1
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Furuya T, Nakane D, Kitanishi K, Katsuumi N, Tsaturyan A, Shcherbakov IN, Unno M, Akitsu T. A novel hybrid protein composed of superoxide-dismutase-active Cu(II) complex and lysozyme. Sci Rep 2023; 13:6892. [PMID: 37106030 PMCID: PMC10140267 DOI: 10.1038/s41598-023-33926-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
A novel hybrid protein composed of a superoxide dismutase-active Cu(II) complex (CuST) and lysozyme (CuST@lysozyme) was prepared. The results of the spectroscopic and electrochemical analyses confirmed that CuST binds to lysozyme. We determined the crystal structure of CuST@lysozyme at 0.92 Å resolution, which revealed that the His15 imidazole group of lysozyme binds to the Cu(II) center of CuST in the equatorial position. In addition, CuST was fixed in position by the weak axial coordination of the Thr89 hydroxyl group and the hydrogen bond between the guanidinium group of the Arg14 residue and the hydroxyl group of CuST. Furthermore, the combination of CuST with lysozyme did not decrease the superoxide dismutase activity of CuST. Based on the spectral, electrochemical, structural studies, and quantum chemical calculations, an O2- disproportionation mechanism catalyzed by CuST@lysozyme is proposed.
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Affiliation(s)
- Tetsundo Furuya
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Daisuke Nakane
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
| | - Kenichi Kitanishi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Natsuki Katsuumi
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Arshak Tsaturyan
- Université Jean Monnet Saint-Etienne, CNRS, Institut d Optique Graduate School, Laboratoire Hubert Curien UMR 5516, 42023, Saint-Étienne, France
- Institute of Physical and Organic Chemistry, Southern Federal University, 194/2 Stachka Ave., Rostov-On-Don, 344090, Russia
| | - Igor N Shcherbakov
- Department of Chemistry, Southern Federal University, 7 Zorge Str., Rostov-On-Don, 344090, Russia
| | - Masaki Unno
- Graduate School of Science and Engineering, Ibaraki University, 4-12-1 Nakanarusawa, Hitachi, Ibaraki, 316-8511, Japan
| | - Takashiro Akitsu
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan.
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2
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de Sá Ribeiro F, Lima LMTR. Linking B-factor and temperature-induced conformational transition. Biophys Chem 2023; 298:107027. [PMID: 37172417 DOI: 10.1016/j.bpc.2023.107027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K-1, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.
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Affiliation(s)
- Fernando de Sá Ribeiro
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Química Biológica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Luís Maurício T R Lima
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Metrologia, Tecnologia e Qualidade (INMETRO), Duque de Caxias, RJ 25250-020, Brazil.
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3
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Ferraro G, Merlino A. Metallodrugs: Mechanisms of Action, Molecular Targets and Biological Activity. Int J Mol Sci 2022; 23:ijms23073504. [PMID: 35408863 PMCID: PMC8998277 DOI: 10.3390/ijms23073504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 01/27/2023] Open
Affiliation(s)
- Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 21, I-80126 Naples, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia 21, I-80126 Naples, Italy
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4
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Kojima M, Abe S, Ueno T. Engineering of protein crystals for use as solid biomaterials. Biomater Sci 2021; 10:354-367. [PMID: 34928275 DOI: 10.1039/d1bm01752g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein crystals have attracted a great deal of attention as solid biomaterials because they have porous structures created by regular assemblies of proteins. The lattice structures of protein crystals are controlled by designing molecular interfacial interactions via covalent bonds and non-covalent bonds. Protein crystals have been functionalized as templates to immobilize foreign molecules such as metal nanoparticles, metal complexes, and proteins. These hybrid crystals are used as functional materials for catalytic reactions and structural analysis. Furthermore, in-cell protein crystals have been studied extensively, providing progress in rapid protein crystallization and crystallography. This review highlights recent advances in crystal engineering for protein crystallization and generation of solid functional materials both in vitro and within cells.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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5
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Loreto D, Merlino A. The interaction of rhodium compounds with proteins: A structural overview. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213999] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Mansour AM, Radacki K, Shehab OR. Sulfonate improves water solubility and cell selective toxicity and alters the lysozyme binding activity of half sandwich Rh(iii) complexes. Dalton Trans 2021; 50:10701-10706. [PMID: 34337627 DOI: 10.1039/d1dt00979f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Introduction of the propyl-sulfonic acid group at N1 of the coordinated 2-(2-pyridyl)benzimidazole ligand (L) in [RhCl(η5-C5Me5)L](CF3SO3) gives rise to a water-soluble complex, which can bind to the model protein lysozyme via non-covalent interactions. The complex shows selective moderate toxicity against Cryptococcus neoformans (MIC = 21.6-43.3 μM) and exhibits no cytotoxicity to healthy HEK293 cells.
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Affiliation(s)
- Ahmed M Mansour
- Department of Chemistry, Faculty of Science, Cairo University, Gamma Street, Giza, Cairo 12613, Egypt.
| | - Krzysztof Radacki
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Ola R Shehab
- Department of Chemistry, Faculty of Science, Cairo University, Gamma Street, Giza, Cairo 12613, Egypt.
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7
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Mansour AM, Radacki K, Shehab OR. Half-sandwich triazolato Rh(III) compound of pyridylbenzimidazole ligand with cell selective toxicity towards Cryptococcus neoformans. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.121928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme. Int J Mol Sci 2021; 22:ijms22031496. [PMID: 33540880 PMCID: PMC7867343 DOI: 10.3390/ijms22031496] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 01/29/2021] [Indexed: 12/11/2022] Open
Abstract
The structures of the adducts formed upon reaction of the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] with the model protein hen egg white lysozyme (HEWL) under different experimental conditions are reported. Results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with HEWL:it in part breaks down, at variance with what happens in reactions with other proteins. A Rh center coordinates the side chains of Arg14 and His15. Dimeric Rh–Rh units with Rh–Rh distances between 2.3 and 2.5 Å are bound to the side chains of Asp18, Asp101, Asn93, and Lys96, while a dirhodium unit with a Rh–Rh distance of 3.2–3.4 Å binds the C-terminal carboxylate and the side chain of Lys13 at the interface between two symmetry-related molecules. An additional monometallic fragment binds the side chain of Lys33. These data, which are supported by replicated structural determinations, shed light on the reactivity of dirhodium tetracarboxylates with proteins, providing useful information for the design of new Rh-containing biomaterials with an array of potential applications in the field of catalysis or of medicinal chemistry and valuable insight into the mechanism of action of these potential anticancer agents.
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9
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Daubit IM, Sullivan MP, John M, Goldstone DC, Hartinger CG, Metzler-Nolte N. A Combined Spectroscopic and Protein Crystallography Study Reveals Protein Interactions of Rh I(NHC) Complexes at the Molecular Level. Inorg Chem 2020; 59:17191-17199. [PMID: 33180473 DOI: 10.1021/acs.inorgchem.0c02438] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While most Rh-N-heterocyclic carbene (NHC) complexes currently investigated in anticancer research contain a Rh(III) metal center, an increasing amount of research is focusing on the cytotoxic activity and mode of action of square-planar [RhCl(COD)(NHC)] (where COD = 1,5-cyclooctadiene) which contains a Rh(I) center. The enzyme thioredoxin reductase (TrxR) and the protein albumin have been proposed as potential targets, but the molecular processes taking place upon protein interaction remain elusive. Herein, we report the preparation of peptide-conjugated and its nonconjugated parent [RhCl(COD)(NHC)] complexes, an in-depth investigation of both their stability in solution, and a crystallographic study of protein interaction. The organorhodium compounds showed a rapid loss of the COD ligand and slow loss of the NHC ligand in aqueous solution. These ligand exchange reactions were reflected in studies on the interaction with hen egg white lysozyme (HEWL) as a model protein in single-crystal X-ray crystallographic investigations. Upon treatment of HEWL with an amino acid functionalized [RhCl(COD)(NHC)] complex, two distinct rhodium adducts were found initially after 7 d of incubation at His15 and after 4 weeks also at Lys33. In both cases, the COD and chlorido ligands had been substituted with aqua and/or hydroxido ligands. While the histidine (His) adduct also indicated a loss of the NHC ligand, the lysine (Lys) adduct retained the NHC core derived from the amino acid l-histidine. In either case, an octahedral coordination environment of the metal center indicates oxidation to Rh(III). This investigation gives the first insight on the interaction of Rh(I)(NHC) complexes and proteins at the molecular level.
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Affiliation(s)
- Isabelle M Daubit
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - Matthew P Sullivan
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.,School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Milena John
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
| | - David C Goldstone
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Christian G Hartinger
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Nils Metzler-Nolte
- Inorganic Chemistry I - Bioinorganic Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Universitätsstr. 150, 44801 Bochum, Germany
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10
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Li X, Yang Z, Bai Y. Fluorescence spectroscopic analysis of the interaction of papain and bromelain with l-ascorbic acid, α-tocopherol, β-carotene and astaxanthin. Int J Biol Macromol 2018; 107:144-156. [DOI: 10.1016/j.ijbiomac.2017.08.150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 08/23/2017] [Accepted: 08/25/2017] [Indexed: 10/18/2022]
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11
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Abe S, Maity B, Ueno T. Design of a confined environment using protein cages and crystals for the development of biohybrid materials. Chem Commun (Camb) 2018; 52:6496-512. [PMID: 27032539 DOI: 10.1039/c6cc01355d] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is growing interest in the design of protein assemblies for use in materials science and bionanotechnology. Protein assemblies, such as cages and crystalline protein structures, provide confined chemical environments that allow immobilization of metal complexes, nanomaterials, and proteins by metal coordination, assembly/disassembly reactions, genetic manipulation and crystallization methods. Protein assembly composites can be used to prepare hybrid materials with catalytic, magnetic and optical properties for cellular applications due to their high stability, solubility and biocompatibility. In this feature article, we focus on the recent development of ferritin as the most promising molecular template protein cage and in vivo and in vitro engineering of protein crystals as solid protein materials with functional properties.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Basudev Maity
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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12
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Functionalization of protein crystals with metal ions, complexes and nanoparticles. Curr Opin Chem Biol 2017; 43:68-76. [PMID: 29245143 DOI: 10.1016/j.cbpa.2017.11.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/09/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects.
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13
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Panneerselvam S, Kumpula EP, Kursula I, Burkhardt A, Meents A. Rapid cadmium SAD phasing at the standard wavelength (1 Å). Acta Crystallogr D Struct Biol 2017; 73:581-590. [PMID: 28695858 PMCID: PMC5505155 DOI: 10.1107/s2059798317006970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/10/2017] [Indexed: 12/26/2022] Open
Abstract
Cadmium ions can be effectively used to promote crystal growth and for experimental phasing. Here, the use of cadmium ions as a suitable anomalous scatterer at the standard wavelength of 1 Å is demonstrated. The structures of three different proteins were determined using cadmium single-wavelength anomalous dispersion (SAD) phasing. Owing to the strong anomalous signal, the structure of lysozyme could be automatically phased and built using a very low anomalous multiplicity (1.1) and low-completeness (77%) data set. Additionally, it is shown that cadmium ions can easily substitute divalent ions in ATP-divalent cation complexes. This property could be generally applied for phasing experiments of a wide range of nucleotide-binding proteins. Improvements in crystal growth and quality, good anomalous signal at standard wavelengths (i.e. no need to change photon energy) and rapid phasing and refinement using a single data set are benefits that should allow cadmium ions to be widely used for experimental phasing.
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Affiliation(s)
| | - Esa-Pekka Kumpula
- Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Inari Kursula
- Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Anja Burkhardt
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
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Abe S, Ueno T. Development of Bio-Hybrid Materials by Design of Supramolecular Protein Assemblies. J SYN ORG CHEM JPN 2017. [DOI: 10.5059/yukigoseikyokaishi.75.1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology
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15
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Li XR, Jia JJ, Yan YH, Ni TJ. Comparative studies on interactions ofl-ascorbic acid, α-tocopherol, procyanidin B3, β-carotene, and astaxanthin with lysozyme using fluorescence spectroscopy and molecular modeling methods. J Food Biochem 2016. [DOI: 10.1111/jfbc.12338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xiang-Rong Li
- Department of Chemistry, School of Basic Medicine; Xinxiang Medical University; Xinxiang Henan 453003 PR China
| | - Jin-Jin Jia
- Grade 2013, School of Pharmacy; Xinxiang Medical University; Xinxiang Henan 453003 PR China
| | - Yun-Hui Yan
- Department of Chemistry, School of Basic Medicine; Xinxiang Medical University; Xinxiang Henan 453003 PR China
| | - Tian-Jun Ni
- Department of Chemistry, School of Basic Medicine; Xinxiang Medical University; Xinxiang Henan 453003 PR China
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16
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Ferraro G, Massai L, Messori L, Merlino A. Cisplatin binding to human serum albumin: a structural study. Chem Commun (Camb) 2016; 51:9436-9. [PMID: 25873085 DOI: 10.1039/c5cc01751c] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The reaction between cisplatin and human serum albumin (HSA) was investigated by X-ray crystallography and crystal structures of the cisplatin/HSA adduct were eventually solved for the first time. Structural data unambiguously prove that cisplatin mainly binds to His105 and Met329 side chains; additional binding sites are detected at His288, Met298, and Met548 and at His535, His67 and His247.
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Affiliation(s)
- Giarita Ferraro
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy.
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17
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Abstract
Protein crystals have been functionalized for applications in preparation of inorganic materials, asymmetric catalysis and accumulation of functional compounds.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takafumi Ueno
- Department of Biomolecular Engineering
- Graduate School of Bioscience and Biotechnology
- Tokyo Institute of Technology
- Midori-ku
- Japan
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18
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Tabe H, Abe S, Hikage T, Kitagawa S, Ueno T. Porous Protein Crystals as Catalytic Vessels for Organometallic Complexes. Chem Asian J 2014; 9:1373-8. [DOI: 10.1002/asia.201301347] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/26/2013] [Indexed: 01/19/2023]
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19
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Bi S, Pang B, Wang T, Zhao T, Yu W. Investigation on the interactions of clenbuterol to bovine serum albumin and lysozyme by molecular fluorescence technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:456-461. [PMID: 24211804 DOI: 10.1016/j.saa.2013.09.137] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 09/13/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Clenbuterol interacting with bovine serum albumin (BSA) or lysozyme (LYS) in physiological buffer (pH 7.4) was investigated by the fluorescence spectroscopy and UV-vis absorption spectroscopy. The results indicated that clenbuterol quenched the intrinsic fluorescence of BSA and LYS via a static quenching procedure. The binding constants of clenbuterol with BSA and LYS were 1.16×10(3) and 1.49×10(3) L mol(-1) at 291 K. The values of ΔH and ΔS implied that hydrophobic and electrostatic interaction played a major role in stabilizing the complex (clenbuterol-BSA or clenbuterol-LYS). In the presence of Fe2+, Fe3+, Cu2+, Mg2+, Ca2+, or Zn2+, the binding constants of clenbuterol to BSA or LYS had no significant differences. The distances between the donor (BSA or LYS) and acceptor (clenbuterol) were 2.61 and 2.19 nm for clenbuterol-BSA and clenbuterol-LYS respectively. Furthermore, synchronous fluorescence spectrometry was used to analyze the conformational changes of BSA and LYS.
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Affiliation(s)
- Shuyun Bi
- College of Chemistry, Changchun Normal University, Changchun 130032, PR China.
| | - Bo Pang
- College of Chemistry, Changchun Normal University, Changchun 130032, PR China
| | - Tianjiao Wang
- College of Chemistry, Changchun Normal University, Changchun 130032, PR China
| | - Tingting Zhao
- College of Chemistry, Changchun Normal University, Changchun 130032, PR China
| | - Wang Yu
- College of Chemistry, Changchun Normal University, Changchun 130032, PR China
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20
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Abstract
Porous protein crystals have the potential to provide new porous materials due to their unique chemical environments composed of amino acid residues periodically exposed at the surface of the solvent channels in the crystal lattice. This enables accumulation of external compounds in special arrangements by metal coordination interactions or by chemical modifications. This article presents a review of advances in the recently established field of porous protein crystals.
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Affiliation(s)
- Takafumi Ueno
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259-B55, Midori-ku, Yokohama 226-8501, Japan.
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21
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Artificial Metalloenzymes Constructed From Hierarchically-Assembled Proteins. Chem Asian J 2013; 8:1646-60. [DOI: 10.1002/asia.201300347] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 01/20/2023]
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22
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Barends TRM, Foucar L, Shoeman RL, Bari S, Epp SW, Hartmann R, Hauser G, Huth M, Kieser C, Lomb L, Motomura K, Nagaya K, Schmidt C, Strecker R, Anielski D, Boll R, Erk B, Fukuzawa H, Hartmann E, Hatsui T, Holl P, Inubushi Y, Ishikawa T, Kassemeyer S, Kaiser C, Koeck F, Kunishima N, Kurka M, Rolles D, Rudek B, Rudenko A, Sato T, Schroeter CD, Soltau H, Strueder L, Tanaka T, Togashi T, Tono K, Ullrich J, Yase S, Wada SI, Yao M, Yabashi M, Ueda K, Schlichting I. Anomalous signal from S atoms in protein crystallographic data from an X-ray free-electron laser. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:838-42. [PMID: 23633593 DOI: 10.1107/s0907444913002448] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/24/2013] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (FELs) enable crystallographic data collection using extremely bright femtosecond pulses from microscopic crystals beyond the limitations of conventional radiation damage. This diffraction-before-destruction approach requires a new crystal for each FEL shot and, since the crystals cannot be rotated during the X-ray pulse, data collection requires averaging over many different crystals and a Monte Carlo integration of the diffraction intensities, making the accurate determination of structure factors challenging. To investigate whether sufficient accuracy can be attained for the measurement of anomalous signal, a large data set was collected from lysozyme microcrystals at the newly established `multi-purpose spectroscopy/imaging instrument' of the SPring-8 Ångstrom Compact Free-Electron Laser (SACLA) at RIKEN Harima. Anomalous difference density maps calculated from these data demonstrate that serial femtosecond crystallography using a free-electron laser is sufficiently accurate to measure even the very weak anomalous signal of naturally occurring S atoms in a protein at a photon energy of 7.3 keV.
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Affiliation(s)
- Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
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23
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Vagenende V, Trout BL. Quantitative characterization of local protein solvation to predict solvent effects on protein structure. Biophys J 2013; 103:1354-62. [PMID: 22995508 DOI: 10.1016/j.bpj.2012.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/19/2012] [Accepted: 08/03/2012] [Indexed: 12/14/2022] Open
Abstract
Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A STAR), Centros, Singapore.
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24
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Sanghamitra NJM, Ueno T. Expanding coordination chemistry from protein to protein assembly. Chem Commun (Camb) 2013; 49:4114-26. [DOI: 10.1039/c2cc36935d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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25
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Maeki M, Yoshizuka S, Yamaguchi H, Kawamoto M, Yamashita K, Nakamura H, Miyazaki M, Maeda H. X-ray diffraction of protein crystal grown in a nano-liter scale droplet in a microchannel and evaluation of its applicability. ANAL SCI 2012; 28:65. [PMID: 22232227 DOI: 10.2116/analsci.28.65] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We describe the technical aspects of the in-situ X-ray diffraction of a protein crystal prepared by a nanodroplet-based crystallization method. We were able to obtain diffraction patterns from a crystal grown in a capillary without any manipulation. Especially in our experimental approach, the crystals that moved to the nanodroplet interface were fixed strongly enough to carry out X-ray diffraction measurements that could be attributed to the high surface tension of the nanodroplet. The crystal was damaged by an indirect action of the X-rays because our in-situ X-ray diffraction measurement was carried out in the liquid phase without freezing the crystal; however, the obtained several diffraction patterns were of sufficiently fine quality for the crystal structure factors to be generated. We consider the technical examination presented in this paper to represent a seamless coupling of crystallization to X-ray analysis.
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Affiliation(s)
- Masatoshi Maeki
- Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Kasuga-Koen, Kasuga, Fukuoka, Japan
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26
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Abe S, Tsujimoto M, Yoneda K, Ohba M, Hikage T, Takano M, Kitagawa S, Ueno T. Porous protein crystals as reaction vessels for controlling magnetic properties of nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2012; 8:1314-1319. [PMID: 22383363 DOI: 10.1002/smll.201101866] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/23/2011] [Indexed: 05/31/2023]
Abstract
Magnetic bimetallic CoPt nanoparticles are synthesized in the solvent channels of hen egg white lysozyme crystals by the reduction of Co(2+) and Pt(2+) ions pre-organized on the interior surface of the solvent channels. By using different lysozyme crystal systems, the magnetic properties of CoPt nanoparticles can be controlled.
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Affiliation(s)
- Satoshi Abe
- Institute for Integrated Cell-Material Sciences, (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto, Japan
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27
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Wei H, Lu Y. Catalysis of gold nanoparticles within lysozyme single crystals. Chem Asian J 2012; 7:680-3. [PMID: 22290848 DOI: 10.1002/asia.201100942] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Indexed: 01/17/2023]
Affiliation(s)
- Hui Wei
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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28
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Koshiyama T, Shirai M, Hikage T, Tabe H, Tanaka K, Kitagawa S, Ueno T. Post-Crystal Engineering of Zinc-Substituted Myoglobin to Construct a Long-Lived Photoinduced Charge-Separation System. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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29
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Koshiyama T, Shirai M, Hikage T, Tabe H, Tanaka K, Kitagawa S, Ueno T. Post-crystal engineering of zinc-substituted myoglobin to construct a long-lived photoinduced charge-separation system. Angew Chem Int Ed Engl 2011; 50:4849-52. [PMID: 21495132 DOI: 10.1002/anie.201008004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 02/14/2011] [Indexed: 12/30/2022]
Affiliation(s)
- Tomomi Koshiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University iCeMS Lab Funai Center, Kyoto University Katsura, Kyoto 615-8510, Japan
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30
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Zhang HM, Chen J, Zhou QH, Shi YQ, Wang YQ. Study on the interaction between cinnamic acid and lysozyme. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Santos-Silva T, Mukhopadhyay A, Seixas JD, Bernardes GJL, Romão CC, Romão MJ. CORM-3 reactivity toward proteins: the crystal structure of a Ru(II) dicarbonyl-lysozyme complex. J Am Chem Soc 2011; 133:1192-5. [PMID: 21204537 DOI: 10.1021/ja108820s] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CORM-3, [fac-Ru(CO)(3)Cl(κ(2)-H(2)NCH(2)CO(2))], is a well-known carbon monoxide releasing molecule (CORM) capable of delivering CO in vivo. Herein we show for the first time that the interactions of CORM-3 with proteins result in the loss of a chloride ion, glycinate, and one CO ligand. The rapid formation of stable adducts between the protein and the remaining cis-Ru(II)(CO)(2) fragments was confirmed by Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), Liquid-Chromatography Mass Spectrometry (LC-MS), Infrared Spectroscopy (IR), and X-ray crystallography. Three Ru coordination sites are observed in the structure of hen egg white lysozyme crystals soaked with CORM-3. The site with highest Ru occupancy (80%) shows a fac-[(His15)Ru(CO)(2)(H(2)O)(3)] structure.
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Affiliation(s)
- Teresa Santos-Silva
- REQUIMTE-CQFB, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
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32
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Pozharski E. Percentile-based spread: a more accurate way to compare crystallographic models. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:970-8. [PMID: 20823548 DOI: 10.1107/s0907444910027927] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 07/13/2010] [Indexed: 11/10/2022]
Abstract
The comparison of biomacromolecular crystal structures is traditionally based on the root-mean-square distance between corresponding atoms. This measure is sensitive to the presence of outliers, which inflate it disproportionately to their fraction. An alternative measure, the percentile-based spread (p.b.s.), is proposed and is shown to represent the average variation in atomic positions more adequately. It is discussed in the context of isomorphous crystal structures, conformational changes and model ensembles generated by repetitive automated rebuilding.
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Abe S, Hikage T, Watanabe Y, Kitagawa S, Ueno T. Mechanism of Accumulation and Incorporation of Organometallic Pd Complexes into the Protein Nanocage of apo-Ferritin. Inorg Chem 2010; 49:6967-73. [DOI: 10.1021/ic1003758] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Satoshi Abe
- Institute for Integrated Cell-Material Sciences (iCeMS), Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | - Susumu Kitagawa
- Institute for Integrated Cell-Material Sciences (iCeMS), Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takafumi Ueno
- Institute for Integrated Cell-Material Sciences (iCeMS), Funai Center, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- PRESTO, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
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