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Naeemi SM, Aminzadeh S, Sari S, Nemati F, Naseroleslami M. In vitro and in silico characterization of a novel glutamate carboxypeptidase from Cohnella sp. A01. Biochimie 2023; 207:83-95. [PMID: 36493965 DOI: 10.1016/j.biochi.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 10/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Glutamate carboxypeptidase is a bacterial enzyme of metallopeptidase superfamily. This enzyme is an exo-peptidase that catalyzes the hydrolysis of glutamate residues at the C-terminus of folic acid. The rCP302 is a novel zinc ion-dependent recombinant glutamate carboxypeptidase derived from a thermophilic bacterium, Cohnella sp. A01 (PTCC No: 1921). By simulating the structure of rCP302, analyzing its activity in various environmental settings, and contrasting it with that of related enzymes, we wanted to evaluate the heterologous production, purification, and characterization of this enzyme. The bioinformatics study showed that rCP302 had maximum similarity to M20 family of metallopeptidases. The purified rCP302 molecular weight was about 41.6 kDa. The optimum temperature and pH for the catalytic activity of rCP302 were 50 °C and 7.2, respectively. Fluorescence spectroscopy data elucidated the secondary structure of rCP302 and determined conformational changes caused by alterations in ambient conditions. Using folate as a substrate, Km and specific activity values were calculated as 0.108 μM and 687 μmol/min/mg, respectively. The enzyme activity was strongly inhibited when EDTA sequestered zinc ions. The half-life of this enzyme at 30 °C was 2012 min. Regarding the ability of rCP302 to degrade folic acid, and its long half-life at 37 °C, the normal temperature of many mammals, this enzyme can be introduced for further study for use in the pharmaceutical industry.
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Affiliation(s)
- Seyed Mahdi Naeemi
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Soyar Sari
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fahimeh Nemati
- Department of Biotechnoligy, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Naseroleslami
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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2
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Nagarajan H, Vetrivel U. Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach. J Biomol Struct Dyn 2022; 40:11758-11770. [PMID: 34402752 DOI: 10.1080/07391102.2021.1965030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Early growth response-1 (Egr1) is a zinc-finger transcription factor that plays a critical role in controlling cell growth, proliferation, differentiation, angiogenesis, and apoptosis. Egr1 is induced by many growth factors, cytokines, and stress signals and is also known to be involved in several pathological conditions like cancer, neurological and ocular disorders. The DNA binding domain of Egr1 is a highly conserved Cys2His2 (C2H2) zinc finger (ZNF) domain which specifically binds to GC-rich consensus sequence GcG (G/T) GGGCG and activates transcription. As the C2H2 domain specifically recognizes its DNA target, the mutations spanning this region shall perturb DNA recognition and may hinder transcription of target genes. Therefore, in this study, the missense mutations occurring specifically at the DNA binding domain (DBD) of Egr1 were probed by computational approaches involving in silico screening of pathogenic and functional mutants coupled with extensive molecular dynamics simulations, to determine the mutants that affect its structural stability and interactions with DNA. From the pathogenicity analysis of 38 missense mutations spanning Egr1-DBD, 17 were predicted as pathogenic, and 7 amongst these were found to have functional impact on Egr1. On combined analysis of molecular dynamics simulation, Residue interaction analysis and Egr1-DNA interaction analysis results, the mutants R371C and R375C showed least impact, whilst, H382R tend to increase the structural stability, whereas R360H, H390R, E393V, and H414Y conferred greater impact by altering the structural stability and DNA interactions. Hence, this study exposes the prospects of considering these 4 deleterious mutations for clinical significance, but needs further experimental validation.HighlightsEgr1's DNA binding domain is a highly conserved Cys2His2 (C2H2) zinc finger domain that specifically recognizes its DNA target.Mutations spanning in the DNA binding domain shall perturb DNA recognition and may hinder transcription.Among the missense mutations, mutants R360H, H390R, E393V, and H414Y were inferred to have a greater impact on Egr1 by altering the structural stability and DNA interactions.
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Affiliation(s)
- Hemavathy Nagarajan
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India.,National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research (Govt. of India), Belagavi, Karnataka, India
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3
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Alfaleh MA, Zawawi A, Al-Amri SS, Hashem AM. David versus goliath: ACE2-Fc receptor traps as potential SARS-CoV-2 inhibitors. MAbs 2022; 14:2057832. [PMID: 35380919 PMCID: PMC8986284 DOI: 10.1080/19420862.2022.2057832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Anti-SARS-CoV-2 monoclonal antibodies and vaccines have shown improvement in lowering viral burden and hospitalization. However, emerging SARS-CoV-2 variants contain neutralizing antibody-escape mutations. Therefore, several reports have suggested the administration of recombinant angiotensin-converting enzyme 2 (rACE2) as a soluble receptor trap to block SARS-CoV-2 infection and limit viral escape potential. Several strategies have been implemented to enhance the efficacy of rACE2 as a therapeutic agent. Fc fusions have been used to improve pharmacokinetics and boost the affinity and avidity of ACE2 decoys for the virus spike protein. Furthermore, the intrinsic catalytic activity of ACE2 can be eliminated by introducing point mutations on the catalytic site of ACE2 to obtain an exclusive antiviral activity. This review summarizes different evolution platforms that have been used to enhance ACE2-Fc (i.e., immunoadhesins) as potential therapeutics for the current pandemic or future outbreaks of SARS-associated betacoronaviruses.
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Affiliation(s)
- Mohamed A Alfaleh
- Department of Pharmaceutics, Faculty of Pharmacy, King Abdulaziz University, Jeddah Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Ayat Zawawi
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah Saudi Arabia
| | - Sawsan S Al-Amri
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah Saudi Arabia
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4
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Lyu X, Tang W, Sasaki Y, Zhao J, Zheng T, Tian Y, Minami T. Toward Food Freshness Monitoring: Coordination Binding-Based Colorimetric Sensor Array for Sulfur-Containing Amino Acids. Front Chem 2021; 9:685783. [PMID: 34222197 PMCID: PMC8248799 DOI: 10.3389/fchem.2021.685783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Herein, a self-assembled colorimetric chemosensor array composed of off-the-shelf catechol dyes and a metal ion (i.e., Zn2+) has been used for the sulfur-containing amino acids (SCAAs; i.e., glutathione, glutathione disulfide, L-cysteine, DL-homocysteine, and L-cystine). The coordination binding-based chemosensor array (CBSA) fabricated by a competitive assay among SCAAs, Zn2+ ions, and catechol dyes [i.e., pyrocatechol violet (PV), bromopyrogallol red (BPR), pyrogallol red (PR), and alizarin red S (ARS)] yielded fingerprint-like colorimetric changes. We succeeded in the qualification of SCAAs based on pattern recognition [i.e., a linear discrimination analysis (LDA)] with 100% correct classification accuracy. The semiquantification of reduced/oxidized forms of SCAAs was also performed based on LDA. Furthermore, we carried out a spike test of glutathione in food samples using the proposed chemosensor array with regression analysis. It is worth mentioning that we achieved a 91-110% recovery rate in real sample tests, which confirmed the accuracy of the constructed model. Thus, this study represents a step forward in assessing food freshness based on supramolecular analytical methods.
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Affiliation(s)
- Xiaojun Lyu
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Wei Tang
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Yui Sasaki
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Jie Zhao
- Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tingting Zheng
- Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Yang Tian
- Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Tsuyoshi Minami
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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5
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Unveiling the N-Terminal Homodimerization of BCL11B by Hybrid Solvent Replica-Exchange Simulations. Int J Mol Sci 2021; 22:ijms22073650. [PMID: 33807484 PMCID: PMC8036541 DOI: 10.3390/ijms22073650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 01/28/2023] Open
Abstract
Transcription factors play a crucial role in regulating biological processes such as cell growth, differentiation, organ development and cellular signaling. Within this group, proteins equipped with zinc finger motifs (ZFs) represent the largest family of sequence-specific DNA-binding transcription regulators. Numerous studies have proven the fundamental role of BCL11B for a variety of tissues and organs such as central nervous system, T cells, skin, teeth, and mammary glands. In a previous work we identified a novel atypical zinc finger domain (CCHC-ZF) which serves as a dimerization interface of BCL11B. This domain and formation of the dimer were shown to be critically important for efficient regulation of the BCL11B target genes and could therefore represent a promising target for novel drug therapies. Here, we report the structural basis for BCL11B-BCL11B interaction mediated by the N-terminal ZF domain. By combining structure prediction algorithms, enhanced sampling molecular dynamics and fluorescence resonance energy transfer (FRET) approaches, we identified amino acid residues indispensable for the formation of the single ZF domain and directly involved in forming the dimer interface. These findings not only provide deep insight into how BCL11B acquires its active structure but also represent an important step towards rational design or selection of potential inhibitors.
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6
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Cuajungco MP, Ramirez MS, Tolmasky ME. Zinc: Multidimensional Effects on Living Organisms. Biomedicines 2021; 9:biomedicines9020208. [PMID: 33671781 PMCID: PMC7926802 DOI: 10.3390/biomedicines9020208] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 12/28/2022] Open
Abstract
Zinc is a redox-inert trace element that is second only to iron in abundance in biological systems. In cells, zinc is typically buffered and bound to metalloproteins, but it may also exist in a labile or chelatable (free ion) form. Zinc plays a critical role in prokaryotes and eukaryotes, ranging from structural to catalytic to replication to demise. This review discusses the influential properties of zinc on various mechanisms of bacterial proliferation and synergistic action as an antimicrobial element. We also touch upon the significance of zinc among eukaryotic cells and how it may modulate their survival and death through its inhibitory or modulatory effect on certain receptors, enzymes, and signaling proteins. A brief discussion on zinc chelators is also presented, and chelating agents may be used with or against zinc to affect therapeutics against human diseases. Overall, the multidimensional effects of zinc in cells attest to the growing number of scientific research that reveal the consequential prominence of this remarkable transition metal in human health and disease.
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7
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Liu P, Xie X, Gao L, Jin J. Designed variants of ACE2-Fc that decouple anti-SARS-CoV-2 activities from unwanted cardiovascular effects. Int J Biol Macromol 2020; 165:1626-1633. [PMID: 33080267 PMCID: PMC7568492 DOI: 10.1016/j.ijbiomac.2020.10.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Angiotensin-converting enzyme 2 (ACE2) is the entry receptor for SARS-CoV-2, and recombinant ACE2 decoys are being evaluated as new antiviral therapies. We designed and tested an antibody-like ACE2-Fc fusion protein, which has the benefit of long pharmacological half-life and the potential to facilitate immune clearance of the virus. Out of a concern that the intrinsic catalytic activity of ACE2 may unintentionally alter the balance of its hormonal substrates and cause adverse cardiovascular effects in treatment, we performed a mutagenesis screening for inactivating the enzyme. Three mutants, R273A, H378A and E402A, completely lost their enzymatic activity for either surrogate or physiological substrates. All of them remained capable of binding SARS-CoV-2 and could suppress the transduction of a pseudotyped virus in cell culture. This study established new ACE2-Fc candidates as antiviral treatment for SARS-CoV-2 without potentially harmful side effects from ACE2's catalytic actions toward its vasoactive substrates.
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Affiliation(s)
- Pan Liu
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine-Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xinfang Xie
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine-Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Li Gao
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine-Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Department of Nephrology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, China
| | - Jing Jin
- Feinberg Cardiovascular and Renal Research Institute, Department of Medicine-Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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8
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Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Laitaoja M, Isoniemi S, Valjakka J, Mándity IM, Jänis J. Deciphering metal ion preference and primary coordination sphere robustness of a designed zinc finger with high-resolution mass spectrometry. Protein Sci 2016; 26:198-207. [PMID: 27750369 DOI: 10.1002/pro.3067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/13/2016] [Accepted: 10/13/2016] [Indexed: 11/10/2022]
Abstract
Small zinc finger (ZnF) motifs are promising molecular scaffolds for protein design owing to their structural robustness and versatility. Moreover, their characterization provides important insights into protein folding in general. ZnF motifs usually possess an exceptional specificity and high affinity towards Zn(II) ion to drive folding. While the Zn(II) ion is canonically coordinated by two cysteine and two histidine residues, many other coordination spheres also exist in small ZnFs, all having four amino acid ligands. Here we used high-resolution mass spectrometry to study metal ion binding specificity and primary coordination sphere robustness of a designed zinc finger, named MM1. Based on the results, MM1 possesses high specificity for zinc with sub-micromolar binding affinity. Surprisingly, MM1 retains metal ion binding affinity even in the presence of selective alanine mutations of the primary zinc coordinating amino acid residues.
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Affiliation(s)
- Mikko Laitaoja
- Department of Chemistry, University of Eastern Finland, Joensuu, FI-80101, Finland
| | - Sari Isoniemi
- Department of Chemistry, University of Eastern Finland, Joensuu, FI-80101, Finland
| | - Jarkko Valjakka
- BioMediTech, University of Tampere, Tampere, FI-33520, Finland
| | - István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Szeged, H-6720, Hungary
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, Joensuu, FI-80101, Finland
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10
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Krężel A, Maret W. The biological inorganic chemistry of zinc ions. Arch Biochem Biophys 2016; 611:3-19. [PMID: 27117234 PMCID: PMC5120989 DOI: 10.1016/j.abb.2016.04.010] [Citation(s) in RCA: 380] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/14/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022]
Abstract
The solution and complexation chemistry of zinc ions is the basis for zinc biology. In living organisms, zinc is redox-inert and has only one valence state: Zn(II). Its coordination environment in proteins is limited by oxygen, nitrogen, and sulfur donors from the side chains of a few amino acids. In an estimated 10% of all human proteins, zinc has a catalytic or structural function and remains bound during the lifetime of the protein. However, in other proteins zinc ions bind reversibly with dissociation and association rates commensurate with the requirements in regulation, transport, transfer, sensing, signalling, and storage. In contrast to the extensive knowledge about zinc proteins, the coordination chemistry of the “mobile” zinc ions in these processes, i.e. when not bound to proteins, is virtually unexplored and the mechanisms of ligand exchange are poorly understood. Knowledge of the biological inorganic chemistry of zinc ions is essential for understanding its cellular biology and for designing complexes that deliver zinc to proteins and chelating agents that remove zinc from proteins, for detecting zinc ion species by qualitative and quantitative analysis, and for proper planning and execution of experiments involving zinc ions and nanoparticles such as zinc oxide (ZnO). In most investigations, reference is made to zinc or Zn2+ without full appreciation of how biological zinc ions are buffered and how the d-block cation Zn2+ differs from s-block cations such as Ca2+ with regard to significantly higher affinity for ligands, preference for the donor atoms of ligands, and coordination dynamics. Zinc needs to be tightly controlled. The interaction with low molecular weight ligands such as water and inorganic and organic anions is highly relevant to its biology but in contrast to its coordination in proteins has not been discussed in the biochemical literature. From the discussion in this article, it is becoming evident that zinc ion speciation is important in zinc biochemistry and for biological recognition as a variety of low molecular weight zinc complexes have already been implicated in biological processes, e.g. with ATP, glutathione, citrate, ethylenediaminedisuccinic acid, nicotianamine, or bacillithiol. Zinc ions not bound to proteins have critical roles in cell biology. Zinc has a unique coordination chemistry, poorly appreciated in the biosciences. Its coordination chemistry is significantly different from that of calcium ions. Specific conditions apply for buffering cellular zinc ions. Investigations with zinc need to consider solution chemistry and metal buffering.
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Affiliation(s)
- Artur Krężel
- Laboratory of Chemical Biology, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14A, 50-383 Wroclaw, Poland.
| | - Wolfgang Maret
- King's College London, Metal Metabolism Group, Division of Diabetes and Nutritional Sciences, Department of Biochemistry, Faculty of Life Sciences of Medicine, 150 Stamford Street, London, SE1 9NH, UK.
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Hartle MD, Delgado M, Gilbertson JD, Pluth MD. Stabilization of a Zn(ii) hydrosulfido complex utilizing a hydrogen-bond accepting ligand. Chem Commun (Camb) 2016; 52:7680-2. [DOI: 10.1039/c6cc01373b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Inclusion of a hydrogen bond accepting motif in the secondary coordination sphere of a pyridinediimine ligand enables formation of a stable Zn–SH adduct. We report here reversible coordination of HS− to Zn(didpa)Cl2 to form [Zn(didpa)Cl2SH]−, which is stabilized by an intramolecular hydrogen bond.
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Affiliation(s)
- Matthew D. Hartle
- Department of Chemistry and Biochemistry
- Materials Science Institute
- Institute of Molecular Biology
- University of Oregon
- Eugene
| | - Mayra Delgado
- Department of Chemistry
- Western Washington University
- Bellingham
- USA
| | | | - Michael D. Pluth
- Department of Chemistry and Biochemistry
- Materials Science Institute
- Institute of Molecular Biology
- University of Oregon
- Eugene
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12
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Lambert LJ, Miller MJ, Huber PW. Tetrahydrofuranyl and tetrahydropyranyl protection of amino acid side-chains enables synthesis of a hydroxamate-containing aminoacylated tRNA. Org Biomol Chem 2015; 13:2341-9. [PMID: 25562392 DOI: 10.1039/c4ob02212b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ability to specifically engineer metal binding sites into target proteins has far-reaching consequences ranging from the development of new biocatalysts and imaging reagents to the production of proteins with increased stability. We report the efficient tRNA-mediated incorporation of the hydroxamate containing amino acid, N(ε)-acetyl-N(ε)-hydroxy-L-lysine, into a transcription factor (TFIIIA). Because this amino acid is compact, hydrophilic, and uncharged at physiological pH, it should have little or no effect on protein folding or solubility. The N(ε)-hydroxy group of the hydroxamate is refractory to photodeprotection and required the identification of reagents for O-protection that are compatible with the synthesis of acylated tRNA. Tetrahydrofuranyl and tetrahydropyranyl O-protecting groups can be removed using mild acid conditions and allowed for an orthogonal protection strategy in which deprotection of the amino acid side chain precedes ligation of an acylated dinucleotide to a truncated suppressor tRNA. These protecting groups will provide a valuable alternative for O-protection, especially in cases where photodeprotection cannot be used.
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Affiliation(s)
- Lester J Lambert
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556.
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13
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Kochańczyk T, Drozd A, Krężel A. Relationship between the architecture of zinc coordination and zinc binding affinity in proteins – insights into zinc regulation. Metallomics 2015; 7:244-57. [DOI: 10.1039/c4mt00094c] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relationship between the architecture and stability of zinc proteins.
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Affiliation(s)
- Tomasz Kochańczyk
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Agnieszka Drozd
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
| | - Artur Krężel
- Laboratory of Chemical Biology
- Faculty of Biotechnology
- University of Wrocław
- 50-383 Wrocław, Poland
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14
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Inhibition of aminoglycoside 6'-N-acetyltransferase type Ib by zinc: reversal of amikacin resistance in Acinetobacter baumannii and Escherichia coli by a zinc ionophore. Antimicrob Agents Chemother 2014; 58:4238-41. [PMID: 24820083 DOI: 10.1128/aac.00129-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In vitro activity of the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] was inhibited by ZnCl2 with a 50% inhibitory concentration (IC50) of 15 μM. Growth of Acinetobacter baumannii or Escherichia coli harboring aac(6')-Ib in cultures containing 8 μg/ml amikacin was significantly inhibited by the addition of 2 μM Zn(2+) in complex with the ionophore pyrithione (ZnPT).
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15
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Zastrow M, Pecoraro VL. Designing hydrolytic zinc metalloenzymes. Biochemistry 2014; 53:957-78. [PMID: 24506795 PMCID: PMC3985962 DOI: 10.1021/bi4016617] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/23/2014] [Indexed: 12/15/2022]
Abstract
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up.
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Affiliation(s)
| | - Vincent L. Pecoraro
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United
States
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16
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Hayes ML, Giang K, Berhane B, Mulligan RM. Identification of two pentatricopeptide repeat genes required for RNA editing and zinc binding by C-terminal cytidine deaminase-like domains. J Biol Chem 2013; 288:36519-29. [PMID: 24194514 DOI: 10.1074/jbc.m113.485755] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many transcripts expressed from plant organelle genomes are modified by C-to-U RNA editing. Nuclear encoded pentatricopeptide repeat (PPR) proteins are required as RNA binding specificity determinants in the RNA editing mechanism. Bioinformatic analysis has shown that most of the Arabidopsis PPR proteins necessary for RNA editing events include a C-terminal portion that shares structural characteristics with a superfamily of deaminases. The DYW deaminase domain includes a highly conserved zinc binding motif that shares characteristics with cytidine deaminases. The Arabidopsis PPR genes, ELI1 and DOT4, both have DYW deaminase domains and are required for single RNA editing events in chloroplasts. The ELI1 DYW deaminase domain was expressed as a recombinant protein in Escherichia coli and was shown to bind two zinc atoms per polypeptide. Thus, the DYW deaminase domain binds a zinc metal ion, as expected for a cytidine deaminase, and is potentially the catalytic component of an editing complex. Genetic complementation experiments demonstrate that large portions of the DYW deaminase domain of ELI1 may be eliminated, but the truncated genes retain the ability to restore editing site conversion in a mutant plant. These results suggest that the catalytic activity can be supplied in trans by uncharacterized protein(s) of the editosome.
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Der BS, Jha RK, Jha RK, Lewis SM, Thompson PM, Guntas G, Kuhlman B. Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding. Proteins 2013; 81:1245-55. [PMID: 23504819 DOI: 10.1002/prot.24280] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/13/2013] [Accepted: 02/26/2013] [Indexed: 11/11/2022]
Abstract
We computationally designed a de novo protein-protein interaction between wild-type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three-residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer-based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (Kd < 10 nM) and binds ubiquitin with a Kd of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple-zinc designs are more likely to promote high-affinity protein interactions.
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Affiliation(s)
- Bryan S Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7260, USA
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