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Bazayeva M, Andreini C, Rosato A. A database overview of metal-coordination distances in metalloproteins. Acta Crystallogr D Struct Biol 2024; 80:S2059798324003152. [PMID: 38682667 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Metalloproteins are ubiquitous in all living organisms and take part in a very wide range of biological processes. For this reason, their experimental characterization is crucial to obtain improved knowledge of their structure and biological functions. The three-dimensional structure represents highly relevant information since it provides insight into the interaction between the metal ion(s) and the protein fold. Such interactions determine the chemical reactivity of the bound metal. The available PDB structures can contain errors due to experimental factors such as poor resolution and radiation damage. A lack of use of distance restraints during the refinement and validation process also impacts the structure quality. Here, the aim was to obtain a thorough overview of the distribution of the distances between metal ions and their donor atoms through the statistical analysis of a data set based on more than 115 000 metal-binding sites in proteins. This analysis not only produced reference data that can be used by experimentalists to support the structure-determination process, for example as refinement restraints, but also resulted in an improved insight into how protein coordination occurs for different metals and the nature of their binding interactions. In particular, the features of carboxylate coordination were inspected, which is the only type of interaction that is commonly present for nearly all metals.
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Affiliation(s)
- Milana Bazayeva
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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2
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Schulz V, Steinhilper R, Oltmanns J, Freibert SA, Krapoth N, Linne U, Welsch S, Hoock MH, Schünemann V, Murphy BJ, Lill R. Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2. Nat Commun 2024; 15:3269. [PMID: 38627381 PMCID: PMC11021402 DOI: 10.1038/s41467-024-47310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Maturation of iron-sulfur proteins in eukaryotes is initiated in mitochondria by the core iron-sulfur cluster assembly (ISC) complex, consisting of the cysteine desulfurase sub-complex NFS1-ISD11-ACP1, the scaffold protein ISCU2, the electron donor ferredoxin FDX2, and frataxin, a protein dysfunctional in Friedreich's ataxia. The core ISC complex synthesizes [2Fe-2S] clusters de novo from Fe and a persulfide (SSH) bound at conserved cluster assembly site residues. Here, we elucidate the poorly understood Fe-dependent mechanism of persulfide transfer from cysteine desulfurase NFS1 to ISCU2. High-resolution cryo-EM structures obtained from anaerobically prepared samples provide snapshots that both visualize different stages of persulfide transfer from Cys381NFS1 to Cys138ISCU2 and clarify the molecular role of frataxin in optimally positioning assembly site residues for fast sulfur transfer. Biochemical analyses assign ISCU2 residues essential for sulfur transfer, and reveal that Cys138ISCU2 rapidly receives the persulfide without a detectable intermediate. Mössbauer spectroscopy assessing the Fe coordination of various sulfur transfer intermediates shows a dynamic equilibrium between pre- and post-sulfur-transfer states shifted by frataxin. Collectively, our study defines crucial mechanistic stages of physiological [2Fe-2S] cluster assembly and clarifies frataxin's molecular role in this fundamental process.
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Affiliation(s)
- Vinzent Schulz
- Institut für Zytobiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Ralf Steinhilper
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Jonathan Oltmanns
- Department of Physics, Biophysics and Medical Physics, University of Kaiserslautern-Landau, Erwin-Schrödinger-Str. 46, 67663, Kaiserslautern, Germany
| | - Sven-A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
- Steinmühle-Schule & Internat, Steinmühlenweg 21, 35043, Marburg, Germany
| | - Nils Krapoth
- Institut für Zytobiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany
| | - Uwe Linne
- Mass Spectrometry Facility of the Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany
| | - Maren H Hoock
- Department of Physics, Biophysics and Medical Physics, University of Kaiserslautern-Landau, Erwin-Schrödinger-Str. 46, 67663, Kaiserslautern, Germany
| | - Volker Schünemann
- Department of Physics, Biophysics and Medical Physics, University of Kaiserslautern-Landau, Erwin-Schrödinger-Str. 46, 67663, Kaiserslautern, Germany
| | - Bonnie J Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438, Frankfurt am Main, Germany.
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.
- Zentrum für Synthetische Mikrobiologie SynMikro, Karl-von-Frisch-Str. 14, 35032, Marburg, Germany.
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3
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Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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4
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Diep P, Stogios PJ, Evdokimova E, Savchenko A, Mahadevan R, Yakunin AF. Ni(II)-binding affinity of CcNikZ-II and its homologs: the role of the HH-prong and variable loop revealed by structural and mutational studies. FEBS J 2024. [PMID: 38555564 DOI: 10.1111/febs.17125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 03/13/2024] [Indexed: 04/02/2024]
Abstract
Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.
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Affiliation(s)
- Patrick Diep
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Systems & Synthetic Biology Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, BioZone - Centre for Applied Bioscience and Bioengineering, University of Toronto, Toronto, Ontario, Canada
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Wales, UK
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5
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Portela PC, Shipps CC, Shen C, Srikanth V, Salgueiro CA, Malvankar NS. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nat Commun 2024; 15:2434. [PMID: 38509081 PMCID: PMC10954620 DOI: 10.1038/s41467-024-46192-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
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Affiliation(s)
- Pilar C Portela
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catharine C Shipps
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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6
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Ma L, Zheng JJ, Zhou N, Zhang R, Fang L, Yang Y, Gao X, Chen C, Yan X, Fan K. A natural biogenic nanozyme for scavenging superoxide radicals. Nat Commun 2024; 15:233. [PMID: 38172125 PMCID: PMC10764798 DOI: 10.1038/s41467-023-44463-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Biominerals, the inorganic minerals of organisms, are known mainly for their physical property-related functions in modern living organisms. Our recent discovery of the enzyme-like activities of nanomaterials, coined as nanozyme, inspires the hypothesis that nano-biominerals might function as enzyme-like catalyzers in cells. Here we report that the iron cores of biogenic ferritins act as natural nanozymes to scavenge superoxide radicals. Through analyzing eighteen representative ferritins from three living kingdoms, we find that the iron core of prokaryote ferritin possesses higher superoxide-diminishing activity than that of eukaryotes. Further investigation reveals that the differences in catalytic capability result from the iron/phosphate ratio changes in the iron core, which is mainly determined by the structures of ferritins. The phosphate in the iron core switches the iron core from single crystalline to amorphous iron phosphate-like structure, resulting in decreased affinity to the hydrogen proton of the ferrihydrite-like core that facilitates its reaction with superoxide in a manner different from that of ferric ions. Furthermore, overexpression of ferritins with high superoxide-diminishing activities in E. coli increases the resistance to superoxide, whereas bacterioferritin knockout or human ferritin knock-in diminishes free radical tolerance, highlighting the physiological antioxidant role of this type of nanozymes.
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Affiliation(s)
- Long Ma
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China
| | - Jia-Jia Zheng
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Ning Zhou
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruofei Zhang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Long Fang
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yili Yang
- China Regional Research Centre, International Centre for Genetic Engineering and Biotechnology, Taizhou, Jiangsu, 225316, China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, National Center for Nanoscience and Technology of China, Beijing, 100190, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xiyun Yan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
| | - Kelong Fan
- CAS Engineering Laboratory for Nanozyme, Key Laboratory of Biomacromolecules (CAS), CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100408, China.
- Nanozyme Medical Center, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Nanozyme Laboratory in Zhongyuan, Zhengzhou, Henan, 451163, China.
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Li L, Jiao L, Feng D, Yuan Y, Yang X, Li J, Jiang D, Chen H, Meng Q, Chen R, Fang B, Zou X, Luo Z, Ye X, Hong Y, Liu C, Li C. Human apical-out nasal organoids reveal an essential role of matrix metalloproteinases in airway epithelial differentiation. Nat Commun 2024; 15:143. [PMID: 38168066 PMCID: PMC10762242 DOI: 10.1038/s41467-023-44488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Extracellular matrix (ECM) assembly/disassembly is a critical regulator for airway epithelial development and remodeling. Airway organoid is widely used in respiratory research, yet there is limited study to indicate the roles and mechanisms of ECM organization in epithelial growth and differentiation by using in vitro organoid system. Moreover, most of current Matrigel-based airway organoids are in basal-out orientation where accessing the apical surface is challenging. We present a human apical-out airway organoid using a biochemically defined hybrid hydrogel system. During human nasal epithelial progenitor cells (hNEPCs) differentiation, the gel gradually degrade, leading to the organoid apical surfaces facing outward. The expression and activity of ECM-degrading enzymes, matrix metalloproteinases (MMP7, MMP9, MMP10 and MMP13) increases during organoid differentiation, where inhibition of MMPs significantly suppresses the normal ciliation, resulting in increased goblet cell proportion. Moreover, a decrease of MMPs is found in goblet cell hyperplastic epithelium in inflammatory mucosa. This system reveals essential roles of epithelial-derived MMPs on epithelial cell fate determination, and provides an applicable platform enabling further study for ECM in regulating airway development in health and diseases.
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Affiliation(s)
- Liyue Li
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Linyi Jiao
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Danni Feng
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yizhang Yuan
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqian Yang
- Precision Medicine Institute, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jian Li
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Dong Jiang
- Precision Medicine Institute, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hexin Chen
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qingxiang Meng
- Department of Otorhinolaryngology Head and Neck Surgery, Guangzhou First People's Hospital, Guangzhou, China
| | - Ruchong Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, Department of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Bixing Fang
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuenong Zou
- Precision Medicine Institute, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhenhua Luo
- Precision Medicine Institute, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Ye
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-sen University, Nanning, China
| | - Yue Hong
- School of Life Sciences, Hainan University, Haikou, China
| | - Chun Liu
- Precision Medicine Institute, Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Chunwei Li
- Department of Otolaryngology, Department of Allergy, Guangzhou Key Laboratory of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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8
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Dixit H, Kulharia M, Verma SK. Metal-binding proteins and proteases in RNA viruses: unravelling functional diversity and expanding therapeutic horizons. J Virol 2023; 97:e0139923. [PMID: 37982624 PMCID: PMC10734521 DOI: 10.1128/jvi.01399-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/18/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Metal-binding proteins are pivotal components with diverse functions in organisms, including viruses. Despite their significance, many metalloproteins in viruses remain uncharacterized, posing challenges to understanding viral systems. This study addresses this knowledge gap by identifying and analyzing metal-binding proteins and proteases in RNA viruses. The findings emphasize the prevalence of these proteins as essential functional classes within viruses and shed light on the role of metal ions and metalloproteins in viral replication and pathogenesis. Moreover, this research serves as a crucial foundation for further investigations in this field, offering the potential for developing innovative antiviral strategies. Additionally, the study enhances our understanding of the distribution and evolutionary patterns of metal-binding proteases in major human viruses. Continually exploring metal-binding proteomes across diverse viruses will deepen our knowledge of metal-dependent biological processes and provide valuable insights for combating viral infections, including respiratory viruses and other life-threatening diseases.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra, India
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9
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Vasquez S, Marquez MD, Brignole EJ, Vo A, Kong S, Park C, Perlstein DL, Drennan CL. Structural and biochemical investigations of a HEAT-repeat protein involved in the cytosolic iron-sulfur cluster assembly pathway. Commun Biol 2023; 6:1276. [PMID: 38110506 PMCID: PMC10728100 DOI: 10.1038/s42003-023-05579-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/13/2023] [Indexed: 12/20/2023] Open
Abstract
Iron-sulfur clusters are essential for life and defects in their biosynthesis lead to human diseases. The mechanism of cluster assembly and delivery to cytosolic and nuclear client proteins via the cytosolic iron-sulfur cluster assembly (CIA) pathway is not well understood. Here we report cryo-EM structures of the HEAT-repeat protein Met18 from Saccharomyces cerevisiae, a key component of the CIA targeting complex (CTC) that identifies cytosolic and nuclear client proteins and delivers a mature iron-sulfur cluster. We find that in the absence of other CTC proteins, Met18 adopts tetrameric and hexameric states. Using mass photometry and negative stain EM, we show that upon the addition of Cia2, these higher order oligomeric states of Met18 disassemble. We also use pulldown assays to identify residues of critical importance for Cia2 binding and recognition of the Leu1 client, many of which are buried when Met18 oligomerizes. Our structures show conformations of Met18 that have not been previously observed in any Met18 homolog, lending support to the idea that a highly flexible Met18 may be key to how the CTC is able to deliver iron-sulfur clusters to client proteins of various sizes and shapes, i.e. Met18 conforms to the dimensions needed.
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Affiliation(s)
- Sheena Vasquez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Edward J Brignole
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- MIT.nano, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Amanda Vo
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Sunnie Kong
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | - Christopher Park
- Department of Chemistry, Boston University, Boston, MA, 02215, USA
| | | | - Catherine L Drennan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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10
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Deblonde GJP, Morrison K, Mattocks JA, Cotruvo JA, Zavarin M, Kersting AB. Impact of a Biological Chelator, Lanmodulin, on Minor Actinide Aqueous Speciation and Transport in the Environment. Environ Sci Technol 2023; 57:20830-20843. [PMID: 37897703 DOI: 10.1021/acs.est.3c06033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Minor actinides are major contributors to the long-term radiotoxicity of nuclear fuels and other radioactive wastes. In this context, understanding their interactions with natural chelators and minerals is key to evaluating their transport behavior in the environment. The lanmodulin family of metalloproteins is produced by ubiquitous bacteria and Methylorubrum extorquens lanmodulin (LanM) was recently identified as one of nature's most selective chelators for trivalent f-elements. Herein, we investigated the behavior of neptunium, americium, and curium in the presence of LanM, carbonate ions, and common minerals (calcite, montmorillonite, quartz, and kaolinite). We show that LanM's aqueous complexes with Am(III) and Cm(III) remain stable in carbonate-bicarbonate solutions. Furthermore, the sorption of Am(III) to these minerals is strongly impacted by LanM, while Np(V) sorption is not. With calcite, even a submicromolar concentration of LanM leads to a significant reduction in the Am(III) distribution coefficient (Kd, from >104 to ∼102 mL/g at pH 8.5), rendering it even more mobile than Np(V). Thus, LanM-type chelators can potentially increase the mobility of trivalent actinides and lanthanide fission products under environmentally relevant conditions. Monitoring biological chelators, including metalloproteins, and their biogenerators should therefore be considered during the evaluation of radioactive waste repository sites and the risk assessment of contaminated sites.
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Affiliation(s)
- Gauthier J-P Deblonde
- Physical and Life Sciences Directorate, Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Keith Morrison
- Physical and Life Sciences Directorate, Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Mavrik Zavarin
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Annie B Kersting
- Glenn T. Seaborg Institute, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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11
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Tokmina-Lukaszewska M, Huang Q, Berry L, Kallas H, Peters JW, Seefeldt LC, Raugei S, Bothner B. Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner. Commun Chem 2023; 6:254. [PMID: 37980448 PMCID: PMC10657360 DOI: 10.1038/s42004-023-01046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.
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Affiliation(s)
| | - Qi Huang
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - John W Peters
- Institute of Biological Chemistry, The University of Oklahoma, Norman, OK, USA
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Simone Raugei
- Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA.
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12
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Díaz-Rueda P, Morales de los Ríos L, Romero LC, García I. Old poisons, new signaling molecules: the case of hydrogen cyanide. J Exp Bot 2023; 74:6040-6051. [PMID: 37586035 PMCID: PMC10575699 DOI: 10.1093/jxb/erad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
The high phenotypic plasticity developed by plants includes rapid responses and adaptations to aggressive or changing environments. To achieve this, they evolved extremely efficient mechanisms of signaling mediated by a wide range of molecules, including small signal molecules. Among them, hydrogen cyanide (HCN) has been largely ignored due to its toxic characteristics. However, not only is it present in living organisms, but it has been shown that it serves several functions in all kingdoms of life. Research using model plants has changed the traditional point of view, and it has been demonstrated that HCN plays a positive role in the plant response to pathogens independently of its toxicity. Indeed, HCN induces a response aimed at protecting the plant from pathogen attack, and the HCN is provided either exogenously (in vitro or by some cyanogenic bacteria species present in the rhizosphere) or endogenously (in reactions involving ethylene, camalexin, or other cyanide-containing compounds). The contribution of different mechanisms to HCN function, including a new post-translational modification of cysteines in proteins, namely S-cyanylation, is discussed here. This work opens up an expanding 'HCN field' of research related to plants and other organisms.
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Affiliation(s)
- Pablo Díaz-Rueda
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
| | | | - Luis C Romero
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
| | - Irene García
- Instituto de Bioquímica Vegetal y Fotosíntesis (IBVF), CSIC-Universidad de Sevilla, 41092-Sevilla, Spain
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13
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Mendoza J, Purchal M, Yamada K, Koutmos M. Structure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo. Nat Commun 2023; 14:6365. [PMID: 37821448 PMCID: PMC10567725 DOI: 10.1038/s41467-023-42037-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Cobalamin-dependent methionine synthase (MS) is a key enzyme in methionine and folate one-carbon metabolism. MS is a large multi-domain protein capable of binding and activating three substrates: homocysteine, folate, and S-adenosylmethionine for methylation. Achieving three chemically distinct methylations necessitates significant domain rearrangements to facilitate substrate access to the cobalamin cofactor at the right time. The distinct conformations required for each reaction have eluded structural characterization as its inherently dynamic nature renders structural studies difficult. Here, we use a thermophilic MS homolog (tMS) as a functional MS model. Its exceptional stability enabled characterization of MS in the absence of cobalamin, marking the only studies of a cobalamin-binding protein in its apoenzyme state. More importantly, we report the high-resolution full-length MS structure, ending a multi-decade quest. We also capture cobalamin loading in crystallo, providing structural insights into holoenzyme formation. Our work paves the way for unraveling how MS orchestrates large-scale domain rearrangements crucial for achieving challenging chemistries.
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Affiliation(s)
- Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Meredith Purchal
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- New England Biolabs, Inc., Ipswich, MA, 01938, England
| | - Kazuhiro Yamada
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Program in Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
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14
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He B, Sachla AJ, Helmann JD. TerC proteins function during protein secretion to metalate exoenzymes. Nat Commun 2023; 14:6186. [PMID: 37794032 PMCID: PMC10550928 DOI: 10.1038/s41467-023-41896-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023] Open
Abstract
Cytosolic metalloenzymes acquire metals from buffered intracellular pools. How exported metalloenzymes are appropriately metalated is less clear. We provide evidence that TerC family proteins function in metalation of enzymes during export through the general secretion (Sec-dependent) pathway. Bacillus subtilis strains lacking MeeF(YceF) and MeeY(YkoY) have a reduced capacity for protein export and a greatly reduced level of manganese (Mn) in the secreted proteome. MeeF and MeeY copurify with proteins of the general secretory pathway, and in their absence the FtsH membrane protease is essential for viability. MeeF and MeeY are also required for efficient function of the Mn2+-dependent lipoteichoic acid synthase (LtaS), a membrane-localized enzyme with an extracytoplasmic active site. Thus, MeeF and MeeY, representative of the widely conserved TerC family of membrane transporters, function in the co-translocational metalation of Mn2+-dependent membrane and extracellular enzymes.
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Affiliation(s)
- Bixi He
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - Ankita J Sachla
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, 370 Wing Hall, 123 Wing Drive, Ithaca, NY, 14853-8101, USA.
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15
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Tian J, Liu J, Knapp M, Donnan PH, Boggs DG, Bridwell-Rabb J. Custom tuning of Rieske oxygenase reactivity. Nat Commun 2023; 14:5858. [PMID: 37730711 PMCID: PMC10511449 DOI: 10.1038/s41467-023-41428-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/27/2023] [Indexed: 09/22/2023] Open
Abstract
Rieske oxygenases use a Rieske-type [2Fe-2S] cluster and a mononuclear iron center to initiate a range of chemical transformations. However, few details exist regarding how this catalytic scaffold can be predictively tuned to catalyze divergent reactions. Therefore, in this work, using a combination of structural analyses, as well as substrate and rational protein-based engineering campaigns, we elucidate the architectural trends that govern catalytic outcome in the Rieske monooxygenase TsaM. We identify structural features that permit a substrate to be functionalized by TsaM and pinpoint active-site residues that can be targeted to manipulate reactivity. Exploiting these findings allowed for custom tuning of TsaM reactivity: substrates are identified that support divergent TsaM-catalyzed reactions and variants are created that exclusively catalyze dioxygenation or sequential monooxygenation chemistry. Importantly, we further leverage these trends to tune the reactivity of additional monooxygenase and dioxygenase enzymes, and thereby provide strategies to custom tune Rieske oxygenase reaction outcomes.
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Affiliation(s)
- Jiayi Tian
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jianxin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madison Knapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Patrick H Donnan
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David G Boggs
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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16
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Fujishiro T, Takaoka K. Class III hybrid cluster protein homodimeric architecture shows evolutionary relationship with Ni, Fe-carbon monoxide dehydrogenases. Nat Commun 2023; 14:5609. [PMID: 37709776 PMCID: PMC10502027 DOI: 10.1038/s41467-023-41289-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Hybrid cluster proteins (HCPs) are Fe-S-O cluster-containing metalloenzymes in three distinct classes (class I and II: monomer, III: homodimer), all of which structurally related to homodimeric Ni, Fe-carbon monoxide dehydrogenases (CODHs). Here we show X-ray crystal structure of class III HCP from Methanothermobacter marburgensis (Mm HCP), demonstrating its homodimeric architecture structurally resembles those of CODHs. Also, despite the different architectures of class III and I/II HCPs, [4Fe-4S] and hybrid clusters are found in equivalent positions in all HCPs. Structural comparison of Mm HCP and CODHs unveils some distinct features such as the environments of their homodimeric interfaces and the active site metalloclusters. Furthermore, structural analysis of Mm HCP C67Y and characterization of several Mm HCP variants with a Cys67 mutation reveal the significance of Cys67 in protein structure, metallocluster binding and hydroxylamine reductase activity. Structure-based bioinformatics analysis of HCPs and CODHs provides insights into the structural evolution of the HCP/CODH superfamily.
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Affiliation(s)
- Takashi Fujishiro
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan.
| | - Kyosei Takaoka
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama, 338-8570, Japan
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17
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Tsutsumi E, Niwa S, Takeda R, Sakamoto N, Okatsu K, Fukai S, Ago H, Nagao S, Sekiguchi H, Takeda K. Structure of a putative immature form of a Rieske-type iron-sulfur protein in complex with zinc chloride. Commun Chem 2023; 6:190. [PMID: 37689761 PMCID: PMC10492824 DOI: 10.1038/s42004-023-01000-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023] Open
Abstract
Iron-sulfur clusters are prosthetic groups of proteins involved in various biological processes. However, details of the immature state of the iron-sulfur cluster into proteins have not yet been elucidated. We report here the first structural analysis of the Zn-containing form of a Rieske-type iron-sulfur protein, PetA, from Thermochromatium tepidum (TtPetA) by X-ray crystallography and small-angle X-ray scattering analysis. The Zn-containing form of TtPetA was indicated to be a dimer in solution. The zinc ion adopts a regular tetra-coordination with two chloride ions and two cysteine residues. Only a histidine residue in the cluster-binding site exhibited a conformational difference from the [2Fe-2S] containing form. The Zn-containing structure indicates that the conformation of the cluster binding site is already constructed and stabilized before insertion of [2Fe-2S]. The binding mode of ZnCl2, similar to the [2Fe-2S] cluster, suggests that the zinc ions might be involved in the insertion of the [2Fe-2S] cluster.
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Affiliation(s)
- Erika Tsutsumi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Satomi Niwa
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryota Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Natsuki Sakamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kei Okatsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shuya Fukai
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hideo Ago
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Satoshi Nagao
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hiroshi Sekiguchi
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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18
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Ilcu L, Denkhaus L, Brausemann A, Zhang L, Einsle O. Architecture of the Heme-translocating CcmABCD/E complex required for Cytochrome c maturation. Nat Commun 2023; 14:5190. [PMID: 37626034 PMCID: PMC10457321 DOI: 10.1038/s41467-023-40881-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Mono- and multiheme cytochromes c are post-translationally matured by the covalent attachment of heme. For this, Escherichia coli employs the most complex type of maturation machineries, the Ccm-system (for cytochrome c maturation). It consists of two membrane protein complexes, one of which shuttles heme across the membrane to a mobile chaperone that then delivers the cofactor to the second complex, an apoprotein:heme lyase, for covalent attachment. Here we report cryo-electron microscopic structures of the heme translocation complex CcmABCD from E. coli, alone and bound to the heme chaperone CcmE. CcmABCD forms a heterooctameric complex centered around the ABC transporter CcmAB that does not by itself transport heme. Our data suggest that the complex flops a heme group from the inner to the outer leaflet at its CcmBC interfaces, driven by ATP hydrolysis at CcmA. A conserved heme-handling motif (WxWD) at the periplasmic side of CcmC rotates the heme by 90° for covalent attachment to the heme chaperone CcmE that we find interacting exclusively with the CcmB subunit.
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Affiliation(s)
- Lorena Ilcu
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Lukas Denkhaus
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Anton Brausemann
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg im Breisgau, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg im Breisgau, Germany.
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, 79104, Freiburg im Breisgau, Germany.
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19
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Mammoser CC, LeMasters BE, Edwards SG, McRae EM, Mullins MH, Wang Y, Garcia NM, Edmonds KA, Giedroc DP, Thielges MC. The structure of plastocyanin tunes the midpoint potential by restricting axial ligation of the reduced copper ion. Commun Chem 2023; 6:175. [PMID: 37612467 PMCID: PMC10447441 DOI: 10.1038/s42004-023-00977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Blue copper proteins are models for illustrating how proteins tune metal properties. Nevertheless, the mechanisms by which the protein controls the metal site remain to be fully elucidated. A hindrance is that the closed shell Cu(I) site is inaccessible to most spectroscopic analyses. Carbon deuterium (C-D) bonds used as vibrational probes afford nonperturbative, selective characterization of the key cysteine and methionine copper ligands in both redox states. The structural integrity of Nostoc plastocyanin was perturbed by disrupting potential hydrogen bonds between loops of the cupredoxin fold via mutagenesis (S9A, N33A, N34A), variably raising the midpoint potential. The C-D vibrations show little change to suggest substantial alteration to the Cu(II) coordination in the oxidized state or in the Cu(I) interaction with the cysteine ligand. They rather indicate, along with visible and NMR spectroscopy, that the methionine ligand distinctly interacts more strongly with the Cu(I) ion, in line with the increases in midpoint potential. Here we show that the protein structure determines the redox properties by restricting the interaction between the methionine ligand and Cu(I) in the reduced state.
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Affiliation(s)
- Claire C Mammoser
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Brynn E LeMasters
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, 53706, USA
| | - Sydney G Edwards
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Emma M McRae
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - M Hunter Mullins
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Yiqi Wang
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nicholas M Garcia
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
- University of Wisconsin School of Medicine and Public Health, Madison, WI, 53726, USA
| | - Katherine A Edmonds
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - David P Giedroc
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA
| | - Megan C Thielges
- Indiana University Department of Chemistry, 800 E. Kirkwood Ave., Bloomington, IN, 47405, USA.
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20
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Bulavko ES, Pak MA, Ivankov DN. In Silico Simulations Reveal Molecular Mechanism of Uranyl Ion Toxicity towards DNA-Binding Domain of PARP-1 Protein. Biomolecules 2023; 13:1269. [PMID: 37627334 PMCID: PMC10452222 DOI: 10.3390/biom13081269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The molecular toxicity of the uranyl ion (UO22+) in living cells is primarily determined by its high affinity to both native and potential metal-binding sites that commonly occur in the structure of biomolecules. Recent advances in computational and experimental research have shed light on the structural properties and functional impacts of uranyl binding to proteins, organic ligands, nucleic acids, and their complexes. In the present work, we report the results of the computational investigation of the uranyl-mediated loss of DNA-binding activity of PARP-1, a eukaryotic enzyme that participates in DNA repair, cell differentiation, and the induction of inflammation. The latest experimental studies have shown that the uranyl ion directly interacts with its DNA-binding subdomains, zinc fingers Zn1 and Zn2, and alters their tertiary structure. Here, we propose an atomistic mechanism underlying this process and compute the free energy change along the suggested pathway. Our Quantum Mechanics/Molecular Mechanics (QM/MM) simulations of the Zn2-UO22+ complex indicate that the uranyl ion replaces zinc in its native binding site. However, the resulting state is destroyed due to the spontaneous internal hydrolysis of the U-Cys162 coordination bond. Despite the enthalpy of hydrolysis being +2.8 kcal/mol, the overall reaction free energy change is -0.6 kcal/mol, which is attributed to the loss of domain's native tertiary structure originally maintained by a zinc ion. The subsequent reorganization of the binding site includes the association of the uranyl ion with the Glu190/Asp191 acidic cluster and significant perturbations in the domain's tertiary structure driven by a further decrease in the free energy by 6.8 kcal/mol. The disruption of the DNA-binding interface revealed in our study is consistent with previous experimental findings and explains the loss of PARP-like zinc fingers' affinity for nucleic acids.
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Affiliation(s)
| | | | - Dmitry N. Ivankov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30/1, Moscow 121205, Russia
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21
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Hay Mele B, Monticelli M, Leone S, Bastoni D, Barosa B, Cascone M, Migliaccio F, Montemagno F, Ricciardelli A, Tonietti L, Rotundi A, Cordone A, Giovannelli D. Oxidoreductases and metal cofactors in the functioning of the earth. Essays Biochem 2023; 67:653-670. [PMID: 37503682 PMCID: PMC10423856 DOI: 10.1042/ebc20230012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 07/29/2023]
Abstract
Life sustains itself using energy generated by thermodynamic disequilibria, commonly existing as redox disequilibria. Metals are significant players in controlling redox reactions, as they are essential components of the engine that life uses to tap into the thermodynamic disequilibria necessary for metabolism. The number of proteins that evolved to catalyze redox reactions is extraordinary, as is the diversification level of metal cofactors and catalytic domain structures involved. Notwithstanding the importance of the topic, the relationship between metals and the redox reactions they are involved in has been poorly explored. This work reviews the structure and function of different prokaryotic organometallic-protein complexes, highlighting their pivotal role in controlling biogeochemistry. We focus on a specific subset of metal-containing oxidoreductases (EC1 or EC7.1), which are directly involved in biogeochemical cycles, i.e., at least one substrate or product is a small inorganic molecule that is or can be exchanged with the environment. Based on these inclusion criteria, we select and report 59 metalloenzymes, describing the organometallic structure of their active sites, the redox reactions in which they are involved, and their biogeochemical roles.
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Affiliation(s)
- Bruno Hay Mele
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Monticelli
- Department of Biology, University of Naples Federico II, Naples, Italy
- National Research Council - Institute of Biomolecular Chemistry - CNR-ICB, Pozzuoli, Italy
| | - Serena Leone
- Dipartimento di Biologia ed Evoluzione degli Organismi Marini, Stazione Zoologica Anton. Dohrn, Napoli, Italy
| | - Deborah Bastoni
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Bernardo Barosa
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Martina Cascone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Flavia Migliaccio
- Department of Biology, University of Naples Federico II, Naples, Italy
| | | | | | - Luca Tonietti
- Department of Biology, University of Naples Federico II, Naples, Italy
- Department of Science and Technology, University of Naples Parthenope, Naples, Italy
| | - Alessandra Rotundi
- Department of Science and Technology, University of Naples Parthenope, Naples, Italy
| | - Angelina Cordone
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Donato Giovannelli
- Department of Biology, University of Naples Federico II, Naples, Italy
- Department of Science and Technology, University of Naples Parthenope, Naples, Italy
- National Research Council - Institute of Marine Biological Resources and Biotechnologies - CNR-IRBIM, Ancona, Italy
- Department of Marine and Coastal Science, Rutgers University, New Brunswick, NJ, U.S.A
- Marine Chemistry and Geochemistry Department - Woods Hole Oceanographic Institution, MA, U.S.A
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
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22
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Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nat Commun 2023; 14:4681. [PMID: 37542031 PMCID: PMC10403576 DOI: 10.1038/s41467-023-40388-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.
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Affiliation(s)
- Ziyu Zhao
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, S. Kensington Campus, London, SW7 2AZ, UK
| | - Irene Vercellino
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
- Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Jana Knoppová
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Opatovický mlýn, Třeboň, 379 81, Czech Republic
| | - Roman Sobotka
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Opatovický mlýn, Třeboň, 379 81, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budĕjovice, 37005, Czech Republic
| | - James W Murray
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, S. Kensington Campus, London, SW7 2AZ, UK
| | - Peter J Nixon
- Sir Ernst Chain Building-Wolfson Laboratories, Department of Life Sciences, Imperial College London, S. Kensington Campus, London, SW7 2AZ, UK.
| | - Leonid A Sazanov
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria.
| | - Josef Komenda
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Opatovický mlýn, Třeboň, 379 81, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, České Budĕjovice, 37005, Czech Republic.
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23
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Buscagan TM, Rees DC. Modeling the Correlation between Z and B in an X-ray Crystal Structure Refinement. bioRxiv 2023:2023.07.04.547724. [PMID: 37461620 PMCID: PMC10350028 DOI: 10.1101/2023.07.04.547724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
We have examined how the refined B-factor changes as a function of Z (the atomic number of a scatterer) at the sulfur site of the [4Fe:4S] cluster of the nitrogenase iron protein by refinement. A simple model is developed that quantitatively captures the observed relationship between Z and B, based on a Gaussian electron density distribution with a constant electron density at the position of the scatterer. From this analysis, the fractional changes in B and Z are found to be similar. The utility of B-factor refinement to potentially distinguish atom types reflects the Z dependence of X-ray atomic scattering factors; the weaker dependence of electron atomic scattering factors on Z implies that distinctions between refined values of B in an electron scattering structure will be less sensitive to the atomic identity of a scatterer than for the case with X-ray-diffraction. This behavior provides an example of the complementary information that can be extracted from different types of scattering studies.
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Affiliation(s)
- Trixia M. Buscagan
- Division of Chemistry and Chemical Engineering 147-75, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering 147-75, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 USA
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24
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Flynn AJ, Antonyuk SV, Eady RR, Muench SP, Hasnain SS. A 2.2 Å cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases. Nat Commun 2023; 14:3416. [PMID: 37296134 PMCID: PMC10256718 DOI: 10.1038/s41467-023-39140-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo3, a respiratory quinol oxidase.
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Affiliation(s)
- Alex J Flynn
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Robert R Eady
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - S Samar Hasnain
- Molecular Biophysics Group, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, L69 7ZB, England.
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25
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Mattocks JA, Jung JJ, Lin CY, Dong Z, Yennawar NH, Featherston ER, Kang-Yun CS, Hamilton TA, Park DM, Boal AK, Cotruvo JA. Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer. Nature 2023; 618:87-93. [PMID: 37259003 PMCID: PMC10232371 DOI: 10.1038/s41586-023-05945-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/13/2023] [Indexed: 06/02/2023]
Abstract
Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number1-3. The natural lanthanide-binding protein lanmodulin (LanM)4,5 is a sustainable alternative to conventional solvent-extraction-based separation6. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM's quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM's greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Jonathan J Jung
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Chi-Yun Lin
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Ziye Dong
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Christina S Kang-Yun
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Timothy A Hamilton
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Dan M Park
- Critical Materials Institute, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Amie K Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
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26
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Hardy BJ, Martin Hermosilla A, Chinthapalli DK, Robinson CV, Anderson JLR, Curnow P. Cellular production of a de novo membrane cytochrome. Proc Natl Acad Sci U S A 2023; 120:e2300137120. [PMID: 37036998 PMCID: PMC10120048 DOI: 10.1073/pnas.2300137120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023] Open
Abstract
Heme-containing integral membrane proteins are at the heart of many bioenergetic complexes and electron transport chains. The importance of these electron relay hubs across biology has inspired the design of de novo proteins that recreate their core features within robust, versatile, and tractable protein folds. To this end, we report here the computational design and in-cell production of a minimal diheme membrane cytochrome which successfully integrates into the cellular membrane of live bacteria. This synthetic construct emulates a four-helix bundle found in modern respiratory complexes but has no sequence homology to any polypeptide sequence found in nature. The two b-type hemes, which appear to be recruited from the endogenous heme pool, have distinct split redox potentials with values close to those of natural membrane-spanning cytochromes. The purified protein can engage in rapid biomimetic electron transport with small molecules, with other redox proteins, and with biologically relevant diffusive electron carriers. We thus report an artificial membrane metalloprotein with the potential to serve as a functional electron transfer module in both synthetic protocells and living systems.
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Affiliation(s)
- Benjamin J Hardy
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
| | | | | | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
| | - Paul Curnow
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, Bristol BS8 1TQ, United Kingdom
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27
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Feehan R, Copeland M, Franklin MW, Slusky JSG. MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. Protein Sci 2023; 32:e4626. [PMID: 36916762 PMCID: PMC10044107 DOI: 10.1002/pro.4626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/15/2023]
Abstract
Recent advances have enabled high-quality computationally generated structures for proteins with no solved crystal structures. However, protein function data remains largely limited to experimental methods and homology mapping. Since structure determines function, it is natural that methods capable of using computationally generated structures for functional annotations need to be advanced. Our laboratory recently developed a method to distinguish between metalloenzyme and nonenzyme sites. Here we report improvements to this method by upgrading our physicochemical features to alleviate the need for structures with sub-angstrom precision and using machine learning to reduce training data labeling error. Our improved classifier identifies protein bound metal sites as enzymatic or nonenzymatic with 94% precision and 92% recall. We demonstrate that both adjustments increased predictive performance and reliability on sites with sub-angstrom variations. We constructed a set of predicted metalloprotein structures with no solved crystal structures and no detectable homology to our training data. Our model had an accuracy of 90%-97.5% depending on the quality of the predicted structures included in our test. Finally, we found the physicochemical trends that drove this model's successful performance were local protein density, second shell ionizable residue burial, and the pocket's accessibility to the site. We anticipate that our model's ability to correctly identify catalytic metal sites could enable identification of new enzymatic mechanisms and improve de novo metalloenzyme design success rates.
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Affiliation(s)
- Ryan Feehan
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Matthew Copeland
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Meghan W. Franklin
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
| | - Joanna S. G. Slusky
- Center for Computational BiologyThe University of Kansas, 2030 Becker Dr66047LawrenceKansasUSA
- Department of Molecular Biosciences|The University of Kansas, Ave. Lawrence KS 66045‐31011200SunnysideKansasUSA
- Present address:
Generate BiomedicinesSomervilleMassachusettsUSA
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28
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Feehan R, Copeland M, Franklin MW, Slusky JSG. MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. bioRxiv 2023:2023.03.08.531790. [PMID: 36945603 PMCID: PMC10028950 DOI: 10.1101/2023.03.08.531790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances have enabled high-quality computationally generated structures for proteins with no solved crystal structures. However, protein function data remains largely limited to experimental methods and homology mapping. Since structure determines function, it is natural that methods capable of using computationally generated structures for functional annotations need to be advanced. Our laboratory recently developed a method to distinguish between metalloenzyme and non-enzyme sites. Here we report improvements to this method by upgrading our physicochemical features to alleviate the need for structures with sub-angstrom precision and using machine learning to reduce training data labeling error. Our improved classifier identifies protein bound metal sites as enzymatic or non-enzymatic with 94% precision and 92% recall. We demonstrate that both adjustments increased predictive performance and reliability on sites with sub-angstrom variations. We constructed a set of predicted metalloprotein structures with no solved crystal structures and no detectable homology to our training data. Our model had an accuracy of 90 - 97.5% depending on the quality of the predicted structures included in our test. Finally, we found the physicochemical trends that drove this model's successful performance were local protein density, second shell ionizable residue burial, and the pocket's accessibility to the site. We anticipate that our model's ability to correctly identify catalytic metal sites could enable identification of new enzymatic mechanisms and improve de novo metalloenzyme design success rates. Significance statement Identification of enzyme active sites on proteins with unsolved crystallographic structures can accelerate discovery of novel biochemical reactions, which can impact healthcare, industrial processes, and environmental remediation. Our lab has developed an ML tool for predicting sites on computationally generated protein structures as enzymatic and non-enzymatic. We have made our tool available on a webserver, allowing the scientific community to rapidly search previously unknown protein function space.
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Affiliation(s)
- Ryan Feehan
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Matthew Copeland
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Meghan W. Franklin
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
| | - Joanna S. G. Slusky
- Center for Computational Biology, The University of Kansas, 2030 Becker Dr., Lawrence, KS 66047
- Department of Molecular Biosciences, The University of Kansas, 1200 Sunnyside Ave. Lawrence KS 66045-3101
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29
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Lahiri D, Agrawal R, Chandravanshi K, Rajput P, Agrawal A, Dwivedi A, Makde RD, Jha SN, Garg N. Assessing the prospect of XAFS experiments of metalloproteins under in vivo conditions at Indus-2 synchrotron facility, India. J Synchrotron Radiat 2023; 30:449-456. [PMID: 36891859 PMCID: PMC10000809 DOI: 10.1107/s1600577522011791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/10/2022] [Indexed: 06/18/2023]
Abstract
The feasibility of X-ray absorption fine-structure (XAFS) experiments of ultra-dilute metalloproteins under in vivo conditions (T = 300 K, pH = 7) at the BL-9 bending-magnet beamline (Indus-2) is reported, using as an example analogous synthetic Zn (0.1 mM) M1dr solution. The (Zn K-edge) XAFS of M1dr solution was measured with a four-element silicon drift detector. The first-shell fit was tested and found to be robust against statistical noise, generating reliable nearest-neighbor bond results. The results are found to be invariant between physiological and non-physiological conditions, which confirms the robust coordination chemistry of Zn with important biological implications. The scope of improving spectral quality for accommodation of higher-shell analysis is addressed.
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Affiliation(s)
- Debdutta Lahiri
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Richa Agrawal
- Department of Biochemistry and Molecular Biology, University of Chicago, 929 E 57th Street, Chicago, IL 60637, USA
| | | | - Parasmani Rajput
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ankur Agrawal
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ashutosh Dwivedi
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Ravindra D. Makde
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - S. N. Jha
- Beamline Development and Application Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Nandini Garg
- High Pressure and Synchrotron Radiation Physics, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
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30
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Warmack RA, Maggiolo AO, Orta A, Wenke BB, Howard JB, Rees DC. Structural consequences of turnover-induced homocitrate loss in nitrogenase. Nat Commun 2023; 14:1091. [PMID: 36841829 PMCID: PMC9968304 DOI: 10.1038/s41467-023-36636-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.
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Affiliation(s)
- Rebeccah A Warmack
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Andres Orta
- Biochemistry and Molecular Biophysics Graduate Program, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Belinda B Wenke
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - James B Howard
- Department of Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
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31
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Chakrabarti S, Sinha S, Tran GN, Na H, Mirica LM. Characterization of paramagnetic states in an organometallic nickel hydrogen evolution electrocatalyst. Nat Commun 2023; 14:905. [PMID: 36807358 DOI: 10.1038/s41467-023-36609-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Significant progress has been made in the bioinorganic modeling of the paramagnetic states believed to be involved in the hydrogen redox chemistry catalyzed by [NiFe] hydrogenase. However, the characterization and isolation of intermediates involved in mononuclear Ni electrocatalysts which are reported to operate through a NiI/III cycle have largely remained elusive. Herein, we report a NiII complex (NCHS2)Ni(OTf)2, where NCHS2 is 3,7-dithia-1(2,6)-pyridina-5(1,3)-benzenacyclooctaphane, that is an efficient electrocatalyst for the hydrogen evolution reaction (HER) with turnover frequencies of ~3,000 s-1 and a overpotential of 670 mV in the presence of trifluoroacetic acid. This electrocatalyst follows a hitherto unobserved HER mechanism involving C-H activation, which manifests as an inverse kinetic isotope effect for the overall hydrogen evolution reaction, and NiI/NiIII intermediates, which have been characterized by EPR spectroscopy. We further validate the possibility of the involvement of NiIII intermediates by the independent synthesis and characterization of organometallic NiIII complexes.
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Aryal B, Tillotson J, Ok K, Stoltzfus AT, Michel SLJ, Rao VA. Metal-induced oxidative stress and human plasma protein oxidation after SARS-CoV-2 infection. Sci Rep 2023; 13:2441. [PMID: 36765106 PMCID: PMC9916496 DOI: 10.1038/s41598-023-29119-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 01/31/2023] [Indexed: 02/12/2023] Open
Abstract
Pathogenesis of COVID-19 by SARS-CoV-2 resulted in a global pandemic and public health emergency in 2020. Viral infection can induce oxidative stress through reactive oxygen species (ROS). Inflammation and environmental stress are major sources of oxidative stress after infection. Micronutrients such as iron, copper, zinc, and manganese play various roles in human tissues and their imbalance in blood can impact immune responses against pathogens including SARS CoV-2. We hypothesized that alteration of free metal ions during infection and metal-catalyzed oxidation plays a critical role towards pathogenesis after infection. We analyzed convalescent and hospitalized COVID-19 patient plasma using orthogonal analytical techniques to determine redox active metal concentrations, overall protein oxidation, oxidative modifications, and protein levels via proteomics to understand the consequences of metal-induced oxidative stress in COVID-19 plasma proteins. Metal analysis using ICP-MS showed significantly greater concentrations of copper in COVID-19 plasma compared to healthy controls. We demonstrate significantly greater total protein carbonylation, other oxidative modifications, and deamidation of plasma proteins in COVID-19 plasma compared to healthy controls. Proteomics analysis showed that levels of redox active proteins including hemoglobulin were elevated in COVID-19 plasma. Molecular modeling concurred with potential interactions between iron binding proteins and SARS CoV-2 surface proteins. Overall, increased levels of redox active metals and protein oxidation indicate that oxidative stress-induced protein oxidation in COVID-19 may be a consequence of the interactions of SARS-CoV-2 proteins with host cell metal binding proteins resulting in altered cellular homeostasis.
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Affiliation(s)
- Baikuntha Aryal
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA
| | - Joseph Tillotson
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA
- Pfizer Inc., Cambridge, MA, USA
| | - Kiwon Ok
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Andrew T Stoltzfus
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, 21201, USA
| | - V Ashutosh Rao
- Laboratory of Applied Biochemistry, Division of Biotechnology Research and Review III, Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, Food and Drug Administrations, Silver Spring, MD, 20993, USA.
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33
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Guffy SL, Pulavarti SVSRK, Harrison J, Fleming D, Szyperski T, Kuhlman B. Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 2023; 62:770-781. [PMID: 36634348 PMCID: PMC9939277 DOI: 10.1021/acs.biochem.2c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The de novo design of functional proteins requires specification of tertiary structure and incorporation of molecular binding sites. Here, we develop an inside-out design strategy in the molecular modeling program Rosetta that begins with amino acid side chains from one or two α-helices making well-defined contacts with a ligand. A full-sized protein is then built around the ligand by adding additional helices that promote the formation of a protein core and allow additional contacts with the ligand. The protocol was tested by designing 12 zinc-binding proteins, each with 4-5 helices. Four of the designs were folded and bound to zinc with equilibrium dissociation constants varying between 95 nM and 1.1 μM. The design with the tightest affinity for zinc, N12, adopts a unique conformation in the folded state as assessed with nuclear magnetic resonance (NMR) and the design model closely matches (backbone root-mean-square deviation (RMSD) < 1 Å) an AlphaFold model of the sequence. Retrospective analysis with AlphaFold suggests that the sequences of many of the failed designs did not encode the desired tertiary packing.
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Affiliation(s)
- Sharon L. Guffy
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Joseph Harrison
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Drew Fleming
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York, Buffalo, NY, 14260, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
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34
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Van V, Brown JB, O'Shea CR, Rosenbach H, Mohamed I, Ejimogu NE, Bui TS, Szalai VA, Chacón KN, Span I, Zhang F, Smith AT. Iron-sulfur clusters are involved in post-translational arginylation. Nat Commun 2023; 14:458. [PMID: 36709327 PMCID: PMC9884297 DOI: 10.1038/s41467-023-36158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Eukaryotic arginylation is an essential post-translational modification that modulates protein stability and regulates protein half-life. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA transferases (ATE1s), which are conserved across the eukaryotic domain. Despite their conservation and importance, little is known regarding the structure, mechanism, and regulation of ATE1s. In this work, we show that ATE1s bind a previously undiscovered [Fe-S] cluster that is conserved across evolution. We characterize the nature of this [Fe-S] cluster and find that the presence of the [Fe-S] cluster in ATE1 is linked to its arginylation activity, both in vitro and in vivo, and the initiation of the yeast stress response. Importantly, the ATE1 [Fe-S] cluster is oxygen-sensitive, which could be a molecular mechanism of the N-degron pathway to sense oxidative stress. Taken together, our data provide the framework of a cluster-based paradigm of ATE1 regulatory control.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Corin R O'Shea
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ijaz Mohamed
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Nna-Emeka Ejimogu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Toan S Bui
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Veronika A Szalai
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kelly N Chacón
- Department of Chemistry, Reed College, Portland, OR, 97202, USA
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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35
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Dixit H, Kulharia M, Verma SK. Metalloproteome of human-infective RNA viruses: a study towards understanding the role of metal ions in virology. Pathog Dis 2023; 81:ftad020. [PMID: 37653445 DOI: 10.1093/femspd/ftad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Metalloproteins and metal-based inhibitors have been shown to effectively combat infectious diseases, particularly those caused by RNA viruses. In this study, a diverse set of bioinformatics methods was employed to identify metal-binding proteins of human RNA viruses. Seventy-three viral proteins with a high probability of being metal-binding proteins were identified. These proteins included 40 zinc-, 47 magnesium- and 14 manganese-binding proteins belonging to 29 viral species and eight significant viral families, including Coronaviridae, Flaviviridae and Retroviridae. Further functional characterization has revealed that these proteins play a critical role in several viral processes, including viral replication, fusion and host viral entry. They fall under the essential categories of viral proteins, including polymerase and protease enzymes. Magnesium ion is abundantly predicted to interact with these viral enzymes, followed by zinc. In addition, this study also examined the evolutionary aspects of predicted viral metalloproteins, offering essential insights into the metal utilization patterns among different viral species. The analysis indicates that the metal utilization patterns are conserved within the functional classes of the proteins. In conclusion, the findings of this study provide significant knowledge on viral metalloproteins that can serve as a valuable foundation for future research in this area.
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Affiliation(s)
- Himisha Dixit
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Mahesh Kulharia
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
| | - Shailender Kumar Verma
- Centre for Computational Biology & Bioinformatics, Central University of Himachal Pradesh, Kangra 176206, Himachal Pradesh, India
- Department of Environmental Studies, University of Delhi 110007, Delhi, India
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36
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Coverdale JPC, Harrington CF, Solovyev N. Review: Advances in the Accuracy and Traceability of Metalloprotein Measurements Using Isotope Dilution Inductively Coupled Plasma Mass Spectrometry. Crit Rev Anal Chem 2023:1-18. [PMID: 36637361 DOI: 10.1080/10408347.2022.2162811] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Advances in inductively coupled plasma mass spectrometry and the methods used to prepare isotopically enriched standards, allow for the high accuracy measurement of metalloproteins by isotope dilution mass spectrometry. This technique has now reached a level of maturity whereby a step change in the accuracy, precision, and traceability of, in particular, clinical, and biomedical measurements is achievable. Current clinical measurements, which require low limits of detection in the presence of complex sample matrices, use indirect methods based on immunochemistry for the study of human disease. However, this approach suffers from poor traceability, requiring comparisons based on provision of matrix-based reference materials, used as analytical standards. This leads to difficulty when changes in the reference material are required, often resulting in a lack of interlaboratory and temporal comparability in clinical results and reference ranges. In this review, we focus on the most important metalloproteins for clinical studies, to illustrate how the attributes of chromatography coupled to inorganic mass spectrometry can be used for the direct measurement of metalloproteins such as hemoglobin, transferrin, and ceruloplasmin. By using this approach, we hope to demonstrate how isotope dilution analysis can be used as a reference method to improve traceability and underpin clinical, biomedical, and other biological measurements.
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Affiliation(s)
- James P C Coverdale
- Supra-Regional Assay Service, Trace Element Laboratory, Surrey Research Park, Guildford, United Kingdom
- School of Pharmacy, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Chris F Harrington
- Supra-Regional Assay Service, Trace Element Laboratory, Surrey Research Park, Guildford, United Kingdom
- Royal Surrey NHS Foundation Trust, Guildford, United Kingdom
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37
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Camponeschi F, Banci L. Metal trafficking in the cell: Combining atomic resolution with cellular dimension. FEBS Lett 2023; 597:122-133. [PMID: 36285633 DOI: 10.1002/1873-3468.14524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/14/2023]
Abstract
Metals are widely present in biological systems as simple ions or complex cofactors, and are involved in a variety of processes essential for life. Their transport inside cells and insertion into the binding sites of the proteins that need metals to function occur through complex and selective pathways involving dedicated multiprotein machineries specifically and transiently interacting with each other, often sharing the coordination of metal ions and/or cofactors. The understanding of these machineries requires integrated approaches, ranging from bioinformatics to experimental investigations, possibly in the cellular context. In this review, we report two case studies where the use of integrated in vitro and in cellulo approaches is necessary to clarify at atomic resolution essential aspects of metal trafficking in cells.
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Affiliation(s)
- Francesca Camponeschi
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy.,Department of Chemistry, University of Florence, Italy
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38
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Dudev T. How Theoretical Evaluations Can Generate Guidelines for Designing/Engineering Metalloproteins with Desired Metal Affinity and Selectivity. Molecules 2022; 28. [PMID: 36615442 DOI: 10.3390/molecules28010249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Almost half of all known proteins contain metal co-factors. Crucial for the flawless performance of a metalloprotein is the selection with high fidelity of the cognate metal cation from the surrounding biological fluids. Therefore, elucidating the factors controlling the metal binding and selectivity in metalloproteins is of particular significance. The knowledge thus acquired not only contributes to better understanding of the intimate mechanism of these events but, also, significantly enriches the researcher's toolbox that could be used in designing/engineering novel metalloprotein structures with pre-programmed properties. A powerful tool in aid of deciphering the physical principles behind the processes of metal recognition and selectivity is theoretical modeling of metal-containing biological structures. This review summarizes recent findings in the field with an emphasis on elucidating the major factors governing these processes. The results from theoretical evaluations are discussed. It is the hope that the physical principles evaluated can serve as guidelines in designing/engineering of novel metalloproteins of interest to both science and industry.
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Howley E, Ki D, Krajmalnik-Brown R, Torres CI. Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content. Microbiol Spectr 2022; 10:e0259322. [PMID: 36301091 PMCID: PMC9769739 DOI: 10.1128/spectrum.02593-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/24/2022] [Indexed: 01/07/2023] Open
Abstract
Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.
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Affiliation(s)
- Ethan Howley
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Dongwon Ki
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Division of Living and the Built Environment Research, Seoul Institute of Technology, Seoul, South Korea
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - César I. Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Engineering of Matter Transport and Energy, Arizona State University, Tempe, Arizona, USA
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40
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Liu Y, Bafaro EM, Cowan AE, Dempski RE. The transmembrane domains mediate oligomerization of the human ZIP4 transporter in vivo. Sci Rep 2022; 12:21083. [PMID: 36473915 PMCID: PMC9727157 DOI: 10.1038/s41598-022-24782-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The human (h) ZIP4 is a plasma membrane transporter that functions to increase cytosolic zinc levels. hZIP4 encodes eight transmembrane domains and a large extracellular domain (ECD). This ECD is cleaved from the holo-transporter when cells are zinc-deficient. At the same time, mutations in the ECD can result in the zinc-deficiency disease Acrodermatitis enteropathica. Previously, it was shown that hZIP4's ECD is comprised of two structurally independent subdomains where contacts between the ECD monomeric units are centered at the PAL motif. These results lead to the hypothesis that ZIP4-ECD is essential to the dimerization of the holo-transporter. To test this hypothesis, we used Fluorescence Correlation Spectroscopy (FCS) to quantify the oligomeric state of full-length hZIP4 and hZIP4 lacking the ECD domain, each tagged with eGFP. Inspection of our experimental results demonstrate that both the full-length and truncated hZIP4 is a dimer when expressed in HEK293 cells. Parallel functional experiments demonstrate that the Km and Vmax for truncated and full-length hZIP4/eGFP are similar. Determining that truncated hZIP4/eGFP forms a dimer is a crucial step for understanding the function of the hZIP4-ECD, which provides more insight into how the diseases related to hZIP4 protein.
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Affiliation(s)
- Yuting Liu
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
| | - Elizabeth M. Bafaro
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
| | - Ann E. Cowan
- grid.63054.340000 0001 0860 4915Department of Molecular Biology and Biophysics and Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT 06030 USA
| | - Robert E. Dempski
- grid.268323.e0000 0001 1957 0327Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609 USA
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41
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Ruckthong L, Pretzler M, Kampatsikas I, Rompel A. Biochemical characterization of Dimocarpus longan polyphenol oxidase provides insights into its catalytic efficiency. Sci Rep 2022; 12:20322. [PMID: 36434079 DOI: 10.1038/s41598-022-20616-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/15/2022] [Indexed: 11/27/2022] Open
Abstract
The "dragon-eye" fruits produced by the tropical longan tree are rich in nutrients and antioxidants. They suffer from post-harvest enzymatic browning, a process for which mainly the polyphenol oxidase (PPO) family of enzymes is responsible. In this study, two cDNAs encoding the PPO have been cloned from leaves of Dimocarpus longan (Dl), heterologously expressed in Escherichia coli and purified by affinity chromatography. The prepro-DlPPO1 contains two signal peptides at its N-terminal end that facilitate transportation of the protein into the chloroplast stroma and to the thylakoid lumen. Removal of the two signal peptides from prepro-DlPPO1 yields pro-DlPPO1. The prepro-DlPPO1 exhibited higher thermal tolerance than pro-DlPPO1 (unfolding at 65 °C vs. 40 °C), suggesting that the signal peptide may stabilize the fold of DlPPO1. DlPPO1 can be classified as a tyrosinase because it accepts both monophenolic and diphenolic substrates. The pro-DlPPO1 exhibited the highest specificity towards the natural diphenol (-)-epicatechin (kcat/KM of 800 ± 120 s-1 mM-1), which is higher than for 4-methylcatechol (590 ± 99 s-1 mM-1), pyrogallol (70 ± 9.7 s-1 mM-1) and caffeic acid (4.3 ± 0.72 s-1 mM-1). The kinetic efficiencies of prepro-DlPPO1 are 23, 36, 1.7 and 4.7-fold lower, respectively, than those observed with pro-DlPPO1 for the four aforementioned diphenolic substrates. Additionally, docking studies showed that (-)-epicatechin has a lower binding energy than any other investigated substrate. Both kinetic and in-silico studies strongly suggest that (-)-epicatechin is a good substrate of DlPPO1 and ascertain the affinity of PPOs towards specific flavonoid compounds.
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Kula-Maximenko M, Zieliński KJ, Depciuch J, Lekki J, Niemiec M, Ślesak I. Application of Spectroscopic Methods for the Identification of Superoxide Dismutases in Cyanobacteria. Int J Mol Sci 2022; 23. [PMID: 36430299 DOI: 10.3390/ijms232213819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
Superoxide dismutases (SODs) belong to the group of metalloenzymes that remove superoxide anion radicals and they have been identified in three domains of life: Bacteria, Archaea and Eucarya. SODs in Synechocystis sp. PCC 6803, Gloeobacter violaceus CCALA 979, and Geitlerinema sp. ZHR1A were investigated. We hypothesized that iron (FeSOD) and/or manganese (MnSOD) dominate as active forms in these cyanobacteria. Activity staining and three different spectroscopic methods of SOD activity bands excised from the gels were used to identify a suitable metal in the separated samples. FeSODs or enzymes belonging to the Fe-MnSOD superfamily were detected. The spectroscopic analyses showed that only Fe is present in the SOD activity bands. We found FeSOD in Synechocystis sp. PCC 6803 while two forms in G. violaceus and Geitlerinema sp. ZHR1A: FeSOD1 and FeSOD2 were present. However, no active Cu/ZnSODs were identified in G. violaceus and Geitlerinema sp. ZHR1A. We have shown that selected spectroscopic techniques can be complementary to the commonly used method of staining for SOD activity in a gel. Furthermore, the occurrence of active SODs in the cyanobacteria studied is also discussed in the context of SOD evolution in oxyphotrophs.
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Chin D, Flannagan RS, Tuffs SW, Chan JK, McCormick JK, Heinrichs DE. Staphylococcus lugdunensis Uses the Agr Regulatory System to Resist Killing by Host Innate Immune Effectors. Infect Immun 2022; 90:e0009922. [PMID: 36069592 DOI: 10.1128/iai.00099-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coagulase-negative staphylococci (CoNS) are frequently commensal bacteria that rarely cause disease in mammals. Staphylococcus lugdunensis is an exceptional CoNS that causes disease in humans similar to virulent Staphylococcus aureus, but the factors that enhance the virulence of this bacterium remain ill defined. Here, we used random transposon insertion mutagenesis to identify the agr quorum sensing system as a regulator of hemolysins in S. lugdunensis. Using RNA sequencing (RNA-seq), we revealed that agr regulates dozens of genes, including hemolytic S. lugdunensis synergistic hemolysins (SLUSH) peptides and the protease lugdulysin. A murine bacteremia model was used to show that mice infected systemically with wild-type S. lugdunensis do not show overt signs of disease despite there being high numbers of bacteria in the livers and kidneys of mice. Moreover, proliferation of the agr mutant in these organs was no different from that of the wild-type strain, leaving the role of the SLUSH peptides and the metalloprotease lugdulysin in pathogenesis still unclear. Nonetheless, the tropism of S. lugdunensis for humans led us to investigate the role of virulence factors in other ways. We show that agr-regulated effectors, but not SLUSH or lugdulysin alone, are important for S. lugdunensis survival in whole human blood. Moreover, we demonstrate that Agr contributes to survival of S. lugdunensis during encounters with murine and primary human macrophages. These findings demonstrate that, in S. lugdunensis, Agr regulates expression of virulence factors and is required for resistance to host innate antimicrobial defenses. This study therefore provides insight into strategies that this Staphylococcus species uses to cause disease.
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Wasilewski M, Gohil VM, Khalimonchuk O. Editorial: Function and formation of mitochondrial metalloproteome. Front Cell Dev Biol 2022; 10:1020441. [PMID: 36247001 PMCID: PMC9554646 DOI: 10.3389/fcell.2022.1020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/01/2022] [Indexed: 01/12/2023] Open
Affiliation(s)
- Michał Wasilewski
- International Institute of Molecular Mechanisms and Machines (IMol), Polish Academy of Sciences, Warsaw, Poland,*Correspondence: Michał Wasilewski,
| | - Vishal M. Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska, Lincoln, NE, United States,Nebraska Redox Biology Center, University of Nebraska, Lincoln, NE, United States,Fred & Pamela Buffett Cancer Center, Omaha, NE, United States
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Guo C, Chadwick RJ, Foulis A, Bedendi G, Lubskyy A, Rodriguez KJ, Pellizzoni MM, Milton RD, Beveridge R, Bruns N. Peroxidase Activity of Myoglobin Variants Reconstituted with Artificial Cofactors. Chembiochem 2022; 23:e202200197. [PMID: 35816250 PMCID: PMC9545363 DOI: 10.1002/cbic.202200197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/08/2022] [Indexed: 02/02/2023]
Abstract
Myoglobin (Mb) can react with hydrogen peroxide (H2 O2 ) to form a highly active intermediate compound and catalyse oxidation reactions. To enhance this activity, known as pseudo-peroxidase activity, previous studies have focused on the modification of key amino acid residues of Mb or the heme cofactor. In this work, the Mb scaffold (apo-Mb) was systematically reconstituted with a set of cofactors based on six metal ions and two ligands. These Mb variants were fully characterised by UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, inductively coupled plasma mass spectrometry (ICP-MS) and native mass spectrometry (nMS). The steady-state kinetics of guaiacol oxidation and 2,4,6-trichlorophenol (TCP) dehalogenation catalysed by Mb variants were determined. Mb variants with iron chlorin e6 (Fe-Ce6) and manganese chlorin e6 (Mn-Ce6) cofactors were found to have improved catalytic efficiency for both guaiacol and TCP substrates in comparison with wild-type Mb, i. e. Fe-protoporphyrin IX-Mb. Furthermore, the selected cofactors were incorporated into the scaffold of a Mb mutant, swMb H64D. Enhanced peroxidase activity for both substrates were found via the reconstitution of Fe-Ce6 into the mutant scaffold.
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Affiliation(s)
- Chao Guo
- Department of Pure and Applied ChemistryUniversity of Strathclyde295 Cathedral StreetG1 1XLGlasgowUK
| | - Robert J. Chadwick
- Department of Pure and Applied ChemistryUniversity of Strathclyde295 Cathedral StreetG1 1XLGlasgowUK
| | - Adam Foulis
- Department of Pure and Applied ChemistryUniversity of Strathclyde295 Cathedral StreetG1 1XLGlasgowUK
| | - Giada Bedendi
- Department of Inorganic and Analytical ChemistryUniversity of Geneva1211Geneva 4Switzerland
| | - Andriy Lubskyy
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Kyle J. Rodriguez
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Michela M. Pellizzoni
- Adolphe Merkle InstituteUniversity of FribourgChemin des Verdiers 41700FribourgSwitzerland
| | - Ross D. Milton
- Department of Inorganic and Analytical ChemistryUniversity of Geneva1211Geneva 4Switzerland
| | - Rebecca Beveridge
- Department of Pure and Applied ChemistryUniversity of Strathclyde295 Cathedral StreetG1 1XLGlasgowUK
| | - Nico Bruns
- Department of Pure and Applied ChemistryUniversity of Strathclyde295 Cathedral StreetG1 1XLGlasgowUK,Department of ChemistryTechnical University of DarmstadtAlarich-Weiss-Str. 464287DarmstadtGermany
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Yuvaraj I, Chaudhary SK, Jeyakanthan J, Sekar K. Structure of the hypothetical protein TTHA1873 from Thermus thermophilus. Acta Crystallogr F Struct Biol Commun 2022; 78:338-346. [PMID: 36048084 PMCID: PMC9435673 DOI: 10.1107/s2053230x22008457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of an uncharacterized hypothetical protein, TTHA1873 from Thermus thermophilus, has been determined by X-ray crystallography to a resolution of 1.78 Å using the single-wavelength anomalous dispersion method. The protein crystallized as a dimer in two space groups: P43212 and P6122. Structural analysis of the hypothetical protein revealed that the overall fold of TTHA1873 has a β-sandwich jelly-roll topology with nine β-strands. TTHA1873 is a dimeric metal-binding protein that binds to two Ca2+ ions per chain, with one on the surface and the other stabilizing the dimeric interface of the two chains. A structural homology search indicates that the protein has moderate structural similarity to one domain of cell-surface proteins or agglutinin receptor proteins. Red blood cells showed visible agglutination at high concentrations of the hypothetical protein.
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Affiliation(s)
- I. Yuvaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Santosh Kumar Chaudhary
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - J. Jeyakanthan
- Structural Biology and Bio Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, India
| | - K. Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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Rose SL, Baba S, Okumura H, Antonyuk SV, Sasaki D, Hedison TM, Shanmugam M, Heyes DJ, Scrutton NS, Kumasaka T, Tosha T, Eady RR, Yamamoto M, Hasnain SS. Single crystal spectroscopy and multiple structures from one crystal (MSOX) define catalysis in copper nitrite reductases. Proc Natl Acad Sci U S A 2022; 119:e2205664119. [PMID: 35862453 DOI: 10.1073/pnas.2205664119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
X-rays used to collect crystallographic data can change the redox states of transition metals utilized by many biological systems including metalloproteins. This disadvantage has been harnessed to drive a complex chemical reaction requiring the delivery of an electron to the active site and recording the structural changes accompanying catalysis, providing a real-time structural movie of an enzymatic reaction, which has been a dream of enzymologists for decades. By coupling the multiple-structures from one crystal technique with single-crystal and solution optical spectroscopy, we show that the electron transfer between the electron accepting type-1 Cu and catalytic type-2 Cu redox centers is gated in a recently characterized copper nitrite reductase. This combined structural/spectroscopic approach is applicable to many complex redox biological systems. Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.
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Soboh B, Adrian L, Stripp ST. An in vitro reconstitution system to monitor iron transfer to the active site during the maturation of [NiFe]-hydrogenase. J Biol Chem 2022; 298:102291. [PMID: 35868564 PMCID: PMC9418501 DOI: 10.1016/j.jbc.2022.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/29/2022] Open
Abstract
[NiFe]-hydrogenases comprise a small and a large subunit. The latter harbors the biologically unique [NiFe](CN)2CO active site cofactor. The maturation process includes the assembly of the [Fe](CN)2CO cofactor precursor, nickel binding, endoproteolytic cleavage of the large subunit, and dimerization with the small subunit to yield active enzyme. The biosynthesis of the [Fe](CN)2CO moiety of [NiFe]-Hydrogenase 1 (Hyd-1) and Hyd-2 occurs on the scaffold complex HybG-HypD (GD), whereas the HypC-HypD complex (CD) is specific for the assembly of Hyd-3. The metabolic source and the route for delivering iron to the active site remain unclear. To investigate the maturation process of O2-tolerant Hyd-1 from Escherichia coli, we developed an enzymatic in vitro reconstitution system that allows for the synthesis of Hyd-1 using only purified components. Together with this in vitro reconstitution system, we employed biochemical analyses, infrared spectroscopy (ATR FTIR), mass spectrometry, and microscale thermophoresis (MST) to monitor the iron transfer during the maturation process and to understand how the [Fe](CN)2CO cofactor precursor is ultimately incorporated into the large subunit. We demonstrate the direct transfer of iron from 57Fe-labeled GD complex to the large subunit of Hyd-1. Our data reveal that the GD complex exclusively interacts with the large subunit of Hyd-1 and Hyd-2 but not with the large subunit of Hyd-3. Furthermore, we show that the presence of iron in the active site is a prerequisite for nickel insertion. Taken together, these findings reveal how the [Fe](CN)2CO cofactor precursor is transferred and incorporated into the active site of [NiFe]-hydrogenase.
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Affiliation(s)
- Basem Soboh
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany.
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany; Chair of Geobiotechnology, Technische Universität Berlin, Ackerstraße 76, 13355 Berlin, Germany
| | - Sven T Stripp
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
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Santos MFA, Sciortino G, Correia I, Fernandes ACP, Santos-Silva T, Pisanu F, Garribba E, Costa Pessoa J. Binding of V IV O 2+ , V IV OL, V IV OL 2 and V V O 2 L Moieties to Proteins: X-ray/Theoretical Characterization and Biological Implications. Chemistry 2022; 28:e202200105. [PMID: 35486702 DOI: 10.1002/chem.202200105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 12/16/2022]
Abstract
Vanadium compounds have frequently been proposed as therapeutics, but their application has been hampered by the lack of information on the different V-containing species that may form and how these interact with blood and cell proteins, and with enzymes. Herein, we report several resolved crystal structures of lysozyme with bound VIV O2+ and VIV OL2+ , where L=2,2'-bipyridine or 1,10-phenanthroline (phen), and of trypsin with VIV O(picolinato)2 and VV O2 (phen)+ moieties. Computational studies complete the refinement and shed light on the relevant role of hydrophobic interactions, hydrogen bonds, and microsolvation in stabilizating the structure. Noteworthy is that the trypsin-VV O2 (phen) and trypsin-VIV O(OH)(phen) adducts correspond to similar energies, thus suggesting a possible interconversion under physiological/biological conditions. The obtained data support the relevance of hydrolysis of VIV and VV complexes in the several types of binding established with proteins and the formation of different adducts that might contribute to their pharmacological action, and significantly widen our knowledge of vanadium-protein interactions.
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Affiliation(s)
- Marino F A Santos
- Centro de Química Estrutural and Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.,UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Giuseppe Sciortino
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007, Tarragona, Spain
| | - Isabel Correia
- Centro de Química Estrutural and Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Andreia C P Fernandes
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.,UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Teresa Santos-Silva
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.,UCIBIO, Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Federico Pisanu
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, I-07100, Sassari, Italy
| | - Eugenio Garribba
- Dipartimento di Medicina, Chirurgia e Farmacia, Università di Sassari, I-07100, Sassari, Italy
| | - João Costa Pessoa
- Centro de Química Estrutural and Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
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50
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Affiliation(s)
- Karrera Djoko
- Department of Biosciences, Durham University, Durham, UK
| | - Jennifer Cavet
- School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
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