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Chavez J, Ceresa L, Kimball J, Kitchner E, Gryczynski Z, Gryczynski I. Room temperature luminescence of 5-chloroindole. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Guðmundsson KE, Marteinsdóttir G, Kristbergsson K, Kvaran Á. Melatonin photoreactivity: phosphorescence formation and quenching processes. CHEMICAL PAPERS 2022. [DOI: 10.1007/s11696-022-02222-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractStudies of melatonin photoreactivity in water solutions: An effect of an external heavy atom I− on UV/Vis absorption, fluorescence and phosphorescence spectra is explored. The data allowed determination of relevant energetics for the system.The heavy atom effect (HAE) of I− on melatonin is clearly found to induce an intersystem crossing from the lowest energy singlet state to the lowest energy triplet state (T1) by a state mixing. Lifetime for the first excited triplet states of melatonin in association with I− and quenching rates for halomethanes (CH2X2, CHX3, CY4, X = Cl, Br, Y = Cl) are determined from Time-Correlated Single-Photon Counting decay curves for the phosphorescence. Dramatic alterations in quenching rate constants with quenchers as CH2X2 < CHX3 < CX4 and Cl < Br are attributed to energy transfer from an I−…Me*(T1) complex to low-lying electronic states of the halomethanes followed by dissociation to form R and X fragments. Relevance of the melatonin photoreactivity to photosensitizer properties in organic media is discussed.
Graphical abstract
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3
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Wu M, Lv K, Li J, Wu B, He B. Coevolutionary analysis reveals a distal amino acid residue pair affecting the catalytic activity of GH5 processive endoglucanase from Bacillus subtilis BS-5. Biotechnol Bioeng 2022; 119:2105-2114. [PMID: 35438195 DOI: 10.1002/bit.28113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/06/2022]
Abstract
EG5C-1, processive endoglucanase from Bacillus subtilis, is a typical bifunctional cellulase with endoglucanase and exoglucanase activities. The engineering of processive endoglucanase focuses on the catalytic pocket or carbohydrate-binding module tailoring based on sequence/structure information. Herein, a computational strategy was applied to identify the desired mutants in the enzyme molecule by evolutionary coupling analysis; subsequently, four residue pairs were selected as evolutionary mutational hotspots. Based on iterative-saturation mutagenesis and subsequent enzymatic activity analysis, a superior mutant K51T/L93T was identified away from the active center. This variant had increased specific activity from 4170 U/µmol of wild-type (WT) to 5678 U/µmol towards CMC-Na and an increase towards the substrate Avicel from 320 U/µmol in WT to 521 U/µmol. In addition, kinetic measurements suggested that superior mutant K51T/L93T had a high substrate affinity (Km ) and a remarkable improvement in catalytic efficiency (kcat /Km ). Furthermore, molecular dynamics simulations revealed that the K51T/L93T mutation altered the spatial conformation at the active site cleft, enhancing the interaction frequency between active site residues and substrate, improving catalytic efficiency and substrate affinity. The current studies provided some perspectives on the effects of distal residue substitution, which might assist in the engineering of processive endoglucanase or other glycoside hydrolases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mujunqi Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Kemin Lv
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Jiahuang Li
- School of Biopharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- School of Pharmaceutical Sciences, Nanjing Tech University, 30 Puzhunan road, Nanjing, 211816, Jiangsu, China
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4
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Zhou M, Li Y. Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation. Chem Res Chin Univ 2022. [DOI: 10.1007/s40242-022-1433-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Chavez J, Ceresa L, Kitchner E, Kimball J, Shtoyko T, Fudala R, Borejdo J, Gryczynski Z, Gryczynski I. On the possibility of direct triplet state excitation of indole. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 208:111897. [PMID: 32447191 DOI: 10.1016/j.jphotobiol.2020.111897] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/26/2020] [Accepted: 05/13/2020] [Indexed: 11/18/2022]
Abstract
We studied the luminescence properties of indole in poly (vinyl alcohol) (PVA) film. The indole molecules are effectively immobilized in this polymer film and display both fluorescence and phosphorescence emission at room temperature. We noticed that the phosphorescence of indole in PVA film can be effectively excited at a longer wavelength than its typical singlet to triplet population route involving intersystem crossing. The maximum of the phosphorescence excitation is about 410 nm which corresponds to the energy of indole's triplet state. Interestingly, the phosphorescence anisotropy excited with the longer wavelength (405 nm) is positive and reaches a value of about 0.25 in contrast to the phosphorescence anisotropy excited within the indole singlet absorption spectrum (290 nm), which is negative. Very different temperature dependences have been observed for fluorescence and phosphorescence of indole in PVA film. While fluorescence depends minimally, the phosphorescence decreases with temperature dramatically. The fluorescence lifetime was measured to be a single component 4.78 ns while the intensity weighted average phosphorescence lifetime with 290 nm and 405 nm excitations were 6.57 and 5.62 ms, respectively. We believe that the possibility of the excitation of indole phosphorescence in the blue region of visible light and its high anisotropy opens a new avenue for future protein studies.
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Affiliation(s)
- Jose Chavez
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA
| | - Luca Ceresa
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA
| | - Emma Kitchner
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA.
| | - Tanya Shtoyko
- Department of Chemistry and Biochemistry, The University of Texas at Tyler, Tyler, TX 75799, USA
| | - Rafal Fudala
- Department of Microbiology, Immunology, and Genetics, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Julian Borejdo
- Department of Microbiology, Immunology, and Genetics, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX 76129, USA; Department of Microbiology, Immunology, and Genetics, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Ignacy Gryczynski
- Department of Microbiology, Immunology, and Genetics, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
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6
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Structural Characterization of an ACP from Thermotoga maritima: Insights into Hyperthermal Adaptation. Int J Mol Sci 2020; 21:ijms21072600. [PMID: 32283632 PMCID: PMC7178038 DOI: 10.3390/ijms21072600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 12/30/2022] Open
Abstract
Thermotoga maritima, a deep-branching hyperthermophilic bacterium, expresses an extraordinarily stable Thermotoga maritima acyl carrier protein (Tm-ACP) that functions as a carrier in the fatty acid synthesis system at near-boiling aqueous environments. Here, to understand the hyperthermal adaptation of Tm-ACP, we investigated the structure and dynamics of Tm-ACP by nuclear magnetic resonance (NMR) spectroscopy. The melting temperature of Tm-ACP (101.4 °C) far exceeds that of other ACPs, owing to extensive ionic interactions and tight hydrophobic packing. The D59 residue, which replaces Pro/Ser of other ACPs, mediates ionic clustering between helices III and IV. This creates a wide pocket entrance to facilitate the accommodation of long acyl chains required for hyperthermal adaptation of the T. maritima cell membrane. Tm-ACP is revealed to be the first ACP that harbor an amide proton hyperprotected against hydrogen/deuterium exchange for I15. The hydrophobic interactions mediated by I15 appear to be the key driving forces of the global folding process of Tm-ACP. Our findings provide insights into the structural basis of the hyperthermal adaptation of ACP, which might have allowed T. maritima to survive in hot ancient oceans.
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Wang X, Jing X, Deng Y, Nie Y, Xu F, Xu Y, Zhao YL, Hunt JF, Montelione GT, Szyperski T. Evolutionary coupling saturation mutagenesis: Coevolution-guided identification of distant sites influencing Bacillus naganoensis pullulanase activity. FEBS Lett 2019; 594:799-812. [PMID: 31665817 DOI: 10.1002/1873-3468.13652] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 01/20/2023]
Abstract
Pullulanases are well-known debranching enzymes hydrolyzing α-1,6-glycosidic linkages. To date, engineering of pullulanase is mainly focused on catalytic pocket or domain tailoring based on structure/sequence information. Saturation mutagenesis-involved directed evolution is, however, limited by the low number of mutational sites compatible with combinatorial libraries of feasible size. Using Bacillus naganoensis pullulanase as a target protein, here we introduce the 'evolutionary coupling saturation mutagenesis' (ECSM) approach: residue pair covariances are calculated to identify residues for saturation mutagenesis, focusing directed evolution on residue pairs playing important roles in natural evolution. Evolutionary coupling (EC) analysis identified seven residue pairs as evolutionary mutational hotspots. Subsequent saturation mutagenesis yielded variants with enhanced catalytic activity. The functional pairs apparently represent distant sites affecting enzyme activity.
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Affiliation(s)
- Xinye Wang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiaoran Jing
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yi Deng
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Fei Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, MOE-LSB & MOE-LSC, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, China
| | - John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Chemistry and Chemical Biology, and Center for Biotechnology and Integrative Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, NY, USA
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Julió Plana L, Nadra AD, Estrin DA, Luque FJ, Capece L. Thermal Stability of Globins: Implications of Flexibility and Heme Coordination Studied by Molecular Dynamics Simulations. J Chem Inf Model 2018; 59:441-452. [PMID: 30516994 DOI: 10.1021/acs.jcim.8b00840] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins are sensitive to temperature, and abrupt changes in the normal temperature conditions can have a profound impact on both structure and function, leading to protein unfolding. However, the adaptation of certain organisms to extreme conditions raises questions about the structural features that permit the structure and function of proteins to be preserved under these adverse conditions. To gain insight into the molecular basis of protein thermostability in the globin family, we have examined three representative examples: human neuroglobin, horse heart myoglobin, and Drosophila hemoglobin, which differ in their melting temperatures and coordination states of the heme iron in the absence of external ligands. In order to elucidate the possible mechanisms that govern the thermostability of these proteins, microsecond-scale classical molecular dynamics simulations were performed at different temperatures. Structural fluctuations and essential dynamics were analyzed, indicating that the flexibility of the CD region, which includes the two short C and D helixes and the connecting CD loop, is directly related to the thermostability. We observed that a larger inherent flexibility of the protein produces higher thermostability, probably concentrating the thermal fluctuations observed at high temperature in flexible regions, preventing unfolding. Globally, the results of this work improve our understanding of thermostability in the globin family.
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Affiliation(s)
- Laia Julió Plana
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - Alejandro D Nadra
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires , Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires/IQUIBICEN-CONICET , C1428EGA Buenos Aires , Argentina
| | - Dario A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
| | - F Javier Luque
- Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences , University of Barcelona , Campus Torribera , 08921 Santa Coloma de Gramenet , Spain.,Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB) , University of Barcelona , 08028 Barcelona , Spain
| | - Luciana Capece
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Universidad de Buenos Aires/Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE-CONICET) , C1428EGA Buenos Aires , Argentina
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9
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Emruzi Z, Aminzadeh S, Karkhane AA, Alikhajeh J, Haghbeen K, Gholami D. Improving the thermostability of Serratia marcescens B4A chitinase via G191V site-directed mutagenesis. Int J Biol Macromol 2018; 116:64-70. [PMID: 29733926 DOI: 10.1016/j.ijbiomac.2018.05.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/26/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
Abstract
Chitinases with high thermostability are important for many industrial and biotechnological applications. This study was conducted to enhance the stability of Serratia marcescens B4A chitinase by site directed mutagenesis of G191 V. Further characterization showed that the thermal stability of the mutant showed marked increase of about 5 and 15 fold at 50 and 60 °C respectively, while the optimum temperature and pH was retained. Kinetic analysis showed decreased Km and Vmax of the mutant in comparison with the wild type chitinase of about 1.3 and 3 fold, respectively. Based on structural prediction, it was speculated that this replacement shortened an important loop concomitant with the extension of adjacent β sheets. Accordingly, a higher thermostability of G191 V up to 90 °C supporting the decreased flexibility of unfolded state was also indicated. Finally, a practical proof of kinetic and thermal stabilization of chitinase was provided through decreased flexibility and entropic stabilization of its surface loops.
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Affiliation(s)
- Zeinab Emruzi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Saeed Aminzadeh
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran.
| | - Ali Asghar Karkhane
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Jahan Alikhajeh
- Departments of Physiology and Cellular Biophysics, Columbia University Medical Center, USA
| | - Kamahldin Haghbeen
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
| | - Dariush Gholami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran, Iran
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10
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Abstract
Using structure and sequence based analysis we can engineer proteins to increase their thermal stability.
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Affiliation(s)
- H. Pezeshgi Modarres
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - M. R. Mofrad
- Molecular Cell Biomechanics Laboratory
- Departments of Bioengineering and Mechanical Engineering
- University of California Berkeley
- Berkeley
- USA
| | - A. Sanati-Nezhad
- BioMEMS and Bioinspired Microfluidic Laboratory
- Department of Mechanical and Manufacturing Engineering
- University of Calgary
- Calgary
- Canada
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11
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Ng CA, Oehme DP, Kato Y, Tanokura M, Brownlee RTC. Binding of an RNA pol II Ligand to the WW Domain of Pin1 Using Molecular Dynamics Docking Simulations. J Chem Theory Comput 2015; 5:2886-97. [PMID: 26631800 DOI: 10.1021/ct900190n] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A novel docking protocol using a long, all atom molecular dynamics (MD) simulation, in an explicit solvent medium, without using any distance constraints is presented. This MD docking protocol is able to dock ligands, based on the C-terminal domain (CTD) of RNA polymerase II, into the tryptophan-tryptophan (WW) domain of Pin1. In this docking process, a significant loop-bending event occurs in order to encircle the ligand into its solvent exposed binding site, which cannot be simulated using current protocols. The simulations were validated structurally and energetically against an X-ray structure to confirm correct sampling of conformational space. Based on these simulations, and justification of the starting structure as a valid intermediate structure, a potential molecular basis for binding was predicted as well as confirming the key residues involved in the formation of the final strong and stable Pin1 WW domain-ligand complex.
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Affiliation(s)
- Chai Ann Ng
- Department of Chemistry, La Trobe University, VIC 3086, Australia, and Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Daniel P Oehme
- Department of Chemistry, La Trobe University, VIC 3086, Australia, and Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yusuke Kato
- Department of Chemistry, La Trobe University, VIC 3086, Australia, and Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Masaru Tanokura
- Department of Chemistry, La Trobe University, VIC 3086, Australia, and Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Robert T C Brownlee
- Department of Chemistry, La Trobe University, VIC 3086, Australia, and Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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12
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Boone CD, Rasi V, Tu C, McKenna R. Structural and catalytic effects of proline substitution and surface loop deletion in the extended active site of human carbonic anhydrase II. FEBS J 2015; 282:1445-57. [PMID: 25683338 PMCID: PMC4400229 DOI: 10.1111/febs.13232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 01/07/2023]
Abstract
UNLABELLED Bioengineering of a thermophilic enzyme starting from a mesophilic scaffold has proven to be a significant challenge, as several stabilizing elements have been proposed to be the foundation of thermal stability, including disulfide bridges, surface loop reduction, ionic pair networks, proline substitutions and aromatic clusters. This study emphasizes the effect of increasing the rigidity of human carbonic anhydrase II (HCA II; EC 4.2.1.1) via incorporation of proline residues at positions 170 and 234, which are located in surface loops that are able to accommodate restrictive main-chain conformations without rearrangement of the surrounding peptide backbone. Additionally, the effect of the compactness of HCA II was examined by deletion of a surface loop (residues 230-240) that had been previously identified as a possible source of thermal stability for the hyperthermophilic carbonic anhydrase isolated from the bacterium Sulfurihydrogenibium yellowstonense YO3AOP1. Differential scanning calorimetry analysis of these HCA II variants revealed that these structural modifications had a minimum effect on the thermal stability of the enzyme, while kinetic studies showed unexpected effects on the catalytic efficiency and proton transfer rates. X-ray crystallographic analysis of these HCA II variants showed that the electrostatic potential and configuration of the highly acidic loop (residues 230-240) play an important role in its high catalytic activity. Based on these observations and previous studies, a picture is emerging of the various components within the general structural architecture of HCA II that are key to stability. These elements may provide blueprints for rational thermal stability engineering of other enzymes. DATABASE Structural data have been submitted to the Protein Data Bank under accession numbers 4QK1 (K170P), 4QK2 (E234P) and 4QK3 (Δ230-240).
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Affiliation(s)
- Christopher D. Boone
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA
| | - Valerio Rasi
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA
| | - Chingkuang Tu
- Pharmacology & Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL, 32610, USA
| | - Robert McKenna
- Biochemistry & Molecular Biology, University of Florida, P.O. Box 100245, Gainesville, FL, 32610, USA,Corresponding author. FAX (352) 392-3422;
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Rawat S, Gupta P, Kumar A, Garg P, Suri CR, Sahoo DK. Molecular Mechanism of Poly(vinyl alcohol) Mediated Prevention of Aggregation and Stabilization of Insulin in Nanoparticles. Mol Pharm 2015; 12:1018-30. [DOI: 10.1021/mp5003653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sanjay Rawat
- CSIR−Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Pawan Gupta
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, Mohali 160062, India
| | - Anil Kumar
- CSIR−Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, Mohali 160062, India
| | - C. Raman Suri
- CSIR−Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Debendra K. Sahoo
- CSIR−Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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14
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Kowalska-Baron A, Gałęcki K, Wysocki S. Room temperature phosphorescence study on the structural flexibility of single tryptophan containing proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:380-387. [PMID: 25025310 DOI: 10.1016/j.saa.2014.06.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/28/2014] [Accepted: 06/21/2014] [Indexed: 06/03/2023]
Abstract
In this study, we have undertaken efforts to find correlation between phosphorescence lifetimes of single tryptophan containing proteins and some structural indicators of protein flexibility/rigidity, such as the degree of tryptophan burial or its exposure to solvent, protein secondary and tertiary structure of the region of localization of tryptophan as well as B factors for tryptophan residue and its immediate surroundings. Bearing in mind that, apart from effective local viscosity of the protein/solvent matrix, the other factor that concur in determining room temperature tryptophan phosphorescence (RTTP) lifetime in proteins is the extent of intramolecular quenching by His, Cys, Tyr and Trp side chains, the crystallographic structures derived from the Brookhaven Protein Data Bank were also analyzed concentrating on the presence of potentially quenching amino acid side chains in the close proximity of the indole chromophore. The obtained results indicated that, in most cases, the phosphorescence lifetimes of tryptophan containing proteins studied tend to correlate with the above mentioned structural indicators of protein rigidity/flexibility. This correlation is expected to provide guidelines for the future development of phosphorescence lifetime-based method for the prediction of structural flexibility of proteins, which is directly linked to their biological function.
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Affiliation(s)
- Agnieszka Kowalska-Baron
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, ul. Stefanowskiego 4/10, 90-924 Lodz, Poland.
| | - Krystian Gałęcki
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, ul. Stefanowskiego 4/10, 90-924 Lodz, Poland
| | - Stanisław Wysocki
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, ul. Stefanowskiego 4/10, 90-924 Lodz, Poland
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15
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Hegde K, Dasu VV. Structural Stability and Unfolding Properties of Cutinases from Thermobifida fusca. Appl Biochem Biotechnol 2014; 174:803-19. [DOI: 10.1007/s12010-014-1037-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/19/2014] [Indexed: 10/24/2022]
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16
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Autodisplay of an archaeal γ-lactamase on the cell surface of Escherichia coli using Xcc_Est as an anchoring scaffold and its application for preparation of the enantiopure antiviral drug intermediate (-) vince lactam. Appl Microbiol Biotechnol 2014; 98:6991-7001. [PMID: 24756321 DOI: 10.1007/s00253-014-5704-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/30/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
At present, autotransporter protein mediated surface display has opened a new dimension in the development of whole-cell biocatalysts. Here, we report the identification of a novel autotransporter Xcc_Est from Xanthomonas campestris pv campestris 8004 by bioinformatic analysis and application of Xcc_Est as an anchoring motif for surface display of γ-lactamase (Gla) from thermophilic archaeon Sulfolobus solfataricus P2 in Escherichia coli. The localization of γ-lactamase in the cell envelope was monitored by Western blot, activity assay and flow cytometry analysis. Either the full-length or truncated Xcc_Est could efficiently transport γ-lactamase to the cell surface. Compared with the free enzyme, the displayed γ-lactamase exhibited optimum temperature of 30 °C other than 90 °C, with a substantial decrease of 60 °C. Under the preparation system, the engineered E. coli with autodisplayed γ-lactamase converted 100 g racemic vince lactam to produce 49.2 g (-) vince lactam at 30 °C within 4 h. By using chiral HPLC, the ee value of the produced (-) vince lactam was determined to be 99.5 %. The whole-cell biocatalyst exhibited excellent stability under the operational conditions. Our results indicate that the E. coli with surface displayed γ-lactamase is an efficient and economical whole cell biocatalyst for preparing the antiviral drug intermediate (-) vince lactam at mild temperature, eliminating expensive energy cost performed at high temperature.
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Molecular basis of thermal stability in truncated (2/2) hemoglobins. Biochim Biophys Acta Gen Subj 2014; 1840:2281-8. [PMID: 24704259 DOI: 10.1016/j.bbagen.2014.03.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/14/2014] [Accepted: 03/25/2014] [Indexed: 11/23/2022]
Abstract
BACKGROUND Understanding the molecular mechanism through which proteins are functional at extreme high and low temperatures is one of the key issues in structural biology. To investigate this phenomenon, we have focused on two instructive truncated hemoglobins from Thermobifida fusca (Tf-trHbO) and Mycobacterium tuberculosis (Mt-trHbO); although the two proteins are structurally nearly identical, only the former is stable at high temperatures. METHODS We used molecular dynamics simulations at different temperatures as well as thermal melting profile measurements of both wild type proteins and two mutants designed to interchange the amino acid residue, either Pro or Gly, at E3 position. RESULTS The results show that the presence of a Pro at the E3 position is able to increase (by 8°) or decrease (by 4°) the melting temperature of Mt-trHbO and Tf-trHbO, respectively. We observed that the ProE3 alters the structure of the CD loop, making it more flexible. CONCLUSIONS This gain in flexibility allows the protein to concentrate its fluctuations in this single loop and avoid unfolding. The alternate conformations of the CD loop also favor the formation of more salt-bridge interactions, together augmenting the protein's thermostability. GENERAL SIGNIFICANCE These results indicate a clear structural and dynamical role of a key residue for thermal stability in truncated hemoglobins.
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Liang J, Corradini MG, Ludescher RD. Influence of antioxidant structure on local molecular mobility in amorphous sucrose. Carbohydr Res 2014; 383:14-20. [PMID: 24239605 DOI: 10.1016/j.carres.2013.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 10/16/2013] [Accepted: 10/19/2013] [Indexed: 11/27/2022]
Abstract
The effect of the antioxidants gallic acid and methyl, propyl, and octyl gallate on the molecular mobility and hydrogen bond network in amorphous sucrose was studied. Solid amorphous sucrose films with and without the addition of antioxidants at a mole ratio of 1:5 (antioxidant/sucrose) were cast from solution onto quartz slides. Local molecular mobility from 0 to 70°C was measured using tryptophan amino acid as a luminescent probe dispersed in the films. Phosphorescence from the tryptophan probe provides spectroscopic characteristics-emission spectrum and lifetime-that are sensitive to changes in molecular mobility induced by the addition of antioxidants. Local molecular mobility detected by tryptophan increased in the following order: sucrose<sucrose-octyl gallate<sucrose-propyl gallate⩽sucrose-methyl gallate⩽sucrose-gallic acid. The antioxidants also modulated the activation energy for matrix motions that quench the tryptophan phosphorescence in a structure-dependent manner. IR measurements as a function of temperature indicated that hydrogen bond strength in these amorphous films followed a rank order (sucrose-methyl gallate>sucrose-gallic acid>sucrose-propyl gallate>sucrose>sucrose-octyl gallate) that was nearly the reverse of that seen in matrix mobility. Analysis of the differential effects of the antioxidants suggests that the presence of the hydroxyl benzoyl head group increased matrix molecular mobility and hydrogen bond strength while the saturated carbon chain decreased mobility and bond strength. The influence of the carboxyl group on matrix properties was comparable to that of the formyloxy group. These results indicate that the addition of specific functional ingredients such as antioxidants may significantly affect the physical properties and consequently functional properties of amorphous edible films in ways that might condition their use. The observed changes are closely related to the chemical structure of the added species.
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Affiliation(s)
- Jun Liang
- Department of Food Science, Rutgers, The State University of New Jersey, 65 Dudley Road, New Brunswick, NJ 08901, United States
| | - Maria G Corradini
- Department of Food Science, Rutgers, The State University of New Jersey, 65 Dudley Road, New Brunswick, NJ 08901, United States
| | - Richard D Ludescher
- Department of Food Science, Rutgers, The State University of New Jersey, 65 Dudley Road, New Brunswick, NJ 08901, United States.
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Boone CD, Habibzadegan A, Tu C, Silverman DN, McKenna R. Structural and catalytic characterization of a thermally stable and acid-stable variant of human carbonic anhydrase II containing an engineered disulfide bond. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1414-22. [PMID: 23897465 PMCID: PMC3727326 DOI: 10.1107/s0907444913008743] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 03/30/2013] [Indexed: 11/10/2022]
Abstract
The carbonic anhydrases (CAs) are a family of mostly zinc metalloenzymes that catalyze the reversible hydration of CO2 to bicarbonate and a proton. Recently, there has been industrial interest in utilizing CAs as biocatalysts for carbon sequestration and biofuel production. The conditions used in these processes, however, result in high temperatures and acidic pH. This unfavorable environment results in rapid destabilization and loss of catalytic activity in CAs, ultimately resulting in cost-inefficient high-maintenance operation of the system. In order to negate these detrimental industrial conditions, cysteines at residues 23 (Ala23Cys) and 203 (Leu203Cys) were engineered into a wild-type variant of human CA II (HCAII) containing the mutation Cys206Ser. The X-ray crystallographic structure of the disulfide-containing HCAII (dsHCAII) was solved to 1.77 Å resolution and revealed that successful oxidation of the cysteine bond was achieved while also retaining desirable active-site geometry. Kinetic studies utilizing the measurement of (18)O-labeled CO2 by mass spectrometry revealed that dsHCAII retained high catalytic efficiency, and differential scanning calorimetry showed acid stability and thermal stability that was enhanced by up to 14 K compared with native HCAII. Together, these studies have shown that dsHCAII has properties that could be used in an industrial setting to help to lower costs and improve the overall reaction efficiency.
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Affiliation(s)
- Christopher D. Boone
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
| | - Andrew Habibzadegan
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
| | - Chingkuang Tu
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - David N. Silverman
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, PO Box 100245, Gainesville, FL 32610, USA
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20
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Lu X, Liu S, Feng Y, Rao S, Zhou X, Wang M, Du G, Chen J. Enhanced thermal stability of Pseudomonas aeruginosa lipoxygenase through modification of two highly flexible regions. Appl Microbiol Biotechnol 2013; 98:1663-9. [DOI: 10.1007/s00253-013-5039-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 01/20/2023]
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21
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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22
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Colletier JP, Aleksandrov A, Coquelle N, Mraihi S, Mendoza-Barbera E, Field M, Madern D. Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions. Mol Biol Evol 2012; 29:1683-94. [DOI: 10.1093/molbev/mss015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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23
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Kim SJ, Lee JA, Joo JC, Yoo YJ, Kim YH, Song BK. The development of a thermostable CiP (Coprinus cinereus peroxidase) through in silico design. Biotechnol Prog 2010; 26:1038-46. [PMID: 20730760 DOI: 10.1002/btpr.408] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein thermostability is a crucial issue in the practical application of enzymes, such as inorganic synthesis and enzymatic polymerization of phenol derivatives. Much attention has been focused on the enhancement and numerous successes have been achieved through protein engineering methods. Despite fruitful results based on random mutagenesis, it was still necessary to develop a novel strategy that can reduce the time and effort involved in this process. In this study, a rapid and effective strategy is described for increasing the thermal stability of a protein. Instead of random mutagenesis, a rational strategy was adopted to theoretically stabilize the thermo labile residues of a protein using computational methods. Protein residues with high flexibility can be thermo labile due to their large range of movement. Here, residue B factor values were used to identify putatively thermo labile residues and the RosettaDesign program was applied to search for stable sequences. Coprinus cinereus (CiP) heme peroxidase was selected as a model protein for its importance in commercial applications, such as the polymerization of phenolic compounds. Eleven CiP residues with the highest B factor values were chosen as target mutation sites for thermostabilization, and then redesigned using RosettaDesign to identify sequences. Eight mutants based on the redesigns, were produced as functional enzymes and two of these (S323Y and E328D) showed increased thermal stability over the wild-type in addition to conserved catalytic activity. Thus, this strategy can be used as a rapid and effective in silico design tool for obtaining thermostable proteins.
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Affiliation(s)
- Su Jin Kim
- Chemical Biotechnology Research Center, Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, Korea
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24
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Zhou HY, Pan HY, Rao LQ, Wu YY. Redesign the α/β fold to enhance the stability of mannanase Man23 from Bacillus subtilis. Appl Biochem Biotechnol 2010; 163:186-94. [PMID: 20640530 DOI: 10.1007/s12010-010-9027-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Accepted: 06/25/2010] [Indexed: 11/30/2022]
Abstract
In this work, we engineered the α/β fold of mannanase Man23 based on its molecular structure analysis to obtain more stable variants. By introducing 31 single-site mutations in the α/β fold and shuffling them, the incorporation of four mutations (K178R, K207R, N340R, and S354R) displayed a good balance between high activity and stability at higher temperature and broader pH. This quartet variant was characterized by an almost threefold increased activity and a sevenfold increased stability compared to native mannanase Man23. Our results suggest that such work is safe to increase our target protein stability with no loss of activity.
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Affiliation(s)
- Hai-Yan Zhou
- The Center of Analysis and Measurement, Hunan Agricultural University, Changsha, China
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25
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You C, Huang Q, Xue H, Xu Y, Lu H. Potential hydrophobic interaction between two cysteines in interior hydrophobic region improves thermostability of a family 11 xylanase fromNeocallimastix Patriciarum. Biotechnol Bioeng 2010; 105:861-70. [DOI: 10.1002/bit.22623] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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26
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Krishnamurthy H, Munro K, Yan H, Vieille C. Dynamics in Thermotoga neapolitana adenylate kinase: 15N relaxation and hydrogen-deuterium exchange studies of a hyperthermophilic enzyme highly active at 30 degrees C. Biochemistry 2009; 48:2723-39. [PMID: 19220019 DOI: 10.1021/bi802001w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Backbone conformational dynamics of Thermotoga neapolitana adenylate kinase in the free form (TNAK) and inhibitor-bound form (TNAK*Ap5A) were investigated at 30 degrees C using (15)N NMR relaxation measurements and NMR monitored hydrogen-deuterium exchange. With kinetic parameters identical to those of Escherichia coli AK (ECAK) at 30 degrees C, TNAK is a unique hyperthermophilic enzyme. These catalytic properties make TNAK an interesting and novel model to study the interplay between protein rigidity, stability, and activity. Comparison of fast time scale dynamics (picosecond to nanosecond) in the open and closed states of TNAK and ECAK at 30 degrees C reveals a uniformly higher rigidity across all domains of TNAK. Within this framework of a rigid TNAK structure, several residues located in the AMP-binding domain and in the core-lid hinge regions display high picosecond to nanosecond time scale flexibility. Together with the recent comparison of ECAK dynamics with those of hyperthermophilic Aquifex aeolicus AK (AAAK), our results provide strong evidence for the role of picosecond to nanosecond time scale fluctuations in both stability and activity. In the slow time scales, TNAK's increased rigidity is not uniform but localized in the AMP-binding and lid domains. The core domain amides of ECAK and TNAK in the open and closed states show comparable protection against exchange. Significantly, the hinges framing the lid domain show similar exchange data in ECAK and TNAK open and closed forms. Our NMR relaxation and hydrogen-deuterium exchange studies therefore suggest that TNAK maintains high activity at 30 degrees C by localizing flexibility to the hinge regions that are key to facilitating conformational changes.
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Affiliation(s)
- Harini Krishnamurthy
- Program in Cell and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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27
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Nonaka Y, Akieda D, Aizawa T, Watanabe N, Kamiya M, Kumaki Y, Mizuguchi M, Kikukawa T, Demura M, Kawano K. X-ray crystallography and structural stability of digestive lysozyme from cow stomach. FEBS J 2009; 276:2192-200. [DOI: 10.1111/j.1742-4658.2009.06948.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Lee CK, Daniel RM, Shepherd C, Saul D, Cary SC, Danson MJ, Eisenthal R, Peterson ME. Eurythermalism and the temperature dependence of enzyme activity. FASEB J 2007; 21:1934-41. [PMID: 17341686 DOI: 10.1096/fj.06-7265com] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The "Equilibrium Model" has provided new tools for describing and investigating enzyme thermal adaptation. It has been shown that the effect of temperature on enzyme activity is not only governed by deltaG(double dagger)(cat) and deltaG(double dagger)(inact) but also by two new intrinsic parameters, deltaH(eq) and T(eq), which describe the enthalpy and midpoint, respectively, of a reversible equilibrium between active and inactive (but not denatured) forms of enzyme. Twenty-one enzymes from organisms with a wide range of growth temperatures were characterized using the Equilibrium Model. Statistical analysis indicates that T(eq) is a better predictor of growth temperature than enzyme stability (deltaG(double dagger)(inact)). As expected from the Equilibrium Model, deltaH(eq) correlates with catalytic temperature tolerance of enzymes and thus can be declared the first intrinsic and quantitative measure of enzyme eurythermalism. Other findings shed light on the evolution of psychrophilic and thermophilic enzymes. The findings suggest that the description of the Equilibrium Model of the effect of temperature on enzyme activity applies to all enzymes regardless of their temperature origins and that its associated parameters, deltaH(eq) and T(eq), are intrinsic and necessary parameters for characterizing the thermal properties of enzymes and their temperature adaptation and evolution.
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Affiliation(s)
- Charles K Lee
- Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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29
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Acidic and proteolytic digestion of α-amylases from Bacillus licheniformis and Bacillus amyloliquefaciens: Stability and flexibility analysis. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Jayasinghe L, Miles G, Bayley H. Role of the amino latch of staphylococcal alpha-hemolysin in pore formation: a co-operative interaction between the N terminus and position 217. J Biol Chem 2005; 281:2195-204. [PMID: 16227199 DOI: 10.1074/jbc.m510841200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Staphylococcal alpha-hemolysin (alphaHL) is a beta barrel pore-forming toxin that is secreted by the bacterium as a water-soluble monomeric protein. Upon binding to susceptible cells, alphaHL assembles via an inactive prepore to form a water-filled homoheptameric transmembrane pore. The N terminus of alphaHL, which in the crystal structure of the fully assembled pore forms a latch between adjacent subunits, has been thought to play a vital role in the prepore to pore conversion. For example, the deletion of two N-terminal residues produced a completely inactive protein that was arrested in assembly at the prepore stage. In the present study, we have re-examined assembly with a comprehensive set of truncation mutants. Surprisingly, we found that after truncation of up to 17 amino acids, the ability of alphaHL to form functional pores was diminished, but still substantial. We then discovered that the mutation Ser(217) --> Asn, which was present in our original set of truncations but not in the new ones, promotes complete inactivation upon truncation of the N terminus. Therefore, the N terminus of alphaHL cannot be critical for the prepore to pore transformation as previously thought. Residue 217 is involved in the assembly process and must interact indirectly with the distant N terminus during the last step in pore formation. In addition, we provide evidence that an intact N terminus prevents the premature oligomerization of alphaHL monomers in solution.
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Affiliation(s)
- Lakmal Jayasinghe
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, United Kingdom
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31
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LeMaster DM, Tang J, Paredes DI, Hernández G. Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: Spatial propagation of differential flexibility in rubredoxin hybrids. Proteins 2005; 61:608-16. [PMID: 16130131 DOI: 10.1002/prot.20594] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The extreme thermal stability of proteins from hyperthermophilic organisms is widely believed to arise from an increased conformational rigidity in the native state. In apparent contrast to this paradigm, both Pyrococcus furiosus (Pf) rubredoxin, the most thermostable protein characterized to date, and its Clostridium pasteurianum (Cp) mesophile homolog undergo a transient conformational opening of their multi-turn segments, which is more favorable in hyperthermophile proteins below room temperature. Substitution of the hyperthermophile multi-turn sequence into the mesophile protein sequence yields a hybrid, (14-33(Pf)) Cp, that exhibits a 12 degrees increase in its reversible thermal unfolding transition midpoint. Nuclear magnetic resonance (NMR) magnetization transfer-based hydrogen exchange was used to monitor backbone conformational dynamics in the subsecond time regime. Despite the substantially increased thermostability, flexibility throughout the entire main chain of the more thermostable hybrid is equal to or greater than that of the wild type mesophile rubredoxin near its normal growth temperature. In comparison to the identical core residues of the (14-33(Pf)) Cp rubredoxin hybrid, six spatially clustered residues in the parental mesophile protein exhibit a substantially larger temperature dependence of exchange. The exchange behavior of these six residues closely matches that observed in the multi-turn segment, consistent with a more extensive conformational process. These six core residues exhibit a much weaker temperature dependence of exchange in the (14-33(Pf)) Cp hybrid, similar to that observed for the multi-turn segment in its parental Pf rubredoxin. These results suggest that differential temperature dependence of flexibility can underlie variations in thermostability observed for mesophile versus hyperthermophile homologs.
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Affiliation(s)
- David M LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, University at Albany- SUNY, 12201-0509, USA
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Sheng Y, Li S, Gou X, Kong X, Wang X, Sun Y, Zhang J. The hybrid enzymes from α-aspartyl dipeptidase and l-aspartase. Biochem Biophys Res Commun 2005; 331:107-12. [PMID: 15845365 DOI: 10.1016/j.bbrc.2005.03.140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2005] [Indexed: 10/25/2022]
Abstract
With combinative functionalities as well as the improved activity and stability, the novel hybrid enzymes (HEs) from the heterogeneous enzymes of alpha-aspartyl dipeptidase (PepE, monomer) and l-aspartase (l-AspA, tetramer) were constructed successfully by gene random deletion strategy. The wild-type hybrid enzyme (WHE) and the evolved hybrid enzyme (EHE) were selected, respectively, upon the phenotype and the enzyme activity. The relative activity of the WHE tested was about 110% of the wild-type PepE and 26% of the wild-type l-AspA, whilst the activity of EHE was about 340% of the PepE and 87% of the l-AspA. In comparison to its individual wild-type enzymes, the EHE exhibited an improved thermostability, when examined at the enzyme concentration of 10(-7)mol/L, but the WHE showed a reduced thermostability. The activity of the EHE was about 3-fold compared to that of the WHE. The current results give a good example that the hybridization of enzymes could be attained between the monomer and multimer enzymes. In addition, they also indicate that construction hybrid enzyme from evolved enzymes is feasible.
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Affiliation(s)
- Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, PR China
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Asghari SM, Khajeh K, Ranjbar B, Sajedi RH, Naderi-Manesh H. Comparative studies on trifluoroethanol (TFE) state of a thermophilic α-amylase and its mesophilic counterpart: limited proteolysis, conformational analysis, aggregation and reactivation of the enzymes. Int J Biol Macromol 2004; 34:173-9. [PMID: 15225989 DOI: 10.1016/j.ijbiomac.2004.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2004] [Indexed: 11/21/2022]
Abstract
Detailed circular dichroism (CD), scattering and quenching studies, 1-anilinonaphthalene-8-sulfonate (ANS) binding, irreversible thermoinactivation, activity measurements and proteolytic digestion of bacterial alpha-amylases have been carried out to elucidate the effect of trifluoroethanol (TFE) on the structure of these enzymes. Under high concentrations of TFE both of the alpha-amylases, a thermostable alpha-amylase from Bacillus licheniformis (BLA) and its mesophilic counterpart from Bacillus amyloliquefaciens (BAA), acquire partially folded state characterized by an enhanced content of the secondary structure (helix) and reduced tertiary structures. According to ANS binding studies, we suggest that the TFE states induced by TFE/water mixture are not the molten globule state in the alpha-amylase folding pathway. In addition, data shows significant reversible aggregation of both enzymes in TFE/water mixtures with concentration between 10 and 60% (v/v). However, reversibility is more in case of BAA. As expected, in the absence of TFE, the thermophilic enzyme compared to mesophilic enzyme, shows a greater resistance to digestion by thermolysin. With respect to fluorescence quenching by acrylamide and potassium iodide, the thermophilic enzyme, BLA, is characterized by higher structural flexibility as compared to the BAA. On the other hand, in the presence of TFE, the enzymes are digested by protease to produce large protein fragments. It is proposed that highly helical secondary structures, acquired by BAA and BLA when dissolved in aqueous TFE, prevent binding and adaptation of the protein substrate at the active site of the protease.
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Affiliation(s)
- S Mohsen Asghari
- Department of Biochemistry and Biophysics, Faculty of Science, Tarbiat Modarres University, P.O. Box 14115-175, Tehran, Iran
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Georlette D, Blaise V, Collins T, D'Amico S, Gratia E, Hoyoux A, Marx JC, Sonan G, Feller G, Gerday C. Some like it cold: biocatalysis at low temperatures. FEMS Microbiol Rev 2004; 28:25-42. [PMID: 14975528 DOI: 10.1016/j.femsre.2003.07.003] [Citation(s) in RCA: 249] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Revised: 07/17/2003] [Accepted: 07/28/2003] [Indexed: 11/21/2022] Open
Abstract
In the last few years, increased attention has been focused on a class of organisms called psychrophiles. These organisms, hosts of permanently cold habitats, often display metabolic fluxes more or less comparable to those exhibited by mesophilic organisms at moderate temperatures. Psychrophiles have evolved by producing, among other peculiarities, "cold-adapted" enzymes which have the properties to cope with the reduction of chemical reaction rates induced by low temperatures. Thermal compensation in these enzymes is reached, in most cases, through a high catalytic efficiency associated, however, with a low thermal stability. Thanks to recent advances provided by X-ray crystallography, structure modelling, protein engineering and biophysical studies, the adaptation strategies are beginning to be understood. The emerging picture suggests that psychrophilic enzymes are characterized by an improved flexibility of the structural components involved in the catalytic cycle, whereas other protein regions, if not implicated in catalysis, may be even more rigid than their mesophilic counterparts. Due to their attractive properties, i.e., a high specific activity and a low thermal stability, these enzymes constitute a tremendous potential for fundamental research and biotechnological applications.
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Affiliation(s)
- D Georlette
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, Liège B-4000, Belgium
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35
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Wintrode PL, Zhang D, Vaidehi N, Arnold FH, Goddard WA. Protein dynamics in a family of laboratory evolved thermophilic enzymes. J Mol Biol 2003; 327:745-57. [PMID: 12634066 DOI: 10.1016/s0022-2836(03)00147-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Molecular dynamics simulations were employed to study how protein solution structure and dynamics are affected by adaptation to high temperature. Simulations were carried out on a para-nitrobenzyl esterase (484 residues) and two thermostable variants that were generated by laboratory evolution. Although these variants display much higher melting temperatures than wild-type (up to 18 degrees C higher) they are both >97% identical in sequence to the wild-type. In simulations at 300 K the thermostable variants remain closer to their crystal structures than wild-type. However, they also display increased fluctuations about their time-averaged structures. Additionally, both variants show a small but significant increase in radius of gyration relative to wild-type. The vibrational density of states was calculated for each of the esterases. While the density of states profiles are similar overall, both thermostable mutants show increased populations of the very lowest frequency modes (<10 cm(-1)), with the more stable mutant showing the larger increase. This indicates that the thermally stable variants experience increased concerted motions relative to wild-type. Taken together, these data suggest that adaptation for high temperature stability has resulted in a restriction of large deviations from the native state and a corresponding increase in smaller scale fluctuations about the native state. These fluctuations contribute to entropy and hence to the stability of the native state. The largest changes in localized dynamics occur in surface loops, while other regions, particularly the active site residues, remain essentially unchanged. Several mutations, most notably L313F and H322Y in variant 8G8, are in the region showing the largest increase in fluctuations, suggesting that these mutations confer more flexibility to the loops. As a validation of our simulations, the fluctuations of Trp102 were examined in detail, and compared with Trp102 phosphorescence lifetimes that were previously measured. Consistent with expectations from the theory of phosphorescence, an inverse correlation between out-of-plane fluctuations on the picosecond time scale and phosphorescence lifetime was observed.
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Affiliation(s)
- Patrick L Wintrode
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125-0001, USA
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36
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Kamal JKA, Behere DV. Activity, stability and conformational flexibility of seed coat soybean peroxidase. J Inorg Biochem 2003; 94:236-42. [PMID: 12628703 DOI: 10.1016/s0162-0134(03)00004-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Seed coat soybean peroxidase (SBP) belongs to class III of the plant peroxidase superfamily that includes the classical peroxidase, namely horseradish peroxidase (HRP). We have measured the catalytic activity (k(cat)) and catalytic efficiency (k(cat)/K(M)) of SBP and that of HRP-C for the oxidation of ABTS [2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulphonate)] by hydrogen peroxide at 25 degrees C. We observed that the k(cat) and k(cat)/K(M) values for SBP are much higher than those for HRP-C at all pH values, rendering SBP a more potent peroxidase. This is attributed to the relatively more solvent exposed delta-meso heme edge in SBP. We observed that the maximum catalytic activity and conformational stability of SBP is at pH approximately 5.5. A pH maximum of 5.0 for the catalytic activity of SBP has recently been reported. Estimation of secondary structural elements at various pH values indicated that there is a maximal reduction of beta-strands and beta-turns at pH 5.5 causing the heme to be further exposed to the solvent and increasing the overall conformational flexibility of the protein.
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Affiliation(s)
- J K Amisha Kamal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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37
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Sehgal AC, Tompson R, Cavanagh J, Kelly RM. Structural and catalytic response to temperature and cosolvents of carboxylesterase EST1 from the extremely thermoacidophilic archaeon Sulfolobus solfataricus P1. Biotechnol Bioeng 2002; 80:784-93. [PMID: 12402324 DOI: 10.1002/bit.10433] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interactive effects of temperature and cosolvents on the kinetic and structural features of a carboxylesterase from the extremely thermoacidophilic archaeon Sulfolobus solfataricus P1 (Sso EST1) were examined. While dimethylformamide, acetonitrile, and dioxane were all found to be deleterious to enzyme function, dimethyl sulfoxide (DMSO) activated Sso EST1 to various extents. This was particularly true at 3.5% (v/v) DMSO, where k(cat) was 20-30% higher than at 1.2% DMSO, over the temperature range of 50-85 degrees C. DMSO compensated for thermal activation in some cases; for example, k(cat) at 60 degrees C in 3.5% DMSO was comparable to k(cat) at 85 degrees C in 1.2% DMSO. The relationship between DMSO activation and enzyme structural characteristics was also investigated. Nuclear magnetic resonance spectroscopy and circular dichroism showed no gross change in enzyme conformation with 3.5% DMSO between 50 and 80 degrees C. However, low levels of DMSO were shown to have a small yet significant change in enzyme conformation. This was evident through the reduction of Sso EST1's melting temperature and changes in the microenvironment of the enzyme's tyrosine and tryptophan residues at 3.5% versus 1.2% (v/v) solvent. Finally, activation parameter analysis based on kinetic data, at 1.2% and 3.5% DMSO, implied an increase in conformational flexibility with additional cosolvent. These results suggest the activating effect of DMSO was related to small changes in the enzyme's structure resulting in an increase in its conformational flexibility. Thus, in addition to their use for solubilizing hydrophobic substrates in water, cosolvents may also serve as activators in applications involving thermostable biocatalysts at sub-optimal temperatures.
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Affiliation(s)
- Amitabh C Sehgal
- Department of Chemical Engineering, North Carolina State University, Raleigh 27695-7905, USA
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38
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Kamal JKA, Nazeerunnisa M, Behere DV, Kizhakkedathu AK. Thermal unfolding of soybean peroxidase. Appropriate high denaturant concentrations induce cooperativity allowing the correct measurement of thermodynamic parameters. J Biol Chem 2002; 277:40717-21. [PMID: 12192011 DOI: 10.1074/jbc.m208129200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have earlier reported that both guanidine hydrochloride (GdnHCl)-induced and heat-induced unfolding of seed coat soybean peroxidase (SBP), monitored by far UV CD, show single step transition. However, although GdnHCl-induced unfolding follows a two-state pathway, the heat-induced denaturation proceeds through intermediates as indicated by the very low cooperativity of transition. In the former case, analysis of the data based on the two-state model gives true thermodynamic parameters, whereas underestimated values are obtained in the latter case. Available complex equations also cannot be applied for the analysis of the thermal unfolding of SBP due to the absence of separate transitions for the intermediates. In the present study, we report a method to obtain true thermodynamic parameters from thermal transition curves of SBP using the two-state model. When SBP is subjected to thermal unfolding at high GdnHCl concentrations (5.8-6.9 M), cooperative behavior is observed, which allowed the analysis by the two-state model to determine their thermodynamic parameters. We then obtained the thermodynamic parameters in the absence of GdnHCl by extrapolating the graph of linear dependence of DeltaH(m) on T(m) to the T(m) corresponding to 0 m GdnHCl. Another key point for checking the validity of our method was the fact that the unfolded state of SBP generated by either heat or GdnHCl is the same by which we could cross-check our results with that obtained from GdnHCl unfolding. Having obtained the true thermodynamic parameters, we report a detailed thermodynamic study of SBP. Further we address the effect of heme in the thermal unfolding mechanism of SBP.
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Affiliation(s)
- J K Amisha Kamal
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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39
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Fischer CJ, Gafni A, Steel DG, Schauerte JA. The triplet-state lifetime of indole in aqueous and viscous environments: significance to the interpretation of room temperature phosphorescence in proteins. J Am Chem Soc 2002; 124:10359-66. [PMID: 12197738 DOI: 10.1021/ja016609x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interpretation of room temperature phosphorescence studies of proteins requires an understanding of the mechanisms governing the tryptophan triplet-state lifetimes of residues fully exposed to solvent and those deeply buried in the hydrophobic core of proteins. Since solvents exposed tryptophans are expected to behave similarly to indole free in solution, it is important to have an accurate measure of the triplet state lifetime of indole in aqueous solution. Using photon counting techniques and low optical fluence (J/cm(2)), we observed the triplet-state lifetime of aqueous, deoxygenated indole and several indole derivatives to be approximately 40 micros, closely matching the previous reports by Bent and Hayon based on flash photolysis (12 micros; Bent, D. V.; Hayon, E. J. Am. Chem. Soc. 1975, 97, 2612-2619) but much shorter than the 1.2 ms lifetime observed more recently (Strambini, G. B.; Gonnelli, M. J. Am. Chem. Soc. 1995, 117, 7646-7651). However, we have now been able to reproduce the long lifetime reported by the latter workers for aqueous indole solutions and show that it likely arises from geminate recombination of the indole radical cation and solvated electron, a conclusion based on studies of the indole radical cation in water (Bent and Hayon, 1975). The evidence for this comes from a fast rise in the phosphorescence emission and measurements of a corresponding enhanced quantum yield in unbuffered solutions. This species can be readily quenched, and the corresponding fast rise disappears, leaving a monoexponential 40 micros decay, which we argue is the true indole triplet lifetime. The work is put in the context of room temperature phosphorescence studies of proteins.
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Affiliation(s)
- Christopher J Fischer
- Biophysics Research Program, Applied Physics Program, Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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40
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D'Amico S, Claverie P, Collins T, Georlette D, Gratia E, Hoyoux A, Meuwis MA, Feller G, Gerday C. Molecular basis of cold adaptation. Philos Trans R Soc Lond B Biol Sci 2002; 357:917-25. [PMID: 12171655 PMCID: PMC1692995 DOI: 10.1098/rstb.2002.1105] [Citation(s) in RCA: 179] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cold-adapted, or psychrophilic, organisms are able to thrive at low temperatures in permanently cold environments, which in fact characterize the greatest proportion of our planet. Psychrophiles include both prokaryotic and eukaryotic organisms and thus represent a significant proportion of the living world. These organisms produce cold-evolved enzymes that are partially able to cope with the reduction in chemical reaction rates induced by low temperatures. As a rule, cold-active enzymes display a high catalytic efficiency, associated however, with a low thermal stability. In most cases, the adaptation to cold is achieved through a reduction in the activation energy that possibly originates from an increased flexibility of either a selected area or of the overall protein structure. This enhanced plasticity seems in turn to be induced by the weak thermal stability of psychrophilic enzymes. The adaptation strategies are beginning to be understood thanks to recent advances in the elucidation of the molecular characteristics of cold-adapted enzymes derived from X-ray crystallography, protein engineering and biophysical methods. Psychrophilic organisms and their enzymes have, in recent years, increasingly attracted the attention of the scientific community due to their peculiar properties that render them particularly useful in investigating the possible relationship existing between stability, flexibility and specific activity and as valuable tools for biotechnological purposes.
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Affiliation(s)
- Salvino D'Amico
- Laboratory of Biochemistry, Institute of Chemistry B6, University of Liège, B-4000 Liège, Belgium
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41
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Zhao H, Chockalingam K, Chen Z. Directed evolution of enzymes and pathways for industrial biocatalysis. Curr Opin Biotechnol 2002; 13:104-10. [PMID: 11950559 DOI: 10.1016/s0958-1669(02)00291-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Directed evolution has become a powerful tool for developing enzyme and whole cell based biocatalysts. Significant recent advances include the creation of novel enzyme functions and the development of several new efficient directed evolution methods. The combination of directed evolution and rational design promises to accelerate the development of biocatalysts for applications in the pharmaceutical, chemical and food industries.
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Affiliation(s)
- Huimin Zhao
- Department of Chemical Engineering, Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.
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42
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Manco G, Mandrich L, Rossi M. Residues at the active site of the esterase 2 from Alicyclobacillus acidocaldarius involved in substrate specificity and catalytic activity at high temperature. J Biol Chem 2001; 276:37482-90. [PMID: 11447219 DOI: 10.1074/jbc.m103017200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recently solved three-dimensional structure of the thermophilic esterase 2 from Alicyclobacillus acidocaldarius allowed us to have a snapshot of an enzyme-sulfonate complex, which mimics the second stage of the catalytic reaction, namely the covalent acyl-enzyme intermediate. The aim of this work was to design, by structure-aided analysis and to generate by site-directed and saturation mutagenesis, EST2 variants with changed substrate specificity in the direction of preference for monoacylesters whose acyl-chain length is greater than eight carbon atoms. Positions 211 and 215 of the polypeptide chain were chosen to introduce mutations. Among five variants with single and double amino acid substitutions, three were obtained, M211S, R215L, and M211S/R215L, that changed the catalytic efficiency profile in the desired direction. Kinetic characterization of mutants and wild type showed that this change was achieved by an increase in k(cat) and a decrease in K(m) values with respect to the parental enzyme. The M211S/R215L specificity constant for p-nitrophenyl decanoate substrate was 6-fold higher than the wild type. However, variants M211T, M211S, and M211V showed strikingly increased activity as well as maximal activity with monoacylesters with four carbon atoms in the acyl chain, compared with the wild type. In the case of mutant M211T, the k(cat) for p-nitrophenyl butanoate was 2.4-fold higher. Overall, depending on the variant and on the substrate, we observed improved catalytic activity at 70 degrees C with respect to the wild type, which was a somewhat unexpected result for an enzyme with already high k(cat) values at high temperature. In addition, variants with altered specificity toward the acyl-chain length were obtained. The results were interpreted in the context of the EST2 three-dimensional structure and a proposed catalytic mechanism in which k(cat), e.g. the limiting step of the reaction, was dependent on the acyl chain length of the ester substrate.
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Affiliation(s)
- G Manco
- Institute of Protein Biochemistry and Enzymology, Consiglio Nazionale delle Ricerche, via G. Marconi 10, Naples 80125, Italy.
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43
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Tsai AM, Udovic TJ, Neumann DA. The inverse relationship between protein dynamics and thermal stability. Biophys J 2001; 81:2339-43. [PMID: 11566803 PMCID: PMC1301704 DOI: 10.1016/s0006-3495(01)75880-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Protein powders that are dehydrated or mixed with a glassy compound are known to have improved thermal stability. We present elastic and quasielastic neutron scattering measurements of the global dynamics of lysozyme and ribonuclease A powders. In the absence of solvation water, both protein powders exhibit largely harmonic motions on the timescale of the measurements. Upon partial hydration, quasielastic scattering indicative of relaxational processes appears at sufficiently high temperature. When the scattering spectrum are analyzed with the Kohlrausch-Williams-Watts formalism, the exponent beta decreases with increasing temperature, suggesting that multiple relaxation modes are emerging. When lysozyme was mixed with glycerol, its beta values were higher than the hydrated sample at comparable temperatures, reflecting the viscosity and stabilizing effects of glycerol.
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Affiliation(s)
- A M Tsai
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
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44
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Berger MD, Lee AM, Simonette RA, Jackson BE, Roca AI, Singleton SF. Design and evaluation of a tryptophanless RecA protein with wild type activity. Biochem Biophys Res Commun 2001; 286:1195-203. [PMID: 11527427 DOI: 10.1006/bbrc.2001.5525] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C-terminal domain of the Escherichia coli RecA protein contains two tryptophan residues whose native fluorescence emission provides an interfering background signal when other fluorophores such as 1,N(6)-ethenoadenine, 2-aminopurine and other tryptophan residues are used to probe the protein's activities. Replacement of the wild type tryptophans with nonfluorescent residues is not trivial because one tryptophan is highly conserved and the C-terminal domain functions in both DNA binding as well as interfilament protein-protein contact. We undertook the task of creating a tryptophanless RecA protein with WT RecA activity by selecting suitable amino acid replacements for Trp290 and Trp308. Mutant proteins were screened in vivo using assays of SOS induction and cell survival following UV irradiation. Based on its activity in these assays, the W290H-W308F W-less RecA was purified for in vitro characterization and functioned like WT RecA in DNA-dependent ATPase and DNA strand exchange assays. Spectrofluorometry indicates that the W290H-W308F RecA protein generates no significant emission when excited with 295-nm light. Based on its ability to function as wild type protein in vivo and in vitro, this dark RecA protein will be useful for future fluorescence experiments.
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Affiliation(s)
- M D Berger
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
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45
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Lehmann M, Wyss M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr Opin Biotechnol 2001; 12:371-5. [PMID: 11551465 DOI: 10.1016/s0958-1669(00)00229-9] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the advent of directed evolution techniques, protein engineering has received a fresh impetus. Engineering proteins for thermostability is a particularly exciting and challenging field, as it is crucial for broadening the industrial use of recombinant proteins. In addition to directed evolution, a variety of partially successful rational concepts for engineering thermostability have been developed in the past. Recent results suggest that amino acid sequence comparisons of mesophilic proteins alone can be used efficiently to engineer thermostable proteins. The potential benefits of the underlying, semirational 'consensus concept' are compared with those of rational design and directed evolution approaches.
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Affiliation(s)
- M Lehmann
- F Hoffmann-La Roche Ltd., Vitamins and Fine Chemicals Division, Department VFB, Building 203, CH-4070 Basel, Switzerland.
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46
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Orencia MC, Hanson MA, Stevens RC. Structural analysis of affinity matured antibodies and laboratory-evolved enzymes. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:227-59. [PMID: 11050935 DOI: 10.1016/s0065-3233(01)55005-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- M C Orencia
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA
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47
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Wintrode PL, Arnold FH. Temperature adaptation of enzymes: lessons from laboratory evolution. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:161-225. [PMID: 11050934 DOI: 10.1016/s0065-3233(01)55004-4] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- P L Wintrode
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena 91125, USA
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48
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Vieille C, Zeikus GJ. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 2001; 65:1-43. [PMID: 11238984 PMCID: PMC99017 DOI: 10.1128/mmbr.65.1.1-43.2001] [Citation(s) in RCA: 1392] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees C), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. These enzymes share the same catalytic mechanisms with their mesophilic counterparts. When cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, indicating that these properties are genetically encoded. Sequence alignments, amino acid content comparisons, crystal structure comparisons, and mutagenesis experiments indicate that hyperthermophilic enzymes are, indeed, very similar to their mesophilic homologues. No single mechanism is responsible for the remarkable stability of hyperthermophilic enzymes. Increased thermostability must be found, instead, in a small number of highly specific alterations that often do not obey any obvious traffic rules. After briefly discussing the diversity of hyperthermophilic organisms, this review concentrates on the remarkable thermostability of their enzymes. The biochemical and molecular properties of hyperthermophilic enzymes are described. Mechanisms responsible for protein inactivation are reviewed. The molecular mechanisms involved in protein thermostabilization are discussed, including ion pairs, hydrogen bonds, hydrophobic interactions, disulfide bridges, packing, decrease of the entropy of unfolding, and intersubunit interactions. Finally, current uses and potential applications of thermophilic and hyperthermophilic enzymes as research reagents and as catalysts for industrial processes are described.
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Affiliation(s)
- C Vieille
- Biochemistry Department, Michigan State University, East Lansing, Michigan 48824, USA
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49
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Arnold FH, Wintrode PL, Miyazaki K, Gershenson A. How enzymes adapt: lessons from directed evolution. Trends Biochem Sci 2001; 26:100-6. [PMID: 11166567 DOI: 10.1016/s0968-0004(00)01755-2] [Citation(s) in RCA: 243] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Enzymes that are adapted to widely different temperature niches are being used to investigate the molecular basis of protein stability and enzyme function. However, natural evolution is complex: random noise, historical accidents and ignorance of the selection pressures at work during adaptation all cloud comparative studies. Here, we review how adaptation in the laboratory by directed evolution can complement studies of natural enzymes in the effort to understand stability and function. Laboratory evolution experiments can attempt to mimic natural evolution and identify different adaptive mechanisms. However, laboratory evolution might make its biggest contribution in explorations of nonnatural functions, by allowing us to distinguish the properties nutured by evolution from those dictated by the laws of physical chemistry.
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Affiliation(s)
- F H Arnold
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA.
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50
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Chapter 3 Cold-adapted enzymes: An unachieved symphony. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1568-1254(01)80005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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