1
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Wang Y, Xie T, Ma C, Zhao Y, Li J, Li Z, Ye X. Biochemical characterization and antifungal activity of a recombinant β-1,3-glucanase FlGluA from Flavobacterium sp. NAU1659. Protein Expr Purif 2024; 224:106563. [PMID: 39122061 DOI: 10.1016/j.pep.2024.106563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/07/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
β-1,3-glucanases can degrade β-1,3-glucoside bonds in β-glucan which is the main cell-wall component of most of fungi, and have the crucial application potential in plant protection and food processing. Herein, a β-1,3-glucanase FlGluA from Flavobacterium sp. NAU1659 composed of 333 amino acids with a predicted molecular mass of 36.6 kDa was expressed in Escherichia coli BL21, purified and characterized. The deduced amino acid sequence of FlGluA showed the high identity with the β-1,3-glucanase belonging to glycoside hydrolase (GH) family 16. Enzymological characterization indicated FlGluA had the highest activity on zymosan A, with a specific activity of 3.87 U/mg, followed by curdlan (1.16 U/mg) and pachymaran (0.88 U/mg). It exhibited optimal catalytic activity at the pH 5.0 and 40 °C, and was stable when placed at 4 °C for 12 h in the range of pH 3.0-8.0 or at a temperature below 50 °C for 3 h. Its catalytic activity was enhanced by approximately 36 % in the presence of 1 mM Cr3+. The detection of thin-layer chromatography and mass spectrometry showed FlGluA hydrolyzed zymosan A mainly to glucose and disaccharide, and trace amounts of tetrasaccharide and pentasaccharide, however, it had no action on laminaribiose, indicating its endo-β-1,3-glucanase activity. The mycelium growth of F. oxysporum treated by FlGluA was inhibited, with approximately 37 % of inhibition rate, revealing the potential antifungal activity of the enzyme. These results revealed the hydrolytic properties and biocontrol activity of FlGluA, laying a crucial foundation for its potential application in agriculture and industry.
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Affiliation(s)
- Yanxin Wang
- College of Life Sciences of Liaocheng University, 252000, Liaocheng, PR China; Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China.
| | - Tingting Xie
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Chenlong Ma
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China
| | - Yujie Zhao
- College of Life Sciences of Liaocheng University, 252000, Liaocheng, PR China
| | - Jingchen Li
- College of Life Sciences of Liaocheng University, 252000, Liaocheng, PR China
| | - Zhendong Li
- College of Life Sciences of Liaocheng University, 252000, Liaocheng, PR China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences of Nanjing Agricultural University, 210095, Nanjing, PR China.
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2
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Mandelli F, Martins MP, Chinaglia M, Lima EAD, Morais MAB, Lima TB, Cabral L, Pirolla RAS, Fuzita FJ, Paixão DAA, Andrade MDO, Wolf LD, Vieira PS, Persinoti GF, Murakami MT. A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary β-glucans. NPJ Biofilms Microbiomes 2024; 10:105. [PMID: 39397008 DOI: 10.1038/s41522-024-00578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 10/01/2024] [Indexed: 10/15/2024] Open
Abstract
Gut microbiota members from the Bacteroidota phylum play a pivotal role in mammalian health and metabolism. They thrive in this diverse ecosystem due to their notable ability to cope with distinct recalcitrant dietary glycans via polysaccharide utilization loci (PULs). Our study reveals that a PUL from an herbivore gut bacterium belonging to the Bacteroidota phylum, with a gene composition similar to that in the human gut, exhibits extended functionality. While the human gut PUL targets mixed-linkage β-glucans specifically, the herbivore gut PUL also efficiently processes linear and substituted β-1,3-glucans. This gain of function emerges from molecular adaptations in recognition proteins and carbohydrate-active enzymes, including a β-glucosidase specialized for β(1,6)-glucosyl linkages, a typical substitution in β(1,3)-glucans. These findings broaden the existing model for non-cellulosic β-glucans utilization by gut bacteria, revealing an additional layer of functional and evolutionary complexity within the gut microbiota, beyond conventional gene insertions/deletions to intricate biochemical interactions.
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Affiliation(s)
- Fernanda Mandelli
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Marcele Pandeló Martins
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Evandro Antonio de Lima
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Mariana Abrahão Bueno Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Tatiani Brenelli Lima
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Lucélia Cabral
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Renan Augusto Siqueira Pirolla
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Felipe Jun Fuzita
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Douglas Antônio Alvaredo Paixão
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Maxuel de Oliveira Andrade
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Lucia Daniela Wolf
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Plinio Salmazo Vieira
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Gabriela Felix Persinoti
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil
| | - Mario Tyago Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-970, Brazil.
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3
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Rodella C, Lazaridi S, Lemmin T. TemBERTure: advancing protein thermostability prediction with deep learning and attention mechanisms. BIOINFORMATICS ADVANCES 2024; 4:vbae103. [PMID: 39040220 PMCID: PMC11262459 DOI: 10.1093/bioadv/vbae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/14/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Motivation Understanding protein thermostability is essential for numerous biotechnological applications, but traditional experimental methods are time-consuming, expensive, and error-prone. Recently, deep learning (DL) techniques from natural language processing (NLP) was extended to the field of biology, since the primary sequence of proteins can be viewed as a string of amino acids that follow a physicochemical grammar. Results In this study, we developed TemBERTure, a DL framework that predicts thermostability class and melting temperature from protein sequences. Our findings emphasize the importance of data diversity for training robust models, especially by including sequences from a wider range of organisms. Additionally, we suggest using attention scores from Deep Learning models to gain deeper insights into protein thermostability. Analyzing these scores in conjunction with the 3D protein structure can enhance understanding of the complex interactions among amino acid properties, their positioning, and the surrounding microenvironment. By addressing the limitations of current prediction methods and introducing new exploration avenues, this research paves the way for more accurate and informative protein thermostability predictions, ultimately accelerating advancements in protein engineering. Availability and implementation TemBERTure model and the data are available at: https://github.com/ibmm-unibe-ch/TemBERTure.
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Affiliation(s)
- Chiara Rodella
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Symela Lazaridi
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Thomas Lemmin
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
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4
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Rocha REO, Mariano DCB, Almeida TS, CorrêaCosta LS, Fischer PHC, Santos LH, Caffarena ER, da Silveira CH, Lamp LM, Fernandez-Quintero ML, Liedl KR, de Melo-Minardi RC, de Lima LHF. Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches. Proteins 2023; 91:218-236. [PMID: 36114781 DOI: 10.1002/prot.26424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 01/07/2023]
Abstract
β-glucosidases play a pivotal role in second-generation biofuel (2G-biofuel) production. For this application, thermostable enzymes are essential due to the denaturing conditions on the bioreactors. Random amino acid substitutions have originated new thermostable β-glucosidases, but without a clear understanding of their molecular mechanisms. Here, we probe by different molecular dynamics simulation approaches with distinct force fields and submitting the results to various computational analyses, the molecular bases of the thermostabilization of the Paenibacillus polymyxa GH1 β-glucosidase by two-point mutations E96K (TR1) and M416I (TR2). Equilibrium molecular dynamic simulations (eMD) at different temperatures, principal component analysis (PCA), virtual docking, metadynamics (MetaDy), accelerated molecular dynamics (aMD), Poisson-Boltzmann surface analysis, grid inhomogeneous solvation theory and colony method estimation of conformational entropy allow to converge to the idea that the stabilization carried by both substitutions depend on different contributions of three classic mechanisms: (i) electrostatic surface stabilization; (ii) efficient isolation of the hydrophobic core from the solvent, with energetic advantages at the solvation cap; (iii) higher distribution of the protein dynamics at the mobile active site loops than at the protein core, with functional and entropic advantages. Mechanisms i and ii predominate for TR1, while in TR2, mechanism iii is dominant. Loop A integrity and loops A, C, D, and E dynamics play critical roles in such mechanisms. Comparison of the dynamic and topological changes observed between the thermostable mutants and the wildtype protein with amino acid co-evolutive networks and thermostabilizing hotspots from the literature allow inferring that the mechanisms here recovered can be related to the thermostability obtained by different substitutions along the whole family GH1. We hope the results and insights discussed here can be helpful for future rational approaches to the engineering of optimized β-glucosidases for 2G-biofuel production for industry, biotechnology, and science.
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Affiliation(s)
- Rafael Eduardo Oliveira Rocha
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Diego César Batista Mariano
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Tiago Silva Almeida
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Leon Sulfierry CorrêaCosta
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Computational Modeling Coordination (COMOD), Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Pedro Henrique Camargo Fischer
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil
| | - Lucianna Helene Santos
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratory of Molecular Modeling and Drug Design, Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Leonida M Lamp
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Monica Lisa Fernandez-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Klaus Roman Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
| | - Raquel Cardoso de Melo-Minardi
- Laboratory of Bioinformatics and Systems (LBS), Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory of Molecular Modelling and Bioinformatics (LAMMB), Department of Physical and Biological Sciences, Campus Sete Lagoas, Universidade Federal de São João Del Rei, Sete Lagoas, Brazil.,Institute of General, Inorganic and Theoretical Chemistry, and Center for Chemistry and Biomedicine Innsbruck (CCB), University of Innsbruck, Innsbruck, Austria
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5
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Cai LN, Lu T, Lin DQ, Yao SJ. Discovery of extremophilic cellobiohydrolases from marine Aspergillus niger with computational analysis. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Ahmed Z, Zulfiqar H, Khan AA, Gul I, Dao FY, Zhang ZY, Yu XL, Tang L. iThermo: A Sequence-Based Model for Identifying Thermophilic Proteins Using a Multi-Feature Fusion Strategy. Front Microbiol 2022; 13:790063. [PMID: 35273581 PMCID: PMC8902591 DOI: 10.3389/fmicb.2022.790063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/10/2022] [Indexed: 01/20/2023] Open
Abstract
Thermophilic proteins have important application value in biotechnology and industrial processes. The correct identification of thermophilic proteins provides important information for the application of these proteins in engineering. The identification method of thermophilic proteins based on biochemistry is laborious, time-consuming, and high cost. Therefore, there is an urgent need for a fast and accurate method to identify thermophilic proteins. Considering this urgency, we constructed a reliable benchmark dataset containing 1,368 thermophilic and 1,443 non-thermophilic proteins. A multi-layer perceptron (MLP) model based on a multi-feature fusion strategy was proposed to discriminate thermophilic proteins from non-thermophilic proteins. On independent data set, the proposed model could achieve an accuracy of 96.26%, which demonstrates that the model has a good application prospect. In order to use the model conveniently, a user-friendly software package called iThermo was established and can be freely accessed at http://lin-group.cn/server/iThermo/index.html. The high accuracy of the model and the practicability of the developed software package indicate that this study can accelerate the discovery and engineering application of thermally stable proteins.
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Affiliation(s)
- Zahoor Ahmed
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hasan Zulfiqar
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Abdullah Aman Khan
- School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China.,Sichuan Artificial Intelligence Research Institute, Yibin, China
| | - Ijaz Gul
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Tsinghua Shenzhen International Graduate School, Institute of Biopharmaceutical and Health Engineering, Tsinghua University, Shenzhen, China
| | - Fu-Ying Dao
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhao-Yue Zhang
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao-Long Yu
- School of Materials Science and Engineering, Hainan University, Haikou, China
| | - Lixia Tang
- School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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7
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Feng C, Ma Z, Yang D, Li X, Zhang J, Li Y. A Method for Prediction of Thermophilic Protein Based on Reduced Amino Acids and Mixed Features. Front Bioeng Biotechnol 2020; 8:285. [PMID: 32432088 PMCID: PMC7214540 DOI: 10.3389/fbioe.2020.00285] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/18/2020] [Indexed: 11/13/2022] Open
Abstract
The thermostability of proteins is a key factor considered during enzyme engineering, and finding a method that can identify thermophilic and non-thermophilic proteins will be helpful for enzyme design. In this study, we established a novel method combining mixed features and machine learning to achieve this recognition task. In this method, an amino acid reduction scheme was adopted to recode the amino acid sequence. Then, the physicochemical characteristics, auto-cross covariance (ACC), and reduced dipeptides were calculated and integrated to form a mixed feature set, which was processed using correlation analysis, feature selection, and principal component analysis (PCA) to remove redundant information. Finally, four machine learning methods and a dataset containing 500 random observations out of 915 thermophilic proteins and 500 random samples out of 793 non-thermophilic proteins were used to train and predict the data. The experimental results showed that 98.2% of thermophilic and non-thermophilic proteins were correctly identified using 10-fold cross-validation. Moreover, our analysis of the final reserved features and removed features yielded information about the crucial, unimportant and insensitive elements, it also provided essential information for enzyme design.
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Affiliation(s)
- Changli Feng
- College of Information Science and Technology, Taishan University, Tai’an, China
| | - Zhaogui Ma
- College of Information Science and Technology, Taishan University, Tai’an, China
| | - Deyun Yang
- College of Information Science and Technology, Taishan University, Tai’an, China
| | - Xin Li
- College of Information Science and Technology, Taishan University, Tai’an, China
| | - Jun Zhang
- Department of Rehabilitation, General Hospital of Heilongjiang Province Land Reclamation Bureau, Harbin, China
| | - Yanjuan Li
- Information and Computer Engineering College, Northeast Forestry University, Harbin, China
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8
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Yu J, Zhang T, Xu H, Dong X, Cai Y, Pan Y, Cao C. Thermostable iron oxide nanoparticle synthesis within recombinant ferritins from the hyperthermophile Pyrococcus yayanosii CH1. RSC Adv 2019; 9:39381-39393. [PMID: 35540659 PMCID: PMC9076106 DOI: 10.1039/c9ra07397c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/14/2019] [Indexed: 12/15/2022] Open
Abstract
Thermostable nanoparticles have numerous applications in catalysis and in the oil/gas industry. However, synthesizing these nanoparticles requires expensive polymers. Here, a novel thermostable ferritin named PcFn, originally from the hyperthermophilic archaeon Pyrococcus yayanosii CH1, was overexpressed in Escherichia coli, purified and characterized, which could successfully direct the synthesis of thermostable magnetoferritins (M-PcFn) with monodispersed iron oxide nanoparticles in one step. Transmission electron microscopy and magnetic measurements show that the cores of the M-PcFn have an average diameter of 4.7 nm, are well-crystalline and superparamagnetic. Both the PcFn and M-PcFn can resist temperatures up to 110 °C, which is significantly higher than for human H-chain ferritin (HFn) and M-HFn, and comparable to temperatures previously reported for Pyrococcus furiosus ferritin (PfFn) and M-PfFn. After heating at 110 °C for 30 minutes, PcFn and M-PcFn maintained their secondary structures and PcFn retained 87.4% of its iron uptake activity. This remarkable thermostability of PcFn and M-PcFn suggests potential applications in elevated temperature environments.
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Affiliation(s)
- Jiacheng Yu
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China.,College of Earth Sciences, University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Tongwei Zhang
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China
| | - Huangtao Xu
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China.,College of Earth Sciences, University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Xiaoli Dong
- Department of Geoscience, University of Calgary Calgary AB T2N 1N4 Canada
| | - Yao Cai
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China
| | - Yongxin Pan
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China.,College of Earth Sciences, University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Changqian Cao
- Biogeomagnetism Group, Paleomagnetism and Geochronology Laboratory, Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences Beijing 100029 P. R. China .,Innovation Academy for Earth Science, CAS Beijing 100029 P. R. China.,College of Earth Sciences, University of Chinese Academy of Sciences Beijing 100049 P. R. China
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9
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Liew KJ, Teo SC, Shamsir MS, Sani RK, Chong CS, Chan KG, Goh KM. Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities. 3 Biotech 2018; 8:376. [PMID: 30105201 PMCID: PMC6087703 DOI: 10.1007/s13205-018-1391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Seng Chong Teo
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, USA
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, 212013 People’s Republic of China
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
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10
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Censoni L, Dos Santos Muniz H, Martínez L. A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics 2018; 33:2106-2113. [PMID: 28334219 DOI: 10.1093/bioinformatics/btx124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/01/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation The flow of vibrational energy in proteins has been shown not to obey expectations for isotropic media. The existence of preferential pathways for energy transport, with probable connections to allostery mechanisms, has been repeatedly demonstrated. Here, we investigate whether, by representing a set of protein structures as networks of interacting amino acid residues, we are able to model heat diffusion and predict residue-protein vibrational couplings, as measured by the Anisotropic Thermal Diffusion (ATD) computational protocol of modified molecular dynamics simulations. Results We revisit the structural rationales for the precise definition of a contact between amino acid residues. Using this definition to describe a set of proteins as contact networks where each node corresponds to a residue, we show that node centrality, particularly closeness centrality and eigenvector centrality , correlates to the strength of the vibrational coupling of each residue to the rest of the structure. We then construct an analytically solvable model of heat diffusion on a network, whose solution incorporates an explicit dependence on the connectivity of the heated node, as described by a perturbed graph Laplacian Matrix. Availability and Implementation An implementation of the described model is available at http://leandro.iqm.unicamp.br/atd-scripts . Contact leandro@iqm.unicamp.br.
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Affiliation(s)
- Luciano Censoni
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | | | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
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11
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Mitsuya D, Sugiyama T, Zhang S, Takeuchi Y, Okai M, Urano N, Ishida M. Enzymatic properties and the gene structure of a cold-adapted laminarinase from Pseudoalteromonas species LA. J Biosci Bioeng 2018; 126:169-175. [PMID: 29627318 DOI: 10.1016/j.jbiosc.2018.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/17/2018] [Accepted: 02/22/2018] [Indexed: 11/18/2022]
Abstract
We isolated a laminarin-degrading cold-adapted bacterium strain LA from coastal seawater in Sagami Bay, Japan and identified it as a Pseudoalteromonas species. We named the extracellular laminarinase LA-Lam, and purified and characterized it. LA-Lam showed high degradation activity for Laminaria digitata laminarin in the ranges of 15-50°C and pH 5.0-9.0. The major terminal products degraded from L. digitata laminarin with LA-Lam were glucose, laminaribiose, and laminaritriose. The degradation profile of laminarioligosaccharides with LA-Lam suggested that the enzyme has a high substrate binding ability toward tetrameric or larger saccharides. Our results of the gene sequence and the SDS-PAGE analyses revealed that the major part of mature LA-Lam is a catalytic domain that belongs to the GH16 family, although its precursor is composed of a signal peptide, the catalytic domain, and three-repeated unknown regions.
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Affiliation(s)
- Daisuke Mitsuya
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Takuya Sugiyama
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Shuo Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Yo Takeuchi
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Masahiko Okai
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Naoto Urano
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Masami Ishida
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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12
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Oda M, Inaba S, Kamiya N, Bekker GJ, Mikami B. Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:415-425. [DOI: 10.1016/j.bbapap.2017.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/24/2017] [Accepted: 12/11/2017] [Indexed: 11/25/2022]
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13
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Kadowaki MAS, Higasi P, de Godoy MO, Prade RA, Polikarpov I. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS J 2018; 285:559-579. [PMID: 29222836 DOI: 10.1111/febs.14356] [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: 08/10/2017] [Revised: 10/20/2017] [Accepted: 12/05/2017] [Indexed: 12/27/2022]
Abstract
Cellobiohydrolases hydrolyze cellulose, a linear polymer with glucose monomers linked exclusively by β-1,4 glycosidic linkages. The widespread hydrogen bonding network tethers individual cellulose polymers forming crystalline cellulose, which prevent the access of hydrolytic enzymes and water molecules. The most abundant enzyme secreted by Myceliophthora thermophila M77 in response to the presence of biomass is the cellobiohydrolase MtCel7A, which is composed by a GH7-catalytic domain (CD), a linker, and a CBM1-type carbohydrate-binding module. GH7 cellobiohydrolases have been studied before, and structural models have been proposed. However, currently available GH7 crystal structures only define separate catalytic domains and/or cellulose-binding modules and do not include the full-length structures that are involved in shaping the catalytic mode of operation. In this study, we determined the 3D structure of catalytic domain using X-ray crystallography and retrieved the full-length enzyme envelope via small-angle X-ray scattering (SAXS) technique. The SAXS data reveal a tadpole-like molecular shape with a rigid linker connecting the CD and CBM. Our biochemical studies show that MtCel7A has higher catalytic efficiency and thermostability as well as lower processivity when compared to the well-studied TrCel7A from Trichoderma reesei. Based on a comparison of the crystallographic structures of CDs and their molecular dynamic simulations, we demonstrate that MtCel7A has considerably higher flexibility than TrCel7A. In particular, loops that cover the active site are more flexible and undergo higher conformational fluctuations, which might account for decreased processivity and enhanced enzymatic efficiency. Our statistical coupling analysis suggests co-evolution of amino acid clusters comprising the catalytic site of MtCel7A, which correlate with the steps in the catalytic cycle of the enzyme. DATABASE The atomic coordinates and structural factors of MtCel7A have been deposited in the Protein Data Bank with accession number 5W11.
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Affiliation(s)
| | - Paula Higasi
- São Carlos Institute of Physics, University of São Paulo, Brazil
| | | | - Rolf A Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, Brazil
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14
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Silva SB, Pinheiro MP, Fuzo CA, Silva SR, Ferreira TL, Lourenzoni MR, Nonato MC, Vieira DS, Ward RJ. The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis. Int J Biol Macromol 2017; 97:574-584. [DOI: 10.1016/j.ijbiomac.2017.01.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/09/2017] [Accepted: 01/11/2017] [Indexed: 12/24/2022]
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15
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Contribution of main chain and side chain atoms and their locations to the stability of thermophilic proteins. J Mol Graph Model 2016; 64:85-93. [DOI: 10.1016/j.jmgm.2016.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/03/2016] [Indexed: 11/21/2022]
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16
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Alvarez TM, Liberato MV, Cairo JPLF, Paixão DAA, Campos BM, Ferreira MR, Almeida RF, Pereira IO, Bernardes A, Ematsu GCG, Chinaglia M, Polikarpov I, de Oliveira Neto M, Squina FM. A Novel Member of GH16 Family Derived from Sugarcane Soil Metagenome. Appl Biochem Biotechnol 2015; 177:304-17. [DOI: 10.1007/s12010-015-1743-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
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17
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Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One 2015; 10:e0119264. [PMID: 25816325 PMCID: PMC4376797 DOI: 10.1371/journal.pone.0119264] [Citation(s) in RCA: 297] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/12/2015] [Indexed: 11/19/2022] Open
Abstract
The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.
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Structural prediction of a novel laminarinase from the psychrophilic Glaciozyma antarctica PI12 and its temperature adaptation analysis. J Mol Model 2015; 21:63. [PMID: 25721655 DOI: 10.1007/s00894-015-2617-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/09/2015] [Indexed: 12/30/2022]
Abstract
Here, we present a novel psychrophilic β-glucanase from Glaciozyma antarctica PI12 yeast that has been structurally modeled and analyzed in detail. To our knowledge, this is the first attempt to model a psychrophilic laminarinase from yeast. Because of the low sequence identity (<40%), a threading method was applied to predict a 3D structure of the enzyme using the MODELLER9v12 program. The results of a comparative study using other mesophilic, thermophilic, and hyperthermophilic laminarinases indicated several amino acid substitutions on the surface of psychrophilic laminarinase that totally increased the flexibility of its structure for efficient catalytic reactions at low temperatures. Whereas several structural factors in the overall structure can explain the weak thermal stability, this research suggests that the psychrophilic adaptation and catalytic activity at low temperatures were achieved through existence of longer loops and shorter or broken helices and strands, an increase in the number of aromatic and hydrophobic residues, a reduction in the number of hydrogen bonds and salt bridges, a higher total solvent accessible surface area, and an increase in the exposure of the hydrophobic side chains to the solvent. The results of comparative molecular dynamics simulation and principal component analysis confirmed the above strategies adopted by psychrophilic laminarinase to increase its catalytic efficiency and structural flexibility to be active at cold temperature.
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Labourel A, Jam M, Legentil L, Sylla B, Hehemann JH, Ferrières V, Czjzek M, Michel G. Structural and biochemical characterization of the laminarinaseZgLamCGH16fromZobellia galactanivoranssuggests preferred recognition of branched laminarin. ACTA ACUST UNITED AC 2015; 71:173-84. [DOI: 10.1107/s139900471402450x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/07/2014] [Indexed: 05/28/2023]
Abstract
Laminarin is a β-1,3-D-glucan displaying occasional β-1,6 branches. This storage polysaccharide of brown algae constitutes an abundant source of carbon for marine bacteria such asZobellia galactanivorans. This marine member of the Bacteroidetes possesses five putative β-1,3-glucanases [four belonging to glycosyl hydrolase family 16 (GH16) and one to GH64] with various modular architectures. Here, the characterization of the β-glucanaseZgLamC is reported. The catalytic GH16 module (ZgLamCGH16) was produced inEscherichia coliand purified. This recombinant enzyme has a preferential specificity for laminarin but also a significant activity on mixed-linked glucan (MLG). The structure of an inactive mutant ofZgLamCGH16in complex with a thio-β-1,3-hexaglucan substrate unravelled a straight active-site cleft with three additional pockets flanking subsites −1, −2 and −3. These lateral pockets are occupied by a glycerol, an acetate ion and a chloride ion, respectively. The presence of these molecules in the vicinity of the O6 hydroxyl group of each glucose moiety suggests thatZgLamCGH16accommodates branched laminarins as substrates. Altogether,ZgLamC is a secreted laminarinase that is likely to be involved in the initial step of degradation of branched laminarin, while the previously characterizedZgLamA efficiently degrades unbranched laminarin and oligo-laminarins.
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20
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Lee CW, Wang HJ, Hwang JK, Tseng CP. Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study. PLoS One 2014; 9:e112751. [PMID: 25393107 PMCID: PMC4231051 DOI: 10.1371/journal.pone.0112751] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 10/18/2014] [Indexed: 11/21/2022] Open
Abstract
Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures. These salt bridges were first categorized based on pairing residues, secondary structure locations, and Cα–Cα distances. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number, relative solvent accessibility, and conservation prescreening to determine the residues appropriate for the thermal adaptive design of salt bridges. According to our method, eight putative salt-bridges were designed on a mesophilic β-glucosidase and 24 variants were constructed to verify the predictions. Six putative salt-bridges leaded to the increase of the enzyme thermal stability. A significant increase in melting temperature of 8.8, 4.8, 3.7, 1.3, 1.2, and 0.7°C of the putative salt-bridges N437K–D49, E96R–D28, E96K–D28, S440K–E70, T231K–D388, and Q277E–D282 was detected, respectively. Reversing the polarity of T231K–D388 to T231D–D388K resulted in a further increase in melting temperatures by 3.6°C, which may be caused by the transformation of an intra-subunit electrostatic interaction into an inter-subunit one depending on the local environment. The combination of the thermostable variants (N437K, E96R, T231D and D388K) generated a melting temperature increase of 15.7°C. Thus, this study demonstrated a novel method for the thermal adaptive design of salt bridges through inference of suitable positions and substitutions.
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Affiliation(s)
- Chi-Wen Lee
- Institute of Bioinformatics and Systems Biology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Hsiu-Jung Wang
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Jenn-Kang Hwang
- Institute of Bioinformatics and Systems Biology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- * E-mail: (JKH); (CPT)
| | - Ching-Ping Tseng
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
- * E-mail: (JKH); (CPT)
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21
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Kim DS, Song HN, Nam HJ, Kim SG, Park YS, Park JC, Woo EJ, Lim HK. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter. PLoS One 2014; 9:e98178. [PMID: 24892548 PMCID: PMC4043505 DOI: 10.1371/journal.pone.0098178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 12/30/2022] Open
Abstract
Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.
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Affiliation(s)
- Dong-Sik Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Hyung-Nam Song
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Hyo Jung Nam
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Sung-Geun Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Young-Seoub Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Jae-Chan Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Eui-Jeon Woo
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Kwon Lim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
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22
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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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23
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Labourel A, Jam M, Jeudy A, Hehemann JH, Czjzek M, Michel G. The β-glucanase ZgLamA from Zobellia galactanivorans evolved a bent active site adapted for efficient degradation of algal laminarin. J Biol Chem 2013; 289:2027-42. [PMID: 24337571 DOI: 10.1074/jbc.m113.538843] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Laminarinase is commonly used to describe β-1,3-glucanases widespread throughout Archaea, bacteria, and several eukaryotic lineages. Some β-1,3-glucanases have already been structurally and biochemically characterized, but very few from organisms that are in contact with genuine laminarin, the storage polysaccharide of brown algae. Here we report the heterologous expression and subsequent biochemical and structural characterization of ZgLamAGH16 from Zobellia galactanivorans, the first GH16 laminarinase from a marine bacterium associated with seaweeds. ZgLamAGH16 contains a unique additional loop, compared with other GH16 laminarinases, which is composed of 17 amino acids and gives a bent shape to the active site cleft of the enzyme. This particular topology is perfectly adapted to the U-shaped conformation of laminarin chains in solution and thus explains the predominant specificity of ZgLamAGH16 for this substrate. The three-dimensional structure of the enzyme and two enzyme-substrate complexes, one with laminaritetraose and the other with a trisaccharide of 1,3-1,4-β-d-glucan, have been determined at 1.5, 1.35, and 1.13 Å resolution, respectively. The structural comparison of substrate recognition pattern between these complexes allows the proposition that ZgLamAGH16 likely diverged from an ancestral broad specificity GH16 β-glucanase and evolved toward a bent active site topology adapted to efficient degradation of algal laminarin.
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Affiliation(s)
- Aurore Labourel
- From Sorbonne Universités, UPMC Université Paris 06, UMR 7139, Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France and
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24
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Lima MA, Oliveira-Neto M, Kadowaki MAS, Rosseto FR, Prates ET, Squina FM, Leme AFP, Skaf MS, Polikarpov I. Aspergillus niger β-glucosidase has a cellulase-like tadpole molecular shape: insights into glycoside hydrolase family 3 (GH3) β-glucosidase structure and function. J Biol Chem 2013; 288:32991-3005. [PMID: 24064212 DOI: 10.1074/jbc.m113.479279] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aspergillus niger is known to secrete large amounts of β-glucosidases, which have a variety of biotechnological and industrial applications. Here, we purified an A. niger β-glucosidase (AnBgl1) and conducted its biochemical and biophysical analyses. Purified enzyme with an apparent molecular mass of 116 kDa forms monomers in solution as judged by native gel electrophoresis and has a pI value of 4.55, as found for most of the fungi of β-glucosidases. Surprisingly, the small angle x-ray experiments reveal that AnBgl1 has a tadpole-like structure, with the N-terminal catalytic domain and C-terminal fibronectin III-like domain (FnIII) connected by the long linker peptide (∼100 amino acid residues) in an extended conformation. This molecular organization resembles the one adopted by other cellulases (such as cellobiohydrolases, for example) that frequently contain a catalytic domain linked to the cellulose-binding module that mediates their binding to insoluble and polymeric cellulose. The reasons why AnBgl1, which acts on the small soluble substrates, has a tadpole molecular shape are not entirely clear. However, our enzyme pulldown assays with different polymeric substrates suggest that AnBgl1 has little or no capacity to bind to and to adsorb cellulose, xylan, and starch, but it has high affinity to lignin. Molecular dynamics simulations suggested that clusters of residues located in the C-terminal FnIII domain interact strongly with lignin fragments. The simulations showed that numerous arginine residues scattered throughout the FnIII surface play an important role in the interaction with lignin by means of cation-π stacking with the lignin aromatic rings. These results indicate that the C-terminal FnIII domain could be operational for immobilization of the enzyme on the cell wall and for the prevention of unproductive binding of cellulase to the biomass lignin.
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Affiliation(s)
- Marisa A Lima
- From the Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos 13560-970, SP
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Manjunath K, Sekar K. Molecular dynamics perspective on the protein thermal stability: a case study using SAICAR synthetase. J Chem Inf Model 2013; 53:2448-61. [PMID: 23962324 DOI: 10.1021/ci400306m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) Cα, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.
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Affiliation(s)
- Kavyashree Manjunath
- Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, Karnataka 560 012, India
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26
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Prates ÉT, Stankovic I, Silveira RL, Liberato MV, Henrique-Silva F, Pereira N, Polikarpov I, Skaf MS. X-ray structure and molecular dynamics simulations of endoglucanase 3 from Trichoderma harzianum: structural organization and substrate recognition by endoglucanases that lack cellulose binding module. PLoS One 2013; 8:e59069. [PMID: 23516599 PMCID: PMC3597598 DOI: 10.1371/journal.pone.0059069] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/11/2013] [Indexed: 11/18/2022] Open
Abstract
Plant biomass holds a promise for the production of second-generation ethanol via enzymatic hydrolysis, but its utilization as a biofuel resource is currently limited to a large extent by the cost and low efficiency of the cellulolytic enzymes. Considerable efforts have been dedicated to elucidate the mechanisms of the enzymatic process. It is well known that most cellulases possess a catalytic core domain and a carbohydrate binding module (CBM), without which the enzymatic activity can be drastically reduced. However, Cel12A members of the glycosyl hydrolases family 12 (GHF12) do not bear a CBM and yet are able to hydrolyze amorphous cellulose quite efficiently. Here, we use X-ray crystallography and molecular dynamics simulations to unravel the molecular basis underlying the catalytic capability of endoglucanase 3 from Trichoderma harzianum (ThEG3), a member of the GHF12 enzymes that lacks a CBM. A comparative analysis with the Cellulomonas fimi CBM identifies important residues mediating interactions of EG3s with amorphous regions of the cellulose. For instance, three aromatic residues constitute a harboring wall of hydrophobic contacts with the substrate in both ThEG3 and CfCBM structures. Moreover, residues at the entrance of the active site cleft of ThEG3 are identified, which might hydrogen bond to the substrate. We advocate that the ThEG3 residues Asn152 and Glu201 interact with the substrate similarly to the corresponding CfCBM residues Asn81 and Arg75. Altogether, these results show that CBM motifs are incorporated within the ThEG3 catalytic domain and suggest that the enzymatic efficiency is associated with the length and position of the substrate chain, being higher when the substrate interact with the aromatic residues at the entrance of the cleft and the catalytic triad. Our results provide guidelines for rational protein engineering aiming to improve interactions of GHF12 enzymes with cellulosic substrates.
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Affiliation(s)
- Érica T. Prates
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Ivana Stankovic
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Rodrigo L. Silveira
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
| | - Marcelo V. Liberato
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Flávio Henrique-Silva
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Nei Pereira
- Centro de Tecnologia, Escola de Química, Laboratório de Desenvolvimento de Bioprocessos (LaDeBio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Igor Polikarpov
- Institute of Physics of São Carlos, University of São Paulo, São Carlos, São Paulo, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, State University of Campinas–UNICAMP. Cx.P. 6154, Campinas, São Paulo, Brazil
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