1
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Schell E, Nouairia G, Steiner E, Weber N, Lundin D, Loderer C. Structural determinants and distribution of phosphate specificity in ribonucleotide reductases. J Biol Chem 2021; 297:101008. [PMID: 34314684 PMCID: PMC8365446 DOI: 10.1016/j.jbc.2021.101008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. RNRs are specific for either ribonucleoside diphosphates or triphosphates as substrates. As far as is known, oxygen-dependent class I RNRs (NrdAB) all reduce ribonucleoside diphosphates, and oxygen-sensitive class III RNRs (NrdD) are all ribonucleoside triphosphate reducers, whereas the adenosylcobalamin-dependent class II (NrdJ) contains both ribonucleoside diphosphate and triphosphate reducers. However, it is unknown how this specificity is conveyed by the active site of the enzymes and how this feature developed in RNR evolution. By structural comparison of the active sites in different RNRs, we identified the apical loop of the phosphate-binding site as a potential structural determinant of substrate specificity. Grafting two residues from this loop from a diphosphate- to a triphosphate-specific RNR caused a change in preference from ribonucleoside triphosphate to diphosphate substrates in a class II model enzyme, confirming them as the structural determinants of phosphate specificity. The investigation of the phylogenetic distribution of this motif in class II RNRs yielded a likely monophyletic clade with the diphosphate-defining motif. This indicates a single evolutionary-split event early in NrdJ evolution in which diphosphate specificity developed from the earlier triphosphate specificity. For those interesting cases where organisms contain more than one nrdJ gene, we observed a preference for encoding enzymes with diverse phosphate specificities, suggesting that this varying phosphate specificity confers a selective advantage.
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Affiliation(s)
- Eugen Schell
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Ghada Nouairia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elisabeth Steiner
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Niclas Weber
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christoph Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany.
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2
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Abstract
Encapsulins are recently discovered protein compartments able to specifically encapsulate cargo proteins in vivo. Encapsulation is dependent on C-terminal targeting peptides (TPs). Here, we characterize and engineer TP-shell interactions in the Thermotoga maritima and Myxococcus xanthus encapsulin systems. Using force-field modeling and particle fluorescence measurements we show that TPs vary in native specificity and binding strength, and that TP-shell interactions are determined by hydrophobic and ionic interactions as well as TP flexibility. We design a set of TPs with a variety of predicted binding strengths and experimentally characterize these designs. This yields a set of TPs with novel binding characteristics representing a potentially useful toolbox for future nanoreactor engineering aimed at controlling cargo loading efficiency and the relative stoichiometry of multiple concurrently loaded cargo proteins.
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Affiliation(s)
- Wiggert J Altenburg
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Nathan Rollins
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA
| | - Tobias W Giessen
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard, Boston, MA, 02115, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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3
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Abstract
Community network analysis (CNA) of correlated protein motions allows modeling of signals propagation in allosteric proteic systems. From standard classical molecular dynamics (MD) simulations, protein motions can be analysed by means of mutual information between pairs of amino acid residues, providing dynamical weighted networks that contains fundamental information of the communication among amino acids. The CNA method has been successfully applied to a variety of allosteric systems including an enzyme, a nuclear receptor and a bacterial adaptive immune system, providing characterization of the allosteric pathways. This method is complementary to network analyses based on different metrics and it is particularly powerful for studying large proteic systems, as it provides a coarse-grained view of the communication flows within large and complex networks.
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Affiliation(s)
- Ivan Rivalta
- Dipartimento di Chimica Industriale "Toso Montanari", Università di Bologna, Bologna, Italy.
- Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, Lyon, France.
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, USA
- Energy Sciences Institute, Yale University, New Haven, CT, USA
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4
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Overbeck JH, Kremer W, Sprangers R. A suite of 19F based relaxation dispersion experiments to assess biomolecular motions. J Biomol NMR 2020; 74:753-766. [PMID: 32997265 PMCID: PMC7701166 DOI: 10.1007/s10858-020-00348-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/18/2020] [Indexed: 05/08/2023]
Abstract
Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1ρ and off-resonance R1ρ RD experiments. We validate these experiments by studying the unfolding transition of a 7.5 kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360 kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.
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Affiliation(s)
- Jan H Overbeck
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Werner Kremer
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany
| | - Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, 93053, Regensburg, Germany.
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5
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Rix G, Watkins-Dulaney EJ, Almhjell PJ, Boville CE, Arnold FH, Liu CC. Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. Nat Commun 2020; 11:5644. [PMID: 33159067 PMCID: PMC7648111 DOI: 10.1038/s41467-020-19539-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/19/2020] [Indexed: 01/11/2023] Open
Abstract
Enzyme orthologs sharing identical primary functions can have different promiscuous activities. While it is possible to mine this natural diversity to obtain useful biocatalysts, generating comparably rich ortholog diversity is difficult, as it is the product of deep evolutionary processes occurring in a multitude of separate species and populations. Here, we take a first step in recapitulating the depth and scale of natural ortholog evolution on laboratory timescales. Using a continuous directed evolution platform called OrthoRep, we rapidly evolve the Thermotoga maritima tryptophan synthase β-subunit (TmTrpB) through multi-mutation pathways in many independent replicates, selecting only on TmTrpB's primary activity of synthesizing L-tryptophan from indole and L-serine. We find that the resulting sequence-diverse TmTrpB variants span a range of substrate profiles useful in industrial biocatalysis and suggest that the depth and scale of evolution that OrthoRep affords will be generally valuable in enzyme engineering and the evolution of biomolecular functions.
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Affiliation(s)
- Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Ella J Watkins-Dulaney
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Patrick J Almhjell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Christina E Boville
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Aralez Bio, Emeryville, CA, USA
| | - Frances H Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Chang C Liu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.
- Department of Chemistry, University of California, Irvine, CA, USA.
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6
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Abstract
Metallo-β-lactamases (MBLs) hydrolyze a wide range of β-lactam antibiotics. While all MBLs share a common αβ/βα-fold, there are many other proteins with the same folding pattern that exhibit different enzymatic activities. These enzymes, together with MBLs, form the MBL superfamily. Thermotoga maritima tRNase Z, a tRNA 3′ processing endoribonuclease of MBL-superfamily, and IMP-1, a clinically isolated MBL, showed a striking similarity in tertiary structure, despite low sequence homology. IMP-1 hydrolyzed both total cellular RNA and synthetic small unstructured RNAs. IMP-1 also hydrolyzed pre-tRNA, but its cleavage site was different from those of T. maritima tRNase Z and human tRNase Z long form, indicating a key difference in substrate recognition. Single-turnover kinetic assays suggested that substrate-binding affinity of T. maritima tRNase Z is much higher than that of IMP-1.
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Affiliation(s)
- Yoshiki Kato
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Takahashi
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Mineaki Seki
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Masayuki Nashimoto
- Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Akiko Shimizu-Ibuka
- Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
- * E-mail:
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7
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Chakraborti S, Korpi A, Kumar M, Stępień P, Kostiainen MA, Heddle JG. Three-Dimensional Protein Cage Array Capable of Active Enzyme Capture and Artificial Chaperone Activity. Nano Lett 2019; 19:3918-3924. [PMID: 31117758 DOI: 10.1021/acs.nanolett.9b01148] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Development of protein cages for encapsulation of active enzyme cargoes and their subsequent arrangement into a controllable three-dimensional array is highly desirable. However, cargo capture is typically challenging because of difficulties in achieving reversible assembly/disassembly of protein cages in mild conditions. Herein we show that by using an unusual ferritin cage protein that undergoes triggerable assembly under mild conditions, we can achieve reversible filling with protein cargoes including an active enzyme. We demonstrate that these filled cages can be arrayed in three-dimensional crystal lattices and have an additional chaperone-like effect, increasing both thermostability and enzymatic activity of the encapsulated enzyme.
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Affiliation(s)
- Soumyananda Chakraborti
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology , Jagiellonian University , Gronostajowa 7A , 30-387 Krakow , Poland
| | - Antti Korpi
- Biohybrid Materials, Department of Bioproducts and Biosystems , Aalto University , FI-00076 Aalto , Finland
| | - Mantu Kumar
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology , Jagiellonian University , Gronostajowa 7A , 30-387 Krakow , Poland
- Postgraduate School of Molecular Medicine ; Żwirki i Wigury 61 , 02-091 Warsaw , Poland
| | - Piotr Stępień
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology , Jagiellonian University , Gronostajowa 7A , 30-387 Krakow , Poland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems , Aalto University , FI-00076 Aalto , Finland
| | - Jonathan G Heddle
- Bionanoscience and Biochemistry Laboratory, Malopolska Centre of Biotechnology , Jagiellonian University , Gronostajowa 7A , 30-387 Krakow , Poland
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8
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Zhou Y, Liu X, Li C, Liu M, Jiang L, Liu Y. Chemical shift assignments of the catalytic and ATP-binding domain of HK853 from Thermotoga maritime. Biomol NMR Assign 2019; 13:173-176. [PMID: 30673936 DOI: 10.1007/s12104-019-09872-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
HK853 is a transmembrane protein from Thermotoga maritime, which belongs to HK853/RR468 two-component signal transduction system (TCS) and acts as a sensor histidine kinase. HK853 is mainly composed of a transmembrane domain, dimerization and histidine-containing phosphotransfer domain (HK853DHp), catalytic and ATP-binding domain (HK853CA) and several linkers. HK853 can be completely autophosphorylated, which is the first step for signal transduction of TCS. HK853CA is an essential domain for its kinase function, since HK853CA could bind with ATP and convert it to ADP. Here, we report the backbone and part of side chain assignments of HK853CA. By analyzing the chemical shifts of HN, N, CO, Cα and Cβ, the secondary structure was predicted and contrasted with the published crystal structure of HK853CA. The result showed that our predicted structure could basically fit into the crystal structure. Thus, the chemical shift assignments of HK853CA are the starting point for further structural and dynamics study.
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Affiliation(s)
- Yuan Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
- Graduate University of Chinese Academy of Science, Beijing, 100049, China
| | - Xinghong Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
- Graduate University of Chinese Academy of Science, Beijing, 100049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, China.
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9
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Zhou Y, Huang L, Ji S, Hou S, Luo L, Li C, Liu M, Liu Y, Jiang L. Structural Basis for the Inhibition of the Autophosphorylation Activity of HK853 by Luteolin. Molecules 2019; 24:molecules24050933. [PMID: 30866470 PMCID: PMC6429454 DOI: 10.3390/molecules24050933] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 02/21/2019] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
The two-component system (TCS) is a significant signal transduction system for bacteria to adapt to complicated and variable environments, and thus has recently been regarded as a novel target for developing antibacterial agents. The natural product luteolin (Lut) can inhibit the autophosphorylation activity of the typical histidine kinase (HK) HK853 from Thermotoga maritime, but the inhibition mechanism is not known. Herein, we report on the binding mechanism of a typical flavone with HK853 by using solution NMR spectroscopy, isothermal titration calorimetry (ITC), and molecular docking. We show that luteolin inhibits the activity of HK853 by occupying the binding pocket of adenosine diphosphate (ADP) through hydrogen bonds and π-π stacking interaction structurally. Our results reveal a detailed mechanism for the inhibition of flavones and observe the conformational and dynamics changes of HK. These results should provide a feasible approach for antibacterial agent design from the view of the histidine kinases.
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Affiliation(s)
- Yuan Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
- Graduate University of Chinese Academy of Science, Beijing 100049, China.
| | - Liqun Huang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
- Graduate University of Chinese Academy of Science, Beijing 100049, China.
| | - Shixia Ji
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
- Graduate University of Chinese Academy of Science, Beijing 100049, China.
| | - Shi Hou
- Laboratory of Computer-Aided Drug Design and Discovery, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.
| | - Liang Luo
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
- Graduate University of Chinese Academy of Science, Beijing 100049, China.
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yixiang Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center of Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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10
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Abstract
Biomolecules can be combined with inorganic compounds to unite biological features with the chemical and physical properties of abiotic materials. In particular, protein containers, with their inherent ability to encapsulate cargo molecules, are perfect platforms for the generation of multifunctional assemblies. However, encapsulation of foreign cargo is immensely challenging due to the lack of specific interactions between cargo and container. Here, we demonstrate that the highly specific cargo-loading mechanism of the bacterial nanocompartment encapsulin can be employed for encapsulation of artificial cargo like inorganic nanoparticles. For this purpose, container-filling gold nanoparticles were decorated with a small number of encapsulin cargo-loading peptides. By lock-and-key interaction between the peptides and the peptide-binding pockets on the inner container surface, the nanoparticles are encapsulated into encapsulin with extremely high efficiency. Most notably, peptide binding is independent from external factors such as ionic strength. Cargo-loading peptides may serve as generally applicable tool for efficient and specific encapsulation of cargo molecules into a proteinaceous compartment.
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Affiliation(s)
- Matthias Künzle
- RWTH Aachen University, Institute of Inorganic Chemistry, JARA-SOFT (Researching Soft Matter), and I3TM, 52074 Aachen, Germany.
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11
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Shukla S, Bafna K, Gullett C, Myles DAA, Agarwal PK, Cuneo MJ. Differential Substrate Recognition by Maltose Binding Proteins Influenced by Structure and Dynamics. Biochemistry 2018; 57:5864-5876. [PMID: 30204415 PMCID: PMC6189639 DOI: 10.1021/acs.biochem.8b00783] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genome of the hyperthermophile Thermotoga maritima contains three isoforms of maltose binding protein (MBP) that are high-affinity receptors for di-, tri-, and tetrasaccharides. Two of these proteins (tmMBP1 and tmMBP2) share significant sequence identity, approximately 90%, while the third (tmMBP3) shares less than 40% identity. MBP from Escherichia coli (ecMBP) shares 35% sequence identity with the tmMBPs. This subset of MBP isoforms offers an interesting opportunity to investigate the mechanisms underlying the evolution of substrate specificity and affinity profiles in a genome where redundant MBP genes are present. In this study, the X-ray crystal structures of tmMBP1, tmMBP2, and tmMBP3 are reported in the absence and presence of oligosaccharides. tmMBP1 and tmMBP2 have binding pockets that are larger than that of tmMBP3, enabling them to bind to larger substrates, while tmMBP1 and tmMBP2 also undergo substrate-induced hinge bending motions (∼52°) that are larger than that of tmMBP3 (∼35°). Small-angle X-ray scattering was used to compare protein behavior in solution, and computer simulations provided insights into dynamics of these proteins. Comparing quantitative protein-substrate interactions and dynamical properties of tmMBPs with those of the promiscuous ecMBP and disaccharide selective Thermococcus litoralis MBP provides insights into the features that enable selective binding. Collectively, the results provide insights into how the structure and dynamics of tmMBP homologues enable them to differentiate between a myriad of chemical entities while maintaining their common fold.
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Affiliation(s)
- Shantanu Shukla
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Khushboo Bafna
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
| | - Caeley Gullett
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dean A. A. Myles
- Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Pratul K. Agarwal
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee
| | - Matthew J. Cuneo
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee
- Deparment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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12
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Abstract
CheY is a response regulator of bacterial chemotaxis that is activated by phosphorylation of a conserved aspartate residue. However, studies of CheY-phosphate have proven challenging due to rapid hydrolysis of the aspartyl-phosphate in vitro. To combat this issue, we have designed a stable analog suitable for structural and functional studies. Herein, we describe a method for the chemical modification of Thermotoga maritima CheY to produce a phospho-analog designated as phosphono-CheY. Our modification produces a stable analog in the constitutively active form that enables the study of signal transfer to the downstream target.
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Affiliation(s)
- Daniel B Lookadoo
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, NC, USA
| | - Matthew S Beyersdorf
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, NC, USA
| | - Christopher J Halkides
- Department of Chemistry and Biochemistry, The University of North Carolina Wilmington, Wilmington, NC, USA.
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13
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Choi MK, Jo S, Lee BH, Kim MH, Choi JB, Kim K, Kim MK. Dynamic characteristics of a flagellar motor protein analyzed using an elastic network model. J Mol Graph Model 2017; 78:81-87. [PMID: 29054097 DOI: 10.1016/j.jmgm.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/23/2022]
Abstract
At the base of a flagellar motor, its rotational direction and speed are regulated by the interaction between rotor and stator proteins. A switching event occurs when the cytoplasmic rotor protein, called C-ring, changes its conformation in response to binding of the CheY signal protein. The C-ring structure consists of FliG, FliM, and FliN proteins and its conformational changes in FliM and FliG including HelixMC play an important role in switching the motor direction. Therefore, clarifying their dynamic properties as well as conformational changes is a key to understanding the switching mechanism of the motor protein. In this study, to elucidate dynamic characteristics of the C-ring structure, both harmonic (intrinsic vibration) and anharmonic (transition pathway) analyses are conducted by using the symmetry-constrained elastic network model. As a result, the first three normal modes successfully capture the essence of transition pathway from wild type to CW-biased state. Their cumulative square overlap value reaches up to 0.842. Remarkably, it is also noted from the transition pathway that the cascade of interactions from the signal protein to FliM to FliG, highlighted by the major mode shapes from the first three normal modes, induces the reorientation (∼100° rotation of FliGC5) of FliG C-terminal that directly interacts with the stator protein. Presumably, the rotational direction of the motor protein is switched by this substantial change in the stator-rotor interaction.
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Affiliation(s)
- Moon-Ki Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Soojin Jo
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Byung Ho Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Min Hyeok Kim
- Korea Institute for Advanced Study, Seoul, 02455, Korea
| | - Jae Boong Choi
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyunghoon Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Moon Ki Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
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14
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Weitz AC, Giri N, Caranto JD, Kurtz DM, Bominaar EL, Hendrich MP. Spectroscopy and DFT Calculations of a Flavo-diiron Enzyme Implicate New Diiron Site Structures. J Am Chem Soc 2017; 139:12009-12019. [PMID: 28756660 PMCID: PMC5898632 DOI: 10.1021/jacs.7b06546] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavo-diiron proteins (FDPs) are non-heme iron containing enzymes that are widespread in anaerobic bacteria, archaea, and protozoa, serving as the terminal components to dioxygen and nitric oxide reductive scavenging pathways in these organisms. FDPs contain a dinuclear iron active site similar to that in hemerythrin, ribonucleotide reductase, and methane monooxygenase, all of which can bind NO and O2. However, only FDP competently turns over NO to N2O. Here, EPR and Mössbauer spectroscopies allow electronic characterization of the diferric and diferrous species of FDP. The exchange-coupling constant J (Hex = JS1·S2) was found to increase from +20 cm-1 to +32 cm-1 upon reduction of the diferric to the diferrous species, indicative of (1) at least one hydroxo bridge between the iron ions for both states and (2) a change to the diiron core structure upon reduction. In comparison to characterized diiron proteins and synthetic complexes, the experimental values were consistent with a dihydroxo bridged diferric core, which loses one hydroxo bridge upon reduction. DFT calculations of these structures gave values of J and Mössbauer parameters in agreement with experiment. Although the crystal structure shows a hydrogen bond between the iron bound aspartate and the bridging solvent molecule, the DFT calculations of structures consistent with the crystal structure gave calculated values of J incompatible with the spectroscopic results. We conclude that the crystal structure of the diferric state does not represent the frozen solution structure and that a mono-μ-hydroxo diferrous species is the catalytically functional state that reacts with NO and O2. The new EPR spectroscopic probe of the diferric state indicated that the diferric structure of FDP prior to and immediately after turnover with NO are flavin mononucleotide (FMN) dependent, implicating an additional proton transfer role for FMN in turnover of NO.
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Affiliation(s)
- Andrew C. Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Nitai Giri
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Jonathan D. Caranto
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Donald M. Kurtz
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Emile L. Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael P. Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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15
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Hughes ML, Paci E, Brockwell DJ, Dougan L. Differential Effects of Hydrophobic Core Packing Residues for Thermodynamic and Mechanical Stability of a Hyperthermophilic Protein. Langmuir 2016; 32:7392-7402. [PMID: 27338140 DOI: 10.1021/acs.langmuir.6b01550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins from organisms that have adapted to environmental extremes provide attractive systems to explore and determine the origins of protein stability. Improved hydrophobic core packing and decreased loop-length flexibility can increase the thermodynamic stability of proteins from hyperthermophilic organisms. However, their impact on protein mechanical stability is not known. Here, we use protein engineering, biophysical characterization, single-molecule force spectroscopy (SMFS), and molecular dynamics (MD) simulations to measure the effect of altering hydrophobic core packing on the stability of the cold shock protein TmCSP from the hyperthermophilic bacterium Thermotoga maritima. We make two variants of TmCSP in which a mutation is made to reduce the size of aliphatic groups from buried hydrophobic side chains. In the first, a mutation is introduced in a long loop (TmCSP L40A); in the other, the mutation is introduced on the C-terminal β-strand (TmCSP V62A). We use MD simulations to confirm that the mutant TmCSP L40A shows the most significant increase in loop flexibility, and mutant TmCSP V62A shows greater disruption to the core packing. We measure the thermodynamic stability (ΔGD-N) of the mutated proteins and show that there is a more significant reduction for TmCSP L40A (ΔΔG = 63%) than TmCSP V62A (ΔΔG = 47%), as might be expected on the basis of the relative reduction in the size of the side chain. By contrast, SMFS measures the mechanical stability (ΔG*) and shows a greater reduction for TmCSP V62A (ΔΔG* = 8.4%) than TmCSP L40A (ΔΔG* = 2.5%). While the impact on the mechanical stability is subtle, the results demonstrate the power of tuning noncovalent interactions to modulate both the thermodynamic and mechanical stability of a protein. Such understanding and control provide the opportunity to design proteins with optimized thermodynamic and mechanical properties.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Matthew Batchelor
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Toni Hoffmann
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Michael C Wilson
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Megan L Hughes
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Emanuele Paci
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - David J Brockwell
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
| | - Lorna Dougan
- School of Physics and Astronomy, ‡Astbury Centre for Structural and Molecular Biology, and §School of Molecular and Cellular Biology, University of Leeds , Leeds, LS2 9JT, United Kingdom
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16
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Talens-Perales D, Polaina J, Marín-Navarro J. Structural Dissection of the Active Site of Thermotoga maritima β-Galactosidase Identifies Key Residues for Transglycosylating Activity. J Agric Food Chem 2016; 64:2917-2924. [PMID: 26998654 DOI: 10.1021/acs.jafc.6b00222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Glycoside hydrolases, specifically β-galactosidases, can be used to synthesize galacto-oligosaccharides (GOS) due to the transglycosylating (secondary) activity of these enzymes. Site-directed mutagenesis of a thermoresistant β-galactosidase from Thermotoga maritima has been carried out to study the structural basis of transgalactosylation and to obtain enzymatic variants with better performance for GOS biosynthesis. Rational design of mutations was based on homologous sequence analysis and structural modeling. Analysis of mutant enzymes indicated that residue W959, or an alternative aromatic residue at this position, is critical for the synthesis of β-3'-galactosyl-lactose, the major GOS obtained with the wild-type enzyme. Mutants W959A and W959C, but not W959F, showed an 80% reduced synthesis of this GOS. Other substitutions, N574S, N574A, and F571L, increased the synthesis of β-3'-galactosyl-lactose about 40%. Double mutants F571L/N574S and F571L/N574A showed an increase of about 2-fold.
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Affiliation(s)
- David Talens-Perales
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
| | - Julio Polaina
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Instituto de Agroquímica y Tecnología de Alimentos, CSIC , Paterna, Valencia, Spain
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17
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Tych KM, Batchelor M, Hoffmann T, Wilson MC, Paci E, Brockwell DJ, Dougan L. Tuning protein mechanics through an ionic cluster graft from an extremophilic protein. Soft Matter 2016; 12:2688-2699. [PMID: 26809452 DOI: 10.1039/c5sm02938d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Proteins from extremophilic organisms provide excellent model systems to determine the role of non-covalent interactions in defining protein stability and dynamics as well as being attractive targets for the development of robust biomaterials. Hyperthermophilic proteins have a prevalence of salt bridges, relative to their mesophilic homologues, which are thought to be important for enhanced thermal stability. However, the impact of salt bridges on the mechanical properties of proteins is far from understood. Here, a combination of protein engineering, biophysical characterisation, single molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations directly investigates the role of salt bridges in the mechanical stability of two cold shock proteins; BsCSP from the mesophilic organism Bacillus subtilis and TmCSP from the hyperthermophilic organism Thermotoga maritima. Single molecule force spectroscopy shows that at ambient temperatures TmCSP is mechanically stronger yet, counter-intuitively, its native state can withstand greater deformation before unfolding (i.e. it is mechanically soft) compared with BsCSP. MD simulations were used to identify the location and quantify the population of salt bridges, and reveal that TmCSP contains a larger number of highly occupied salt bridges than BsCSP. To test the hypothesis that salt-bridges endow these mechanical properties on the hyperthermophilic CSP, a charged triple mutant (CTM) variant of BsCSP was generated by grafting an ionic cluster from TmCSP into the BsCSP scaffold. As expected CTM is thermodynamically more stable and mechanically softer than BsCSP. We show that a grafted ionic cluster can increase the mechanical softness of a protein and speculate that it could provide a mechanical recovery mechanism and that it may be a design feature applicable to other proteins.
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Affiliation(s)
- Katarzyna M Tych
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK.
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18
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Zhou W, You C, Ma H, Ma Y, Zhang YHP. One-Pot Biosynthesis of High-Concentration α-Glucose 1-Phosphate from Starch by Sequential Addition of Three Hyperthermophilic Enzymes. J Agric Food Chem 2016; 64:1777-1783. [PMID: 26832825 DOI: 10.1021/acs.jafc.5b05648] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
α-Glucose 1-phosphate (G1P) is synthesized from 5% (w/v) corn starch and 1 M phosphate mediated by α-glucan phosphorylase (αGP) from the thermophilic bacterium Thermotoga maritima at pH 7.2 and 70 °C. To increase G1P yield from corn starch containing branched amylopectin, a hyper-thermostable isoamylase from Sulfolobus tokodaii was added for simultaneous starch gelatinization and starch-debranching hydrolysis at 85 °C and pH 5.5 before αGP use. The pretreatment of isoamylase increased G1P titer from 120 mM to 170 mM. To increase maltose and maltotriose utilization, the third thermostable enzyme, 4-glucanotransferase (4GT) from Thermococcus litoralis, was added during the late stage of G1P biotransformation, further increasing G1P titer to 200 mM. This titer is the highest G1P level obtained on starch or its derived products (maltodextrin and soluble starch). This study suggests that in vitro multienzyme biotransformation has an advantage of great engineering flexibility in terms of space and time compared with microbial fermentation.
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Affiliation(s)
- Wei Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Chun You
- Cell Free Bioinnovations Inc. , 1800 Kraft Drive, Suite 222, Blacksburg, Virginia 24060, United States
| | - Hongwu Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Y-H Percival Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 West Seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- Cell Free Bioinnovations Inc. , 1800 Kraft Drive, Suite 222, Blacksburg, Virginia 24060, United States
- Biological Systems Engineering Department, Virginia Tech , 304 Seitz Hall, Blacksburg, Virginia 24061, United States
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19
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Burban DJ, Haglund E, Capraro DT, Jennings PA. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil. J Phys Condens Matter 2015; 27:354108. [PMID: 26291198 PMCID: PMC4681393 DOI: 10.1088/0953-8984/27/35/354108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region.
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Affiliation(s)
- David J Burban
- Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA USA
| | - Ellinor Haglund
- Center for Theoretical Biological Physics (CTBP) and Department of Physics, University of California at San Diego (UCSD), La Jolla, CA USA
- Center for Theoretical Biological Physics (CTBP) and Departments of Physics and Astronomy, Chemistry and Biochemistry and Cell Biology, Rice University, Houston, TX USA
| | - Dominique T Capraro
- Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA USA
| | - Patricia A Jennings
- Departments of Chemistry and Biochemistry, University of California at San Diego (UCSD), La Jolla, CA USA
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20
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Abstract
Ultracentrifugation, particularly the use of sucrose or cesium chloride density gradients, is a highly reliable and efficient technique for the purification of virus-like particles and protein cages. Since virus-like particles and protein cages have a unique size compared to cellular macromolecules and organelles, the rate of migration can be used as a tool for purification. Here we describe a detailed protocol for the purification of recently discovered virus-like assemblies called bacterial encapsulins from Thermotoga maritima and Brevibacterium linens.
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Affiliation(s)
- W Frederik Rurup
- Laboratory for Biomolecular Nanotechnology, MESA + Institute for Nanotechnology, University of Twente, 217, 7500 AE, Enschede, The Netherlands
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21
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Abstract
The role of protein dynamics in the reaction catalyzed by dihydrofolate reductase from the hyperthermophile Thermotoga maritima (TmDHFR) has been examined by enzyme isotope substitution ((15)N, (13)C, (2)H). In contrast to all other enzyme reactions investigated previously, including DHFR from Escherichia coli (EcDHFR), for which isotopic substitution led to decreased reactivity, the rate constant for the hydride transfer step is not affected by isotopic substitution of TmDHFR. TmDHFR therefore appears to lack the coupling of protein motions to the reaction coordinate that have been identified for EcDHFR catalysis. Clearly, dynamical coupling is not a universal phenomenon that affects the efficiency of enzyme catalysis.
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Affiliation(s)
- Louis
Y. P. Luk
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - E. Joel Loveridge
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
- Cardiff
Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
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22
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Ferris HU, Zeth K, Hulko M, Dunin-Horkawicz S, Lupas AN. Axial helix rotation as a mechanism for signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor. J Struct Biol 2014; 186:349-56. [PMID: 24680785 DOI: 10.1016/j.jsb.2014.03.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/19/2022]
Abstract
Bacterial chemotaxis receptors are elongated homodimeric coiled-coil bundles, which transduce signals generated in an N-terminal sensor domain across 15-20nm to a conserved C-terminal signaling subdomain. This signal transduction regulates the activity of associated kinases, altering the behavior of the flagellar motor and hence cell motility. Signaling is in turn modulated by selective methylation and demethylation of specific glutamate and glutamine residues in an adaptation subdomain. We have determined the structure of a chimeric protein, consisting of the HAMP domain from Archaeoglobus fulgidus Af1503 and the methyl-accepting domain of Escherichia coli Tsr. It shows a 21nm coiled coil that alternates between two coiled-coil packing modes: canonical knobs-into-holes and complementary x-da, a variant form related to the canonical one by axial rotation of the helices. Comparison of the obtained structure to the Thermotoga maritima chemoreceptor TM1143 reveals that they adopt different axial rotation states in their adaptation subdomains. This conformational change is presumably induced by the upstream HAMP domain and may modulate the affinity of the chemoreceptor to the methylation-demethylation system. The presented findings extend the cogwheel model for signal transmission to chemoreceptors.
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Affiliation(s)
- Hedda U Ferris
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Kornelius Zeth
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Hulko
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Stanislaw Dunin-Horkawicz
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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23
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Berggren G, Garcia-Serres R, Brazzolotto X, Clemancey M, Gambarelli S, Atta M, Latour JM, Hernández HL, Subramanian S, Johnson MK, Fontecave M. An EPR/HYSCORE, Mössbauer, and resonance Raman study of the hydrogenase maturation enzyme HydF: a model for N-coordination to [4Fe-4S] clusters. J Biol Inorg Chem 2014; 19:75-84. [PMID: 24240692 PMCID: PMC4439245 DOI: 10.1007/s00775-013-1062-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 10/30/2013] [Indexed: 10/26/2022]
Abstract
The biosynthesis of the organometallic H cluster of [Fe-Fe] hydrogenase requires three accessory proteins, two of which (HydE and HydG) belong to the radical S-adenosylmethionine enzyme superfamily. The third, HydF, is an Fe-S protein with GTPase activity. The [4Fe-4S] cluster of HydF is bound to the polypeptide chain through only the three, conserved, cysteine residues present in the binding sequence motif CysXHisX(46-53)HisCysXXCys. However, the involvement of the two highly conserved histidines as a fourth ligand for the cluster coordination is controversial. In this study, we set out to characterize further the [4Fe-4S] cluster of HydF using Mössbauer, EPR, hyperfine sublevel correlation (HYSCORE), and resonance Raman spectroscopy in order to investigate the influence of nitrogen ligands on the spectroscopic properties of [4Fe-4S](2+/+) clusters. Our results show that Mössbauer, resonance Raman, and EPR spectroscopy are not able to readily discriminate between the imidazole-coordinated [4Fe-4S] cluster and the non-imidazole-bound [4Fe-4S] cluster with an exchangeable fourth ligand that is present in wild-type HydF. HYSCORE spectroscopy, on the other hand, detects the presence of an imidazole/histidine ligand on the cluster on the basis of the appearance of a specific spectral pattern in the strongly coupled region, with a coupling constant of approximately 6 MHz. We also discovered that a His-tagged version of HydF, with a hexahistidine tag at the N-terminus, has a [4Fe-4S] cluster coordinated by one histidine from the tag. This observation strongly indicates that care has to be taken in the analysis of data obtained on tagged forms of metalloproteins.
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Affiliation(s)
- Gustav Berggren
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Ricardo Garcia-Serres
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Xavier Brazzolotto
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Martin Clemancey
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Serge Gambarelli
- Laboratoire “Résonance Magnétique”, Université Joseph Fourier, Grenoble 1/CEA/Institut Nanoscience et Cryogénie/SCIB, UMR-E3, Grenoble, France
| | - Mohamed Atta
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
| | - Jean-Marc Latour
- Laboratoire de Chimie et Biologie des Métaux, Équipe “Physicochimie des Métaux en Biologie”, Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/pmb, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, Grenoble, France
| | - Heather L. Hernández
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Sowmya Subramanian
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Michael K. Johnson
- Department of Chemistry and Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
| | - Marc Fontecave
- Laboratoire de Chimie et Biologie des Métaux, Équipe «Biocatalyse», Institut de Recherches en Technologies et Sciences pour le Vivant, iRTSV-LCBM/Biocat, UMR 5249 CEA/CNRS/UJF, CEA/Grenoble, 17, rue des Martyrs, Grenoble, France
- Collége de France, 11 place Marcellin-Berthelot, Paris, France
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24
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An JY, Kim TG, Park KR, Lee JG, Youn HS, Lee Y, Kang JY, Kang GB, Eom SH. Crystal structure of the N-terminal domain of MinC dimerized via domain swapping. J Synchrotron Radiat 2013; 20:984-8. [PMID: 24121353 PMCID: PMC3795569 DOI: 10.1107/s0909049513022760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/13/2013] [Indexed: 06/02/2023]
Abstract
Proper cell division at the mid-site of gram-negative bacteria reflects critical regulation by the min system (MinC, MinD and MinE) of the cytokinetic Z ring, which is a polymer composed of FtsZ subunits. MinC and MinD act together to inhibit aberrantly positioned Z-ring formation. MinC consists of two domains: an N-terminal domain (MinCNTD), which interacts with FtsZ and inhibits FtsZ polymerization, and a C-terminal domain (MinCCTD), which interacts with MinD and inhibits the bundling of FtsZ filaments. These two domains reportedly function together, and both are essential for normal cell division. The full-length dimeric structure of MinC from Thermotoga maritima has been reported, and shows that MinC dimerization occurs via MinCCTD; MinCNTD is not involved in dimerization. Here the crystal structure of Escherichia coli MinCNTD (EcoMinCNTD) is reported. EcoMinCNTD forms a dimer via domain swapping between the first β strands in each subunit. It is therefore suggested that the dimerization of full-length EcoMinC occurs via both MinCCTD and MinCNTD, and that the dimerized EcoMinCNTD likely plays an important role in inhibiting aberrant Z-ring localization.
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Affiliation(s)
- Jun Yop An
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Tae Gyun Kim
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Hyung-Seop Youn
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Youngjin Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Gil Bu Kang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
- Steitz Center for Structural Biology, Gwangju Institute of Science and Technology, Gwangju 500-712, Republic of Korea
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25
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Abstract
Cell-free biosystems comprised of synthetic enzymatic pathways would be a promising biomanufacturing platform due to several advantages, such as high product yield, fast reaction rate, easy control and access, and so on. However, it was essential to produce (purified) enzymes at low costs and stabilize them for a long time so to decrease biocatalyst costs. We studied the stability of the four recombinant enzyme mixtures, all of which originated from thermophilic microorganisms: triosephosphate isomerase (TIM) from Thermus thermophiles, fructose bisphosphate aldolase (ALD) from Thermotoga maritima, fructose bisphosphatase (FBP) from T. maritima, and phosphoglucose isomerase (PGI) from Clostridium thermocellum. It was found that TIM and ALD were very stable at evaluated temperature so that they were purified by heat precipitation followed by gradient ammonia sulfate precipitation. In contrast, PGI was not stable enough for heat treatment. In addition, the stability of a low concentration PGI was enhanced by more than 25 times in the presence of 20 mg/L bovine serum albumin or the other three enzymes. At a practical enzyme loading of 1000 U/L for each enzyme, the half-life time of free PGI was prolong to 433 h in the presence of the other three enzymes, resulting in a great increase in the total turn-over number of PGI to 6.2×109 mole of product per mole of enzyme. This study clearly suggested that the presence of other proteins had a strong synergetic effect on the stabilization of the thermolabile enzyme PGI due to in vitro macromolecular crowding effect. Also, this result could be used to explain why not all enzymes isolated from thermophilic microorganisms are stable in vitro because of a lack of the macromolecular crowding environment.
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Affiliation(s)
- Suwan Myung
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States of America
- Institute for Critical Technology and Applied Science (ICTAS), Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia, United States of America
- Institute for Critical Technology and Applied Science (ICTAS), Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Cell Free Bioinnovations Inc., Blacksburg, Virginia, United States of America
- Gate Fuels Inc., Blacksburg, Virginia, United States of America
- * E-mail:
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26
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Jeong E, Jo H, Kim TG, Ban C. Characterization of multi-functional properties and conformational analysis of MutS2 from Thermotoga maritima MSB8. PLoS One 2012; 7:e34529. [PMID: 22545085 PMCID: PMC3335848 DOI: 10.1371/journal.pone.0034529] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/01/2012] [Indexed: 11/18/2022] Open
Abstract
The MutS2 homologues have received attention because of their unusual activities that differ from those of MutS. In this work, we report on the functional characteristics and conformational diversities of Thermotoga maritima MutS2 (TmMutS2). Various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (SPM), ATPase assays, analytical ultracentrifugation, DNA binding assays, size chromatography, and limited proteolytic analysis. Dimeric TmMutS2 showed the temperature-dependent ATPase activity. The non-specific nicking endonuclease activities of TmMutS2 were inactivated in the presence of nonhydrolytic ATP (ADPnP) and enhanced by the addition of TmMutL. In addition, TmMutS2 suppressed the TmRecA-mediated DNA strand exchange reaction in a TmMutL-dependent manner. We also demonstrated that small-angle X-ray scattering (SAXS) analysis of dimeric TmMutS2 exhibited nucleotide- and DNA-dependent conformational transitions. Particularly, TmMutS2-ADPnP showed the most compressed form rather than apo-TmMutS2 and the TmMutS2-ADP complex, in accordance with the results of biochemical assays. In the case of the DNA-binding complexes, the stretched conformation appeared in the TmMutS2-four-way junction (FWJ)-DNA complex. Convergences of biochemical- and SAXS analysis provided abundant information for TmMutS2 and clarified ambiguous experimental results.
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Affiliation(s)
- Euiyoung Jeong
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Hunho Jo
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Tae Gyun Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
| | - Changill Ban
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk, South Korea
- * E-mail:
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27
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Fredslund F, Hachem MA, Larsen RJ, Sørensen PG, Coutinho PM, Lo Leggio L, Svensson B. Crystal structure of α-galactosidase from Lactobacillus acidophilus NCFM: insight into tetramer formation and substrate binding. J Mol Biol 2011; 412:466-80. [PMID: 21827767 DOI: 10.1016/j.jmb.2011.07.057] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/21/2011] [Accepted: 07/25/2011] [Indexed: 11/19/2022]
Abstract
Lactobacillus acidophilus NCFM is a probiotic bacterium known for its beneficial effects on human health. The importance of α-galactosidases (α-Gals) for growth of probiotic organisms on oligosaccharides of the raffinose family present in many foods is increasingly recognized. Here, the crystal structure of α-Gal from L. acidophilus NCFM (LaMel36A) of glycoside hydrolase (GH) family 36 (GH36) is determined by single-wavelength anomalous dispersion. In addition, a 1.58-Å-resolution crystallographic complex with α-d-galactose at substrate binding subsite -1 was determined. LaMel36A has a large N-terminal twisted β-sandwich domain, connected by a long α-helix to the catalytic (β/α)(8)-barrel domain, and a C-terminal β-sheet domain. Four identical monomers form a tightly packed tetramer where three monomers contribute to the structural integrity of the active site in each monomer. Structural comparison of LaMel36A with the monomeric Thermotoga maritima α-Gal (TmGal36A) reveals that O2 of α-d-galactose in LaMel36A interacts with a backbone nitrogen in a glycine-rich loop of the catalytic domain, whereas the corresponding atom in TmGal36A is from a tryptophan side chain belonging to the N-terminal domain. Thus, two distinctly different structural motifs participate in substrate recognition. The tetrameric LaMel36A furthermore has a much deeper active site than the monomeric TmGal36A, which possibly modulates substrate specificity. Sequence analysis of GH36, inspired by the observed structural differences, results in four distinct subgroups having clearly different active-site sequence motifs. This novel subdivision incorporates functional and architectural features and may aid further biochemical and structural analyses within GH36.
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Affiliation(s)
- Folmer Fredslund
- Department of Systems Biology, Enzyme and Protein Chemistry, Technical University of Denmark, Søltofts Plads, Building 224, DK-2800 Kongens Lyngby, Denmark
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28
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Wan Q, Ahmad MF, Fairman J, Gorzelle B, de la Fuente M, Dealwis C, Maguire ME. X-ray crystallography and isothermal titration calorimetry studies of the Salmonella zinc transporter ZntB. Structure 2011; 19:700-10. [PMID: 21565704 PMCID: PMC3094545 DOI: 10.1016/j.str.2011.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 02/11/2011] [Accepted: 02/21/2011] [Indexed: 11/17/2022]
Abstract
The ZntB Zn(2+) efflux system is important for maintenance of Zn(2+) homeostasis in Enterobacteria. We report crystal structures of ZntB cytoplasmic domains from Salmonella enterica serovar Typhimurium (StZntB) in dimeric and physiologically relevant homopentameric forms at 2.3 Å and 3.1 Å resolutions, respectively. The funnel-like structure is similar to that of the homologous Thermotoga maritima CorA Mg(2+) channel and a Vibrio parahaemolyticus ZntB (VpZntB) soluble domain structure. However, the central α7 helix forming the inner wall of the StZntB funnel is oriented perpendicular to the membrane instead of the marked angle seen in CorA or VpZntB. Consequently, the StZntB funnel pore is cylindrical, not tapered, which may represent an "open" form of the ZntB soluble domain. Our crystal structures and isothermal titration calorimetry data indicate that there are three Zn(2+) binding sites in the full-length ZntB, two of which could be involved in Zn(2+) transport.
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Affiliation(s)
- Qun Wan
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - Md Faiz Ahmad
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - James Fairman
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Bonnie Gorzelle
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - María de la Fuente
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - Chris Dealwis
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
| | - Michael E. Maguire
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4965, USA
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29
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Minamino T, Imada K, Kinoshita M, Nakamura S, Morimoto YV, Namba K. Structural insight into the rotational switching mechanism of the bacterial flagellar motor. PLoS Biol 2011; 9:e1000616. [PMID: 21572987 PMCID: PMC3091841 DOI: 10.1371/journal.pbio.1000616] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 03/29/2011] [Indexed: 01/09/2023] Open
Abstract
Structural analysis of a clockwise-biased rotation mutant of the bacterial
flagellar rotor protein FliG provides a new model for the arrangement of FliG
subunits in the motor, and novel insights into rotation switching. The bacterial flagellar motor can rotate either clockwise (CW) or
counterclockwise (CCW). Three flagellar proteins, FliG, FliM, and FliN, are
required for rapid switching between the CW and CCW directions. Switching is
achieved by a conformational change in FliG induced by the binding of a
chemotaxis signaling protein, phospho-CheY, to FliM and FliN. FliG consists of
three domains, FliGN, FliGM, and FliGC, and
forms a ring on the cytoplasmic face of the MS ring of the flagellar basal body.
Crystal structures have been reported for the FliGMC domains of
Thermotoga maritima, which consist of the FliGM
and FliGC domains and a helix E that connects these two domains, and
full-length FliG of Aquifex aeolicus. However, the basis for
the switching mechanism is based only on previously obtained genetic data and is
hence rather indirect. We characterized a CW-biased mutant
(fliG(ΔPAA)) of Salmonella enterica by
direct observation of rotation of a single motor at high temporal and spatial
resolution. We also determined the crystal structure of the FliGMC
domains of an equivalent deletion mutant variant of T. maritima
(fliG(ΔPEV)). The FliG(ΔPAA) motor produced torque
at wild-type levels under a wide range of external load conditions. The
wild-type motors rotated exclusively in the CCW direction under our experimental
conditions, whereas the mutant motors rotated only in the CW direction. This
result suggests that wild-type FliG is more stable in the CCW state than in the
CW state, whereas FliG(ΔPAA) is more stable in the CW state than in the CCW
state. The structure of the TM-FliGMC(ΔPEV) revealed that
extremely CW-biased rotation was caused by a conformational change in helix E.
Although the arrangement of FliGC relative to FliGM in a
single molecule was different among the three crystals, a conserved
FliGM-FliGC unit was observed in all three of them. We
suggest that the conserved FliGM-FliGC unit is the basic
functional element in the rotor ring and that the PAA deletion induces a
conformational change in a hinge-loop between FliGM and helix E to
achieve the CW state of the FliG ring. We also propose a novel model for the
arrangement of FliG subunits within the motor. The model is in agreement with
the previous mutational and cross-linking experiments and explains the
cooperative switching mechanism of the flagellar motor. The bacterial flagellum is a rotating organelle that governs cell motility. At
the base of each flagellum is a motor powered by the electrochemical potential
difference of specific ions across the cytoplasmic membrane. In response to
environmental stimuli, rotation of the motor switches between counterclockwise
and clockwise, with a corresponding effect on the swimming direction of the
cell. Switching is triggered by the binding of the signaling protein
phospho-CheY to FliM and FliN, and achieved by conformational changes in the
rotor protein FliG. The actual switching mechanism, however, remains unclear. In
this study, we characterized a fliG mutant of
Salmonella that shows an extreme clockwise-biased rotation,
and determined the structure of a fragment of FliG (FliGMC) of the
equivalent mutant variant of Thermotoga maritima.
FliGMC is composed of two domains and covers the regions
essential for torque generation and FliM binding. We showed that the mutant
structure has a conformational change in the helix connecting the two domains,
leading to a domain orientation distinct from that of the wild-type FliG. On the
basis of this structure, we propose a new model for the arrangement of FliG
subunits in the rotor that is consistent with the previous mutational studies
and explains how cooperative switching occurs in the motor.
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Affiliation(s)
- Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- PRESTO, JST, Saitama, Japan
| | - Katsumi Imada
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- Department of Macromolecular Science, Osaka
University, Osaka, Japan
- * E-mail: (KI); (KN)
| | - Miki Kinoshita
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
| | - Shuichi Nakamura
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
| | | | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka
University, Osaka, Japan
- * E-mail: (KI); (KN)
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30
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Serrano P, Pedrini B, Geralt M, Jaudzems K, Mohanty B, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K. Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1393-405. [PMID: 20944236 PMCID: PMC2954230 DOI: 10.1107/s1744309110033658] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 08/20/2010] [Indexed: 05/12/2023]
Abstract
The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this paper, the extent to which this approach can provide function-related information on the two functionally annotated proteins TM1081, a Thermotoga maritima anti-σ factor antagonist, and A2LD1 (gi:13879369), a mouse γ-glutamylamine cyclotransferase, is explored. The NMR structures of the two proteins have been determined in solution at 313 and 298 K, respectively, using the current JCSG protocol based on the software package UNIO for extensive automation. The corresponding crystal structures were solved by the JCSG at 100 K and 1.6 Å resolution and at 100 K and 1.9 Å resolution, respectively. The NMR and crystal structures of the two proteins share the same overall molecular architectures. However, the precision of the structure determination along the amino-acid sequence varies over a significantly wider range in the NMR structures than in the crystal structures. Thereby, in each of the two NMR structures about 65% of the residues have displacements below the average and in both proteins the less well ordered residues include large parts of the active sites, in addition to some highly solvent-exposed surface areas. Whereas the latter show increased disorder in the crystal and in solution, the active-site regions display increased displacements only in the NMR structures, where they undergo local conformational exchange on the millisecond time scale that appears to be frozen in the crystals. These observations suggest that a search for molecular regions showing increased structural disorder and slow dynamic processes in solution while being well ordered in the corresponding crystal structure might be a valid initial step in the challenge of identifying putative active sites in functionally unannotated proteins with known three-dimensional structure.
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Affiliation(s)
- Pedro Serrano
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Bill Pedrini
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Michael Geralt
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kristaps Jaudzems
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Biswaranjan Mohanty
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Reto Horst
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Torsten Herrmann
- Centre Européen de RMN à Très Hauts Champs, Université de Lyon FRE 3008 CNRS, F-69100 Villeurbanne, France
| | - Marc-André Elsliger
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
| | - Ian A. Wilson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kurt Wüthrich
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
- Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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31
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Xu Q, McMullan D, Jaroszewski L, Krishna SS, Elsliger MA, Yeh AP, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chiu HJ, Clayton T, Duan L, Feuerhelm J, Grant J, Han GW, Jin KK, Klock HE, Knuth MW, Miller MD, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, van den Bedem H, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Structure of an essential bacterial protein YeaZ (TM0874) from Thermotoga maritima at 2.5 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1230-6. [PMID: 20944216 PMCID: PMC2954210 DOI: 10.1107/s1744309109022192] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 06/10/2009] [Indexed: 11/24/2022]
Abstract
YeaZ is involved in a protein network that is essential for bacteria. The crystal structure of YeaZ from Thermotoga maritima was determined to 2.5 Å resolution. Although this protein belongs to a family of ancient actin-like ATPases, it appears that it has lost the ability to bind ATP since it lacks some key structural features that are important for interaction with ATP. A conserved surface was identified, supporting its role in the formation of protein complexes.
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Affiliation(s)
- Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew P. Yeh
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Herbert L. Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Joanna Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Silvya Oommachen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Jessica Paulsen
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, CA, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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32
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Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science 2009; 325:1544-9. [PMID: 19762644 PMCID: PMC2833182 DOI: 10.1126/science.1174671] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.
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Affiliation(s)
- Ying Zhang
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Ines Thiele
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Zhanwen Li
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Krzysztof Ginalski
- Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Warsaw, Poland
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, Structure Determination Core, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - John Wooley
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, Crystallomics Core, Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bernhard Palsson
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093-0412, USA
| | - Andrei Osterman
- Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Adam Godzik
- Joint Center for Molecular Modeling, Burnham Institute for Medical Research La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
- Joint Center for Structural Genomics, Bioinformatics Core, University of California at San Diego, La Jolla, CA 92093, USA
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Zheng M, Cooper DR, Grossoehme NE, Yu M, Hung LW, Cieslik M, Derewenda U, Lesley SA, Wilson IA, Giedroc DP, Derewenda ZS. Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains. Acta Crystallogr D Biol Crystallogr 2009; 65:356-65. [PMID: 19307717 PMCID: PMC2659884 DOI: 10.1107/s0907444909004727] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 02/09/2009] [Indexed: 11/10/2022]
Abstract
The GntR superfamily of dimeric transcription factors, with more than 6200 members encoded in bacterial genomes, are characterized by N-terminal winged-helix DNA-binding domains and diverse C-terminal regulatory domains which provide a basis for the classification of the constituent families. The largest of these families, FadR, contains nearly 3000 proteins with all-alpha-helical regulatory domains classified into two related Pfam families: FadR_C and FCD. Only two crystal structures of FadR-family members, those of Escherichia coli FadR protein and LldR from Corynebacterium glutamicum, have been described to date in the literature. Here, the crystal structure of TM0439, a GntR regulator with an FCD domain found in the Thermotoga maritima genome, is described. The FCD domain is similar to that of the LldR regulator and contains a buried metal-binding site. Using atomic absorption spectroscopy and Trp fluorescence, it is shown that the recombinant protein contains bound Ni(2+) ions but that it is able to bind Zn(2+) with K(d) < 70 nM. It is concluded that Zn(2+) is the likely physiological metal and that it may perform either structural or regulatory roles or both. Finally, the TM0439 structure is compared with two other FadR-family structures recently deposited by structural genomics consortia. The results call for a revision in the classification of the FadR family of transcription factors.
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Affiliation(s)
- Meiying Zheng
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - David R. Cooper
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | | | - Minmin Yu
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
| | - Li-Wei Hung
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS4R0230, Berkeley, CA 94720, USA
- Physics Division, MS D454, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Marcin Cieslik
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Urszula Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
| | - Scott A. Lesley
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ian A. Wilson
- The Scripps Research Institute, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, USA
| | - Zygmunt S. Derewenda
- Integrated Center for Structure–Function Innovation, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
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Ethayathulla AS, Bessho Y, Shinkai A, Padmanabhan B, Singh TP, Kaur P, Yokoyama S. Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:498-500. [PMID: 18540059 PMCID: PMC2496867 DOI: 10.1107/s1744309108013778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2007] [Accepted: 05/08/2008] [Indexed: 12/19/2022]
Abstract
Adenosine triphosphate (ATP) binding cassette transporters (ABC transporters) are ATP hydrolysis-dependent transmembrane transporters. Here, the overproduction, purification and crystallization of the putative ABC transporter ATP-binding protein TM0222 from Thermotoga maritima are reported. The protein was crystallized in the hexagonal space group P6(4)22, with unit-cell parameters a = b = 148.49, c = 106.96 A, gamma = 120.0 degrees . Assuming the presence of two molecules in the asymmetric unit, the calculated V(M) is 2.84 A(3) Da(-1), which corresponds to a solvent content of 56.6%. A three-wavelength MAD data set was collected to 2.3 A resolution from SeMet-substituted TM0222 crystals. Data sets were collected on the BL38B1 beamline at SPring-8, Japan.
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Affiliation(s)
- Abdul S. Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India
| | - Yoshitaka Bessho
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Akeo Shinkai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Balasundaram Padmanabhan
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Tej P. Singh
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India
| | - Shigeyuki Yokoyama
- Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Barbey C, Rouhier N, Haouz A, Navaza A, Jacquot JP. Overproduction, purification, crystallization and preliminary X-ray analysis of the peroxiredoxin domain of a larger natural hybrid protein from Thermotoga maritima. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:29-31. [PMID: 18097097 PMCID: PMC2374002 DOI: 10.1107/s1744309107064391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 11/29/2007] [Indexed: 11/10/2022]
Abstract
Thermotoga maritima contains a natural hybrid protein constituted of two moieties: a peroxiredoxin domain at the N-terminus and a nitroreductase domain at the C-terminus. The peroxiredoxin (Prx) domain has been overproduced and purified from Escherichia coli cells. The recombinant Prx domain, which is homologous to bacterial Prx BCP and plant Prx Q, folds properly into a stable protein that possesses biological activity. The recombinant protein was crystallized and synchrotron data were collected to 2.9 A resolution. The crystals belonged to the tetragonal space group I422, with unit-cell parameters a = b = 176.67, c = 141.20 A.
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Affiliation(s)
- Carole Barbey
- Laboratoire de Biophysique Moléculaire, Cellulaire et Tissulaire, UMR 7033, Université Paris 13, UFR SMBH, 74 Rue Marcel Cachin, 93017 Bobigny Cedex, France.
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Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins 2007; 68:418-24. [PMID: 17444523 DOI: 10.1002/prot.21436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Huang S, Romanchuk G, Pattridge K, Lesley SA, Wilson IA, Matthews RG, Ludwig M. Reactivation of methionine synthase from Thermotoga maritima (TM0268) requires the downstream gene product TM0269. Protein Sci 2007; 16:1588-95. [PMID: 17656578 PMCID: PMC2203375 DOI: 10.1110/ps.072936307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome-wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin-dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, which shows sequence homology with the first three modules of E. coli MetH. The fourth module of E. coli MetH is required for reductive remethylation of the cob(II)alamin form of the cofactor and binds the methyl donor for this reactivation, S-adenosylmethionine (AdoMet). Measurements of the rates of methionine formation in the presence and absence of TM0269 and AdoMet demonstrate that both TM0269 and AdoMet are required for reactivation of the inactive cob(II)alamin form of TM0268. These activity measurements confirm the structure-based assignment of the function of the TM0269 gene product. In the presence of TM0269, AdoMet, and reductants, the measured activity of T. maritima MetH is maximal near 80 degrees C, where the specific activity of the purified protein is approximately 15% of that of E. coli methionine synthase (MetH) at 37 degrees C. Comparisons of the structures and sequences of TM0269 and the reactivation domain of E. coli MetH suggest that AdoMet may be bound somewhat differently by the homologous proteins. However, the conformation of a hairpin that is critical for cobalamin binding in E. coli MetH, which constitutes an essential structural element, is retained in the T. maritima reactivation protein despite striking divergence of the sequences.
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Affiliation(s)
- Sha Huang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
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Danciulescu C, Ladenstein R, Nilsson L. Dynamic Arrangement of Ion Pairs and Individual Contributions to the Thermal Stability of the Cofactor-Binding Domain of Glutamate Dehydrogenase from Thermotoga maritima. Biochemistry 2007; 46:8537-49. [PMID: 17602502 DOI: 10.1021/bi7004398] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of a hyperthermophilic protein fragment in a water environment, as studied by performing molecular dynamics (MD) simulations at various temperatures, is compared to the dynamical behavior of a homologous mesophilic protein simulated under identical conditions. The effects on the stability of the spatial arrangement and mobility of the charged residues in solution were quantified by calculating free energy changes upon salt bridge formation in these proteins. Electrostatic free energy terms derived from a thermodynamic cycle were obtained by solving the linearized Poisson-Boltzmann equation for a series of protein conformations generated by MD simulations and placed subsequently in a continuum solvent medium. Our results show that the ion pairs are electrostatically stabilizing in most of the cases, but their individual contributions vary significantly. The greater contribution of the charged residues to the stability of the hyperthermophilic protein as compared with the mesophilic counterpart was evidenced only by the calculations that included conformations sampled at 343 and 373 K. The "dynamic" structure of the hyperthermophilic protein fragment simulated at elevated temperatures reveals an optimum placement of the ionizable residues within the protein structure as well as the role of their cooperative interactions in promoting thermal stability. The thermodynamic properties such as electrostatic free energy differences, configurational entropies, and specific heat capacities calculated in the dynamic context of the protein structure provided new insight into the mechanism of protein thermostabilization.
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Affiliation(s)
- Cristian Danciulescu
- Department of Biosciences and Nutrition, Karolinska Institutet, S-141 57 Huddinge, Sweden
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39
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Weekes D, Miller MD, Krishna SS, McMullan D, McPhillips TM, Acosta C, Canaves JM, Elsliger MA, Floyd R, Grzechnik SK, Jaroszewski L, Klock HE, Koesema E, Kovarik JS, Kreusch A, Morse AT, Quijano K, Spraggon G, van den Bedem H, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of a transcription regulator (TM1602) from Thermotoga maritima at 2.3 A resolution. Proteins 2007; 67:247-52. [PMID: 17256761 DOI: 10.1002/prot.21221] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Casino P, Fernández-Alvarez A, Alfonso C, Rivas G, Marina A. Identification of a novel two component system in Thermotoga maritima. Complex stoichiometry and crystallization. Biochim Biophys Acta 2007; 1774:603-9. [PMID: 17478132 DOI: 10.1016/j.bbapap.2007.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Revised: 02/06/2007] [Accepted: 02/12/2007] [Indexed: 11/25/2022]
Abstract
Two-component signal transduction systems, comprised of histidine kinase and its cognate response regulator, are the predominant mechanism by which microorganisms sense and respond to changes in many different environmental conditions. Different Thermotoga maritima histidine kinases have been used as prototypes; among them, the orphan TM0853 has been presented as a structural model of class I histidine kinases. We used phosphotransfer assays to identify TM0468 as the partner response regulator of TM0853. Since full-length TM0853 can be produced as a soluble protein in Escherichia coli, it was used to analyze the union stoichiometry in an intact two-component system for the first time. We demonstrate that TM0853, or its cytoplasmic catalytic portion, form a 1:1 complex with TM0468 with native PAGE. The complex band is unique, even in the presence of an excess of each individual protein, indicating that the union is cooperative. We corroborated these findings by using ultracentrifugation assays. Therefore, we propose that the general mode of interaction in an orthodox two-component system may be the stoichiometric and cooperative complex between a dimeric histidine kinase and two response regulators. Finally, we have been able to produce protein crystals of the complex between the cytoplasmic portion of TM0853 and TM0468 that diffract to 2.8 A Bragg spacing.
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Affiliation(s)
- Patricia Casino
- Departamento de Genómica y Proteómica, Instituto de Biomedicina de Valencia (CSIC), Jaume Roig 11, 46010, Valencia, Spain
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41
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Xu Q, Krishna SS, McMullan D, Schwarzenbacher R, Miller MD, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rife CL, Spraggon G, Stevens RC, van den Bedem H, White A, Wolf G, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p. Proteins 2007; 65:777-82. [PMID: 16948158 DOI: 10.1002/prot.21015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Salomo M, Keyser UF, Kegler K, Gutsche C, Struhalla M, Immisch C, Hahn U, Kremer F. Kinetics of TmHU binding to DNA as observed by optical tweezers. Microsc Res Tech 2007; 70:938-43. [PMID: 17661366 DOI: 10.1002/jemt.20498] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The kinetics of binding for the histone-like protein TmHU (from Thermotoga maritima) to DNA is analyzed on a single molecule level by use of optical tweezers. For the reaction rate a pronounced concentration-dependence is found with an "all or nothing"-limit which suggests the cooperative nature of the binding-reaction. By analyzing the statistics of mechanically induced dissociation-events of TmHU from DNA multiple reaction sites are observed to become more likely with increasing TmHU concentration. This is interpreted as a hint for a secondary organizational level of the TmHU/DNA complex. The reaction rate of TmHU binding to DNA is remarkably higher than that of the HU protein from Escherichia coli which will be discussed.
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Affiliation(s)
- Mathias Salomo
- Faculty of Experimental Physics 1, University of Leipzig, Linnèstrasse 5, D-04103 Leipzig, Germany.
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Gloster TM, Roberts S, Perugino G, Rossi M, Moracci M, Panday N, Terinek M, Vasella A, Davies GJ. Structural, Kinetic, and Thermodynamic Analysis of Glucoimidazole-Derived Glycosidase Inhibitors†,‡. Biochemistry 2006; 45:11879-84. [PMID: 17002288 DOI: 10.1021/bi060973x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inhibition of glycosidases has great potential in the quest for highly potent and specific drugs to treat diseases such as diabetes, cancer, and viral infections. One of the most effective ways of designing such compounds is by mimicking the transition state. Here we describe the structural, kinetic, and thermodynamic dissection of binding of two glucoimidazole-derived compounds, which are among the most potent glycosidase inhibitors reported to date, with two family 1 beta-glycosidases. Provocatively, while inclusion of the phenethyl moiety improves binding by a factor of 20-80-fold, this does not appear to result from better noncovalent interactions with the enzyme; instead, improved affinity may be derived from significantly better entropic contributions to binding displayed by the phenethyl-substituted imidazole compound.
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Affiliation(s)
- Tracey M Gloster
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom
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Han GW, Sri Krishna S, Schwarzenbacher R, McMullan D, Ginalski K, Elsliger MA, Brittain SM, Abdubek P, Agarwalla S, Ambing E, Astakhova T, Axelrod H, Canaves JM, Chiu HJ, DiDonato M, Grzechnik SK, Hale J, Hampton E, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kreusch A, Kuhn P, Miller MD, Morse AT, Moy K, Nigoghossian E, Oommachen S, Ouyang J, Paulsen J, Quijano K, Reyes R, Rife C, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Wang X, West B, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution. Proteins 2006; 64:1083-90. [PMID: 16779835 DOI: 10.1002/prot.20950] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gye Won Han
- Joint Center for Structural Genomics, La Jolla, CA 92037, USA
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Yamada S, Akiyama S, Sugimoto H, Kumita H, Ito K, Fujisawa T, Nakamura H, Shiro Y. The Signaling Pathway in Histidine Kinase and the Response Regulator Complex Revealed by X-ray Crystallography and Solution Scattering. J Mol Biol 2006; 362:123-39. [PMID: 16890956 DOI: 10.1016/j.jmb.2006.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 07/05/2006] [Accepted: 07/06/2006] [Indexed: 11/16/2022]
Abstract
The structure of a histidine kinase (ThkA) complexed with a response regulator (TrrA) in the two-component regulatory system from hyperthermophile Thermotoga maritima was determined by a combination of X-ray crystallography at a resolution of 4.2 A and small-angle X-ray scattering (SAXS). The boundary of the three component domains (PAS-sensor, dimerization and catalytic domains) of ThkA and the bound TrrA molecule were unambiguously assigned in the electron density map at 4.2 A resolution. ThkA forms a dimer with crystallographic 2-fold symmetry and two monomeric TrrAs bind to the ThkA dimer. SAXS experiments also confirmed this association state in solution and specific binding between ThkA and TrrA (Kd=8.2x10(-11) M(-2)). The association interface between ThkA and TrrA contains the phosphotransfer His residue in the ThkA, indicative of an efficient receipt of the phosphoryl group. One Per-Arnt-Sim (PAS) domain does not interact with the other PAS domain, but with the catalytic domain of the same polypeptide chain and with one TrrA molecule. Observed inter-domain and inter-molecular interactions reveal a definite pathway of signal transduction in the kinase/regulator complex. In addition, we propose a responsible role of TrrA for the feedback regulation of sensing and/or kinase activities of ThkA.
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Affiliation(s)
- Seiji Yamada
- Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Hyogo 679-5148, Japan
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Eshaghi S, Niegowski D, Kohl A, Martinez Molina D, Lesley SA, Nordlund P. Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution. Science 2006; 313:354-7. [PMID: 16857941 DOI: 10.1126/science.1127121] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.
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Affiliation(s)
- Said Eshaghi
- Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden.
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de Lorimier RM, Tian Y, Hellinga HW. Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins. Protein Sci 2006; 15:1936-44. [PMID: 16823040 PMCID: PMC2242582 DOI: 10.1110/ps.062261606] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Development of biosensor devices typically requires incorporation of the molecular recognition element into a solid surface for interfacing with a signal detector. One approach is to immobilize the signal transducing protein directly on a solid surface. Here we compare the effects of two direct immobilization methods on ligand binding, kinetics, and signal transduction of reagentless fluorescent biosensors based on engineered periplasmic binding proteins. We used thermostable ribose and glucose binding proteins cloned from Thermoanaerobacter tengcongensis and Thermotoga maritima, respectively. To test the behavior of these proteins in semispecifically oriented layers, we covalently modified lysine residues with biotin or sulfhydryl functions, and attached the conjugates to plastic surfaces derivatized with streptavidin or maleimide, respectively. The immobilized proteins retained ligand binding and signal transduction but with adversely affected affinities and signal amplitudes for the thiolated, but not the biotinylated, proteins. We also immobilized these proteins in a more specifically oriented layer to maleimide-derivatized plates using a His(2)Cys(2) zinc finger domain fused at either their N or C termini. Proteins immobilized this way either retained, or displayed enhanced, ligand affinity and signal amplitude. In all cases tested ligand binding by immobilized proteins is reversible, as demonstrated by several iterations of ligand loading and elution. The kinetics of ligand exchange with the immobilized proteins are on the order of seconds.
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Affiliation(s)
- Robert M de Lorimier
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA
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Page R, Deacon AM, Lesley SA, Stevens RC. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins. ACTA ACUST UNITED AC 2006; 6:209-17. [PMID: 16211521 DOI: 10.1007/s10969-005-1916-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Accepted: 01/16/2005] [Indexed: 11/27/2022]
Abstract
Currently, 119 high resolution structures of Thermotoga maritima proteins have been determined by the Joint Center for Structural Genomics (JCSG, www.jcsg.org). Sixty-seven of these were solved using the first implementation of the multi-tiered crystallization strategy at the JCSG for the efficient crystallization of large numbers of protein targets. Previously, we reported the analysis of all proteins crystallized using this multi-tiered strategy [Lesley, S.A. et al. (2002) Proc. Natl. Acad. Sci. USA 99, 11664-11669; Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028-1037]. Here, we extend the analysis and describe the crystallization characteristics of those proteins that produced diffraction quality crystals, ultimately resulting in high resolution structures. First, we found that over 77% (52) of the crystals used for structure determination were produced directly from high-throughput coarse screens, indicating that less than one quarter of the crystals (15) required fine screening. In addition, as observed for the proteome screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028-1037], the majority of conditions that produced crystals for natively expressed proteins, whose structures have been determined, were distinct from those of their more extensively purified and selenomethionine-labeled counterparts. Finally, 99% of the proteins whose structures were solved crystallized in conditions contained in the JCSG Minimal Core Screen [Page, R. et al. (2003) Acta Crystallogr. D Biol. Crystallogr. 59, 1028-1037; Page, R. and Stevens, R.C. (2004) Methods 34, 373-389], a set of 67 conditions previously identified as those most likely to produce crystals of a diverse set of proteins, confirming its success for rapid identification of proteins with a natural propensity to crystallize.
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Columbus L, Peti W, Etezady-Esfarjani T, Herrmann T, Wüthrich K. NMR structure determination of the conserved hypothetical protein TM1816 from Thermotoga maritima. Proteins 2006; 60:552-7. [PMID: 15937903 DOI: 10.1002/prot.20465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Linda Columbus
- Joint Center of Structural Genomics and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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Duguet M, Serre MC, Bouthier de La Tour C. A universal type IA topoisomerase fold. J Mol Biol 2006; 359:805-12. [PMID: 16647715 DOI: 10.1016/j.jmb.2006.04.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2006] [Revised: 04/05/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
A class of enzymes, called DNA topoisomerases, is responsible for controlling the topological state of cellular DNA. Among these, type IA topoisomerases form a vast family that is present in all living organisms, including higher eukaryotes, in which they play important roles in genome stability. The known 3D structures of three of these enzymes indicate that they share a common toroidal architecture. We previously showed that the toroidal structure could be split off from the core enzyme of Thermotoga maritima topoisomerase I by limited proteolysis. This structure is produced by the association of two tandemly repeated elementary folds in a head-to-tail orientation. By using a combination of structural and sequence data analysis, we show that the elementary fold of about 150 amino acid residues, referred to as the topofold, is likely to be present in the whole topoisomerase IA family. Within each enzyme, the successive topofolds share two conserved sequence motifs located at the base of the ring, and referred to as the MI and MII motifs. However, the overall sequences of the folds have largely diverged. By contrast, secondary and tertiary structures appear remarkably conserved. We suggest that this twofold repeat has evolved by gene duplication/fusion from an ancestral topofold.
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Affiliation(s)
- Michel Duguet
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, Université Paris-Sud, Unité Mixte de Recherche 8621, Centre National de la Recherche Scientifique, 91405 Orsay, France
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