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Counterbalance of Stability and Activity Observed for Thermostable Transaminase from Thermobaculum terrenum in the Presence of Organic Solvents. Catalysts 2020. [DOI: 10.3390/catal10091024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pyridoxal-5’-phosphate-dependent transaminases catalyze stereoselective amination of organic compounds and are highly important for industrial applications. Catalysis by transaminases often requires organic solvents to increase the solubility of reactants. However, natural transaminases are prone to inactivation in the presence of water-miscible organic solvents. Here, we present the solvent tolerant thermostable transaminase from Thermobaculum terrenum (TaTT) that catalyzes transamination between L-leucine and alpha-ketoglutarate with an optimum at 75 °C and increases the activity ~1.8-fold upon addition of 15% dimethyl sulfoxide or 15% methanol at high but suboptimal temperature, 50 °C. The enhancement of the activity correlates with a decrease in the thermal denaturation midpoint temperature. The blue-shift of tryptophan fluorescence suggested that solvent molecules penetrate the hydration shell of the enzyme. Analysis of hydrogen bonds in the TaTT dimer revealed a high number of salt bridges and surface hydrogen bonds formed by backbone atoms. The latter are sensitive to the presence of organic solvents; they rearrange, conferring the relaxation of some constraints inherent to a thermostable enzyme at low temperatures. Our data support the idea that the counterbalance of stability and activity is crucial for the catalysis under given conditions; the obtained results may be useful for fine-tuning biocatalyst efficiency.
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Affiliation(s)
- Toshiyuki Itoh
- Department
of Chemistry and Biotechnology, Graduate School of Engineering and ‡Center for Research
on Green Sustainable Chemistry, Tottori University, 4-101 Koyama-minami, Tottori 680-8552, Japan
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Nordwald EM, Plaks JG, Snell JR, Sousa MC, Kaar JL. Crystallographic Investigation of Imidazolium Ionic Liquid Effects on Enzyme Structure. Chembiochem 2015; 16:2456-9. [PMID: 26388426 DOI: 10.1002/cbic.201500398] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 01/11/2023]
Abstract
We present the first crystallographic insight into the interactions of an ionic liquid (IL) with an enzyme, which has widespread implications for stabilizing enzymes in IL media for biocatalysis. Structures of Bacillus subtilis lipase A (lipA) and an IL-stable variant (QM-lipA) were obtained in the presence of increasing concentrations of 1-butyl-3-methylimidazolium chloride ([BMIM][Cl]). These studies revealed that the [BMIM] cation interacts with surface residues through hydrophobic and cation-π interactions. Of specific interest was the disruption of internal stacking interactions of aromatic side chains by [BMIM], which provides structural evidence for the mechanism of enzyme denaturation by ILs. The interaction of [BMIM] and Cl ions with lipA was reduced by the stabilizing mutations Y49E and G158E in QM-lipA. Ultimately, these findings present the molecular basis for stabilizing enzymes from IL-induced inactivation, as well as the selection of ILs that are less denaturing.
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Affiliation(s)
- Erik M Nordwald
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Jared R Snell
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA
| | - Marcelo C Sousa
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, CO, 80309, USA.
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Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Shibazaki C, Shimizu R, Yamada M, Adachi M, Tamada T, Kawamoto M, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R. Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:541-54. [PMID: 25760604 PMCID: PMC4356365 DOI: 10.1107/s1399004714027734] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/19/2014] [Indexed: 11/17/2022]
Abstract
Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+). The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P31 using X-ray crystallography. Moreover, the locations of bound Sr(2+) and Cs(+) ions were identified by anomalous X-ray diffraction. The location of one Cs(+)-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na(+) (90 mM Na(+)/10 mM Cs(+)). From an activity assay using isothermal titration calorimetry, the bound Sr(2+) and Cs(+) ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs(+)-binding site provides important information that is useful for the design of artificial Cs(+)-binding sites that may be useful in the bioremediation of radioactive isotopes.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Yasushi Yonezawa
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Nobuo Okazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Fumiko Matsumoto
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Chie Shibazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Rumi Shimizu
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Mitsugu Yamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Masahide Kawamoto
- Saga Prefectural Regional Industry Support Center, Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005, Japan
| | - Hiroko Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Matsujiro Ishibashi
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Michael Blaber
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
- College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300, USA
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ryota Kuroki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
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Cianci M, Negroni J, Helliwell JR, Halling PJ. Extensive counter-ion interactions seen at the surface of subtilisin in an aqueous medium. RSC Adv 2014. [DOI: 10.1039/c4ra06448h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The extent of counter-ion interaction within subtilisin in aqueous medium has been investigated using CsCl soak and anomalous diffraction, revealing that in aqueous salt solutions ions can bind at defined points around the protein surface.
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Affiliation(s)
- Michele Cianci
- European Molecular Biology Laboratory c/o DESY
- 22603 Hamburg, Germany
| | - Jacopo Negroni
- European Molecular Biology Laboratory c/o DESY
- 22603 Hamburg, Germany
| | | | - Peter J. Halling
- WestCHEM
- Department of P & A Chemistry
- University of Strathclyde
- Glasgow G1 1XL, UK
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The putative propeptide of MycP1 in mycobacterial type VII secretion system does not inhibit protease activity but improves protein stability. Protein Cell 2013; 4:921-31. [PMID: 24248472 DOI: 10.1007/s13238-013-3089-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022] Open
Abstract
Mycosin-1 protease (MycP1) is a serine protease anchored to the inner membrane of Mycobacterium tuberculosis, and is essential in virulence factor secretion through the ESX-1 type VII secretion system (T7SS). Bacterial physiology studies demonstrated that MycP1 plays a dual role in the regulation of ESX-1 secretion and virulence, primarily through cleavage of its secretion substrate EspB. MycP1 contains a putative N-terminal inhibitory propeptide and a catalytic triad of Asp-His-Ser, classic hallmarks of a subtilase family serine protease. The MycP1 propeptide was previously reported to be initially inactive and activated after prolonged incubation. In this study, we have determined crystal structures of MycP1 with (MycP1²⁴⁻⁴²²) and without (MycP1⁶³⁻⁴²²) the propeptide, and conducted EspB cleavage assays using the two proteins. Very high structural similarity was observed in the two crystal structures. Interestingly, protease assays demonstrated positive EspB cleavage for both proteins, indicating that the putative propeptide does not inhibit protease activity. Molecular dynamic simulations showed higher rigidity in regions guarding the entrance to the catalytic site in MycP1²⁴⁻⁴²² than in MycP1⁶³⁻⁴²², suggesting that the putative propeptide might contribute to the conformational stability of the active site cleft and surrounding regions.
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Liu J, Cukier RI, Bu Y. Bending Vibration-Governed Solvation Dynamics of an Excess Electron in Liquid Acetonitrile Revealed by Ab Initio Molecular Dynamics Simulation. J Chem Theory Comput 2013; 9:4727-34. [DOI: 10.1021/ct4002174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jinxiang Liu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100 Shandong, P. R. China
| | - Robert I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, 48824 Michigan, United States
| | - Yuxiang Bu
- School
of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100 Shandong, P. R. China
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9
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Lousa D, Cianci M, Helliwell JR, Halling PJ, Baptista AM, Soares CM. Interaction of Counterions with Subtilisin in Acetonitrile: Insights from Molecular Dynamics Simulations. J Phys Chem B 2012; 116:5838-48. [DOI: 10.1021/jp303008g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diana Lousa
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Michele Cianci
- European Molecular
Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestraße 85, 22603 Hamburg, Germany
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Peter J. Halling
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Cláudio M. Soares
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
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