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Kwong RWM. Trace metals in the teleost fish gill: biological roles, uptake regulation, and detoxification mechanisms. J Comp Physiol B 2024:10.1007/s00360-024-01565-1. [PMID: 38916671 DOI: 10.1007/s00360-024-01565-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 06/26/2024]
Abstract
In fish, the gill plays a vital role in regulating the absorption of trace metals and is also highly susceptible to metal toxicity. Trace metals such as iron (Fe), copper (Cu), zinc (Zn), and manganese (Mn) are involved in various catalytic activities and molecular binding within the gill, thereby supporting a range of physiological processes in this organ. While beneficial at normal levels, these metals can become toxic when present in excess. Conversely, nonessential metals like cadmium (Cd) and lead (Pb) can gain entry into gill cells through similar metal transport pathways, potentially interfering with various cellular processes. The transepithelial transport of these metals across the gill epithelium is governed by a variety of metal transport and metal binding proteins. These include the Cu transporter 1 (CTR1), divalent metal transporter 1 (DMT1), and members of the Zrt-/Irt-like protein (ZIP) and zinc transport (ZnT) families. Additionally, some of these metals can compete with major ions (e.g., calcium, sodium) for absorption sites in the gill. This complex crosstalk suggests an interdependent mechanism that balances metal uptake to meet physiological needs while preventing excessive accumulation. In this article, I review the roles of trace metals in proteins/enzymes that support the different functions in the gill of teleost fish. I also discuss current understanding of the pathways involved in regulating the branchial uptake of metals and their influence on ionic regulation, and the potential detoxification mechanisms in the gill. Finally, I summarize knowledge gaps and potential areas for further investigation.
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Affiliation(s)
- Raymond W M Kwong
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada.
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2
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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; 80:362-376. [PMID: 38682667 PMCID: PMC11066882 DOI: 10.1107/s2059798324003152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
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3
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Mydy LS, Hungerford J, Chigumba DN, Konwerski JR, Jantzi SC, Wang D, Smith JL, Kersten RD. An intramolecular macrocyclase in plant ribosomal peptide biosynthesis. Nat Chem Biol 2024; 20:530-540. [PMID: 38355722 PMCID: PMC11049724 DOI: 10.1038/s41589-024-01552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
The biosynthetic dogma of ribosomally synthesized and posttranslationally modified peptides (RiPP) involves enzymatic intermolecular modification of core peptide motifs in precursor peptides. The plant-specific BURP-domain protein family, named after their four founding members, includes autocatalytic peptide cyclases involved in the biosynthesis of side-chain-macrocyclic plant RiPPs. Here we show that AhyBURP, a representative of the founding Unknown Seed Protein-type BURP-domain subfamily, catalyzes intramolecular macrocyclizations of its core peptide during the sequential biosynthesis of monocyclic lyciumin I via glycine-tryptophan crosslinking and bicyclic legumenin via glutamine-tyrosine crosslinking. X-ray crystallography of AhyBURP reveals the BURP-domain fold with two type II copper centers derived from a conserved stapled-disulfide and His motif. We show the macrocyclization of lyciumin-C(sp3)-N-bond formation followed by legumenin-C(sp3)-O-bond formation requires dioxygen and radical involvement based on enzyme assays in anoxic conditions and isotopic labeling. Our study expands enzymatic intramolecular modifications beyond catalytic moiety and chromophore biogenesis to RiPP biosynthesis.
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Affiliation(s)
- Lisa S Mydy
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
| | - Jordan Hungerford
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Desnor N Chigumba
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Sarah C Jantzi
- Plasma Chemistry Laboratory, Center for Applied Isotope Studies, University of Georgia, Athens, GA, USA
| | - Di Wang
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Roland D Kersten
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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4
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Killian MM, Brophy MB, Nolan EM, Brunold TC. Spectroscopic and computational investigations of Cobalt(II) binding to the innate immune protein human calprotectin. J Biol Inorg Chem 2024; 29:127-137. [PMID: 38233645 DOI: 10.1007/s00775-023-02034-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/30/2023] [Indexed: 01/19/2024]
Abstract
Human calprotectin (CP) is an innate immune protein that participates in the metal-withholding response to infection by sequestering essential metal nutrients from invading microbial pathogens. CP is comprised of S100A8 (α subunit, 10.8 kDa) and S100A9 (β subunit, 13.2 kDa). Two transition-metal binding sites of CP form at the S100A8/S100A9 dimer interface. Site 1 is a His3Asp motif comprised of His83 and His87 from the S100A8 subunit and His20 and Asp30 from the S100A9 subunit. Site 2 is an unusual hexahistidine motif composed of S100A8 residues His17 and His27 and S100A9 residues His91, His95, His103, and His105. In the present study, the His3Asp and His6 sites of CP were further characterized by utilizing Co2+ as a spectroscopic probe. Magnetic circular dichroism spectroscopy was employed in conjunction with electron paramagnetic resonance spectroscopy and density functional theory computations to characterize the Co2+-bound S100A8(C42S)/S100A9(C3S) CP-Ser variant and six site variants that allowed the His3Asp and His6 sites to be further probed. Our results provide new insight into the metal-binding sites of CP-Ser and the effect of amino acid substitutions on the structure of site 2.
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Affiliation(s)
- Michelle M Killian
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan B Brophy
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elizabeth M Nolan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Thomas C Brunold
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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5
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Gebretsadik H, Kahsay G, Adams E, Van Schepdael A. A comprehensive review of capillary electrophoresis-based techniques for erythropoietin isoforms analysis. J Chromatogr A 2023; 1708:464331. [PMID: 37660565 DOI: 10.1016/j.chroma.2023.464331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Different CE techniques have been used to analyze erythropoietin. These techniques have been shown to be effective in differentiating and quantifying erythropoietin isoforms, including natural and recombinant origins. This review provides a comprehensive overview of various capillary electrophoresis-based techniques used for the analysis of erythropoietin isoforms. The importance of erythropoietin in clinical practice and the necessity for the accurate analysis of its isoforms are first discussed. Various techniques that have been used for erythropoietin isoform analysis are then described. The main body of the review focuses on the different capillary electrophoresis-based methods that have been developed for erythropoietin isoform analysis, including capillary zone electrophoresis and capillary isoelectric focusing. The advantages and drawbacks of each method as well as their applications are discussed. Suggestions into the future directions of the area are also described.
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Affiliation(s)
- Hailekiros Gebretsadik
- KU Leuven - University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, Herestraat 49, O&N2, PB 923, 3000 Leuven, Belgium
| | - Getu Kahsay
- KU Leuven - University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, Herestraat 49, O&N2, PB 923, 3000 Leuven, Belgium
| | - Erwin Adams
- KU Leuven - University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, Herestraat 49, O&N2, PB 923, 3000 Leuven, Belgium
| | - Ann Van Schepdael
- KU Leuven - University of Leuven, Department of Pharmaceutical and Pharmacological Sciences, Pharmaceutical Analysis, Herestraat 49, O&N2, PB 923, 3000 Leuven, Belgium.
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6
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Feng X, Su Z, Cheng Y, Ma G, Zhang S. Messenger RNA chromatographic purification: advances and challenges. J Chromatogr A 2023; 1707:464321. [PMID: 37639849 DOI: 10.1016/j.chroma.2023.464321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/16/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023]
Abstract
Messenger RNA (mRNA) technologies have shown great potential in prophylactic vaccines and therapeutic medicines due to their adaptability, rapidity, efficacy, and safety. The purity of mRNA determines the efficacy and safety of mRNA drugs. Though chromatographic technologies are currently employed in mRNA purification, they are facing challenges, mainly arising from the large size, relatively simple chemical composition, instability, and high resemblance of by-products to the target mRNA. In this review, we will first make a comprehensive analysis of physiochemical properties differences between mRNA and proteins, then the major challenges facing in mRNA purification and general considerations are highlighted. A detailed summary of the state-of-arts in mRNA chromatographic purification will be provided, which are mainly classified into physicochemical property-based (size, charge, and hydrophobicity) and chemical structure-based (phosphate backbone, bases, cap structure, and poly A tail) technologies. Efforts in eliminating dsRNA byproducts via post in vitro transcript (IVT) purification and by manipulating the IVT process to reduce the generation of dsRNA are highlighted. Finally, a brief summary of the current status of chromatographic purification of the emerging circular mRNA (circRNA) is provided. We hope this review will provide some useful guidance for the Quality by Design (QbD) of mRNA downstream process development.
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Affiliation(s)
- Xue Feng
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China; Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia; Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China
| | - Yuan Cheng
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia; Monash Suzhou Research Institute, Monash University, SIP, Suzhou 215000, China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinses Academy of Sciences, Beijing 100190, China.
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7
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Ravnik V, Jukič M, Bren U. Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. J Chem Inf Model 2023; 63:5204-5219. [PMID: 37557084 PMCID: PMC10466382 DOI: 10.1021/acs.jcim.3c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Indexed: 08/11/2023]
Abstract
In order to identify the locations of metal ions in the binding sites of proteins, we have developed a method named the MADE (MAcromolecular DEnsity and Structure Analysis) approach. The MADE approach represents an evolution of our previous toolset, the ProBiS H2O (MD) methodology, for the identification of conserved water molecules. Our method uses experimental structures of proteins homologous to a query, which are subsequently superimposed upon it. Areas with a particular species present in a similar location among many homologous protein structures are identified using a clustering algorithm. Dense clusters likely represent positions containing species important to the query protein structure or function. We analyze well-characterized apo protein structures and show that the MADE approach can identify clusters corresponding to the expected positions of metal ions in their binding sites. The greatest advantage of our method lies in its generality. It can in principle be applied to any species found in protein records; it is not only limited to metal ions. We additionally demonstrate that the MADE approach can be successfully applied to predict the location of cofactors in computer-modeled structures, e.g., via AlphaFold. We also conduct a careful protein superposition method comparison and find our methodology robust and the results largely independent of the selected protein superposition algorithm. We postulate that with increasing structural data availability, additional applications of the MADE approach will be possible such as non-protein systems, water network identification, protein binding site elaboration, and analysis of binding events, all in a dynamic manner. We have implemented the MADE approach as a plugin for the PyMOL molecular visualization tool. The MADE plugin is available free of charge at https://gitlab.com/Jukic/made_software.
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Affiliation(s)
- Vid Ravnik
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
| | - Marko Jukič
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
- The
Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper SI-6000, Slovenia
- Institute
for Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
| | - Urban Bren
- Faculty
of Chemistry and Chemical Engineering, University
of Maribor, Smetanova
ulica 17, Maribor SI-2000, Slovenia
- The
Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper SI-6000, Slovenia
- Institute
for Environmental Protection and Sensors, Beloruska ulica 7, Maribor SI-2000, Slovenia
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8
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Wu D, Gucwa M, Czub MP, Cooper DR, Shabalin IG, Fritzen R, Arya S, Schwarz-Linek U, Blindauer CA, Minor W, Stewart AJ. Structural and biochemical characterisation of Co 2+-binding sites on serum albumins and their interplay with fatty acids. Chem Sci 2023; 14:6244-6258. [PMID: 37325156 PMCID: PMC10266443 DOI: 10.1039/d3sc01723k] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
Serum albumin-Co2+ interactions are of clinical importance. They play a role in mediating the physiological effects associated with cobalt toxicity and are central to the albumin cobalt binding (ACB) assay for diagnosis of myocardial ischemia. To further understand these processes, a deeper understanding of albumin-Co2+ interactions is required. Here, we present the first crystallographic structures of human serum albumin (HSA; three structures) and equine serum albumin (ESA; one structure) in complex with Co2+. Amongst a total of sixteen sites bearing a cobalt ion across the structures, two locations were prominent, and they relate to metal-binding sites A and B. Site-directed mutagenesis and isothermal titration calorimetry (ITC) were employed to characterise sites on HSA. The results indicate that His9 and His67 contribute to the primary (putatively corresponding to site B) and secondary Co2+-binding sites (site A), respectively. The presence of additional multiple weak-affinity Co2+ binding sites on HSA was also supported by ITC studies. Furthermore, addition of 5 molar equivalents of the non-esterified fatty acid palmitate (C16:0) reduced the Co2+-binding affinity at both sites A and B. The presence of bound myristate (C14:0) in the HSA crystal structures provided insight into the fatty acid-mediated structural changes that diminish the affinity of the protein toward Co2+. Together, these data provide further support for the idea that ischemia-modified albumin corresponds to albumin with excessive fatty-acid loading. Collectively, our findings provide a comprehensive understanding of the molecular underpinnings governing Co2+ binding to serum albumin.
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Affiliation(s)
- Dongmei Wu
- School of Medicine, University of St Andrews St Andrews UK +44 (0)1334 463546
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville VA 22908-0736 USA +1 434-243-6865
- Doctoral School of Exact and Natural Sciences, Jagiellonian University Krakow Poland
| | - Mateusz P Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville VA 22908-0736 USA +1 434-243-6865
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville VA 22908-0736 USA +1 434-243-6865
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville VA 22908-0736 USA +1 434-243-6865
| | - Remi Fritzen
- School of Medicine, University of St Andrews St Andrews UK +44 (0)1334 463546
| | - Swati Arya
- School of Medicine, University of St Andrews St Andrews UK +44 (0)1334 463546
| | | | | | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville VA 22908-0736 USA +1 434-243-6865
| | - Alan J Stewart
- School of Medicine, University of St Andrews St Andrews UK +44 (0)1334 463546
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9
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Jafari-Nodoushan H, Fazeli MR, Faramarzi MA, Samadi N. Hierarchically-structured laccase@Ni 3(PO 4) 2 hybrid nanoflowers for antibiotic degradation: Application in real wastewater effluent and toxicity evaluation. Int J Biol Macromol 2023; 234:123574. [PMID: 36764346 DOI: 10.1016/j.ijbiomac.2023.123574] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/26/2023] [Accepted: 02/03/2023] [Indexed: 02/11/2023]
Abstract
Laccase@Ni3(PO4)2 hybrid nanoflowers (HNFs) were prepared by the anisotropic growth of biomineralized nickel phosphate. The immobilization yield was 77.5 ± 3.6 %, and the immobilized enzyme retained 50 % of its initial activity after 18 reusability cycles. The immobilized and free enzymes lost 80 % of their activity after 18 and 6 h incubation in municipal wastewater effluent (MWWE), respectively. The increase in α-helix content (8 %) following immobilization led to a more rigid enzyme structure, potentially contributing to its improved stability. The removal of ciprofloxacin from MWWE by laccase@Ni3(PO4)2·HNFs/p-coumaric acid oxidation system was optimized using a Box-Behnken design. Under the optimized conditions [initial laccase activity (0.05 U mL-1), the concentration of p-coumaric acid (2.9 mM), and treatment time (4.9 h)], the biocatalyst removed 90 % of ciprofloxacin (10 mg L-1) from MWWE. The toxicity of ciprofloxacin against some G+ and G- bacteria was reduced by 35-70 %, depending on their strain. The EC50 of ciprofloxacin for the alga Raphidocelis subcapitata reduced from 3.08 to 1.07 mg L-1 (p-value <0.05) after the bioremoval. Also, the acute and chronic toxicity of identified biodegradation products was lower than ciprofloxacin at three trophic levels, as predicted by ECOSAR software.
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Affiliation(s)
- Hossein Jafari-Nodoushan
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran; Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran
| | - Mohammad Reza Fazeli
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran
| | - Mohammad Ali Faramarzi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran.
| | - Nasrin Samadi
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran; Pharmaceutical Quality Assurance Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran.
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10
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Gucwa M, Lenkiewicz J, Zheng H, Cymborowski M, Cooper DR, Murzyn K, Minor W. CMM-An enhanced platform for interactive validation of metal binding sites. Protein Sci 2023; 32:e4525. [PMID: 36464767 PMCID: PMC9794025 DOI: 10.1002/pro.4525] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022]
Abstract
Metal ions bound to macromolecules play an integral role in many cellular processes. They can directly participate in catalytic mechanisms or be essential for the structural integrity of proteins and nucleic acids. However, their unique nature in macromolecules can make them difficult to model and refine, and a substantial portion of metal ions in the PDB are misidentified or poorly refined. CheckMyMetal (CMM) is a validation tool that has gained widespread acceptance as an essential tool for researchers working on metal-macromolecule complexes. CMM can be used during structure determination or to validate metal binding sites in structural models within the PDB. The functionalities of CMM have recently been greatly enhanced and provide researchers with additional information that can guide modeling decisions. The new version of CMM shows metals in the context of electron density maps and allows for on-the-fly refinement of metal binding sites. The improvements should increase the reproducibility of biomedical research. The web server is available at https://cmm.minorlab.org.
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Affiliation(s)
- Michal Gucwa
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA,Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heping Zheng
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA,Present address:
Hunan University College of BiologyBioinformatics CenterHunanPeople's Republic of China
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Krzysztof Murzyn
- Department of Computational Biophysics and BioinformaticsJagiellonian UniversityKrakowPoland
| | - Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginiaUSA
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11
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Victor-Lovelace TW, Miller LM. The development and use of metal-based probes for X-ray fluorescence microscopy. METALLOMICS : INTEGRATED BIOMETAL SCIENCE 2022; 14:6852953. [PMID: 36537552 DOI: 10.1093/mtomcs/mfac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
Abstract
X-ray fluorescence microscopy (XFM) has become a widely used technique for imaging the concentration and distribution of metal ions in cells and tissues. Recent advances in synchrotron sources, optics, and detectors have improved the spatial resolution of the technique to <10 nm with attogram detection sensitivity. However, to make XFM most beneficial for bioimaging-especially at the nanoscale-the metal ion distribution must be visualized within the subcellular context of the cell. Over the years, a number of approaches have been taken to develop X-ray-sensitive tags that permit the visualization of specific organelles or proteins using XFM. In this review, we examine the types of X-ray fluorophore used, including nanomaterials and metal ions, and the approaches used to incorporate the metal into their target binding site via antibodies, genetically encoded metal-binding peptides, affinity labeling, or cell-specific peptides. We evaluate their advantages and disadvantages, review the scientific findings, and discuss the needs for future development.
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Affiliation(s)
| | - Lisa M Miller
- N ational Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973,USA.,Department of Chemistry, Stony Brook University, Stony Brook, NY 11794,USA
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12
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Conservation and Diversification of tRNA t6A-Modifying Enzymes across the Three Domains of Life. Int J Mol Sci 2022; 23:ijms232113600. [PMID: 36362385 PMCID: PMC9654439 DOI: 10.3390/ijms232113600] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification occurs at position 37 of tRNAs that decipher codons starting with adenosine. Mechanistically, t6A stabilizes structural configurations of the anticodon stem loop, promotes anticodon–codon pairing and safeguards the translational fidelity. The biosynthesis of tRNA t6A is co-catalyzed by two universally conserved protein families of TsaC/Sua5 (COG0009) and TsaD/Kae1/Qri7 (COG0533). Enzymatically, TsaC/Sua5 protein utilizes the substrates of L-threonine, HCO3−/CO2 and ATP to synthesize an intermediate L-threonylcarbamoyladenylate, of which the threonylcarbamoyl-moiety is subsequently transferred onto the A37 of substrate tRNAs by the TsaD–TsaB –TsaE complex in bacteria or by the KEOPS complex in archaea and eukaryotic cytoplasm, whereas Qri7/OSGEPL1 protein functions on its own in mitochondria. Depletion of tRNA t6A interferes with protein homeostasis and gravely affects the life of unicellular organisms and the fitness of higher eukaryotes. Pathogenic mutations of YRDC, OSGEPL1 and KEOPS are implicated in a number of human mitochondrial and neurological diseases, including autosomal recessive Galloway–Mowat syndrome. The molecular mechanisms underscoring both the biosynthesis and cellular roles of tRNA t6A are presently not well elucidated. This review summarizes current mechanistic understandings of the catalysis, regulation and disease implications of tRNA t6A-biosynthetic machineries of three kingdoms of life, with a special focus on delineating the structure–function relationship from perspectives of conservation and diversity.
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Kiliszek A, Pluta M, Bejger M, Rypniewski W. Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair. RNA (NEW YORK, N.Y.) 2022; 29:rna.079414.122. [PMID: 36319090 PMCID: PMC9808570 DOI: 10.1261/rna.079414.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The self-complementary triplet 5'UGG3'/5'UGG3' is a particular structural motif containing noncanonical G-G pair and two U·G wobble pairs. It constitutes a specific structural and electrostatic environment attracting metal ions, particularly Ba2+ ions. Crystallographic research has shown that two Ba2+ cations are located in the major groove of the helix and interact directly with the UGG triplet. A comparison with the unliganded structure has revealed global changes in the RNA structure in the presence of metal ions, whereas thermodynamic measurements have shown increased stability. Moreover, in the structure with Ba2+, an unusual noncanonical G(syn)-G(syn) pair is observed instead of the common G(anti)-G(syn). We further elucidate the metal binding properties of the UGG/UGG triplet by performing crystallographic and thermodynamic studies using DSC and UV melting with other metal ions. The results explain the preferences of the UGG sequence for Ba2+ cations and point to possible applications of this metal-binding propensity.
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14
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Hosseinzadeh B, Ahmadi M. Coordination geometry in metallo-supramolecular polymer networks. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Lee J, Yang M, Song WJ. The expanded landscape of metalloproteins by genetic incorporation of noncanonical amino acids. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jaehee Lee
- Department of Chemistry Seoul National University Seoul South Korea
| | - Minwoo Yang
- Department of Chemistry Seoul National University Seoul South Korea
| | - Woon Ju Song
- Department of Chemistry Seoul National University Seoul South Korea
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16
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Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins. J Mol Model 2022; 28:201. [PMID: 35748949 DOI: 10.1007/s00894-022-05154-3] [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: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 10/17/2022]
Abstract
Metal ions play important biological roles, e.g., activation or deactivation of enzymatic reactions and signal transduction. Moreover, they can stabilize protein structure, or even be actively involved in the protein folding process. Therefore, accurate treatment of the ions is crucial to model and investigate biological phenomena properly. In this work the coarse-grained UNRES (UNited RESidue) force field was extended to include the interactions between proteins and four alkali or alkaline earth metal cations of biological significance, i.e., calcium, magnesium, sodium and potassium. Additionally, chloride anions were introduced as counter-ions. Parameters were derived from all-atom simulations and incorporate water in an implicit manner. The new force field was tested on the set of the proteins and was able to reproduce the ion-binding preferences.
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17
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Krošl I, Košćak M, Ribičić K, Žinić B, Majhen D, Božinović K, Piantanida I. Impact of the Histidine-Triazole and Tryptophan-Pyrene Exchange in the WHW Peptide: Cu(II) Binding, DNA/RNA Interactions and Bioactivity. Int J Mol Sci 2022; 23:ijms23137006. [PMID: 35806009 PMCID: PMC9266797 DOI: 10.3390/ijms23137006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
In three novel peptidoids based on the tryptophan—histidine—tryptophan (WHW) peptide, the central histidine was replaced by Ala-(triazole), and two derivatives also had one tryptophan replaced with pyrene-alkyls of different lengths and flexibility. Pyrene analogues show strong fluorescence at 480–500 nm, attributed to intramolecular exciplex formation with tryptophan. All three peptidoids bind Cu2+ cation in water with strong affinity, with Trp- Ala-(triazole)-Trp binding comparably to the parent WHW, and the pyrene analogues even stronger, demonstrating that replacement of histidine with triazole in peptides does not hamper Cu2+ coordination. The studied peptidoids strongly bind to ds-DNA and ds-RNA, whereby their complexes with Cu2+ exhibit distinctively different interactions in comparison to metal-free analogues, particularly in the stabilization of ds-DNA against thermal denaturation. The pyrene peptidoids efficiently enter living cells with no apparent cytotoxic effect, whereby their red-shifted emission compared to the parent pyrene allows intracellular confocal microscopy imaging, showing accumulation in cytoplasmic organelles. However, irradiation with 350 nm light resulted in evident antiproliferative effect on cells treated with micromolar concentrations of the pyrene analogues, presumably attributed to pyrene-induced production of singlet oxygen and consecutive cellular damage.
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Affiliation(s)
- Ivona Krošl
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Karla Ribičić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Biserka Žinić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
- Correspondence: ; Tel.: +385-1-4571-326
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18
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Knox HL, Booker SJ. Structural characterization of cobalamin-dependent radical S-adenosylmethionine methylases. Methods Enzymol 2022; 669:3-27. [PMID: 35644177 DOI: 10.1016/bs.mie.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cobalamin-dependent radical S-adenosylmethionine (SAM) methylases catalyze key steps in the biosynthesis of numerous biomolecules, including protein cofactors, antibiotics, herbicides, and other natural products, but have remained a relatively understudied subclass of radical SAM enzymes due to their inherent insolubility upon overproduction in Escherichia coli. These enzymes contain two cofactors: a [4Fe-4S] cluster that is ligated by three cysteine residues, and a cobalamin cofactor typically bound by residues in the N-terminal portion of the enzyme. Recent advances in the expression and purification of these enzymes in their active states and with both cofactors present has allowed for more detailed biochemical studies as well as structure determination by X-ray crystallography. Herein, we use KsTsrM and TokK to highlight methods for the structural characterization of cobalamin-dependent radical SAM (RS) enzymes and describe recent advances in in the overproduction and purification of these enzymes.
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Affiliation(s)
- Hayley L Knox
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Squire J Booker
- The Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States.
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19
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Lennartz F, Jeoung JH, Ruenger S, Dobbek H, Weiss MS. Determining the oxidation state of elements by X-ray crystallography. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:238-247. [PMID: 35102889 PMCID: PMC8805299 DOI: 10.1107/s2059798321013048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022]
Abstract
Protein-mediated redox reactions play a critical role in many biological processes and often occur at centres that contain metal ions as cofactors. In order to understand the exact mechanisms behind these reactions it is important to not only characterize the three-dimensional structures of these proteins and their cofactors, but also to identify the oxidation states of the cofactors involved and to correlate this knowledge with structural information. The only suitable approach for this based on crystallographic measurements is spatially resolved anomalous dispersion (SpReAD) refinement, a method that has been used previously to determine the redox states of metals in iron–sulfur cluster-containing proteins. In this article, the feasibility of this approach for small, non-iron–sulfur redox centres is demonstrated by employing SpReAD analysis to characterize Sulfolobus tokodaii sulerythrin, a ruberythrin-like protein that contains a binuclear metal centre. Differences in oxidation states between the individual iron ions of the binuclear metal centre are revealed in sulerythrin crystals treated with H2O2. Furthermore, data collection at high X-ray doses leads to photoreduction of this metal centre, showing that careful control of the total absorbed dose is a prerequisite for successfully determining the oxidation state through SpReAD analysis.
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20
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Fluorescent Analogues of FRH Peptide: Cu(II) Binding and Interactions with ds-DNA/RNA. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Four novel peptidoids, derived from the Phe-Arg-His (FRH) peptide motif, were prepared by replacing the histidine heterocycle with triazole and consequent triazole-fluorophore (coumarin) extension and also replacing arginine with less voluminous lysine. So the constructed Phe-Lys-Ala(triazole) (FKA(triazole)) peptidoids bind Cu2+ cations in water with a strong, nanomolar affinity comparable to the parent FRH and its known analogs, demonstrating that triazole can coordinate copper similarly as histidine. Moreover, even short KA(triazole)coumarin showed submicromolar affinity to Cu2+. Only FKA(triazole)coumarin with free amino groups and its shorter analog KA(triazole)coumarin showed strong induced CD spectra upon Cu2+ cation binding. Thus, KA(triazole)coumarin can be considered as the shortest peptidoid sequence with highly sensitive fluorescent and chiral CD response for Cu2+ cation, encouraging further studies with other metal cations. The FKA(triazole) coumarin peptidoids show biorelevant, 10 µM affinity to ds-DNA and ds-RNA, binding within DNA/RNA grooves. Intriguingly, only peptidoid complexes with Cu2+ strongly stabilize ds-DNA and ds-RNA against thermal denaturation, suggesting significant interactions of Cu2+ cation within the DNA/RNA binding site.
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21
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Engineering potassium activation into biosynthetic thiolase. Biochem J 2021; 478:3047-3062. [PMID: 34338286 DOI: 10.1042/bcj20210455] [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: 06/18/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 11/17/2022]
Abstract
Activation of enzymes by monovalent cations (M+) is a widespread phenomenon in biology. Despite this, there are few structure-based studies describing the underlying molecular details. Thiolases are a ubiquitous and highly conserved family of enzymes containing both K+-activated and K+-independent members. Guided by structures of naturally occurring K+-activated thiolases, we have used a structure-based approach to engineer K+-activation into a K+-independent thiolase. To our knowledge, this is the first demonstration of engineering K+-activation into an enzyme, showing the malleability of proteins to accommodate M+ ions as allosteric regulators. We show that a few protein structural features encode K+-activation in this class of enzyme. Specifically, two residues near the substrate-binding site are sufficient for K+-activation: A tyrosine residue is required to complete the K+ coordination sphere, and a glutamate residue provides a compensating charge for the bound K+ ion. Further to these, a distal residue is important for positioning a K+-coordinating water molecule that forms a direct hydrogen bond to the substrate. The stability of a cation-π interaction between a positively charged residue and the substrate is determined by the conformation of the loop surrounding the substrate-binding site. Our results suggest that this cation-π interaction effectively overrides K+-activation, and is, therefore, destabilised in K+-activated thiolases. Evolutionary conservation of these amino acids provides a promising signature sequence for predicting K+-activation in thiolases. Together, our structural, biochemical and bioinformatic work provide important mechanistic insights into how enzymes can be allosterically activated by M+ ions.
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22
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Boychuk BTA, Rebecca Jeong YE, Wetmore SD. Assessment of the Accuracy of DFT-Predicted Li +-Nucleic Acid Binding Energies. J Chem Theory Comput 2021; 17:5392-5408. [PMID: 34339194 DOI: 10.1021/acs.jctc.1c00401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li+ binding to nucleic acids is required. Herein, a new database of Li+-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li+-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li+-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.
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Affiliation(s)
- Briana T A Boychuk
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Ye Eun Rebecca Jeong
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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23
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Moulahoum H, Ghorbani Zamani F, Timur S, Zihnioglu F. Metal Binding Antimicrobial Peptides in Nanoparticle Bio-functionalization: New Heights in Drug Delivery and Therapy. Probiotics Antimicrob Proteins 2021; 12:48-63. [PMID: 31001788 DOI: 10.1007/s12602-019-09546-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides are considered very important due to the diversity expressed through their amino acid sequence, structure variation, large spectrum, and their essential role in biological systems. Antimicrobial peptides (AMPs) emerged as a potent tool in therapy owing to their antimicrobial properties but also their ability to trespass the membranes, specificity, and low toxicity. They comprise a variety of peptides from which specific amino acid-rich peptides are of interest to the current review due to their features in metal interaction and cell penetration. Histidine-rich peptides such as Histatins belong to the metal binding salivary residing peptides with efficient antibacterial, antifungal, and wound-healing activities. Furthermore, their ability to activate in acidic environment attracted the attention to their potential in therapy. The current review covers the current knowledge about AMPs and critically assess the potential of associating with metal ions both structurally and functionally. This review provides interesting hints for the advantages provided by AMPs and metal ions in biomedicine, making use of their direct properties in brain diseases therapy or in the creation of new bio-functionalized nanoparticles for cancer diagnosis and treatment.
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Affiliation(s)
- Hichem Moulahoum
- Biochemistry Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Faezeh Ghorbani Zamani
- Biochemistry Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Suna Timur
- Biochemistry Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey
| | - Figen Zihnioglu
- Biochemistry Department, Faculty of Science, Ege University, 35100, Bornova, Izmir, Turkey.
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24
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Vadivel K, Schmidt AE, Cascio D, Padmanabhan K, Krishnaswamy S, Brandstetter H, Bajaj SP. Structure of human factor VIIa-soluble tissue factor with calcium, magnesium and rubidium. Acta Crystallogr D Struct Biol 2021; 77:809-819. [PMID: 34076594 PMCID: PMC8171065 DOI: 10.1107/s2059798321003922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/12/2021] [Indexed: 11/10/2022] Open
Abstract
Coagulation factor VIIa (FVIIa) consists of a γ-carboxyglutamic acid (GLA) domain, two epidermal growth factor-like (EGF) domains and a protease domain. FVIIa binds three Mg2+ ions and four Ca2+ ions in the GLA domain, one Ca2+ ion in the EGF1 domain and one Ca2+ ion in the protease domain. Further, FVIIa contains an Na+ site in the protease domain. Since Na+ and water share the same number of electrons, Na+ sites in proteins are difficult to distinguish from waters in X-ray structures. Here, to verify the Na+ site in FVIIa, the structure of the FVIIa-soluble tissue factor (TF) complex was solved at 1.8 Å resolution containing Mg2+, Ca2+ and Rb+ ions. In this structure, Rb+ replaced two Ca2+ sites in the GLA domain and occupied three non-metal sites in the protease domain. However, Rb+ was not detected at the expected Na+ site. In kinetic experiments, Na+ increased the amidolytic activity of FVIIa towards the synthetic substrate S-2288 (H-D-Ile-Pro-Arg-p-nitroanilide) by ∼20-fold; however, in the presence of Ca2+, Na+ had a negligible effect. Ca2+ increased the hydrolytic activity of FVIIa towards S-2288 by ∼60-fold in the absence of Na+ and by ∼82-fold in the presence of Na+. In molecular-dynamics simulations, Na+ stabilized the two Na+-binding loops (the 184-loop and 220-loop) and the TF-binding region spanning residues 163-180. Ca2+ stabilized the Ca2+-binding loop (the 70-loop) and Na+-binding loops but not the TF-binding region. Na+ and Ca2+ together stabilized both the Na+-binding and Ca2+-binding loops and the TF-binding region. Previously, Rb+ has been used to define the Na+ site in thrombin; however, it was unsuccessful in detecting the Na+ site in FVIIa. A conceivable explanation for this observation is provided.
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Affiliation(s)
- Kanagasabai Vadivel
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Amy E. Schmidt
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Duilio Cascio
- DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | | | - Sriram Krishnaswamy
- Division of Hematology, The Children’s Hospital of Philadelphia University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - S. Paul Bajaj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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25
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Abstract
Combining crosslinking strategies with electrophysiology, biochemistry, and structural in silico analysis is a powerful tool to study transient movements of ion channels during gating. This chapter describes crosslinking in living cells using cysteine and photoactive unnatural amino acids (UAAs) that we have used on glutamate receptor ion channels. Here, we share the protocol for building a perfusion tool to enable rapid chemical modification of glutamate-gated AMPA receptors, optimized for their fast activation. This system can be used to perform state-dependent crosslinking in receptors modified by cysteines or UAA incorporation on the millisecond timescale. Introducing UAAs results in receptors with lower expression levels relative to the introduction of cysteine residues. Reduced expression is principally a challenge for biochemical studies, and we share here our approach to capture the light driven oligomerization of AMPA receptors containing UAA crosslinkers. Finally, we describe strategies for computational analysis to make sense of the crosslinking results in terms of structure and function.
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Affiliation(s)
- Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany; NeuroCure Cluster of Excellence, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Mette H Poulsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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26
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Vrancken JPM, Noguchi H, Zhang KYJ, Tame JRH, Voet ARD. The symmetric designer protein Pizza as a scaffold for metal coordination. Proteins 2021; 89:945-951. [PMID: 33713051 DOI: 10.1002/prot.26072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 12/14/2020] [Accepted: 03/04/2021] [Indexed: 01/17/2023]
Abstract
Symmetric proteins are currently of interest as they allow creation of larger assemblies and facilitate the incorporation of metal ions in the larger complexes. Recently this was demonstrated by the biomineralization of the cadmium-chloride nanocrystal via the Pizza designer protein. However, the mechanism behind this formation remained unclear. Here, we set out to investigate the mechanism driving the formation of this nanocrystal via truncation, mutation, and circular permutations. In addition, the interaction of other biologically relevant metal ions with these symmetric proteins to form larger symmetric complexes was also studied. The formation of the initial nanocrystal is shown to originate from steric strain, where His 58 induces a different rotameric conformation on His 73, thereby distorting an otherwise perfect planar ring of alternating cadmium and chlorine ions, resulting in the smallest nanocrystal. Similar highly symmetric complexes were also observed for the other biological relevant metal ions. However, the flexibility of the coordinating histidine residues allows each metal ion to adopt its preferred geometry leading to either monomeric or dimeric β-propeller units, where the metal ions are located at the interface between both propeller units. These results demonstrate that symmetric proteins are not only interesting to generate larger assemblies, but are also the perfect scaffold to create more complex metal based assemblies. Such metal protein assemblies may then find applications in bionanotechnology or biocatalysis.
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Affiliation(s)
- Jeroen P M Vrancken
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Kanagawa, Japan
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Arnout R D Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Leuven, Belgium
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27
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Zhou W, Trinco G, Slotboom DJ, Forrest LR, Faraldo-Gómez JD. On the Role of a Conserved Methionine in the Na +-Coupling Mechanism of a Neurotransmitter Transporter Homolog. Neurochem Res 2021; 47:163-175. [PMID: 33565025 PMCID: PMC8431971 DOI: 10.1007/s11064-021-03253-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/17/2021] [Accepted: 01/19/2021] [Indexed: 11/26/2022]
Abstract
Excitatory amino acid transporters (EAAT) play a key role in glutamatergic synaptic communication. Driven by transmembrane cation gradients, these transporters catalyze the reuptake of glutamate from the synaptic cleft once this neurotransmitter has been utilized for signaling. Two decades ago, pioneering studies in the Kanner lab identified a conserved methionine within the transmembrane domain as key for substrate turnover rate and specificity; later structural work, particularly for the prokaryotic homologs GltPh and GltTk, revealed that this methionine is involved in the coordination of one of the three Na+ ions that are co-transported with the substrate. Albeit extremely atypical, the existence of this interaction is consistent with biophysical analyses of GltPh showing that mutations of this methionine diminish the binding cooperativity between substrates and Na+. It has been unclear, however, whether this intriguing methionine influences the thermodynamics of the transport reaction, i.e., its substrate:ion stoichiometry, or whether it simply fosters a specific kinetics in the binding reaction, which, while influential for the turnover rate, do not fundamentally explain the ion-coupling mechanism of this class of transporters. Here, studies of GltTk using experimental and computational methods independently arrive at the conclusion that the latter hypothesis is the most plausible, and lay the groundwork for future efforts to uncover the underlying mechanism.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Gianluca Trinco
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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Knox HL, Chen PYT, Blaszczyk AJ, Mukherjee A, Grove TL, Schwalm EL, Wang B, Drennan CL, Booker SJ. Structural basis for non-radical catalysis by TsrM, a radical SAM methylase. Nat Chem Biol 2021; 17:485-491. [PMID: 33462497 PMCID: PMC7990684 DOI: 10.1038/s41589-020-00717-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 12/19/2022]
Abstract
TsrM methylates C2 of the indole ring of L-tryptophan (Trp) during the biosynthesis of the quinaldic acid moiety of thiostrepton. It is annotated as a cobalamin-dependent radical S-adenosylmethionine (SAM) methylase; however, TsrM does not reductively cleave SAM to the universal 5ʹ-deoxyadenosyl 5ʹ-radical intermediate, a hallmark of radical-SAM (RS) enzymes. Herein, we report structures of TsrM from Kitasatospora setae, the first of a cobalamin-dependent radical SAM methylase. Unexpectedly, the structures show an essential arginine residue that resides in the proximal coordination sphere of the cobalamin cofactor and a [4Fe–4S] cluster that is ligated by a glutamyl residue and three cysteines in a canonical CxxxCxxC RS motif. Structures in the presence of substrates suggest a substrate-assisted mechanism of catalysis, wherein the carboxylate group of SAM serves as a general base to deprotonate N1 of the tryptophan substrate, facilitating formation of a C2 carbanion. The first crystal structures of a cobalamin-dependent radical SAM methylase reveal an unexpected mode of methylation.
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Affiliation(s)
- Hayley L Knox
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Percival Yang-Ting Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Anthony J Blaszczyk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.,Catalent Pharma Solutions, Gaithersburg, MD, USA
| | - Arnab Mukherjee
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erica L Schwalm
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.,Merck & Co., Inc., Rahway, NJ, USA
| | - Bo Wang
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Squire J Booker
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA. .,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA. .,Howard Hughes Medical Institute, Pennsylvania State University, University Park, PA, USA.
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29
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Anirudhan A, Prabu P, Sanyal J, Banerjee TK, Guha G, Murugesan R, Ahmed SSSJ. Interdependence of metals and its binding proteins in Parkinson's disease for diagnosis. NPJ Parkinsons Dis 2021; 7:3. [PMID: 33398051 PMCID: PMC7782529 DOI: 10.1038/s41531-020-00146-7] [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: 05/01/2020] [Accepted: 11/12/2020] [Indexed: 01/29/2023] Open
Abstract
Metalloproteins utilizes cellular metals which plays a crucial function in brain that linked with neurodegenerative disorders. Parkinson's disease (PD) is a neurodegenerative disorder that affects geriatric population world-wide. Twenty-four metal-binding protein networks were investigated to identify key regulating protein hubs in PD blood and brain. Amongst, aluminum, calcium, copper, iron, and magnesium protein hubs are the key regulators showing the ability to classify PD from control based on thirty-four classification algorithms. Analysis of these five metal proteins hubs showed involvement in environmental information processing, immune, neuronal, endocrine, aging, and signal transduction pathways. Furthermore, gene expression of functional protein in each hub showed significant upregulation of EFEMP2, MMP9, B2M, MEAF2A, and TARDBP in PD. Dysregulating hub proteins imprint the metal availability in a biological system. Hence, metal concentration in serum and cerebrospinal fluid were tested, which were altered and showed significant contribution towards gene expression of metal hub proteins along with the previously reported PD markers. In conclusion, analyzing the levels of serum metals along with the gene expression in PD opens up an ideal and feasible diagnostic intervention for PD. Hence, this will be a cost effective and rapid method for the detection of Parkinson's disease.
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Affiliation(s)
- Athira Anirudhan
- Faculty of Allied Health Sciences, Chettinad Academy of Research and Education CARE, Kelambakkam, 603103 India
| | - Paramasivam Prabu
- grid.266832.b0000 0001 2188 8502School of Medicine, Department of Neurology, University of New Mexico Health Sciences Center, University of New Mexico, New Mexico, USA
| | - Jaya Sanyal
- grid.8195.50000 0001 2109 4999Department of Anthropology, University of Delhi, Delhi, 110007 India
| | - Tapas Kumar Banerjee
- grid.459884.cDepartment of Neurology, National Neurosciences Centre, Kolkata, India
| | - Gautam Guha
- grid.416241.4Department of Neurology, Nil Ratan Sircar Medical College and Hospital, Kolkata, India
| | - Ram Murugesan
- Drug Discovery & Omics Lab, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, 603103 India
| | - Shiek S. S. J. Ahmed
- Drug Discovery & Omics Lab, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Kelambakkam, 603103 India
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Auffinger P, Ennifar E, D'Ascenzo L. Deflating the RNA Mg 2+ bubble. Stereochemistry to the rescue! RNA (NEW YORK, N.Y.) 2020; 27:rna.076067.120. [PMID: 33268500 PMCID: PMC7901845 DOI: 10.1261/rna.076067.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/20/2020] [Indexed: 05/03/2023]
Abstract
Proper evaluation of the ionic structure of biomolecular systems through X ray and cryo-EM techniques remains challenging but is essential for advancing our understanding of the underlying structure/activity/solvent relationships. However, numerous studies overestimate the number of Mg2+ in deposited structures due to assignment errors finding their origin in improper consideration of stereochemical rules. Herein, to tackle such issues, we re-evaluate the PDBid 6QNR and 6SJ6 models of the ribosome ionic structure. We establish that stereochemical principles need to be carefully pondered when evaluating ion binding features, even when K+ anomalous signals are available as it is the case for the 6QNR PDB entry. For ribosomes, assignment errors can result in misleading conceptions of their solvent structure. For instance, present stereochemical analysis result in a significant decrease of the number of assigned Mg2+ in 6QNR, suggesting that K+ and not Mg2+ is the prevalent ion in the ribosome 1st solvation shell. We stress that the use of proper stereochemical guidelines in combination or not with other identification techniques, such as those pertaining to the detection of transition metals, of some anions and of K+ anomalous signals, is critical for deflating the current Mg2+ bubble witnessed in many ribosome and other RNA structures. We also stress that for the identification of lighter ions such as Mg2+, Na+, …, for which no anomalous signals can be detected, stereochemistry coupled with high resolution structures (<2.4 Å) remain the best currently available option.
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31
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Loreto D, Ferraro G, Merlino A. Protein-metallodrugs interactions: Effects on the overall protein structure and characterization of Au, Ru and Pt binding sites. Int J Biol Macromol 2020; 163:970-976. [DOI: 10.1016/j.ijbiomac.2020.07.053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/22/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022]
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32
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Masmaliyeva RC, Babai KH, Murshudov GN. Local and global analysis of macromolecular atomic displacement parameters. Acta Crystallogr D Struct Biol 2020; 76:926-937. [PMID: 33021494 PMCID: PMC7543658 DOI: 10.1107/s2059798320011043] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/11/2020] [Indexed: 04/13/2023] Open
Abstract
This paper describes the global and local analysis of atomic displacement parameters (ADPs) of macromolecules in X-ray crystallography. The distribution of ADPs is shown to follow the shifted inverse-gamma distribution or a mixture of these distributions. The mixture parameters are estimated using the expectation-maximization algorithm. In addition, a method for the resolution- and individual ADP-dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of mismodelled atoms, heavy-metal atoms and disordered and/or incorrectly modelled ligands. Both global and local analyses can be used to detect errors in atomic models, thus helping in the (re)building, refinement and validation of macromolecular structures. This method can also serve as an additional validation tool during PDB deposition.
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Affiliation(s)
| | - Kave H. Babai
- R.I.S.K. Scientific Production Company, Baku, Azerbaijan
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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33
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Abstract
The light-driven sodium pump KR2, found in 2013 in the marine bacteria Krokinobacter eikastus, serves as a model protein for the studies of the sodium-pumping microbial rhodopsins (NaRs). KR2 possesses a unique NDQ (N112, D116, and Q123) set of the amino acid residues in the functionally relevant positions, named the NDQ motif. The N112 was shown to determine the Na+/H+ selectivity and pumping efficiency of the protein. Thus, N112A mutation converts KR2 into an outward proton pump. However, no structural data on the functional conversions of the light-driven sodium pumps are available at the moment. Here we present the crystal structure of the N112A mutant of KR2 in the ground state at the resolution of 2.4 Å. The structure revealed a minor deflection in the central part of the helix C and a double conformation of the L74 residue in the mutant. The organization of the retinal Schiff base and neighboring water molecules is preserved in the ground state of KR2-N112A. The presented data provide structural insights into the effects of the alterations of the characteristic NDQ motif of NaRs. Our findings also demonstrate that for the rational design of the KR2 variants with modified ion selectivity for optogenetic applications, the structures of the intermediate states of both the protein and its functional variants are required.
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34
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Investigation of manganese metal coordination in proteins: a comprehensive PDB analysis and quantum mechanical study. Struct Chem 2020. [DOI: 10.1007/s11224-020-01488-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE. Sci Rep 2020; 10:5830. [PMID: 32242052 PMCID: PMC7118094 DOI: 10.1038/s41598-020-62847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/20/2020] [Indexed: 11/16/2022] Open
Abstract
Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.
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36
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Lee C, Choi SE, Kim JW, Lee SY. Boston Ivy Disk-Inspired Pressure-Mediated Adhesive Film Patches. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904282. [PMID: 31755646 DOI: 10.1002/smll.201904282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Boston ivy (Parthenocissus tricuspidata) climbs brick walls using its tendril disks, which excrete a sticky substance to perform binding and attachment. While the cellular structures and adhesive substances involved have been identified for decades, their practical applicability as an adhesive has not yet been demonstrated. A Boston ivy disk-inspired adhesive film patch system is reported in which structural and compositional features of the Boston ivy disk are mimicked with a form of thin adhesive film patches. In analogy to the sticky disk of a mature ivy in which porous microchannels are occupied by catechol-containing microgranules on the bound site, 3,4-dihydroxylphenylalanine bolaamphiphile nanoparticle (DOPA-C7 NP)-coated alginate microgels are two-dimensionally positioned into the cylindrical holes that are periodically micropatterned on the flexible stencil film. Finally, it is demonstrated that the pressurization of the patch breaks the microgels filled in the holes, releasing the polysaccharides and leading to crosslinking with DOPA-C7 NPs via ligandation with combined Ca2+ and Fe3+ ions, thus enabling development of a pressure-mediated adhesion technology.
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Affiliation(s)
- Chaemyeong Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Song-Ee Choi
- Department of Bionano Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Jin Woong Kim
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sang-Yup Lee
- Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea
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37
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López R, Díaz N, Suárez D. Alkali and Alkaline-Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition. Chemphyschem 2020; 21:99-112. [PMID: 31674092 DOI: 10.1002/cphc.201900877] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 10/15/2019] [Indexed: 12/20/2022]
Abstract
Herein, we report a computational database for the complexes of alkali [Li(I), Na(I), K(I)] and alkaline-earth [Be(II), Mg(II) and Ca(II)] cations with 25 small ligands with varying charge and donor atoms ("O", "N", and "S") that provides geometries and accurate bond energies useful to analyze metal-ligand interactions in proteins and nucleic acids. The role of the ligand→metal charge transfer, the equilibrium bond distance, the electronegativity of the donor atom, the ligand polarizability, and the relative stability of the complexes are discussed in detail. The interacting quantum atoms (IQA) method is used to decompose the binding energy into electrostatic and quantum mechanical contributions. In addition, bond energies are also estimated by means of multipolar electrostatic calculations. No simple correlation exists between bond energies and structural/electronic descriptors unless the data are segregated by the type of ligand or metal. The electrostatic attraction of some molecules (H2 O, NH3 , CH3 OH) towards the metal cations is well reproduced using their (unrelaxed) atomic multipoles, but the same comparison is much less satisfactory for other ligands (e. g. benzene, thiol/thiolate groups, etc.). Besides providing reference structures and bond energies, the database can contribute to validate molecular mechanics potentials capable of yielding a balanced description of alkali and alkaline-earth metals binding to biomolecules.
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Affiliation(s)
- Roberto López
- Departamento de Química y Física Aplicadas, Universidad de León, Campus de Vegazana, s/n., 24071, León (Castilla y León, Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo (Asturias, Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Clavería 8, 33006, Oviedo (Asturias, Spain
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38
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Grime GW, Zeldin OB, Snell ME, Lowe ED, Hunt JF, Montelione GT, Tong L, Snell EH, Garman EF. High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application. J Am Chem Soc 2019; 142:185-197. [PMID: 31794207 DOI: 10.1021/jacs.9b09186] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Metalloproteins comprise over one-third of proteins, with approximately half of all enzymes requiring metal to function. Accurate identification of these metal atoms and their environment is a prerequisite to understanding biological mechanism. Using ion beam analysis through particle induced X-ray emission (PIXE), we have quantitatively identified the metal atoms in 30 previously structurally characterized proteins using minimal sample volume and a high-throughput approach. Over half of these metals had been misidentified in the deposited structural models. Some of the PIXE detected metals not seen in the models were explainable as artifacts from promiscuous crystallization reagents. For others, using the correct metal improved the structural models. For multinuclear sites, anomalous diffraction signals enabled the positioning of the correct metals to reveal previously obscured biological information. PIXE is insensitive to the chemical environment, but coupled with experimental diffraction data deposited alongside the structural model it enables validation and potential remediation of metalloprotein models, improving structural and, more importantly, mechanistic knowledge.
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Affiliation(s)
- Geoffrey W Grime
- Ion Beam Centre, Advanced Technology Institute , University of Surrey , Guildford, Surrey GU2 7XH , United Kingdom
| | - Oliver B Zeldin
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - Mary E Snell
- Hauptman-Woodward Medical Research Institute , 700 Ellicott St. , Buffalo , New York 14203 , United States
| | - Edward D Lowe
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
| | - John F Hunt
- Department of Biological Sciences , Columbia University , New York , New York 10027 , United States
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences , Rensselaer Polytechnic Institute , Troy New York 12180 United States
| | - Liang Tong
- Department of Biological Sciences , Columbia University , New York , New York 10027 , United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute , 700 Ellicott St. , Buffalo , New York 14203 , United States.,Materials Design and Innovation , SUNY Buffalo , 700 Ellicott St. , Buffalo , New York 14203 , United States
| | - Elspeth F Garman
- Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , United Kingdom
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Lisnyansky M, Yariv E, Segal O, Marom M, Loewenstein A, Ben-Tal N, Giladi M, Haitin Y. Metal Coordination Is Crucial for Geranylgeranyl Diphosphate Synthase–Bisphosphonate Interactions: A Crystallographic and Computational Analysis. Mol Pharmacol 2019; 96:580-588. [DOI: 10.1124/mol.119.117499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022] Open
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40
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Rasool N, Husssain W, Khan YD. Revelation of enzyme activity of mutant pyrazinamidases from Mycobacterium tuberculosis upon binding with various metals using quantum mechanical approach. Comput Biol Chem 2019; 83:107108. [PMID: 31442707 DOI: 10.1016/j.compbiolchem.2019.107108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 12/11/2018] [Accepted: 08/13/2019] [Indexed: 01/11/2023]
Abstract
Pyrazinamide (PZA) is one of the most potent bacteriostatic drug against tuberculosis, a deadliest disease with high mortality and morbidity rate. PZA metabolizes into its active form pyrazinoic acid (POA) with the help of a metalloenzyme, pyrazinamidase (PZase). Mutagenicity and metal substitution in PZase weakens the binding of PZA with PZase and increases the drug resistance in Mycobacterium tuberculosis. The present study aims at the quantum mechanistic analysis of mutant-metal substituted PZase complexes by studying the mechanics of metals and PZA binding at MCS and catalytic site, respectively. A total of 66 complexes are scrutinised in this study to elucidate the effect of mutations on the enzymatic function of PZase. Among the 10 mutations considered in this study, 7 different mutations i.e. Asp49 → Asn, His51 → Arg, Gly78 → Cys, Asp12 → Gly, Asp12 → Ala, Thr135 → Pro and Asp136 → Gly cause a detrimental effect on the activity of PZase. In addition to this, the substitution of iron with cobalt enhances the enzymatic activity of both wild type and mutant PZase while zinc, magnesium and copper reduce it. Based on these results, it is concluded that upon substitution of iron with zinc, magnesium and copper, PZase cannot function properly. Due to mutations, the reactivity of the drug also reduces as its binding with PZase weakens and this phenomenon enhances the resistance of Mycobacterium tuberculosis against drug.
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Affiliation(s)
- Nouman Rasool
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
| | - Waqar Husssain
- Department of Computer Science, University of Management and Technology, Lahore, Pakistan
| | - Yaser Daanial Khan
- Department of Computer Science, University of Management and Technology, Lahore, Pakistan
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41
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Hickman AB, Voth AR, Ewis H, Li X, Craig NL, Dyda F. Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase. Nucleic Acids Res 2019; 46:10286-10301. [PMID: 30239795 PMCID: PMC6212770 DOI: 10.1093/nar/gky838] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
Some DNA transposons relocate from one genomic location to another using a mechanism that involves generating double-strand breaks at their transposon ends by forming hairpins on flanking DNA. The same double-strand break mode is employed by the V(D)J recombinase at signal-end/coding-end junctions during the generation of antibody diversity. How flanking hairpins are formed during DNA transposition has remained elusive. Here, we describe several co-crystal structures of the Hermes transposase bound to DNA that mimics the reaction step immediately prior to hairpin formation. Our results reveal a large DNA conformational change between the initial cleavage step and subsequent hairpin formation that changes which strand is acted upon by a single active site. We observed that two factors affect the conformational change: the complement of divalent metal ions bound by the catalytically essential DDE residues, and the identity of the –2 flanking base pair. Our data also provides a mechanistic link between the efficiency of hairpin formation (an A:T basepair is favored at the –2 position) and Hermes' strong target site preference. Furthermore, we have established that the histidine residue within a conserved C/DxxH motif present in many transposase families interacts directly with the scissile phosphate, suggesting a crucial role in catalysis.
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Affiliation(s)
- Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Regier Voth
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hosam Ewis
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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42
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Listyarini RV, Gesto DS, Paiva P, Ramos MJ, Fernandes PA. Benchmark of Density Functionals for the Calculation of the Redox Potential of Fe 3+/Fe 2+ Within Protein Coordination Shells. Front Chem 2019; 7:391. [PMID: 31231631 PMCID: PMC6560050 DOI: 10.3389/fchem.2019.00391] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/15/2019] [Indexed: 11/13/2022] Open
Abstract
Iron is a very important transition metal often found in proteins. In enzymes specifically, it is often found at the core of reaction mechanisms, participating in the reaction cycle, more often than not in oxidation/reduction reactions, where it cycles between its most common Fe(III)/Fe(II) oxidation states. QM and QM/MM computational methods that study these catalytic reaction mechanisms mostly use density functional theory (DFT) to describe the chemical transformations. Unfortunately, density functional is known to be plagued by system-specific and property-specific inaccuracies that cast a shadow of uncertainty over the results. Here we have modeled 12 iron coordination complexes, using ligands that represent amino acid sidechains, and calculated the accuracy with which the most common density functionals reproduce the redox properties of the iron complexes (specifically the electronic component of the redox potential at 0 K, ΔEelecFe3+/Fe2+), using the same property calculated with CCSD(T)/CBS as reference for the evaluation. A number of hybrid and hybrid-meta density functionals, generally with a large % of HF exchange (such as BB1K, mPWB1K, and mPW1B95) provided systematically accurate values for ΔEelecFe3+/Fe2+, with MUEs of ~2 kcal/mol. The very popular B3LYP density functional was found to be quite precise as well, with a MUE of 2.51 kcal/mol. Overall, the study provides guidelines to estimate the inaccuracies coming from the density functionals in the study of enzyme reaction mechanisms that involve an iron cofactor, and to choose appropriate density functionals for the study of the same reactions.
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Affiliation(s)
- Risnita Vicky Listyarini
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Diana Sofia Gesto
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Paiva
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Maria João Ramos
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Pedro Alexandrino Fernandes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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43
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Disruption of the Metal Ion Environment by EDTA for Silk Formation Affects the Mechanical Properties of Silkworm Silk. Int J Mol Sci 2019; 20:ijms20123026. [PMID: 31234286 PMCID: PMC6627089 DOI: 10.3390/ijms20123026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 06/16/2019] [Accepted: 06/16/2019] [Indexed: 11/22/2022] Open
Abstract
Silk fiber has become a research focus because of its comprehensive mechanical properties. Metal ions can influence the conformational transition of silk fibroin. Current research is mainly focused on the role of a single ion, rather than the whole metal ion environment. Here, we report the effects of the overall metal ion environment on the secondary structure and mechanical properties of silk fibers after direct injection and feeding of silkworms with EDTA. The metal composition of the hemolymph, silk gland, and silk fiber changed significantly post EDTA treatment. Synchrotron FTIR analysis indicated that the secondary structure of silk fiber after EDTA treatment changed dramatically; particularly, the β-sheets decreased and the β-turns increased. Post EDTA treatment, the silk fiber had significantly decreased strength, Young’s modulus, and toughness as compared with the control groups, while the strain exhibited no obvious change. These changes can be attributed to the change in the metal ion environment in the silk fibroin and sericin in the silk gland. Our investigation provides a new theoretical basis for the natural silk spinning process, and our findings could help develop a method to modify the mechanical properties of silk fiber using metal ions.
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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Pernil R, Schleiff E. Metalloproteins in the Biology of Heterocysts. Life (Basel) 2019; 9:E32. [PMID: 30987221 PMCID: PMC6616624 DOI: 10.3390/life9020032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 12/15/2022] Open
Abstract
Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.
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Affiliation(s)
- Rafael Pernil
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
| | - Enrico Schleiff
- Institute for Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straβe 9, 60438 Frankfurt am Main, Germany.
- Frankfurt Institute for Advanced Studies, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straβe 15, 60438 Frankfurt am Main, Germany.
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Zechel S, Hager MD, Priemel T, Harrington MJ. Healing through Histidine: Bioinspired Pathways to Self-Healing Polymers via Imidazole⁻Metal Coordination. Biomimetics (Basel) 2019; 4:E20. [PMID: 31105205 PMCID: PMC6477608 DOI: 10.3390/biomimetics4010020] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 12/03/2022] Open
Abstract
Biology offers a valuable inspiration toward the development of self-healing engineering composites and polymers. In particular, chemical level design principles extracted from proteinaceous biopolymers, especially the mussel byssus, provide inspiration for design of autonomous and intrinsic healing in synthetic polymers. The mussel byssus is an acellular tissue comprised of extremely tough protein-based fibers, produced by mussels to secure attachment on rocky surfaces. Threads exhibit self-healing response following an apparent plastic yield event, recovering initial material properties in a time-dependent fashion. Recent biochemical analysis of the structure-function relationships defining this response reveal a key role of sacrificial cross-links based on metal coordination bonds between Zn2+ ions and histidine amino acid residues. Inspired by this example, many research groups have developed self-healing polymeric materials based on histidine (imidazole)-metal chemistry. In this review, we provide a detailed overview of the current understanding of the self-healing mechanism in byssal threads, and an overview of the current state of the art in histidine- and imidazole-based synthetic polymers.
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Affiliation(s)
- Stefan Zechel
- Laboratory for Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
| | - Martin D Hager
- Laboratory for Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany.
- Jena Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743 Jena, Germany.
| | - Tobias Priemel
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.
| | - Matthew J Harrington
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada.
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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Yuliarto B, Septiani NLW, Kaneti YV, Iqbal M, Gumilar G, Kim M, Na J, Wu KCW, Yamauchi Y. Green synthesis of metal oxide nanostructures using naturally occurring compounds for energy, environmental, and bio-related applications. NEW J CHEM 2019. [DOI: 10.1039/c9nj03311d] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review summarizes the synthesis and functional applications of metal oxide nanostructures synthesized using plant-derived phytochemicals for energy, environmental, and biomedical applications.
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Affiliation(s)
- Brian Yuliarto
- Advanced Functional Materials Research Group
- Department of Engineering Physics
- Institute of Technology Bandung
- Bandung 40132
- Indonesia
| | - Ni Luh Wulan Septiani
- Advanced Functional Materials Research Group
- Department of Engineering Physics
- Institute of Technology Bandung
- Bandung 40132
- Indonesia
| | - Yusuf Valentino Kaneti
- International Research Center for Materials Nanoarchitectonics (WPI-MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba
- Japan
| | - Muhammad Iqbal
- Advanced Functional Materials Research Group
- Department of Engineering Physics
- Institute of Technology Bandung
- Bandung 40132
- Indonesia
| | - Gilang Gumilar
- Advanced Functional Materials Research Group
- Department of Engineering Physics
- Institute of Technology Bandung
- Bandung 40132
- Indonesia
| | - Minjun Kim
- School of Chemical Engineering and Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Jongbeom Na
- School of Chemical Engineering and Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- College of Chemistry and Molecular Engineering
| | - Kevin C.-W. Wu
- Department of Chemical Engineering
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Yusuke Yamauchi
- School of Chemical Engineering and Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- College of Chemistry and Molecular Engineering
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49
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Pu Z, Zhao M, Zhang Y, Sun W, Bao Y. Dynamic Description of the Catalytic Cycle of Malate Enzyme: Stereoselective Recognition of Substrate, Chemical Reaction, and Ligand Release. J Phys Chem B 2018; 122:12241-12250. [PMID: 30500201 DOI: 10.1021/acs.jpcb.8b05135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In protein engineering, investigations of catalytic cycle facilitate rational design of enzymes. In the present work, deeper analysis on the catalytic cycle of malate enzyme (EC 1.1.1.40), an enzyme involved in cancer metabolic and fatty acid synthesis, was performed. In substrate binding, stereoselective recognition of a substrate originates from distance and angle difference between two chiral substrates and Mn2+ as well as monodentate or coplanar ion reaction with Arg165. In catalytic transformation, the activation barrier for the hydride transfer of d-malate is 20.28 kcal/mol higher than that for l-malate. The activation barrier for β-decarboxylation of oxaloacetate is about 4.59 kcal/mol higher than the activation barrier for the hydride transfer of l-malate. The effective activation barrier is 16.44 kcal/mol, which is in close agreement with the value derived from the application of transition-state theory and the Eyring equation to kcat. In ligand release, l/d-malate needs to overcome a higher barrier than pyruvate to break all bonds in parallel and then to escape from the binding pocket. Leu167 and Asn421 comprise a swinging gate to control the product release. The more open gate is possibly required in the direction of pyruvate to l-malate. Our studies are focused on extending structural knowledge regarding the malate enzyme and provided a powerful strategy for future experimental investigations.
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Affiliation(s)
- Zhongji Pu
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Mengdi Zhao
- Department of Nanoenergy Engineering , Pusan National University , Busan 46241 , Republic of Korea
| | - Yue Zhang
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Wenhui Sun
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China
| | - Yongming Bao
- School of Life Science and Biotechnology , Dalian University of Technology , Dalian 116024 , China.,School of Food and Environment Science and Engineering , Dalian University of Technology , Panjin 124221 , China
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50
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Kurniawan I, Kawaguchi K, Sugimori K, Sakurai T, Nagao H. Quantum Chemical Study of Axial Ligand Effect on the Electronic Properties of Type I Copper Protein. CHEM LETT 2018. [DOI: 10.1246/cl.180521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isman Kurniawan
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- School of Computing, Telkom University, Jl. Telekomunikasi, Terusan Buah Batu, Bandung, Indonesia 40257
| | - Kazutomo Kawaguchi
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Kimikazu Sugimori
- Division of Higher Education Research and Development, Institute of Liberal Arts and Science, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takeshi Sakurai
- Division of Material Chemistry, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Hidemi Nagao
- Division of Mathematical and Physical Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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