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Dou Z, He J, Han C, Wu X, Wan L, Yang J, Zheng Y, Gong B, Wang L. qProtein: Exploring Physical Features of Protein Thermostability Based on Structural Proteomics. J Chem Inf Model 2024. [PMID: 39375829 DOI: 10.1021/acs.jcim.4c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2024]
Abstract
Thermostability, which is essential for the functional performance of enzymes, is largely determined by intramolecular physical interactions. Although many tools have been developed, existing computational methods have struggled to find the universal principles of protein thermostability. Recent advancements in structural proteomics have been driven by the introduction of deep neural networks such as AlphaFold2 and ESMFold. These innovations have enabled the characterization of protein structures with unprecedented speed and accuracy. Here, we introduce qProtein, a Python-implemented workflow designed for the quantitative analysis of physical interactions on the scale of structural proteomics. This platform accepts protein sequences as input and produces four structural features, including hydrophobic clusters, hydrogen bonds, electrostatic interactions, and disulfide bonds. To demonstrate the use of qProtein, we investigate the structural features related to protein thermostability in six glycoside hydrolase (GH) families, comprising a total of 3,811 protein structures. Our results indicate that in five enzyme families (GH11, GH12, GH5_2, GH10, and GH48), the thermophilic enzymes have a larger average area of hydrophobic clusters compared to the nonthermophilic enzymes within each family. Furthermore, our analysis of the local-structure regions reveals that the hydrophobic clusters are predominantly distributed in the distal regions of the GH11 enzymes. In addition, the average hydrophobic cluster area of the thermophilic enzymes is significantly higher than that of the nonthermophilic enzymes in the distal regions of the GH11 enzymes. Therefore, qProtein is a well-suited platform for analyzing the structural features of thermal stability at the level of structural proteomics. We provide the source code for qProtein at https://github.com/bj600800/qProtein, and the web server is available at http://qProtein.sdu.edu.cn:8888.
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Affiliation(s)
- Zhixin Dou
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
| | - Jiaxin He
- School of Computer Science and Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
| | - Chao Han
- Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an 271018, China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
| | - Lin Wan
- School of Software, Shandong University, Shunhua Road, Jinan 250101, P.R. China
| | - Jian Yang
- School of Computer Science and Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
| | - Yanwei Zheng
- School of Computer Science and Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
| | - Bin Gong
- School of Software, Shandong University, Shunhua Road, Jinan 250101, P.R. China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P.R. China
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2
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Koenekoop L, Åqvist J. Computational Analysis of Heat Capacity Effects in Protein-Ligand Binding. J Chem Theory Comput 2024; 20:5708-5716. [PMID: 38870420 PMCID: PMC11238534 DOI: 10.1021/acs.jctc.4c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Heat capacity effects in protein-ligand binding as measured by calorimetric experiments have recently attracted considerable attention, particularly in the field of enzyme inhibitor design. A significant negative heat capacity change upon ligand binding implies a marked temperature dependence of the binding enthalpy, which is of high relevance for attempts to optimize protein-ligand interactions. In this work, we address the question of how well such heat capacity changes can be predicted by computer simulations. We examine a series of human thrombin inhibitors that all bind with ΔCp values of about -0.4 kcal/mol/K and calculate heat capacity changes from plain molecular dynamics simulations of the bound and free states of the enzyme and ligand. The results show that accurate ΔCp estimates within a few tenths of a kcal/mol/K of the experimental values can be obtained with this approach. This allows us to address the structural and energetic origin of the negative heat capacity changes for the thrombin inhibitors, and it is found that conformational equilibria of the free ligands in solution make a major contribution to the observed effect.
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Affiliation(s)
- Lucien Koenekoop
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
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3
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Xin S, Zhang H, Sun J, Mao X. Characterization and Hydrolysis Mechanism Analysis of a Cold-Adapted Trypsin-Like Protease from Antarctic Krill. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9955-9966. [PMID: 38628059 DOI: 10.1021/acs.jafc.4c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Cold-adapted proteases are capable of efficient protein hydrolysis at reduced temperatures, which offer significant potential applications in the area of low temperature food processing. In this paper, we attempted to characterize cold-adapted proteases from Antarctic krill. Antarctic krill possesses an extremely active autolytic enzyme system in their bodies, and the production of peptides and free amino acids accompanies the rapid breakdown of muscle proteins following the death. The crucial role of trypsin in this process is recognized. A cold-adapted trypsin named OUC-Pp-20 from Antarctic krill genome was cloned and expressed in Pichia pastoris. Recombinant trypsin is a monomeric protein of 26.8 ± 1.0 kDa with optimum reaction temperature at 25 °C. In addition, the catalytic specificity of OUC-Pp-20 was assessed by identifying its hydrolysis sites through LC-MS/MS. OUC-Pp-20 appeared to prefer Gln and Asn at the P1 position, which is an amino acid with an amide group in its side chain. Hydrolysis reactions on milk and shrimp meat revealed that it can effectively degrade allergenic components in milk and arginine kinase in shrimp meat. These findings update the current knowledge of cold-adapted trypsin and demonstrate the potential application of OUC-Pp-20 in low temperature food processing.
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Affiliation(s)
- Shanglin Xin
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Haiyang Zhang
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Jianan Sun
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Xiangzhao Mao
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
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4
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Bian F, Liang XY, Wang M, Sun ZZ, Xie BB. Comparative molecular dynamics simulations provided insights into the mechanisms of cold-adaption of alginate lyases from the PL7 family. Extremophiles 2024; 28:24. [PMID: 38598094 DOI: 10.1007/s00792-024-01340-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Alginate is an important polysaccharide that is abundant in the marine environments, including the Polar Regions, and bacterial alginate lyases play key roles in its degradation. Many reported alginate lyases show characteristics of cold-adapted enzymes, including relatively low temperature optimum of activities (Topt) and low thermal stabilities. However, the cold-adaption mechanisms of alginate lyases remain unclear. Here, we studied the cold-adaptation mechanisms of alginate lyases by comparing four members of the PL7 family from different environments: AlyC3 from the Arctic ocean (Psychromonas sp. C-3), AlyA1 from the temperate ocean (Zobellia galactanivorans), PA1167 from the human pathogen (Pseudomonas aeruginosa PAO1), and AlyQ from the tropic ocean (Persicobacter sp. CCB-QB2). Sequence comparison and comparative molecular dynamics (MD) simulations revealed two main strategies of cold adaptation. First, the Arctic AlyC3 and temperate AlyA1 increased the flexibility of the loops close to the catalytic center by introducing insertions at these loops. Second, the Arctic AlyC3 increased the electrostatic attractions with the negatively charged substrate by introducing a high portion of positively charged lysine at three of the insertions mentioned above. Furthermore, our study also revealed that the root mean square fluctuation (RMSF) increased greatly when the temperature was increased to Topt or higher, suggesting the RMSF increase temperature as a potential indicator of the cold adaptation level of the PL7 family. This study provided new insights into the cold-adaptation mechanisms of bacterial alginate lyases and the marine carbon cycling at low temperatures.
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Affiliation(s)
- Fei Bian
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Xiao-Yue Liang
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meng Wang
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhong-Zhi Sun
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Bin-Bin Xie
- Microbial Technology Institute and State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Zheng J, Guo N, Huang Y, Guo X, Wagner A. High temperature delays and low temperature accelerates evolution of a new protein phenotype. Nat Commun 2024; 15:2495. [PMID: 38553445 PMCID: PMC10980763 DOI: 10.1038/s41467-024-46332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/19/2024] [Indexed: 04/02/2024] Open
Abstract
Since the origin of life, temperatures on earth have fluctuated both on short and long time scales. How such changes affect the rate at which Darwinian evolution can bring forth new phenotypes remains unclear. On the one hand, high temperature may accelerate phenotypic evolution because it accelerates most biological processes. On the other hand, it may slow phenotypic evolution, because proteins are usually less stable at high temperatures and therefore less evolvable. Here, to test these hypotheses experimentally, we evolved a green fluorescent protein in E. coli towards the new phenotype of yellow fluorescence at different temperatures. Yellow fluorescence evolved most slowly at high temperature and most rapidly at low temperature, in contradiction to the first hypothesis. Using high-throughput population sequencing, protein engineering, and biochemical assays, we determined that this is due to the protein-destabilizing effect of neofunctionalizing mutations. Destabilization is highly detrimental at high temperature, where neofunctionalizing mutations cannot be tolerated. Their detrimental effects can be mitigated through excess stability at low temperature, leading to accelerated adaptive evolution. By modifying protein folding stability, temperature alters the accessibility of mutational paths towards high-fitness genotypes. Our observations have broad implications for our understanding of how temperature changes affect evolutionary adaptations and innovations.
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Affiliation(s)
- Jia Zheng
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Ning Guo
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuxiang Huang
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xiang Guo
- Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- The Santa Fe Institute, Santa Fe, USA.
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6
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Wilkins RS, Lund BA, Isaksen GV, Åqvist J, Brandsdal BO. Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations. J Chem Theory Comput 2024; 20:451-458. [PMID: 38112329 PMCID: PMC10782440 DOI: 10.1021/acs.jctc.3c01105] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
Chorismate mutase (CM) enzymes have long served as model systems for benchmarking new methods and tools in computational chemistry. Despite the enzymes' prominence in the literature, the extent of the roles that activation enthalpy and entropy play in catalyzing the conversion of chorismate to prephenate is still subject to debate. Knowledge of these parameters is a key piece in fully understanding the mechanism of chorismate mutases. Within this study, we utilize EVB/MD free energy perturbation calculations at a range of temperatures, allowing us to extract activation enthalpies and entropies from an Arrhenius plot of activation free energies of the reaction catalyzed by a monofunctional Bacillus subtilis CM and the promiscuous enzyme isochorismate pyruvate lyase of Pseudomonas aeruginosa. In comparison to the uncatalyzed reaction, our results show that both enzyme-catalyzed reactions exhibit a substantial reduction in activation enthalpy, while the effect on activation entropy is relatively minor, demonstrating that enzyme-catalyzed CM reactions are enthalpically driven. Furthermore, we observe that the monofunctional CM from B. subtilis more efficiently catalyzes this reaction than its promiscuous counterpart. This is supported by a structural analysis of the reaction pathway at the transition state, from which we identified key residues explaining the enthalpically driven nature of the reactions and also the difference in efficiencies between the two enzymes.
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Affiliation(s)
- Ryan Scott Wilkins
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | - Bjarte Aarmo Lund
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | - Geir Villy Isaksen
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
| | | | - Bjørn Olav Brandsdal
- Hylleraas Centre for Quantum Molecular
Sciences, Department of Chemistry, University
of Tromsø, N9037 Tromsø, Norway
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7
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Lee MJ, Kim B, Kim K, Lee JH, Do H. Heterologous protein production using Psychrobacter sp. PAMC 21119 analyzed with a green fluorescent protein-based reporter system. Protein Expr Purif 2023; 212:106352. [PMID: 37595854 DOI: 10.1016/j.pep.2023.106352] [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: 05/02/2023] [Revised: 07/11/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Insolubility and low expression are typical bottlenecks in the production of proteins for studying their function and structure using X-ray crystallography or nuclear magnetic resonance spectroscopy. Cold-active enzymes from polar microorganisms have unique structural features that render them unstable and thermolabile, and are responsible for decreased protein yield in heterologous expression systems. To address these challenges, we developed a heterologous protein expression system using a psychrophilic organism, Psychrobacter sp. PAMC 21119, as a protein expression host with its own promoter. We screened 11 promoters and evaluated their strength using quantitative real-time polymerase chain reaction and a reporter system harboring the SfGFP gene. The highest expression was achieved using promoters RH96_RS13655 (P21119_20930) and RH96_RS15090 (P21119_23410), regardless of the temperature used. The p20930 strain exhibited a maximum expression level 19.6-fold higher than that of its control at 20 °C and produced approximately 0.5 mg of protein per gram of dry cell weight. To our knowledge, this is the first report of a low-temperature recombinant protein expression system developed using Psychrobacter sp. that can be used to express various difficult-to-express and cold-active proteins.
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Affiliation(s)
- Min Ju Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Bomi Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Kitae Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, 21990, Republic of Korea; Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea.
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8
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Huang A, Lu F, Liu F. Exploring the molecular mechanism of cold-adaption of an alkaline protease mutant by molecular dynamics simulations and residue interaction network. Protein Sci 2023; 32:e4837. [PMID: 37984374 PMCID: PMC10682693 DOI: 10.1002/pro.4837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Psychrophilic proteases have attracted enormous attention in past decades, due to their high catalytic activity at low temperatures in a wide range of industrial processes, especially in the detergent and leather industries. Among them, H5 is an alkaline protease mutant, which featuring psychrophilic-like behavior, but the reasons that H5 with higher activity at low temperatures are still poorly understood. Herein, the molecular dynamics (MD) simulations combined with residue interaction network (RIN) were utilized to investigate the mechanisms of the cold-adaption of mutant H5. The results demonstrated that two loops involved in the substrate binding G100-S104 and S125-S129 in H5 had higher mobility, and the distance enlargement between the two loops modulated the substrate's accessibility compared with wild type counterpart. Besides, H5 enhanced conformational flexibility by weakening salt bridges and increasing interaction with the solvent. In particular, the absence of Lys251-Asp197-Arg247 salt bridge network may contribute to the structural mobility. Based on the free energy landscape and molecular mechanics Poisson-Boltzmann surface area of the wild type and H5, it was elucidated that H5 possessed a large population of interconvertible conformations, resulting in the weaker substrate binding free energy. The calculated RIN topology parameters such as the average degree, average cluster coefficient, and average path length further verified that the mutant H5 attenuated residue-to-residue interactions. The investigation of the mechanisms by which how the residue mutation affects the stability and activity of enzymes provides a theoretical basis for the development of cold-adapted protease.
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Affiliation(s)
- Ailan Huang
- College of BiotechnologyTianjin University of Science & TechnologyTianjinChina
| | - Fuping Lu
- College of BiotechnologyTianjin University of Science & TechnologyTianjinChina
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyTianjinChina
| | - Fufeng Liu
- College of BiotechnologyTianjin University of Science & TechnologyTianjinChina
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of EducationTianjin Key Laboratory of Industrial MicrobiologyTianjinChina
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9
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Hussain A, Ray MK. Functional activity of E. coli RNase R in the Antarctic Pseudomonas syringae Lz4W. J Genet Eng Biotechnol 2023; 21:101. [PMID: 37843651 PMCID: PMC10579198 DOI: 10.1186/s43141-023-00553-2] [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: 09/09/2022] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
BACKGROUND In Antarctic P. syringae RNase R play an essential role in the processing of 16S and 5S rRNA, thereby playing an important role in cold-adapted growth of the bacterium. This study is focused on deciphering the in vivo functional activity of mesophilic exoribonuclease R and its catalytic domain (RNB) in an evolutionary distant psychrophilic bacterium Pseudomonas syringae Lz4W. RESULTS Our results confirm that E. coli RNase R complemented the physiological functions of the psychrophilic bacterium P. syringae RNase R and rescued the cold-sensitive phenotype of Pseudomonas syringae ∆rnr mutant. More importantly, the catalytic domain (RNB) of the E. coli RNase R is also capable of alleviating the cold-sensitive growth defects of ∆rnr mutant as seen with the catalytic domain (RNB) of the P. syringae enzyme. The Catalytic domain of E. coli RNase R was less efficient than the Catalytic domain of P. syringae RNase R in rescuing the cold-sensitive growth of ∆rnr mutant at 4°C, as the ∆rnr expressing the RNBEc (catalytic domain of E. coli RNase R) displayed longer lag phase than the RNBPs (Catalytic domain of P. syringae RNase R) complemented ∆rnr mutant at 4°C. Altogether it appears that the E. coli RNase R and P. syringae RNase R are functionally exchangeable for the growth requirements of P. syringae at low temperature (4°C). Our results also confirm that in P. syringae the requirement of RNase R for supporting the growth at 4°C is independent of the degradosomal complex. CONCLUSION E. coli RNase R (RNase REc) rescues the cold-sensitive phenotype of the P. syringae Δrnr mutant. Similarly, the catalytic domain of E. coli RNase R (RNBEc) is also capable of supporting the growth of Δrnr mutant at low temperatures. These findings have a vast scope in the design and development of low-temperature-based expression systems.
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Affiliation(s)
- Ashaq Hussain
- Centre for Cellular and Molecular Biology, Hyderabad, India.
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10
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Komp E, Alanzi HN, Francis R, Vuong C, Roberts L, Mosallanejad A, Beck DAC. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023; 10:682. [PMID: 37805601 PMCID: PMC10560248 DOI: 10.1038/s41597-023-02553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
Stability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Humood N Alanzi
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Ryan Francis
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Chau Vuong
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Logan Roberts
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Amin Mosallanejad
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
- Paul G. Allen School of Computer Science, University of Washington, Seattle, USA.
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11
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Lee SH, Seo H, Hong H, Park J, Ki D, Kim M, Kim HJ, Kim KJ. Three-directional engineering of IsPETase with enhanced protein yield, activity, and durability. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132297. [PMID: 37595467 DOI: 10.1016/j.jhazmat.2023.132297] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/25/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Abstract
The mesophilic PETase from Ideonella sakaiensis (IsPETase) has been shown to exhibit high PET hydrolysis activity, but its low stability limits its industrial applications. Here, we developed a variant, Z1-PETase, with enhanced soluble protein yield and durability while maintaining or improving activity at lower temperatures. The selected Z1-PETase not only exhibited a 20-fold improvement in soluble protein yield compared to the previously engineered IsPETaseS121E/D186H/S242T/N246D (4p) variant, but also demonstrated a 30% increase in low-temperature activity at 40 °C, along with an 11 °C increase in its TmD value. The PET depolymerization test across a temperature range low to high (30-70 °C) confirmed that Z1-PETase exhibits high accessibility of mesophilic PET hydrolase and rapid depolymerizing rate at higher temperature in accordance with the thermal behaviors of polymer and enzyme. Additionally, structural interpretation indicated that the stabilization of specific active site loops in Z1-PETase contributes to enhanced thermostability without adversely impacting enzymatic activity. In a pH-stat bioreactor, Z1-PETase depolymerized > 90% of both transparent and colored post-consumer PET powders within 24 and 8 h at 40 °C and 55 °C, respectively, demonstrating that the utility of this IsPETase variant in the bio-recycling of PET.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hogyun Seo
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hwaseok Hong
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jiyoung Park
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dongwoo Ki
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mijeong Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyung-Joon Kim
- Bioresearch Research Institute, CJ CheilJedang Co., Suwon 16495, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea; Zyen Co, Daegu 41566, Republic of Korea.
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12
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Wendering P, Nikoloski Z. Model-driven insights into the effects of temperature on metabolism. Biotechnol Adv 2023; 67:108203. [PMID: 37348662 DOI: 10.1016/j.biotechadv.2023.108203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/22/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023]
Abstract
Temperature affects cellular processes at different spatiotemporal scales, and identifying the genetic and molecular mechanisms underlying temperature responses paves the way to develop approaches for mitigating the effects of future climate scenarios. A systems view of the effects of temperature on cellular physiology can be obtained by focusing on metabolism since: (i) its functions depend on transcription and translation and (ii) its outcomes support organisms' development, growth, and reproduction. Here we provide a systematic review of modelling efforts directed at investigating temperature effects on properties of single biochemical reactions, system-level traits, metabolic subsystems, and whole-cell metabolism across different prokaryotes and eukaryotes. We compare and contrast computational approaches and theories that facilitate modelling of temperature effects on key properties of enzymes and their consideration in constraint-based as well as kinetic models of metabolism. In addition, we provide a summary of insights from computational approaches, facilitating integration of omics data from temperature-modulated experiments with models of metabolic networks, and review the resulting biotechnological applications. Lastly, we provide a perspective on how different types of metabolic modelling can profit from developments in machine learning and models of different cellular layers to improve model-driven insights into the effects of temperature relevant for biotechnological applications.
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Affiliation(s)
- Philipp Wendering
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany.
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13
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Chen L, Hong T, Wu Z, Song W, Chen SX, Liu Y, Shen L. Genomic analyses reveal a low-temperature adapted clade in Halorubrum, a widespread haloarchaeon across global hypersaline environments. BMC Genomics 2023; 24:508. [PMID: 37653415 PMCID: PMC10468875 DOI: 10.1186/s12864-023-09597-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions. RESULTS In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments ('PD group' hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test. CONCLUSIONS The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea.
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Affiliation(s)
- Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Auhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu, 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Zirui Wu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Shaoxing X Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
| | - Yongqin Liu
- Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou, 730000, China
- State Key Laboratory of Tibetan Plateau Earth System Science, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- Anhui Provincial Key Laboratory of Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu, 241000, China.
- State Key Laboratory of Tibetan Plateau Earth System Science, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100085, Beijing, China.
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14
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Collins T, Feller G. Psychrophilic enzymes: strategies for cold-adaptation. Essays Biochem 2023; 67:701-713. [PMID: 37021674 DOI: 10.1042/ebc20220193] [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: 03/02/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023]
Abstract
Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes.
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Affiliation(s)
- Tony Collins
- Department of Biology, Center of Molecular and Environmental Biology (CBMA), University of Minho, 4710-057 Braga, Portugal
| | - Georges Feller
- Department of Life Sciences, Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, 4000 Liège, Belgium
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15
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van der Ent F, Skagseth S, Lund BA, Sǒan J, Griese JJ, Brandsdal BO, Åqvist J. Computational design of the temperature optimum of an enzyme reaction. SCIENCE ADVANCES 2023; 9:eadi0963. [PMID: 37379391 DOI: 10.1126/sciadv.adi0963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023]
Abstract
Cold-adapted enzymes are characterized both by a higher catalytic activity at low temperatures and by having their temperature optimum down-shifted, compared to mesophilic orthologs. In several cases, the optimum does not coincide with the onset of protein melting but reflects some other type of inactivation. In the psychrophilic α-amylase from an Antarctic bacterium, the inactivation is thought to originate from a specific enzyme-substrate interaction that breaks around room temperature. Here, we report a computational redesign of this enzyme aimed at shifting its temperature optimum upward. A set of mutations designed to stabilize the enzyme-substrate interaction were predicted by computer simulations of the catalytic reaction at different temperatures. The predictions were verified by kinetic experiments and crystal structures of the redesigned α-amylase, showing that the temperature optimum is indeed markedly shifted upward and that the critical surface loop controlling the temperature dependence approaches the target conformation observed in a mesophilic ortholog.
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Affiliation(s)
- Florian van der Ent
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Susann Skagseth
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjarte A Lund
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Jaka Sǒan
- National Institute of Chemistry, SI-1001 Ljubljana, Slovenia
| | - Julia J Griese
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø-The Arctic University of Norway, N9037 Tromsø, Norway
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16
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Hou Q, Rooman M, Pucci F. Enzyme Stability-Activity Trade-Off: New Insights from Protein Stability Weaknesses and Evolutionary Conservation. J Chem Theory Comput 2023. [PMID: 37276063 DOI: 10.1021/acs.jctc.3c00036] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A general limitation of the use of enzymes in biotechnological processes under sometimes nonphysiological conditions is the complex interplay between two key quantities, enzyme activity and stability, where the increase of one is often associated with the decrease of the other. A precise stability-activity trade-off is necessary for the enzymes to be fully functional, but its weight in different protein regions and its dependence on environmental conditions is not yet elucidated. To advance this issue, we used the formalism that we have recently developed to effectively identify stability strength and weakness regions in protein structures and applied it to a large set of globular enzymes with known experimental structure and catalytic sites. Our analysis showed a striking oscillatory pattern of free energy compensation centered on the catalytic region. Indeed, catalytic residues are usually nonoptimal with respect to stability, but residues in the first shell around the catalytic site are, on the average, stability strengths and thus compensate for this lack of stability; residues in the second shell are weaker again, and so on. This trend is consistent across all enzyme families. It is accompanied by a similar, but less pronounced, pattern of residue conservation across evolution. In addition, we analyzed cold- and heat-adapted enzymes separately and highlighted different patterns of stability strengths and weaknesses, which provide insight into the longstanding problem of catalytic rate enhancement in cold environments. The successful comparison of our stability and conservation results with experimental fitness data, obtained by deep mutagenesis scanning, led us to propose criteria for improving catalytic activity while maintaining enzyme stability, a key goal in enzyme design.
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Affiliation(s)
- Qingzhen Hou
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
- National Institute of Health Data Science of China, Shandong University, Jinan, Shandong 250002, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, 1050 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
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17
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Rasmussen CB, Scavenius C, Thøgersen IB, Harwood SL, Larsen Ø, Bjerga GEK, Stougaard P, Enghild JJ, Thøgersen MS. Characterization of a novel cold-adapted intracellular serine protease from the extremophile Planococcus halocryophilus Or1. Front Microbiol 2023; 14:1121857. [PMID: 36910232 PMCID: PMC9995970 DOI: 10.3389/fmicb.2023.1121857] [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: 12/12/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
The enzymes of microorganisms that live in cold environments must be able to function at ambient temperatures. Cold-adapted enzymes generally have less ordered structures that convey a higher catalytic rate, but at the cost of lower thermodynamic stability. In this study, we characterized P355, a novel intracellular subtilisin protease (ISP) derived from the genome of Planococcus halocryophilus Or1, which is a bacterium metabolically active down to -25°C. P355's stability and activity at varying pH values, temperatures, and salt concentrations, as well as its temperature-dependent kinetics, were determined and compared to an uncharacterized thermophilic ISP (T0099) from Parageobacillus thermoglucosidasius, a previously characterized ISP (T0034) from Planococcus sp. AW02J18, and Subtilisin Carlsberg (SC). The results showed that P355 was the most heat-labile of these enzymes, closely followed by T0034. P355 and T0034 exhibited catalytic constants (k cat ) that were much higher than those of T0099 and SC. Thus, both P355 and T0034 demonstrate the characteristics of the stability-activity trade-off that has been widely observed in cold-adapted proteases.
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Affiliation(s)
| | | | - Ida B. Thøgersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Øivind Larsen
- NORCE Climate and Environment, NORCE Norwegian Research Centre AS, Bergen, Norway
| | | | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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18
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Huang A, Lu F, Liu F. Discrimination of psychrophilic enzymes using machine learning algorithms with amino acid composition descriptor. Front Microbiol 2023; 14:1130594. [PMID: 36860491 PMCID: PMC9968940 DOI: 10.3389/fmicb.2023.1130594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Introduction Psychrophilic enzymes are a class of macromolecules with high catalytic activity at low temperatures. Cold-active enzymes possessing eco-friendly and cost-effective properties, are of huge potential application in detergent, textiles, environmental remediation, pharmaceutical as well as food industry. Compared with the time-consuming and labor-intensive experiments, computational modeling especially the machine learning (ML) algorithm is a high-throughput screening tool to identify psychrophilic enzymes efficiently. Methods In this study, the influence of 4 ML methods (support vector machines, K-nearest neighbor, random forest, and naïve Bayes), and three descriptors, i.e., amino acid composition (AAC), dipeptide combinations (DPC), and AAC + DPC on the model performance were systematically analyzed. Results and discussion Among the 4 ML methods, the support vector machine model based on the AAC descriptor using 5-fold cross-validation achieved the best prediction accuracy with 80.6%. The AAC outperformed than the DPC and AAC + DPC descriptors regardless of the ML methods used. In addition, amino acid frequencies between psychrophilic and non-psychrophilic proteins revealed that higher frequencies of Ala, Gly, Ser, and Thr, and lower frequencies of Glu, Lys, Arg, Ile,Val, and Leu could be related to the protein psychrophilicity. Further, ternary models were also developed that could classify psychrophilic, mesophilic, and thermophilic proteins effectively. The predictive accuracy of the ternary classification model using AAC descriptor via the support vector machine algorithm was 75.8%. These findings would enhance our insight into the cold-adaption mechanisms of psychrophilic proteins and aid in the design of engineered cold-active enzymes. Moreover, the proposed model could be used as a screening tool to identify novel cold-adapted proteins.
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Affiliation(s)
- Ailan Huang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
| | - Fufeng Liu
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, China,Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China,*Correspondence: Fufeng Liu, ✉ ;
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19
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Laye VJ, Solieva S, Voelz VA, DasSarma S. Effects of Salinity and Temperature on the Flexibility and Function of a Polyextremophilic Enzyme. Int J Mol Sci 2022; 23:15620. [PMID: 36555259 PMCID: PMC9779221 DOI: 10.3390/ijms232415620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The polyextremophilic β-galactosidase enzyme of the haloarchaeon Halorubrum lacusprofundi functions in extremely cold and hypersaline conditions. To better understand the basis of polyextremophilic activity, the enzyme was studied using steady-state kinetics and molecular dynamics at temperatures ranging from 10 °C to 50 °C and salt concentrations from 1 M to 4 M KCl. Kinetic analysis showed that while catalytic efficiency (kcat/Km) improves with increasing temperature and salinity, Km is reduced with decreasing temperatures and increasing salinity, consistent with improved substrate binding at low temperatures. In contrast, kcat was similar from 2-4 M KCl across the temperature range, with the calculated enthalpic and entropic components indicating a threshold of 2 M KCl to lower the activation barrier for catalysis. With molecular dynamics simulations, the increase in per-residue root-mean-square fluctuation (RMSF) was observed with higher temperature and salinity, with trends like those seen with the catalytic efficiency, consistent with the enzyme's function being related to its flexibility. Domain A had the smallest change in flexibility across the conditions tested, suggesting the adaptation to extreme conditions occurs via regions distant to the active site and surface accessible residues. Increased flexibility was most apparent in the distal active sites, indicating their importance in conferring salinity and temperature-dependent effects.
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Affiliation(s)
- Victoria J. Laye
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD 21202, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
| | - Shahlo Solieva
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Vincent A. Voelz
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, University System of Maryland, Baltimore, MD 21202, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21202, USA
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20
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:2355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
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21
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Åqvist J, van der Ent F. Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding. J Chem Theory Comput 2022; 18:6345-6353. [PMID: 36094903 PMCID: PMC9558309 DOI: 10.1021/acs.jctc.2c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Indexed: 11/30/2022]
Abstract
It has been suggested that heat capacity changes in enzyme catalysis may be the underlying reason for temperature optima that are not related to unfolding of the enzyme. If this were to be a common phenomenon, it would have major implications for our interpretation of enzyme kinetics. In most cases, the support for the possible existence of a nonzero (negative) activation heat capacity, however, only relies on fitting such a kinetic model to experimental data. It is therefore of fundamental interest to try to use computer simulations to address this issue. One way is simply to calculate the temperature dependence of the activation free energy and determine whether the relationship is linear or not. An alternative approach is to calculate the absolute heat capacities of the reactant and transition states from plain molecular dynamics simulations using either the temperature derivative or fluctuation formula for the enthalpy. Here, we examine these different approaches for a designer enzyme with a temperature optimum that is not caused by unfolding. Benchmark calculations for the heat capacity of liquid water are first carried out using different thermostats. It is shown that the derivative formula for the heat capacity is generally the most robust and insensitive to the thermostat used and its parameters. The enzyme calculations using this method give results in agreement with direct calculations of activation free energies and show no sign of a negative activation heat capacity. We also provide a simple scheme for the calculation of binding heat capacity changes, which is of clear interest in ligand design, and demonstrate it for substrate binding to the designer enzyme. Neither in that case do the simulations predict any negative heat capacity change.
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Affiliation(s)
- Johan Åqvist
- Department of Cell &
Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Florian van der Ent
- Department of Cell &
Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
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22
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Markússon S, Hjörleifsson JG, Kursula P, Ásgeirsson B. Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Biochemistry 2022; 61:2248-2260. [PMID: 36194497 DOI: 10.1021/acs.biochem.2c00438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzyme stability and function can be affected by various environmental factors, such as temperature, pH, and ionic strength. Enzymes that are located outside the relatively unchanging environment of the cytosol, such as those residing in the periplasmic space of bacteria or extracellularly secreted, are challenged by more fluctuations in the aqueous medium. Bacterial alkaline phosphatases (APs) are generally affected by ionic strength of the medium, but this varies substantially between species. An AP from the marine bacterium Vibrio splendidus (VAP) shows complex pH-dependent activation and stabilization in the 0-1.0 M range of halogen salts and has been hypothesized to specifically bind chloride anions. Here, using X-ray crystallography and anomalous scattering, we have located two chloride binding sites in the structure of VAP, one in the active site and another one at a peripheral site. Further characterization of the binding sites using site-directed mutagenesis and small-angle X-ray scattering showed that upon binding of chloride to the peripheral site, structural dynamics decreased locally, resulting in thermal stabilization of the VAP active conformation. Binding of the chloride ion in the active site did not displace the bound inorganic phosphate product, but it may promote product release by facilitating rotational stabilization of the substrate-binding Arg129. Overall, these results reveal the complex nature and dynamics of chloride binding to enzymes through long-range modulation of electronic potential in the vicinity of the active site, resulting in increased catalytic efficiency and stability.
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Affiliation(s)
- Sigurbjörn Markússon
- Science Institute, University of Iceland, 107 Reykjavik, Iceland.,Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
| | | | - Petri Kursula
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90570 Oulu, Finland.,Biocenter Oulu, University of Oulu, 90570 Oulu, Finland
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23
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Identification and Characterization of a Novel Cold-Adapted GH15 Family Trehalase from the Psychrotolerant Microbacterium phyllosphaerae LW106. FERMENTATION 2022. [DOI: 10.3390/fermentation8100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Psychrophiles inhabiting various cold environments are regarded as having evolved diverse physiological and molecular strategies, such as the accumulation of trehalose to alleviate cold stress. To investigate the possible contributions of trehalose metabolism-related enzymes to cold-adaption in psychrotrophic bacteria and enrich the resource bank of trehalose hydrolysis enzymes, a novel cold-adapted GH15 GA-like trehalase (MpTre15A) from psychrotolerant Microbacteriumphyllosphaerae LW106 isolated from glacier sediments was cloned and characterized. The recombinant MpTre15A from M. phyllosphaerae LW106 was expressed and purified in Escherichia coli BL21(DE3). The purified MpTre15A functioned as a hexamer and displayed maximal activity at pH 5.0 and 50 °C. Substrate specificity assay proved MpTre15A only showed hydrolytic activity toward α,α-trehalose. Site-directed mutation verified the key catalytic sites of Glu392 and Glu557 in MpTre15A. The kcat and kcat/Km values of MpTre15A at 4 °C (104.50 s−1 and 1.6 s−1 mM−1, respectively) were comparable to those observed for thermophilic GH15 trehalases at 50 °C, revealing its typical cold-adaptability. MpTre15A showed a trehalose conversion rate of 100% and 99.4% after 10 min and 15 min of incubation at 50 °C and 37 °C, respectively. In conclusion, this novel cold-adapted α,α-trehalase MpTre15A showed potential application for developing therapeutic enzymes, enzyme-based biosensors, and enzyme additives in the fermentation industry.
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24
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Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect. Int J Mol Sci 2022; 23:ijms23158119. [PMID: 35897698 PMCID: PMC9332260 DOI: 10.3390/ijms23158119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of temperature effects on the structure and function of enzymes is necessary to understand the mechanisms underlying their adaptation to a constantly changing environment. In the current study, we investigated the influence of temperature variation on the activity, structural dynamics, thermal inactivation and denaturation of Photobacterium leiognathi and Vibrio harveyi luciferases belonging to different subfamilies, as well as the role of sucrose in maintaining the enzymes functioning and stability. We used the stopped-flow technique, differential scanning calorimetry and molecular dynamics to study the activity, inactivation rate, denaturation and structural features of the enzymes under various temperatures. It was found that P. leiognathi luciferase resembles the properties of cold-adapted enzymes with high activity in a narrow temperature range and slightly lower thermal stability than V. harveyi luciferase, which is less active, but more thermostable. Differences in activity at the studied temperatures can be associated with the peculiarities of the mobile loop conformational changes. The presence of sucrose does not provide an advantage in activity but increases the stability of the enzymes. Differential scanning calorimetry experiments showed that luciferases probably follow different denaturation schemes.
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25
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Cold-active enzymes in the dairy industry: Insight into cold adaption mechanisms and their applications. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Biochemical Characterisation and Structure Determination of a Novel Cold-Active Proline Iminopeptidase from the Psychrophilic Yeast, Glaciozyma antarctica PI12. Catalysts 2022. [DOI: 10.3390/catal12070722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Microbial proteases constitute one of the most important groups of industrially relevant enzymes. Proline iminopeptidases (PIPs) that specifically release amino-terminal proline from peptides are of major interest for applications in food biotechnology. Proline iminopeptidase has been extensively characterised in bacteria and filamentous fungi. However, no similar reports exist for yeasts. In this study, a protease gene from Glaciozyma antarctica designated as GaPIP was cloned and overexpressed in Escherichia coli. Sequence analyses of the gene revealed a 960 bp open reading frame encoding a 319 amino acid protein (35,406 Da). The purified recombinant GaPIP showed a specific activity of 3561 Umg−1 towards L-proline-p-nitroanilide, confirming its identity as a proline iminopeptidase. GaPIP is a cold-active enzyme with an optimum activity of 30 °C at pH 7.0. The enzyme is stable between pH 7.0 and 8.0 and able to retain its activity at 10–30 °C. Although GaPIP is a serine protease, only 25% inhibition by the serine protease inhibitor, phenylmethanesulfonylfluoride (PMSF) was recorded. This enzyme is strongly inhibited by the presence of EDTA, suggesting that it is a metalloenzyme. The dimeric structure of GaPIP was determined at a resolution of 2.4 Å. To date, GaPIP is the first characterised PIP from yeasts and the structure of GaPIP is the first structure for PIP from eukaryotes.
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van der Ent F, Lund BA, Svalberg L, Purg M, Chukwu G, Widersten M, Isaksen GV, Brandsdal BO, Åqvist J. Structure and Mechanism of a Cold-Adapted Bacterial Lipase. Biochemistry 2022; 61:933-942. [PMID: 35503728 PMCID: PMC9118546 DOI: 10.1021/acs.biochem.2c00087] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural origin of enzyme cold-adaptation has been the subject of considerable research efforts in recent years. Comparative studies of orthologous mesophilic-psychrophilic enzyme pairs found in nature are an obvious strategy for solving this problem, but they often suffer from relatively low sequence identity of the enzyme pairs. Small bacterial lipases adapted to distinctly different temperatures appear to provide an excellent model system for these types of studies, as they may show a very high degree of sequence conservation. Here, we report the first crystal structures of lipase A from the psychrophilic bacterium Bacillus pumilus, which confirm the high structural similarity to the mesophilic Bacillus subtilis enzyme, as indicated by their 81% sequence identity. We further employ extensive QM/MM calculations to delineate the catalytic reaction path and its energetics. The computational prediction of a rate-limiting deacylation step of the enzymatic ester hydrolysis reaction is verified by stopped-flow experiments, and steady-state kinetics confirms the psychrophilic nature of the B. pumilus enzyme. These results provide a useful benchmark for examining the structural basis of cold-adaptation and should now make it possible to disentangle the effects of the 34 mutations between the two enzymes on catalytic properties and thermal stability.
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Affiliation(s)
- Florian van der Ent
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Bjarte A Lund
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Linn Svalberg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Miha Purg
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden
| | - Ghislean Chukwu
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry─BMC, Uppsala University, Biomedical Center, SE-751 23 Uppsala, Sweden
| | - Geir V Isaksen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Bjørn O Brandsdal
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
| | - Johan Åqvist
- Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Tromsø─The Arctic University of Norway, N9037 Tromsø, Norway
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Sheikh T, Hamid B, Baba Z, Iqbal S, Yatoo A, Fatima S, Nabi A, Kanth R, Dar K, Hussain N, Alturki AI, Sunita K, Sayyed R. Extracellular polymeric substances in psychrophilic cyanobacteria: A potential bioflocculant and carbon sink to mitigate cold stress. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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29
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The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization. Biochemistry 2022; 61:514-522. [PMID: 35229609 PMCID: PMC8988307 DOI: 10.1021/acs.biochem.2c00024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The structural principles
of enzyme cold adaptation are of fundamental
interest both for understanding protein evolution and for biotechnological
applications. It has become clear in recent years that structural
flexibility plays a major role in tuning enzyme activity at low temperatures,
which is reflected by characteristic changes in the thermodynamic
activation parameters for psychrophilic enzymes, compared to those
of mesophilic and thermophilic ones. Hence, increased flexibility
of the enzyme surface has been shown to lead to a lower enthalpy and
a more negative entropy of activation, which leads to higher activity
in the cold. This immediately raises the question of how enzyme oligomerization
affects the temperature dependence of catalysis. Here, we address
this issue by computer simulations of the catalytic reaction of a
cold-adapted bacterial short chain dehydrogenase in different oligomeric
states. Reaction free energy profiles are calculated at different
temperatures for the tetrameric, dimeric, and monomeric states of
the enzyme, and activation parameters are obtained from the corresponding
computational Arrhenius plots. The results show that the activation
free energy, enthalpy, and entropy are remarkably insensitive to the
oligomeric state, leading to the conclusion that assembly of the subunit
interfaces does not compromise cold adaptation, even though the mobilities
of interfacial residues are indeed affected.
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Laye VJ, DasSarma S. Double mutations far from the active site affect cold activity in an Antarctic halophilic β-galactosidase. Protein Sci 2022; 31:677-687. [PMID: 34939242 PMCID: PMC8862438 DOI: 10.1002/pro.4264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022]
Abstract
The Antarctic haloarchaeon, Halorubrum lacusprofundi, contains a polyextremophilic family 42 β-galactosidase, which we are using as a model for cold-active enzymes. Divergent amino acid residues in this 78 kDa protein were identified through comparative genomics and hypothesized to be important for cold activity. Six amino acid residues were previously mutated and five were shown by steady-state kinetic analysis to have altered temperature-dependent catalytic activity profiles via effects on Km and/or kcat compared to the wild-type enzyme. In this follow-up study, double-mutated enzymes were constructed and tested for temperature effects, including two new tandem residue pairs (N180T/A181T and T383A/S384A), and pairwise combination of the single residue mutations (N251D, F387L, I476V, and V482L). All double-mutated enzymes were found to be more catalytically active at moderate and/or less active at colder temperatures than wild-type, with both Km and kcat effects observed for the two tandem mutations. For pairwise combinations, a Km effect was seen when the surface exposed F387L mutation located in a domain A TIM barrel α helix 19 Å from the active site was combined with two internal residues, N251D or V482L. When another surface exposed mutation I476V located in a coiled region of domain B 25 Å from the active site was paired with N251D or V482L, a kcat effect was observed. These results indicate that temperature-dependent kinetic effects may be complex and subtle and are mediated by a combination of a small number of residues distant from the active site via changes to the hydration shell and/or perturbation of internal packing.
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Affiliation(s)
- Victoria J. Laye
- Institute of Marine and Environmental TechnologyUniversity System of MarylandBaltimoreMarylandUSA,Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
| | - Shiladitya DasSarma
- Institute of Marine and Environmental TechnologyUniversity System of MarylandBaltimoreMarylandUSA,Department of Microbiology and ImmunologyUniversity of Maryland School of MedicineBaltimoreMarylandUSA
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31
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Biochemical Characterization and Cold-Adaption Mechanism of A PL-17 Family Alginate Lyase Aly23 from Marine Bacterium Pseudoalteromonas sp. ASY5 and Its Application for Oligosaccharides Production. Mar Drugs 2022; 20:md20020126. [PMID: 35200655 PMCID: PMC8876620 DOI: 10.3390/md20020126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 02/01/2023] Open
Abstract
As an important enzyme involved in the marine carbon cycle, alginate lyase has received extensive attention because of its excellent degradation ability on brown algae, which is widely utilized for alginate oligosaccharide preparation or bioethanol production. In comparison with endo-type alginate lyases (PL-5, PL-7, and PL-18 families), limited studies have focused on PL-17 family alginate lyases, especially for those with special characteristics. In this study, a novel PL-17 family alginate lyase, Aly23, was identified and cloned from the marine bacterium Pseudoalteromonas carrageenovora ASY5. Aly23 exhibited maximum activity at 35 °C and retained 48.93% of its highest activity at 4 °C, representing an excellent cold-adaptation property. Comparative molecular dynamics analysis was implemented to explore the structural basis for the cold-adaptation property of Aly23. Aly23 had a high substrate preference for poly β-D-mannuronate and exhibited both endolytic and exolytic activities; its hydrolysis reaction mainly produced monosaccharides, disaccharides, and trisaccharides. Furthermore, the enzymatic hydrolyzed oligosaccharides displayed good antioxidant activities to reduce ferric and scavenge radicals, such as hydroxyl, ABTS+, and DPPH. Our work demonstrated that Aly23 is a promising cold-adapted biocatalyst for the preparation of natural antioxidants from brown algae.
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Stark C, Bautista-Leung T, Siegfried J, Herschlag D. Systematic investigation of the link between enzyme catalysis and cold adaptation. eLife 2022; 11:72884. [PMID: 35019838 PMCID: PMC8754429 DOI: 10.7554/elife.72884] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/24/2021] [Indexed: 11/13/2022] Open
Abstract
Cold temperature is prevalent across the biosphere and slows the rates of chemical reactions. Increased catalysis has been predicted to be a dominant adaptive trait of enzymes to reduced temperature, and this expectation has informed physical models for enzyme catalysis and influenced bioprospecting strategies. To systematically test rate enhancement as an adaptive trait to cold, we paired kinetic constants of 2223 enzyme reactions with their organism's optimal growth temperature (TGrowth) and analyzed trends of rate constants as a function of TGrowth. These data do not support a general increase in rate enhancement in cold adaptation. In the model enzyme ketosteroid isomerase (KSI), there is prior evidence for temperature adaptation from a change in an active site residue that results in a tradeoff between activity and stability. Nevertheless, we found that little of the rate constant variation for 20 KSI variants was accounted for by TGrowth. In contrast, and consistent with prior expectations, we observed a correlation between stability and TGrowth across 433 proteins. These results suggest that temperature exerts a weaker selection pressure on enzyme rate constants than stability and that evolutionary forces other than temperature are responsible for the majority of enzymatic rate constant variation.
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Affiliation(s)
- Catherine Stark
- ChEM-H, Stanford University, Stanford, United States.,Department of Biochemistry, Stanford University, Stanford, United States
| | | | - Joanna Siegfried
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Daniel Herschlag
- ChEM-H, Stanford University, Stanford, United States.,Department of Biochemistry, Stanford University, Stanford, United States.,Department of Chemical Engineering, Stanford University, Stanford, United States
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Piszkin L, Bowman J. Extremophile enzyme optimization for low temperature and high salinity are fundamentally incompatible. Extremophiles 2021; 26:5. [PMID: 34940913 DOI: 10.1007/s00792-021-01254-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/09/2021] [Indexed: 11/25/2022]
Abstract
The evolutionary mechanisms behind cold and high-saline co-adaptation of proteins are not thoroughly understood. To explore how enzymes evolve in response to multiple environmental pressures we developed a novel in silico method to model the directed evolution of proteins, the Protein Evolution Parameter Calculator (PEPC). PEPC carries out single amino acid substitutions that lead to improvements in the selected user-defined parameters. To investigate the evolutionary relationship between increased flexibility and decreased isoelectric point, which are presumed indicators of cold and saline adaptation in proteins, we applied PEPC to a subset of core haloarchaea orthologous group (cHOG) proteins from the mesophilic Halobacterium salinarum NRC-1 and cold-tolerant Halorubrum lacusprofundi strain ATCC 49239. The results suggest that mutations that increase flexibility will also generally increase isoelectric point. These findings suggest that enzyme adaptation to low temperature and high salinity might be evolutionarily counterposed based on the structural characteristics of probable amino acid mutations. This may help to explain the apparent lack of truly psychrophilic halophiles in nature, and why microbes adapted to polar hypersaline environments typically have mesophilic temperature optima. A better understanding of protein evolution to extremely cold and salty conditions will aid in our understanding of where and how life is distributed on Earth and in our solar system.
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Affiliation(s)
- Luke Piszkin
- Department of Physics, UC San Diego, La Jolla, CA, USA.
| | - Jeff Bowman
- Scripps Institution of Oceanography, UC San Diego, La Jolla, CA, USA
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34
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Nguyen TT, Hoang T, Tran KN, Kim H, Jang SH, Lee C. Essential roles of buried phenylalanine in the structural stability of thioredoxin from a psychrophilic Arctic bacterium Sphingomonas sp. PLoS One 2021; 16:e0261123. [PMID: 34910731 PMCID: PMC8673628 DOI: 10.1371/journal.pone.0261123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 11/21/2022] Open
Abstract
Thioredoxin (Trx), a small redox protein, exhibits thermal stability at high temperatures regardless of its origin, including psychrophiles. Trxs have a common structure consisting of the central β-sheet flanked by an aliphatic cluster on one side and an aromatic cluster on the other side. Although the roles of aromatic amino acids in the folding and stability of proteins have been studied extensively, the contributions of aromatic residues to the stability and function of Trx, particularly Trxs from cold-adapted organisms, have not been fully elucidated. This study examined the roles of aromatic amino acids in the aromatic cluster of a Trx from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621 (SpTrx). The aromatic cluster of SpTrx was comprised of W11, F26, F69, and F80, in which F26 at the β2 terminus was buried inside. The substitution of tyrosine for F26 changed the SpTrx conformation substantially compared to that of F69 and F80. Further biochemical and spectroscopic investigations on F26 showed that the F26Y, F26W, and F26A mutants resulted in structural instability of SpTrx in both urea- and temperature-induced unfolding and lower insulin reduction activities. The Trx reductase (SpTR) showed lower catalytic efficiencies against F26 mutants compared to the wild-type SpTrx. These results suggest that buried F26 is essential for maintaining the active-site conformation of SpTrx as an oxidoreductase and its structural stability for interactions with SpTR at colder temperatures.
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Affiliation(s)
- Thu-Thuy Nguyen
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Kiet N. Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Hyeonji Kim
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Sei-Heon Jang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
- * E-mail:
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35
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Shen L, Zhang S, Chen G. Regulated strategies of cold-adapted microorganisms in response to cold: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:68006-68024. [PMID: 34648167 DOI: 10.1007/s11356-021-16843-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
There are a large number of active cold-adapted microorganisms in the perennial cold environment. Due to their high-efficiency and energy-saving catalytic properties, cold-adapted microorganisms have become valuable natural resources with potential in various biological fields. In this study, a series of cold response strategies for microorganisms were summarized. This mainly involves the regulation of cell membrane fluidity, synthesis of cold adaptation proteins, regulators and metabolic changes, energy supply, and reactive oxygen species. Also, the potential of biocatalysts produced by cold-adapted microorganisms including cold-active enzymes, ice-binding proteins, polyhydroxyalkanoates, and surfactants was introduced, which provided a guidance for expanding its application values. Overall, new insights were obtained on response strategies of microorganisms to cold environments in this review. This will deepen the understanding of the cold tolerance mechanism of cold-adapted microorganisms, thus promoting the establishment and application of low-temperature biotechnology.
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Affiliation(s)
- Lijun Shen
- College of Life Sciences, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
| | - Guang Chen
- College of Life Sciences, Jilin Agricultural University, Changchun, China.
- Key Laboratory of Straw Biology and Utilization, The Ministry of Education, Changchun, China.
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36
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Lund BA, Brandsdal BO. ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments. Molecules 2021; 26:molecules26237155. [PMID: 34885737 PMCID: PMC8658824 DOI: 10.3390/molecules26237155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/03/2022] Open
Abstract
The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by characterizing the Bacillus pumilus LipA enzyme. Our results for the lipase show that the enzyme is psychrotolerant, with an activation energy of 15.3 kcal/mol for the chromogenic substrate para-nitrophenyl butyrate. Our results demonstrate that this can produce equivalent curves to the traditional approach while requiring significantly less sample, labour and time. Our method is further validated by characterizing three α-amylases from different species and habitats. The experiments with the α-amylases show that the approach works over a wide range of temperatures and clearly differentiates between psychrophilic, mesophilic and thermophilic enzymes. The methodology is released as an open-source implementation in Python, available online or used locally. This method of determining the activation parameters can make studies of the temperature dependence of enzyme catalysis more widely adapted to understand how enzymes have evolved to function in extreme environments. Moreover, the thermodynamic parameters that are estimated serve as functional validations of the empirical valence bond calculations of enzyme catalysis.
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Zhang LL, Jiang XH, Xiao XF, Zhang WX, Shi YQ, Wang ZP, Zhou HX. Expression and Characterization of a Novel Cold-Adapted Chitosanase from Marine Renibacterium sp. Suitable for Chitooligosaccharides Preparation. Mar Drugs 2021; 19:596. [PMID: 34822467 PMCID: PMC8620120 DOI: 10.3390/md19110596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/10/2021] [Accepted: 10/19/2021] [Indexed: 01/07/2023] Open
Abstract
(1) Background: Chitooligosaccharides (COS) have numerous applications due to their excellent properties. Chitosan hydrolysis using chitosanases has been proposed as an advisable method for COS preparation. Although many chitosanases from various sources have been identified, the cold-adapted ones with high stability are still rather rare but required. (2) Methods: A novel chitosanase named CsnY from marine bacterium Renibacterium sp. Y82 was expressed in Escherichia coli, following sequence analysis. Then, the characterizations of recombinant CsnY purified through Ni-NTA affinity chromatography were conducted, including effects of pH and temperature, effects of metal ions and chemicals, and final product analysis. (3) Results: The GH46 family chitosanase CsnY possessed promising thermostability at broad temperature range (0-50 °C), and with optimal activity at 40 °C and pH 6.0, especially showing relatively high activity (over 80% of its maximum activity) at low temperatures (20-30 °C), which demonstrated the cold-adapted property. Common metal ions or chemicals had no obvious effect on CsnY except Mn2+ and Co2+. Finally, CsnY was determined to be an endo-type chitosanase generating chitodisaccharides and -trisaccharides as main products, whose total concentration reached 56.74 mM within 2 h against 2% (w/v) initial chitosan substrate. (4) Conclusions: The results suggest the cold-adapted CsnY with favorable stability has desirable potential for the industrial production of COS.
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Affiliation(s)
- Lin-Lin Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266510, China; (L.-L.Z.); (X.-F.X.); (W.-X.Z.); (Y.-Q.S.)
| | - Xiao-Hua Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
| | - Xin-Feng Xiao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266510, China; (L.-L.Z.); (X.-F.X.); (W.-X.Z.); (Y.-Q.S.)
| | - Wen-Xiu Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266510, China; (L.-L.Z.); (X.-F.X.); (W.-X.Z.); (Y.-Q.S.)
| | - Yi-Qian Shi
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266510, China; (L.-L.Z.); (X.-F.X.); (W.-X.Z.); (Y.-Q.S.)
| | - Zhi-Peng Wang
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao 266109, China
| | - Hai-Xiang Zhou
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
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38
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Wang W, Dasetty S, Sarupria S, Blenner M. Rational engineering of low temperature activity in thermoalkalophilic Geobacillus thermocatenulatus lipase. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Mozzicafreddo M, Pucciarelli S, Swart EC, Piersanti A, Emmerich C, Migliorelli G, Ballarini P, Miceli C. The macronuclear genome of the Antarctic psychrophilic marine ciliate Euplotes focardii reveals new insights on molecular cold adaptation. Sci Rep 2021; 11:18782. [PMID: 34548559 PMCID: PMC8455672 DOI: 10.1038/s41598-021-98168-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/05/2021] [Indexed: 11/23/2022] Open
Abstract
The macronuclear (MAC) genomes of ciliates belonging to the genus Euplotes species are comprised of numerous small DNA molecules, nanochromosomes, each typically encoding a single gene. These genomes are responsible for all gene expression during vegetative cell growth. Here, we report the analysis of the MAC genome from the Antarctic psychrophile Euplotes focardii. Nanochromosomes containing bacterial sequences were not found, suggesting that phenomena of horizontal gene transfer did not occur recently, even though this ciliate species has a substantial associated bacterial consortium. As in other euplotid species, E. focardii MAC genes are characterized by a high frequency of translational frameshifting. Furthermore, in order to characterize differences that may be consequent to cold adaptation and defense to oxidative stress, the main constraints of the Antarctic marine microorganisms, we compared E. focardii MAC genome with those available from mesophilic Euplotes species. We focussed mainly on the comparison of tubulin, antioxidant enzymes and heat shock protein (HSP) 70 families, molecules which possess peculiar characteristic correlated with cold adaptation in E. focardii. We found that α-tubulin genes and those encoding SODs and CATs antioxidant enzymes are more numerous than in the mesophilic Euplotes species. Furthermore, the phylogenetic trees showed that these molecules are divergent in the Antarctic species. In contrast, there are fewer hsp70 genes in E. focardii compared to mesophilic Euplotes and these genes do not respond to thermal stress but only to oxidative stress. Our results suggest that molecular adaptation to cold and oxidative stress in the Antarctic environment may not only be due to particular amino acid substitutions but also due to duplication and divergence of paralogous genes.
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Affiliation(s)
- Matteo Mozzicafreddo
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy.
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Estienne C Swart
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | | | - Giovanna Migliorelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Patrizia Ballarini
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032, Camerino, MC, Italy
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40
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Varliero G, Rafiq M, Singh S, Summerfield A, Sgouridis F, Cowan DA, Barker G. Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost. FEMS Microbiol Ecol 2021; 97:fiab127. [PMID: 34468725 PMCID: PMC8445667 DOI: 10.1093/femsec/fiab127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Permafrost represents a reservoir for the biodiscovery of cold-adapted proteins which are advantageous in industrial and medical settings. Comparisons between different thermo-adapted proteins can give important information for cold-adaptation bioengineering. We collected permafrost active layer samples from 34 points along a proglacial transect in southwest Greenland. We obtained a deep read coverage assembly (>164x) from nanopore and Illumina sequences for the purposes of i) analysing metagenomic and metatranscriptomic trends of the microbial community of this area, and ii) creating the Cold-Adapted Predicted Protein (CAPP) database. The community showed a similar taxonomic composition in all samples along the transect, with a solid permafrost-shaped community, rather than microbial trends typical of proglacial systems. We retrieved 69 high- and medium-quality metagenome-assembled clusters, 213 complete biosynthetic gene clusters and more than three million predicted proteins. The latter constitute the CAPP database that can provide cold-adapted protein sequence information for protein- and taxon-focused amino acid sequence modifications for the future bioengineering of cold-adapted enzymes. As an example, we focused on the enzyme polyphenol oxidase, and demonstrated how sequence variation information could inform its protein engineering.
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Affiliation(s)
- Gilda Varliero
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Muhammad Rafiq
- Department of Microbiology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology, Engineering and Management Sciences, Airport Road, Baleli, Quetta, Balochistan, Pakistan
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Swati Singh
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
- School of Chemistry, University of Bristol, Cantock's Cl, Bristol BS8 1TS, United Kingdom
| | - Annabel Summerfield
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
| | - Fotis Sgouridis
- School of Geographical Sciences, University of Bristol, Wills Memorial Building, Bristol BS8 1RL, United Kingdom
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Natural Sciences 2 Building, Private Bag X20, Hatfield 0028, South Africa
| | - Gary Barker
- School of Life Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom
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41
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Chen Q, Wu Y, Huang Z, Zhang W, Mu W. Molecular Characterization of a Mesophilic Cellobiose 2-Epimerase That Maintains a High Catalytic Efficiency at Low Temperatures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8268-8275. [PMID: 34231359 DOI: 10.1021/acs.jafc.1c02025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cellobiose 2-epimerase (CE) can catalyze bioconversion of lactose to its prebiotic derivative epilactose. The catalytic property of a novel CE from Treponema brennaborense (Trbr-CE) was investigated. Trbr-CE showed the highest catalytic efficiency of epimerization toward lactose among all of the previously reported CEs. This enzyme's specific activity could reach as high as 208.5 ± 5.3 U/mg at its optimum temperature, which is 45 °C. More importantly, this enzyme demonstrated a considerably high activity at low temperatures, suggesting Trbr-CE as a promising enzyme for industrial low-temperature production of epilactose. This structurally flexible enzyme exhibited a comparatively high binding affinity toward substrates, which was confirmed by both experimental verification and computational analysis. Molecular dynamics (MD) simulations and binding free energy calculations were applied to provide insights into molecular recognition upon temperature changes. Compared with thermophilic CEs, Trbr-CE presents a more negative enthalpy change and a higher entropy change when the temperature drops.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yanchang Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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42
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Kaspar F, Wolff DS, Neubauer P, Kurreck A, Arcus VL. pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius. Biochemistry 2021; 60:1573-1577. [PMID: 33955225 DOI: 10.1021/acs.biochem.1c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, the effects of pH and (de)protonation on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from Geobacillus thermoglucosidasius across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pKa values. Our analysis revealed the presence of a measurable activation heat capacity change ΔCp⧧ in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution that has a minor influence on ΔCp⧧ but conveys a significant kinetic effect by decreasing the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction conditions can affect the rate, affinity, and thermodynamic phenomena independently of one another.
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Affiliation(s)
- Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Darian S Wolff
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Vickery L Arcus
- Te Aka Ma̅tuatua-School of Science, Te Whare Wa̅nanga o Waikato-University of Waikato, Hamilton 3240, New Zealand
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43
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Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
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Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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44
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Mangiagalli M, Barbiroli A, Santambrogio C, Ferrari C, Nardini M, Lotti M, Brocca S. The activity and stability of a cold-active acylaminoacyl peptidase rely on its dimerization by domain swapping. Int J Biol Macromol 2021; 181:263-274. [PMID: 33775759 DOI: 10.1016/j.ijbiomac.2021.03.150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023]
Abstract
The study of enzymes from extremophiles arouses interest in Protein Science because of the amazing solutions these proteins adopt to cope with extreme conditions. Recently solved, the structure of the psychrophilic acyl aminoacyl peptidase from Sporosarcina psychrophila (SpAAP) pinpoints a mechanism of dimerization unusual for this class of enzymes. The quaternary structure of SpAAP relies on a domain-swapping mechanism involving the N-terminal A1 helix. The A1 helix is conserved among homologous mesophilic and psychrophilic proteins and its deletion causes the formation of a monomeric enzyme, which is inactive and prone to aggregate. Here, we investigate the dimerization mechanism of SpAAP through the analysis of chimeric heterodimers where a protomer lacking the A1 helix combines with a protomer carrying the inactivated catalytic site. Our results indicate that the two active sites are independent, and that a single A1 helix is sufficient to partially recover the quaternary structure and the activity of chimeric heterodimers. Since catalytically competent protomers are unstable and inactive unless they dimerize, SpAAP reveals as an "obligomer" for both structural and functional reasons.
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Affiliation(s)
- Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
| | - Alberto Barbiroli
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Cristian Ferrari
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Marco Nardini
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy.
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45
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Abstract
QM/MM simulations have become an indispensable tool in many chemical and biochemical investigations. Considering the tremendous degree of success, including recognition by a 2013 Nobel Prize in Chemistry, are there still "burning challenges" in QM/MM methods, especially for biomolecular systems? In this short Perspective, we discuss several issues that we believe greatly impact the robustness and quantitative applicability of QM/MM simulations to many, if not all, biomolecules. We highlight these issues with observations and relevant advances from recent studies in our group and others in the field. Despite such limited scope, we hope the discussions are of general interest and will stimulate additional developments that help push the field forward in meaningful directions.
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Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics, and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Tanmoy Pal
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Luke Xie
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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46
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Hjörleifsson JG, Helland R, Magnúsdóttir M, Ásgeirsson B. The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop. FEBS Open Bio 2020; 11:173-184. [PMID: 33197282 PMCID: PMC7780099 DOI: 10.1002/2211-5463.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold‐adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B‐factors of the R336L crystal structure to that of the wild‐type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half‐of‐sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).
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Affiliation(s)
| | - Ronny Helland
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT, The Arctic University of Tromsø, Norway
| | - Manuela Magnúsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
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47
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Carretas-Valdez MI, Moreno-Cordova EN, Ibarra-Hernandez BG, Cinco-Moroyoqui FJ, Castillo-Yañez FJ, Casas-Flores S, Osuna-Amarillas PS, Islas-Osuna MA, Arvizu-Flores AA. Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant. Int J Biol Macromol 2020; 164:2701-2710. [PMID: 32827617 DOI: 10.1016/j.ijbiomac.2020.08.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.
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Affiliation(s)
- Manuel I Carretas-Valdez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Elena N Moreno-Cordova
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Brisa G Ibarra-Hernandez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Cinco-Moroyoqui
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Castillo-Yañez
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, Col. Lomas 4a sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Pablo S Osuna-Amarillas
- Universidad Estatal de Sonora, Carretera Navojoa-Huatabampo km 5, Navojoa, Sonora 85874, Mexico
| | - Maria A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, Laboratorio de Genética y Biología Molecular de Plantas, Carr. Gustavo Enrique Astiazarán Rosas, N0. 46. Col. La Victoria, Hermosillo, Sonora 83304, Mexico.
| | - Aldo A Arvizu-Flores
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico.
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48
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Arcus VL, van der Kamp MW, Pudney CR, Mulholland AJ. Enzyme evolution and the temperature dependence of enzyme catalysis. Curr Opin Struct Biol 2020; 65:96-101. [DOI: 10.1016/j.sbi.2020.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/25/2020] [Accepted: 06/04/2020] [Indexed: 10/23/2022]
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49
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Orlando M, Pucciarelli S, Lotti M. Endolysins from Antarctic Pseudomonas Display Lysozyme Activity at Low Temperature. Mar Drugs 2020; 18:E579. [PMID: 33233712 PMCID: PMC7699920 DOI: 10.3390/md18110579] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/18/2022] Open
Abstract
Organisms specialized to thrive in cold environments (so-called psychrophiles) produce enzymes with the remarkable ability to catalyze chemical reactions at low temperature. Cold activity relies on adaptive changes in the proteins' sequence and structural organization that result in high conformational flexibility. As a consequence of flexibility, several such enzymes are inherently heat sensitive. Cold-active enzymes are of interest for application in a number of bioprocesses, where cold activity coupled with easy thermal inactivation can be of advantage. We describe the biochemical and functional properties of two glycosyl hydrolases (named LYS177 and LYS188) of family 19 (GH19), identified in the genome of an Antarctic marine Pseudomonas. Molecular evolutionary analysis placed them in a group of characterized GH19 endolysins active on lysozyme substrates, such as peptidoglycan. Enzyme activity peaks at about 25-35 °C and 40% residual activity is retained at 5 °C. LYS177 and LYS188 are thermolabile, with Tm of 52 and 45 °C and half-lives of 48 and 12 h at 37 °C, respectively. Bioinformatics analyses suggest that low heat stability may be associated to temperature-driven increases in local flexibility occurring mainly in a specific region of the polypeptide that is predicted to contain hot spots for aggregation.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy;
| | - Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, 20126 Milano, Italy;
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50
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Matricon P, Suresh RR, Gao ZG, Panel N, Jacobson KA, Carlsson J. Ligand design by targeting a binding site water. Chem Sci 2020; 12:960-968. [PMID: 34163862 PMCID: PMC8179138 DOI: 10.1039/d0sc04938g] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design. Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.![]()
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Affiliation(s)
- Pierre Matricon
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Nicolas Panel
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
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