Biotechnology and Medicine, Robert Wood Johnson Medical School, Rutgers University, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Will A Hansen
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and the Center for Integrated Proteomics Research, Rutgers University, 174 Frelinghuysen Rd, Piscataway, NJ 08854, USA
| | - Dror Noy
- Bioenergetics and Protein Design Laboratory, Migal - Galilee Research Institute, South Industrial Zone, Kiryat Shmona 11016, Israel
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13
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Sun CC, Dong WR, Zhao J, Nie L, Xiang LX, Zhu G, Shao JZ. Cysteine-independent Catalase-like Activity of Vertebrate Peroxiredoxin 1 (Prx1). J Biol Chem 2015; 290:19942-54. [PMID: 26088136 DOI: 10.1074/jbc.m115.659011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 11/06/2022] Open
Abstract
Peroxiredoxins (Prxs) are a ubiquitous family of antioxidant proteins that are known as thioredoxin peroxidases. Here we report that Prx1 proteins from Tetraodon nigroviridis and humans also possess a previously unknown catalase-like activity that is independent of Cys residues and reductants but dependent on iron. We identified that the GVL motif was essential to the catalase (CAT)-like activity of Prx1 but not to the Cys-dependent thioredoxin peroxidase (POX) activity, and we generated mutants lacking POX and/or CAT activities for individually delineating their functional features. We discovered that the TnPrx1 POX and CAT activities possessed different kinetic features in reducing H2O2. The overexpression of wild-type TnPrx1 and mutants differentially regulated the intracellular levels of reactive oxygen species and p38 phosphorylation in HEK-293T cells treated with H2O2. These observations suggest that the dual antioxidant activities of Prx1 may be crucial for organisms to mediate intracellular redox homeostasis.
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Affiliation(s)
- Cen-Cen Sun
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
| | - Wei-Ren Dong
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
| | - Jing Zhao
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
| | - Li Nie
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
| | - Li-Xin Xiang
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
| | - Guan Zhu
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and the Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843
| | - Jian-Zhong Shao
- From the College of Life Sciences, Zhejiang University and Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou 310058, China and
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14
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Zhang C. Involvement of Iron-Containing Proteins in Genome Integrity in Arabidopsis Thaliana. Genome Integr 2015; 6:2. [PMID: 27330736 PMCID: PMC4911903 DOI: 10.4103/2041-9414.155953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/12/2015] [Indexed: 01/03/2023] Open
Abstract
The Arabidopsis genome encodes numerous iron-containing proteins such as iron-sulfur (Fe-S) cluster proteins and hemoproteins. These proteins generally utilize iron as a cofactor, and they perform critical roles in photosynthesis, genome stability, electron transfer, and oxidation-reduction reactions. Plants have evolved sophisticated mechanisms to maintain iron homeostasis for the assembly of functional iron-containing proteins, thereby ensuring genome stability, cell development, and plant growth. Over the past few years, our understanding of iron-containing proteins and their functions involved in genome stability has expanded enormously. In this review, I provide the current perspectives on iron homeostasis in Arabidopsis, followed by a summary of iron-containing protein functions involved in genome stability maintenance and a discussion of their possible molecular mechanisms.
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Affiliation(s)
- Caiguo Zhang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
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15
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Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites. Sci Rep 2015; 5:9486. [PMID: 25820752 PMCID: PMC4377587 DOI: 10.1038/srep09486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/02/2015] [Indexed: 12/25/2022] Open
Abstract
Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the proposed computational protocol to all heme-binding proteins and zinc-binding proteins of known structure highlighted the existence of structural subtypes, validated known evolutionary links and shed new light on the occurrence of similar sites in systems at different evolutionary distances. The present approach thus makes available an innovative viewpoint on metalloproteins, where the functionally crucial metal sites effectively lead the discovery of structural and functional relationships in a largely protein-independent manner.
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16
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Piccioli M, Turano P. Transient iron coordination sites in proteins: Exploiting the dual nature of paramagnetic NMR. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Anand P, Nagarajan D, Mukherjee S, Chandra N. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res 2014; 3:214. [PMID: 25685322 DOI: 10.12688/f1000research.5165.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/01/2014] [Indexed: 03/24/2024] Open
Abstract
Most physiological processes in living systems are fundamentally regulated by protein-ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are computed by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide clues to researchers about residues to obtain loss-of-function mutations and to understand drug resistant mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
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Affiliation(s)
- Praveen Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sumanta Mukherjee
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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Anand P, Nagarajan D, Mukherjee S, Chandra N. ABS-Scan: In silico alanine scanning mutagenesis for binding site residues in protein-ligand complex. F1000Res 2014; 3:214. [PMID: 25685322 PMCID: PMC4319546 DOI: 10.12688/f1000research.5165.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/24/2014] [Indexed: 12/27/2022] Open
Abstract
Most physiological processes in living systems are fundamentally regulated by protein-ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
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Affiliation(s)
- Praveen Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Deepesh Nagarajan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Sumanta Mukherjee
- IISc Mathematics Initiative, Indian Institute of Science, Bangalore, 560012, India
| | - Nagasuma Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
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Valasatava Y, Rosato A, Cavallaro G, Andreini C. MetalS(3), a database-mining tool for the identification of structurally similar metal sites. J Biol Inorg Chem 2014; 19:937-45. [PMID: 24699831 DOI: 10.1007/s00775-014-1128-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 03/19/2014] [Indexed: 12/14/2022]
Abstract
We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.
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Affiliation(s)
- Yana Valasatava
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy
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21
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Andreini C, Cavallaro G, Rosato A, Valasatava Y. MetalS2: a tool for the structural alignment of minimal functional sites in metal-binding proteins and nucleic acids. J Chem Inf Model 2013; 53:3064-75. [PMID: 24117467 DOI: 10.1021/ci400459w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We developed a new software tool, MetalS(2), for the structural alignment of Minimal Functional Sites (MFSs) in metal-binding biological macromolecules. MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. On our example data sets, MetalS(2) unveiled structural similarities that other programs for protein structure comparison do not consistently point out and overall identified a larger number of structurally similar MFSs. MetalS(2) supports the comparison of MFSs harboring different metals and/or with different nuclearity and is available both as a stand-alone program and a Web tool ( http://metalweb.cerm.unifi.it/tools/metals2/).
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM) - University of Florence , Via L. Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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22
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Human anamorsin binds [2Fe–2S] clusters with unique electronic properties. J Biol Inorg Chem 2013; 18:883-93. [DOI: 10.1007/s00775-013-1033-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/05/2013] [Indexed: 11/27/2022]
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23
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Tam W, Pell LG, Bona D, Tsai A, Dai XX, Edwards AM, Hendrix RW, Maxwell KL, Davidson AR. Tail tip proteins related to bacteriophage λ gpL coordinate an iron-sulfur cluster. J Mol Biol 2013; 425:2450-62. [PMID: 23542343 DOI: 10.1016/j.jmb.2013.03.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/12/2013] [Accepted: 03/23/2013] [Indexed: 01/20/2023]
Abstract
The assembly of long non-contractile phage tails begins with the formation of the tail tip complex (TTC). TTCs are multi-functional protein structures that mediate host cell adsorption and genome injection. The TTC of phage λ is assembled from multiple copies of eight different proteins, including gpL. Purified preparations of gpL and several homologues all displayed a distinct reddish color, suggesting the binding of iron by these proteins. Further characterization of the gpL homologue from phage N15, which was most amenable to in vitro analyses, showed that it contains two domains. The C-terminal domain was demonstrated to coordinate an iron-sulfur cluster, providing the first example of a viral structural protein binding to this type of metal group. We characterized the iron-sulfur cluster using inductively coupled plasma-atomic emission spectroscopy, absorbance spectroscopy, and electron paramagnetic resonance spectroscopy and found that it is an oxygen-sensitive [4Fe-4S](2+) cluster. Four highly conserved cysteine residues were shown to be required for coordinating the iron-sulfur cluster, and substitution of any of these Cys residues with Ser or Ala within the context of λ gpL abolished biological activity. These data imply that the intact iron-sulfur cluster is required for function. The presence of four conserved Cys residues in the C-terminal regions of very diverse gpL homologues suggest that utilization of an iron-sulfur cluster is a widespread feature of non-contractile tailed phages that infect Gram-negative bacteria. In addition, this is the first example of a viral structural protein that binds an iron-sulfur cluster.
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Affiliation(s)
- William Tam
- Department of Biochemistry, University of Toronto, Medical Sciences Building, Toronto, ON, Canada M5S 1A8
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24
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Abstract
The nature of the cytosolic iron pool remains largely uncharacterized, although a range of candidate ligands and chaperones have been proposed. Herein an overview is presented of cytosolic non heme and non iron-sulphur cluster protein iron binding sites and the influence of ligands on the redox activity of iron. This analysis leads to the concept of iron(II) glutathione functioning as the labile cytosolic iron pool and offers a means for the selection of iron over manganese in subsequent incorporation into a wide range of iron-dependent enzymes and electron transfer proteins. Glutathione and glutathione-binding glutaredoxins play a critical role in iron sulfur cluster synthesis and Fe(II)GS (iron(II) coordinated by the thiol function of glutathione) is a suitable iron donor for this biosynthetic route. Significantly, both glutathione and glutaredoxins are universally distributed and thus a controlling influence of glutathione on intracellular iron trafficking is likely to be a common feature of the majority of living organisms.
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Affiliation(s)
- Robert C Hider
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK.
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25
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Cun S, Lai YT, Chang YY, Sun H. Structure-oriented bioinformatic approach exploring histidine-rich clusters in proteins. Metallomics 2013; 5:904-12. [DOI: 10.1039/c3mt00026e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Abstract
Iron is a redox active metal which is abundant in the Earth's crust. It has played a key role in the evolution of living systems and as such is an essential element in a wide range of biological phenomena, being critical for the function of an enormous array of enzymes, energy transduction mechanisms, and oxygen carriers. The redox nature of iron renders the metal toxic in excess and consequently all biological organisms carefully control iron levels. In this overview the mechanisms adopted by man to control body iron levels are described.Low body iron levels are related to anemia which can be treated by various forms of iron fortification and supplementation. Elevated iron levels can occur systemically or locally, each giving rise to specific symptoms. Systemic iron overload results from either the hyperabsorption of iron or regular blood transfusion and can be treated by the use of a selection of iron chelating molecules. The symptoms of many forms of neurodegeneration are associated with elevated levels of iron in certain regions of the brain and iron chelation therapy is beginning to find an application in the treatment of such diseases. Iron chelators have also been widely investigated for the treatment of cancer, tuberculosis, and malaria. In these latter studies, selective removal of iron from key enzymes or iron binding proteins is sought. Sufficient selectivity between the invading organism and the host has yet to be established for such chelators to find application in the clinic.Iron chelation for systemic iron overload and iron supplementation therapy for the treatment of various forms of anemia are now established procedures in clinical medicine. Chelation therapy may find an important role in the treatment of various neurodegenerative diseases in the near future.
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Andreini C, Cavallaro G, Lorenzini S, Rosato A. MetalPDB: a database of metal sites in biological macromolecular structures. Nucleic Acids Res 2012; 41:D312-9. [PMID: 23155064 PMCID: PMC3531106 DOI: 10.1093/nar/gks1063] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal–macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto, Fiorentino, Italy.
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28
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Armstrong CT, Watkins DW, Anderson JLR. Constructing manmade enzymes for oxygen activation. Dalton Trans 2012; 42:3136-50. [PMID: 23076271 DOI: 10.1039/c2dt32010j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Natural oxygenases catalyse the insertion of oxygen into an impressive array of organic substrates with exquisite efficiency, specificity and power unparalleled by current biomimetic catalysts. However, their true potential to provide tailor-made oxygenation catalysts remains largely untapped, perhaps a consequence of the evolutionary complexity imprinted into their three-dimensional structures through millennia of exposure to parallel selective pressures. In this perspective we describe how we may take inspiration from natural enzymes to design manmade oxygenase enzymes free from such complexity. We explore the differing chemistries accessed by natural oxygenases and outline a stepwise methodology whereby functional elements key to oxygenase catalysis are assembled within artificially designed protein scaffolds.
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Affiliation(s)
- Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
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29
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Reig AJ, Pires MM, Snyder RA, Wu Y, Jo H, Kulp DW, Butch SE, Calhoun JR, Szyperski T, Szyperski TG, Solomon EI, DeGrado WF. Alteration of the oxygen-dependent reactivity of de novo Due Ferri proteins. Nat Chem 2012; 4:900-6. [PMID: 23089864 PMCID: PMC3568993 DOI: 10.1038/nchem.1454] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 08/09/2012] [Indexed: 12/18/2022]
Abstract
De novo proteins provide a unique opportunity for investigating the structure-function relationships of metalloproteins in a minimal, well-defined, and controlled scaffold. Herein, we describe the rational programming of function in a de novo designed di-iron carboxylate protein from the due ferri family. Originally created to catalyze O2-dependent, two-electron oxidation of hydroquinones, the protein was reprogrammed to catalyze the selective N-hydroxylation of arylamines by remodeling the substrate access cavity and introducing a critical third His ligand to the metal binding cavity. Additional second-and third-shell modifications were required to stabilize the His ligand in the core of the protein. These changes resulted in at least a 106 –fold increase in the relative rates of the two reactions. This result highlights the potential for using de novo proteins as scaffolds for future investigations of geometric and electronic factors that influence the catalytic tuning of di-iron active sites.
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Affiliation(s)
- Amanda J Reig
- Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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30
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Andreini C, Cavallaro G, Lorenzini S. FindGeo: a tool for determining metal coordination geometry. ACTA ACUST UNITED AC 2012; 28:1658-60. [PMID: 22556364 DOI: 10.1093/bioinformatics/bts246] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
UNLABELLED Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment. AVAILABILITY FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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31
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Abstract
Metals are present in about one-half of the protein structures available and also have critical roles in nucleic acid biochemistry. This prologue introduces the fourth of the Thematic Minireview Series on Metals in Biology, which deals with several topics involving iron, manganese, copper, and other metals. The six minireviews discuss metal transport and intracellular homeostasis, including chaperones and siderophores, maturation of the diiron active sites in hydrogenases, the balance between manganese and iron, and copper homeostasis relevant to pathogens.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA.
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32
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Huang K, Li H, Shen H, Li M. Psychological stress expands low molecular weight iron pool in cerebral cortex, hippocampus, and striatum of rats. Biol Trace Elem Res 2012; 146:79-85. [PMID: 21993966 DOI: 10.1007/s12011-011-9230-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Accepted: 10/04/2011] [Indexed: 01/30/2023]
Abstract
We have previously demonstrated that psychological stress (PS) can cause iron to accumulate in the cerebral cortex, hippocampus, and striatum of rats. However, why iron accumulates and in what oxidation state iron it accumulates in the brain of PS-exposed rats has not been well elucidated. In the present study, we investigated the influence of PS on the low molecular weight iron pool (LMWIP) in the rat brain. The results showed that: (1) PS significantly expanded LMWIP in the cerebral cortex, hippocampus, and striatum in rats; (2) PS caused derangement of pyramidal cells and reduced the layers of pyramidal CA1 and CA2 neurons; (3) PS exposure greatly lowered the expression of ferritin (Fn) and hephaestin (HP) in the rat cortex and hippocampus; and (4) PS decreased superoxide dismutase, glutathione peroxidase, and glutathione level and increased malondialdehyde level in the cerebral cortex, hippocampus, and striatum in rats. These results indicated that PS could expand LMWIP significantly, which may be attributed to PS-induced decrease in Fn, HP expression, and the subsequent reduction in iron storage and utilization, and expansion of LMWIP could in turn lead to aggravation of oxidative damage.
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Affiliation(s)
- Kai Huang
- Department of Military Hygiene, Second Military Medical University, No. 800 Xiangyin Road, Yangpu District, Shanghai, 200433, China
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33
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Amrein B, Schmid M, Collet G, Cuniasse P, Gilardoni F, Seebeck FP, Ward TR. Identification of two-histidines one-carboxylate binding motifs in proteins amenable to facial coordination to metals. Metallomics 2012; 4:379-88. [DOI: 10.1039/c2mt20010d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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Andreini C, Bertini I. A bioinformatics view of zinc enzymes. J Inorg Biochem 2011; 111:150-6. [PMID: 22209023 DOI: 10.1016/j.jinorgbio.2011.11.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 11/02/2011] [Accepted: 11/23/2011] [Indexed: 11/17/2022]
Abstract
Thanks to the contributions of scientists like Bert Vallee, zinc enzymology is an area of research with a rich history and a strong basis of biochemical and biophysical knowledge. In recent years, the dramatic development of the genomic and post-genomic research has provided this as well as all other fields of life sciences with a massive body of new data, including, but not limited to, protein sequence and structural data. By integrating these new data with the wealth of information available in the literature, it is possible to achieve an unprecedented overview of the properties and functions of zinc enzymes in the context of biological systems. To this aim, the role of bioinformatics is essential. In this work, we use bioinformatics tools and databases that we have developed for the study of metalloproteins to gain insights into the functions of zinc in zinc enzymes, its coordination properties, and the usage of zinc enzymes in living organisms.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy
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35
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Andreini C, Bertini I, Cavallaro G. Minimal functional sites allow a classification of zinc sites in proteins. PLoS One 2011; 6:e26325. [PMID: 22043316 PMCID: PMC3197139 DOI: 10.1371/journal.pone.0026325] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.
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Affiliation(s)
- Claudia Andreini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Ivano Bertini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
- * E-mail:
| | - Gabriele Cavallaro
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
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36
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Choi H, Kang H, Park H. MetLigDB: a web-based database for the identification of chemical groups to design metalloprotein inhibitors. J Appl Crystallogr 2011. [DOI: 10.1107/s0021889811022503] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
MetLigDB (http://silver.sejong.ac.kr/MetLigDB) is a publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail. Additional information can also be retrieved, including protein and inhibitor names, the amino acid residues coordinated to the central metal ion, and the binding affinity of the inhibitor for the target metalloprotein. Although many metalloproteins have been considered promising targets for drug discovery, it is difficult to discover new inhibitors because of the difficulty in designing a suitable chelating moiety to impair the catalytic activity of the central metal ion. Because both common and specific chelating groups can be identified for varying metal ions and the associated coordination environments, MetLigDB is expected to give users insight into designing new inhibitors of metalloproteins for drug discovery.
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Anamorsin Is a [2Fe-2S] Cluster-Containing Substrate of the Mia40-Dependent Mitochondrial Protein Trapping Machinery. ACTA ACUST UNITED AC 2011; 18:794-804. [DOI: 10.1016/j.chembiol.2011.03.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 02/24/2011] [Accepted: 03/08/2011] [Indexed: 11/24/2022]
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38
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Zhou P, Tian F, Zou J, Ren Y, Liu X, Shang Z. Do Halide Motifs Stabilize Protein Architecture? J Phys Chem B 2010; 114:15673-86. [DOI: 10.1021/jp105259d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Feifei Tian
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Jianwei Zou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Yanrong Ren
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Xiuhong Liu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
| | - Zhicai Shang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, Department of Biological and Chemical Engineering, Chongqing Education College, Chongqing 400067, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United
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Kell DB. Towards a unifying, systems biology understanding of large-scale cellular death and destruction caused by poorly liganded iron: Parkinson's, Huntington's, Alzheimer's, prions, bactericides, chemical toxicology and others as examples. Arch Toxicol 2010; 84:825-89. [PMID: 20967426 PMCID: PMC2988997 DOI: 10.1007/s00204-010-0577-x] [Citation(s) in RCA: 286] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/14/2010] [Indexed: 12/11/2022]
Abstract
Exposure to a variety of toxins and/or infectious agents leads to disease, degeneration and death, often characterised by circumstances in which cells or tissues do not merely die and cease to function but may be more or less entirely obliterated. It is then legitimate to ask the question as to whether, despite the many kinds of agent involved, there may be at least some unifying mechanisms of such cell death and destruction. I summarise the evidence that in a great many cases, one underlying mechanism, providing major stresses of this type, entails continuing and autocatalytic production (based on positive feedback mechanisms) of hydroxyl radicals via Fenton chemistry involving poorly liganded iron, leading to cell death via apoptosis (probably including via pathways induced by changes in the NF-κB system). While every pathway is in some sense connected to every other one, I highlight the literature evidence suggesting that the degenerative effects of many diseases and toxicological insults converge on iron dysregulation. This highlights specifically the role of iron metabolism, and the detailed speciation of iron, in chemical and other toxicology, and has significant implications for the use of iron chelating substances (probably in partnership with appropriate anti-oxidants) as nutritional or therapeutic agents in inhibiting both the progression of these mainly degenerative diseases and the sequelae of both chronic and acute toxin exposure. The complexity of biochemical networks, especially those involving autocatalytic behaviour and positive feedbacks, means that multiple interventions (e.g. of iron chelators plus antioxidants) are likely to prove most effective. A variety of systems biology approaches, that I summarise, can predict both the mechanisms involved in these cell death pathways and the optimal sites of action for nutritional or pharmacological interventions.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and the Manchester Interdisciplinary Biocentre, The University of Manchester, Manchester M1 7DN, UK.
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Abstract
Bioinformatics is a central discipline in modern life sciences aimed at describing the complex properties of living organisms starting from large-scale data sets of cellular constituents such as genes and proteins. In order for this wealth of information to provide useful biological knowledge, databases and software tools for data collection, analysis and interpretation need to be developed. In this paper, we review recent advances in the design and implementation of bioinformatics resources devoted to the study of metals in biological systems, a research field traditionally at the heart of bioinorganic chemistry. We show how metalloproteomes can be extracted from genome sequences, how structural properties can be related to function, how databases can be implemented, and how hints on interactions can be obtained from bioinformatics.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center (CERM)-University of Florence, Via L. Sacconi 6, Sesto Fiorentino, Italy.
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Leitgeb S, Straganz GD, Nidetzky B. Functional characterization of an orphan cupin protein from Burkholderia xenovorans reveals a mononuclear nonheme Fe2+-dependent oxygenase that cleaves β-diketones. FEBS J 2009; 276:5983-97. [DOI: 10.1111/j.1742-4658.2009.07308.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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