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Rodella C, Lazaridi S, Lemmin T. TemBERTure: advancing protein thermostability prediction with deep learning and attention mechanisms. BIOINFORMATICS ADVANCES 2024; 4:vbae103. [PMID: 39040220 PMCID: PMC11262459 DOI: 10.1093/bioadv/vbae103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/14/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024]
Abstract
Motivation Understanding protein thermostability is essential for numerous biotechnological applications, but traditional experimental methods are time-consuming, expensive, and error-prone. Recently, deep learning (DL) techniques from natural language processing (NLP) was extended to the field of biology, since the primary sequence of proteins can be viewed as a string of amino acids that follow a physicochemical grammar. Results In this study, we developed TemBERTure, a DL framework that predicts thermostability class and melting temperature from protein sequences. Our findings emphasize the importance of data diversity for training robust models, especially by including sequences from a wider range of organisms. Additionally, we suggest using attention scores from Deep Learning models to gain deeper insights into protein thermostability. Analyzing these scores in conjunction with the 3D protein structure can enhance understanding of the complex interactions among amino acid properties, their positioning, and the surrounding microenvironment. By addressing the limitations of current prediction methods and introducing new exploration avenues, this research paves the way for more accurate and informative protein thermostability predictions, ultimately accelerating advancements in protein engineering. Availability and implementation TemBERTure model and the data are available at: https://github.com/ibmm-unibe-ch/TemBERTure.
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Affiliation(s)
- Chiara Rodella
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Symela Lazaridi
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern CH-3012, Switzerland
| | - Thomas Lemmin
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bern CH-3012, Switzerland
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2
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Sánchez-Morán H, Kaar JL, Schwartz DK. Supra-biological performance of immobilized enzymes enabled by chaperone-like specific non-covalent interactions. Nat Commun 2024; 15:2299. [PMID: 38485940 PMCID: PMC10940687 DOI: 10.1038/s41467-024-46719-5] [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: 09/07/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Designing complex synthetic materials for enzyme immobilization could unlock the utility of biocatalysis in extreme environments. Inspired by biology, we investigate the use of random copolymer brushes as dynamic immobilization supports that enable supra-biological catalytic performance of immobilized enzymes. This is demonstrated by immobilizing Bacillus subtilis Lipase A on brushes doped with aromatic moieties, which can interact with the lipase through multiple non-covalent interactions. Incorporation of aromatic groups leads to a 50 °C increase in the optimal temperature of lipase, as well as a 50-fold enhancement in enzyme activity. Single-molecule FRET studies reveal that these supports act as biomimetic chaperones by promoting enzyme refolding and stabilizing the enzyme's folded and catalytically active state. This effect is diminished when aromatic residues are mutated out, suggesting the importance of π-stacking and π-cation interactions for stabilization. Our results underscore how unexplored enzyme-support interactions may enable uncharted opportunities for using enzymes in industrial biotransformations.
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Affiliation(s)
- Héctor Sánchez-Morán
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA.
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA.
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3
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Benrezkallah D. Molecular dynamics simulations at high temperatures of the Aeropyrum pernix L7Ae thermostable protein: Insight into the unfolding pathway. J Mol Graph Model 2024; 127:108700. [PMID: 38183846 DOI: 10.1016/j.jmgm.2023.108700] [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: 09/07/2023] [Revised: 11/27/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Most life forms on earth live at temperatures below 50 °C. Within these organisms are proteins that form the three-dimensional structures essential to their biological activity and function. However, some thermophilic life forms can resist higher temperatures and have corresponding adaptations to preserve protein function at these high temperatures. Among the structural factors responsible for this resistance of thermophilic proteins to high temperatures is the presence of additional hydrogen bonds in the thermophilic proteins, which means that the structure of the protein is more resistant to unfolding. Similarly, thermostable proteins are rich in structure-stabilizing salt bridges and/or disulfide bridges. In this context, we perform multiple replica molecular dynamics simulations at different temperatures on the Aeropyrum pernix (L7Ae) protein (from the crenarchaeal species A. pernix), known for its high melting temperature, and this in the aim to elucidate the structural factors responsible for its high thermostability. The results reveal that between the most sensitive regions of the protein to the increase of temperature are the loops L1, and L5, which surround the hydrophobic core region of the protein, besides the loop L9, and the C-terminal α5 region. This latter is the longer alpha helix of the protein secondary structure motifs and it is the first to be denaturated at 450 K, while the rest of the protein secondary structure motifs at this temperature were intact. The mechanism of unfolding that follows this protein at 550 K is similar to other thermophile proteins found in literature, with the opening of the loops that surround the hydrophobic core of the protein. So, the latter is completely exposed to the solvent, and partially denatured. The total denaturation process of the protein takes an average time of 40 ns to be achieved. Our investigation also shows that all the calculated salt bridges, with distances less than or equal to 6 A°, are on the periphery part of the protein, exposed to the solvent. However, the hydrophobic core of the protein is not involved in the formation of salt bridges, but rather with formation of some important hydrogen bondings that still persist even at 450 K. So, optimizing hydrogen bonding, near or within the core region, at high temperatures is a strategy that follows this thermostable protein to protect its hydrophobic core from denaturation, and ensure the thermal stability of the protein.
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Affiliation(s)
- Djamila Benrezkallah
- Department of Basic Teachings in Sciences and Technologies (EBST), Faculty of Technology, Djillali Liabes University, Ben M'Hidi BP 89, Sidi Bel Abbes 22000, Algeria; LCPM Laboratory, Chemistry Department, Faculty of Exact and Applied Sciences, University Oran 1 Ahmed Ben Bella, El Mnaouer BP 1524, Oran 31000, Algeria.
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4
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Senthilkumar S, Mahesh S, Jaisankar S, Yennamalli RM. Surface exposed and charged residues drive thermostability in fungi. Proteins 2023. [PMID: 37909647 DOI: 10.1002/prot.26623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023]
Abstract
Fungi, though mesophilic, include thermophilic and thermostable species, as well. The thermostability of proteins observed in these fungi is most likely to be attributed to several molecular factors, such as the presence of salt bridges and hydrogen bond interactions between side chains. These factors cannot be generalized for all fungi. Factors impacting thermostability can guide how fungal thermophilic proteins gain thermostability. We curated a dataset of proteins for 14 thermophilic fungi and their evolutionarily closer mesophiles. Additionally, the proteome of Chaetomium thermophilum and its evolutionarily related mesophile Chaetomium globosum was analyzed. Using eggNOG, we categorized the proteomes into clusters of orthologous groups (COGs). While the individual count of proteins is over-represented in mesophiles (for COGs S, G, L, and Q), there are certain features that are significantly enriched in thermophiles (such as charged residues, exposed residues, polar residues, etc.). Since fungi are known to be cellulolytic and chitinolytic by nature, we selected 37 existing carbohydrate-active enzymes (CAZyme) families in Eurotiales, Mucorales, and Sordariales. We looked at closely similar sequences and their modeled structures for further comparison. Comparing solvent accessibilities of thermophilic and mesophilic proteins, exposed and intermediate residues are observed higher in thermophiles whereas buried residues are observed higher in mesophiles. For specific five CAZYme families (GH7, GH11, GH18, GH45, and CBM1) we looked at position-specific substitutions between thermophiles and mesophiles. We also found that there are relatively more intramolecular interactions in thermophiles compared to mesophiles. Thus, we found factors such as surface exposed residues and charged residues that are highly likely to impart thermostability in fungi, and this study sets the stage for further studies in the area of fungal thermostability.
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Affiliation(s)
- Shricharan Senthilkumar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sankar Mahesh
- Department of Biotechnology, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Subachandran Jaisankar
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Ragothaman M Yennamalli
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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5
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Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins. Pharmaceutics 2022; 14:pharmaceutics14112533. [PMID: 36432723 PMCID: PMC9699111 DOI: 10.3390/pharmaceutics14112533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
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Öten AM, Atak E, Taktak Karaca B, Fırtına S, Kutlu A. Discussing the roles of proline and glycine from the perspective of cold adaptation in lipases and cellulases. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2124111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Ahmet Melih Öten
- Biology Education Center, Faculty of Science and Technology, Uppsala University, Uppsala, Sweden
| | - Evren Atak
- Bioinformatics and System Biology, Bioengineering Department, Gebze Technical University, Kocaeli, Turkey
| | - Banu Taktak Karaca
- Molecular Biology & Genetics Department, Faculty of Natural Science and Engineering, Atlas University, Istanbul, Turkey
| | - Sinem Fırtına
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
| | - Aslı Kutlu
- Bioinformatics & Genetics, Faculty of Natural Science and Engineering, İstinye University, Istanbul, Turkey
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Zhang W, Zhang Y, Lu Y, Herman RA, Zhang S, Hu Y, Zhao W, Wang J, You S. More efficient barley malting under catalyst: thermostability improvement of a β-1,3-1,4-glucanase through surface charge engineering with higher activity. Enzyme Microb Technol 2022; 162:110151. [DOI: 10.1016/j.enzmictec.2022.110151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/25/2022]
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Yuvaraj I, Chaudhary SK, Jeyakanthan J, Sekar K. Structure of the hypothetical protein TTHA1873 from Thermus thermophilus. Acta Crystallogr F Struct Biol Commun 2022; 78:338-346. [PMID: 36048084 PMCID: PMC9435673 DOI: 10.1107/s2053230x22008457] [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: 06/01/2022] [Accepted: 08/23/2022] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of an uncharacterized hypothetical protein, TTHA1873 from Thermus thermophilus, has been determined by X-ray crystallography to a resolution of 1.78 Å using the single-wavelength anomalous dispersion method. The protein crystallized as a dimer in two space groups: P43212 and P6122. Structural analysis of the hypothetical protein revealed that the overall fold of TTHA1873 has a β-sandwich jelly-roll topology with nine β-strands. TTHA1873 is a dimeric metal-binding protein that binds to two Ca2+ ions per chain, with one on the surface and the other stabilizing the dimeric interface of the two chains. A structural homology search indicates that the protein has moderate structural similarity to one domain of cell-surface proteins or agglutinin receptor proteins. Red blood cells showed visible agglutination at high concentrations of the hypothetical protein.
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Affiliation(s)
- I. Yuvaraj
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Santosh Kumar Chaudhary
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - J. Jeyakanthan
- Structural Biology and Bio Computing Laboratory, Department of Bioinformatics, Alagappa University, Karaikudi 630 004, India
| | - K. Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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9
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Fever as an evolutionary agent to select immune complexes interfaces. Immunogenetics 2022; 74:465-474. [PMID: 35545703 PMCID: PMC9094598 DOI: 10.1007/s00251-022-01263-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/08/2022] [Indexed: 11/10/2022]
Abstract
We herein analyzed all available protein–protein interfaces of the immune complexes from the Protein Data Bank whose antigens belong to pathogens or cancers that are modulated by fever in mammalian hosts. We also included, for comparison, protein interfaces from immune complexes that are not significantly modulated by the fever response. We highlight the distribution of amino acids at these viral, bacterial, protozoan and cancer epitopes, and at their corresponding paratopes that belong strictly to monoclonal antibodies. We identify the “hotspots”, i.e. residues that are highly connected at such interfaces, and assess the structural, kinetic and thermodynamic parameters responsible for complex formation. We argue for an evolutionary pressure for the types of residues at these protein interfaces that may explain the role of fever as a selective force for optimizing antibody binding to antigens.
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10
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Sen S, Sarkar M. Insights on Rigidity and Flexibility at the Global and Local Levels of Protein Structures and Their Roles in Homologous Psychrophilic, Mesophilic, and Thermophilic Proteins: A Computational Study. J Chem Inf Model 2022; 62:1916-1932. [PMID: 35412825 DOI: 10.1021/acs.jcim.1c01381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rigidity and flexibility of homologous psychrophilic (P), mesophilic (M), and thermophilic (T) proteins have been investigated at the global and local levels in terms of "packing factors" and "atomic fluctuations" obtained from B-factors. For comparison of atomic fluctuations, correction of errors by considering errors in B-factors from all sources in a consolidated manner and conversion of the fluctuations to the same temperature have been suggested and validated. The results indicate no differences in the global values like the average packing factor among the three classes of protein homologues, but at local levels there are differences. A comparison of homologous protein triplets show that the average atomic fluctuations at a given temperature mainly obey the order P > M > T. Packing factors and the atomic fluctuations are anti-correlated, suggesting that altering the rigidity of the active site might be a potential strategy to make tailor-made psychrophilic or thermophilic proteins from their mesophilic homologues. The computer codes developed and used in this work are available at the link https://github.com/Munna-Sarkar/proteins-rigidity-flexibility.git.
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Affiliation(s)
- Srikanta Sen
- Molecular Modeling Section, Biolab, Chembiotek, TCG Lifesciences Limited, Bengal Intelligent Park, Salt Lake Electronic Complex, Sector-V, Kolkata 700091, India
| | - Munna Sarkar
- Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India
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11
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Charoenkwan P, Chotpatiwetchkul W, Lee VS, Nantasenamat C, Shoombuatong W. A novel sequence-based predictor for identifying and characterizing thermophilic proteins using estimated propensity scores of dipeptides. Sci Rep 2021; 11:23782. [PMID: 34893688 PMCID: PMC8664844 DOI: 10.1038/s41598-021-03293-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/01/2021] [Indexed: 02/08/2023] Open
Abstract
Owing to their ability to maintain a thermodynamically stable fold at extremely high temperatures, thermophilic proteins (TTPs) play a critical role in basic research and a variety of applications in the food industry. As a result, the development of computation models for rapidly and accurately identifying novel TTPs from a large number of uncharacterized protein sequences is desirable. In spite of existing computational models that have already been developed for characterizing thermophilic proteins, their performance and interpretability remain unsatisfactory. We present a novel sequence-based thermophilic protein predictor, termed SCMTPP, for improving model predictability and interpretability. First, an up-to-date and high-quality dataset consisting of 1853 TPPs and 3233 non-TPPs was compiled from published literature. Second, the SCMTPP predictor was created by combining the scoring card method (SCM) with estimated propensity scores of g-gap dipeptides. Benchmarking experiments revealed that SCMTPP had a cross-validation accuracy of 0.883, which was comparable to that of a support vector machine-based predictor (0.906-0.910) and 2-17% higher than that of commonly used machine learning models. Furthermore, SCMTPP outperformed the state-of-the-art approach (ThermoPred) on the independent test dataset, with accuracy and MCC of 0.865 and 0.731, respectively. Finally, the SCMTPP-derived propensity scores were used to elucidate the critical physicochemical properties for protein thermostability enhancement. In terms of interpretability and generalizability, comparative results showed that SCMTPP was effective for identifying and characterizing TPPs. We had implemented the proposed predictor as a user-friendly online web server at http://pmlabstack.pythonanywhere.com/SCMTPP in order to allow easy access to the model. SCMTPP is expected to be a powerful tool for facilitating community-wide efforts to identify TPPs on a large scale and guiding experimental characterization of TPPs.
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Affiliation(s)
- Phasit Charoenkwan
- grid.7132.70000 0000 9039 7662Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200 Thailand
| | - Warot Chotpatiwetchkul
- grid.419784.70000 0001 0816 7508Applied Computational Chemistry Research Unit, Department of Chemistry, School of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520 Thailand
| | - Vannajan Sanghiran Lee
- grid.10347.310000 0001 2308 5949Department of Chemistry, Centre of Theoretical and Computational Physics, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chanin Nantasenamat
- grid.10223.320000 0004 1937 0490Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700 Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
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12
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Villain E, Fort P, Kajava AV. Aspartate-phobia of thermophiles as a reaction to deleterious chemical transformations. Bioessays 2021; 44:e2100213. [PMID: 34791689 DOI: 10.1002/bies.202100213] [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: 09/09/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 11/08/2022]
Abstract
Prokaryotes growing at high temperatures have a high proportion of charged residues in their proteins to stabilize their 3D structure. By mining 175 disparate bacterial and archaeal proteomes we found that, against the general trend for charged residues, the frequency of aspartic acid residues decreases strongly as natural growth temperature increases. In search of the explanation, we hypothesized that the reason for such unusual correlation is the deleterious consequences of spontaneous chemical transformations of aspartate at high temperatures. Our subsequent statistical analysis supported this hypothesis. This finding reveals that organisms have likely adapted to high temperatures by minimizing the harmful consequences of spontaneous chemical transformations.
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Affiliation(s)
- Etienne Villain
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
| | - Philippe Fort
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Université de Montpellier 1919 Route de Mende, Montpellier, France
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13
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Akanuma S, Yamaguchi M, Yamagishi A. Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins. PLoS One 2021; 16:e0258821. [PMID: 34673819 PMCID: PMC8530338 DOI: 10.1371/journal.pone.0258821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Further improvement of the thermostability of inherently thermostable proteins is an attractive challenge because more thermostable proteins are industrially more useful and serve as better scaffolds for protein engineering. To establish guidelines that can be applied for the rational design of hyperthermostable proteins, we compared the amino acid sequences of two ancestral nucleoside diphosphate kinases, Arc1 and Bac1, reconstructed in our previous study. Although Bac1 is a thermostable protein whose unfolding temperature is around 100°C, Arc1 is much more thermostable with an unfolding temperature of 114°C. However, only 12 out of 139 amino acids are different between the two sequences. In this study, one or a combination of amino acid(s) in Bac1 was/were substituted by a residue(s) found in Arc1 at the same position(s). The best mutant, which contained three amino acid substitutions (S108D, G116A and L120P substitutions), showed an unfolding temperature more than 10°C higher than that of Bac1. Furthermore, a combination of the other nine amino acid substitutions also led to improved thermostability of Bac1, although the effects of individual substitutions were small. Therefore, not only the sum of the contributions of individual amino acids, but also the synergistic effects of multiple amino acids are deeply involved in the stability of a hyperthermostable protein. Such insights will be helpful for future rational design of hyperthermostable proteins.
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Affiliation(s)
- Satoshi Akanuma
- Faculty of Human Sciences, Waseda University, Tokorozawa, Saitama, Japan
- * E-mail:
| | - Minako Yamaguchi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Akihiko Yamagishi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
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14
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Wu H, Chen Q, Zhang W, Mu W. Overview of strategies for developing high thermostability industrial enzymes: Discovery, mechanism, modification and challenges. Crit Rev Food Sci Nutr 2021; 63:2057-2073. [PMID: 34445912 DOI: 10.1080/10408398.2021.1970508] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biocatalysts such as enzymes are environmentally friendly and have substrate specificity, which are preferred in the production of various industrial products. However, the strict reaction conditions in industry including high temperature, organic solvents, strong acids and bases and other harsh environments often destabilize enzymes, and thus substantially compromise their catalytic functions, and greatly restrict their applications in food, pharmaceutical, textile, bio-refining and feed industries. Therefore, developing industrial enzymes with high thermostability becomes very important in industry as thermozymes have more advantages under high temperature. Discovering new thermostable enzymes using genome sequencing, metagenomics and sample isolation from extreme environments, or performing molecular modification of the existing enzymes with poor thermostability using emerging protein engineering technology have become an effective means of obtaining thermozymes. Based on the thermozymes as biocatalytic chips in industry, this review systematically analyzes the ways to discover thermostable enzymes from extreme environment, clarifies various interaction forces that will affect thermal stability of enzymes, and proposes different strategies to improve enzymes' thermostability. Furthermore, latest development in the thermal stability modification of industrial enzymes through rational design strategies is comprehensively introduced from structure-activity relationship point of view. Challenges and future research perspectives are put forward as well.
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Affiliation(s)
- Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China
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15
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The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference? Life (Basel) 2021; 11:life11080773. [PMID: 34440517 PMCID: PMC8398314 DOI: 10.3390/life11080773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.
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16
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Qu Y, Wang L, Yin S, Zhang B, Jiao Y, Sun Y, Middelberg A, Bi J. Stability of Engineered Ferritin Nanovaccines Investigated by Combined Molecular Simulation and Experiments. J Phys Chem B 2021; 125:3830-3842. [PMID: 33825471 DOI: 10.1021/acs.jpcb.1c00276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human ferritin is regarded as an attractive and promising vaccine platform because of its uniform structure, good plasticity, and desirable thermal and chemical stabilities. Besides, it is biocompatible and presumed safe when used as a vaccine carrier. However, there is a lack of knowledge of how different antigen insertion sites on the ferritin nanocage impact the resulting protein stability and performance. To address this question, we selected Epstein-Barr nuclear antigen 1 as a model epitope and fused it at the DNA level with different insertion sites, namely, the N- and C-termini of ferritin, to engineer proteins E1F1 and F1E1, respectively. Protein properties including hydrophobicity and thermal, pH, and chemical stability were investigated both by molecular dynamics (MD) simulation and by experiments. Both methods demonstrate that the insertion site plays an important role in protein properties. The C-terminus insertion (F1E1) leads to a less hydrophobic surface and more tolerance to the external influence of high temperature, pH, and high concentration of chemical denaturants compared to N-terminus insertion (E1F1). Simulated protein hydrophobicity and thermal stability by MD were in high accordance with experimental results. Thus, MD simulation can be used as a valuable tool to engineer nanovaccine candidates, cutting down costs by reducing the experimental effort and accelerating vaccine design.
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Affiliation(s)
- Yiran Qu
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Lijie Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Shuang Yin
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bingyang Zhang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Jiao
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Anton Middelberg
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jingxiu Bi
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, South Australia 5005, Australia
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17
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Cruse CA, Goodpaster JV. Thermal and spectroscopic analysis of nitrated compounds and their break-down products using gas chromatography/vacuum UV spectroscopy (GC/VUV). Anal Chim Acta 2021; 1143:117-123. [PMID: 33384109 DOI: 10.1016/j.aca.2020.11.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/22/2020] [Accepted: 11/28/2020] [Indexed: 11/29/2022]
Abstract
Gas chromatography/vacuum UV spectroscopy (GC/VUV) was utilized to study various explosives and pharmaceuticals in the nitrate ester and nitramine structural classes. In addition to generating specific VUV spectra for each compound, VUV was used to indicate the onset of thermal decomposition based upon the appearance of break-down products such as nitric oxide, carbon monoxide, formaldehyde, water, and molecular oxygen. The effect of temperature on decomposition could be fit to a logistical function where the fraction of intact compound remaining decreased as the transfer line/flow cell temperature was increased from 200 °C to 300 °C. Utilizing this relationship, the decomposition temperatures for the nitrate ester and nitramine compounds were determined to range between 244 °C and 277 °C. It was also discovered that the decomposition temperature was dependent on the GC carrier gas flow rate and, therefore, the residence time of the compounds in the transfer line/flow cell. For example, the measured decomposition temperature of nitroglycerine ranged from 222 °C to 253 °C across four flow rates. Tracking the appearance/disappearance of decomposition products across this temperature range indicated that NO, CO, and H2CO are final decomposition products while O2 and H2O are intermediate products. The decomposition temperatures for all explosives were highly correlated to similar decomposition measurements taken by differential scanning calorimetry (DSC) (r = 0.91) and thermal gravimetric analysis (TGA) (r = 0.90-0.98). In addition, the decomposition temperatures for all explosives were negatively correlated to the heat of explosion at constant volume (r = -0.68) and strongly positively correlated to the oxygen balance (r = 0.92).
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Affiliation(s)
- Courtney A Cruse
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, LD326, Indianapolis, IN, 46202, USA
| | - John V Goodpaster
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, LD326, Indianapolis, IN, 46202, USA; Forensic and Investigative Sciences Program, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, LD326, Indianapolis, IN, 46202, USA.
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18
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Liu Y, Sun Q, Pan Y, Wei S, Xia Q, Liu S, Ji H, Deng C, Hao J. Investigation on the correlation between changes in water and texture properties during the processing of surimi from golden pompano (Trachinotus ovatus). J Food Sci 2021; 86:376-384. [PMID: 33438246 DOI: 10.1111/1750-3841.15581] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/28/2022]
Abstract
Water and texture properties are important indicators for evaluating surimi and surimi seafood quality. The present study assessed the impact of surimi processing on the water and texture properties and analyzed their correlations. The results showed that the moisture content exhibited significant positive correlations with T22 and A22 (P < 0.05). However, water-holding capacity (WHC) revealed significant negative correlation with T21 and A22 (P < 0.05). Moreover, correlations between water and texture properties were observed. Moisture content and A22 displayed significant negative correlation with hardness (P < 0.05). WHC exhibited significant positive correlations with cohesiveness, springiness, and chewiness (P < 0.05), whereas T21 exhibited significant negative correlation with those properties (P < 0.05). Springiness is an important indicator for texture properties of surimi gel. T21 and WHC exhibited significant correlations with springiness (P < 0.05). We used two equations to assess the relationship between springiness and T21 (y = 9.64 × x2 - 33.79 × x + 29.62, R2 = 0.995, P < 0.05) and between springiness and WHC (y = 0.57 + 9.05/{1+e[-29.29 × ( x - 83.90)] }0.01 , R2 = 0.999, P < 0.05), respectively. Verification experiments proved that these two regression equations could be used to predict the change law among feature indicators during the processing of surimi seafood. The present study finds an easy-to-control method to monitor the quality of surimi production and processing for all the stages, and provides ideas for quality design of surimi products. PRACTICAL APPLICATION: The quality of surimi seafood is affected by the process used for surimi production. Early detection of the material quality can efficiently prevent resource wastage. The feature indicators and their correlations help in easy-to-control of all surimi processing stages. Low-field nuclear magnetic resonance (LF-NMR) is a fast, nondestructive method for monitoring food real-time, but the instrument is expensive; whereas water-holding capacity and texture profile analysis (TPA) are traditional methods but time-consuming and material-consuming. Surimi enterprises or researchers choose the right methods based on their needs.
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Affiliation(s)
- Yang Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Qinxiu Sun
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Yanmo Pan
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Shuai Wei
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Qiuyu Xia
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Shucheng Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Hongwu Ji
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Chujin Deng
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
| | - Jiming Hao
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, 524088, China.,Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, 116034, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524088, China
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19
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Bi J, Chen S, Zhao X, Nie Y, Xu Y. Computation-aided engineering of starch-debranching pullulanase from Bacillus thermoleovorans for enhanced thermostability. Appl Microbiol Biotechnol 2020; 104:7551-7562. [PMID: 32632476 DOI: 10.1007/s00253-020-10764-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/17/2020] [Accepted: 06/30/2020] [Indexed: 12/26/2022]
Abstract
Pullulanases are widely used in food, medicine, and other industries because they specifically hydrolyze α-1,6-glycosidic linkages in starch and oligosaccharides. In addition, high-temperature thermostable pullulanase has multiple advantages, including decreasing saccharification solution viscosity accompanied with enhanced mass transfer and reducing microbial contamination in starch hydrolysis. However, thermophilic pullulanase availability remains limited. Additionally, most do not meet starch-manufacturing requirements due to weak thermostability. Here, we developed a computation-aided strategy to engineer the thermophilic pullulanase from Bacillus thermoleovorans. First, three computational design predictors (FoldX, I-Mutant 3.0, and dDFIRE) were combined to predict stability changes introduced by mutations. After excluding conserved and catalytic sites, 17 mutants were identified. After further experimental verification, we confirmed six positive mutants. Among them, the G692M mutant had the highest thermostability improvement, with 3.8 °C increased Tm and 2.1-fold longer half-life than the wild type at 70 °C. We then characterized the mechanism underlying increased thermostability, such as rigidity enhancement, closer conformation, and strengthened motion correlation using root mean square fluctuation (RMSF), principal component analysis (PCA), dynamic cross-correlation map (DCCM), and free energy landscape (FEL) analysis. KEY POINTS: • A computation-aided strategy was developed to engineer pullulanase thermostability. • Seventeen mutants were identified by combining three computational design predictors. • The G692M mutant was obtained with increased Tmand half-life at 70 °C.
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Affiliation(s)
- Jiahua Bi
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shuhui Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xianghan Zhao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yao Nie
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Suqian Industrial Technology Research Institute of Jiangnan University, Suqian, 223814, China.
| | - Yan Xu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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20
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Jia Y, Selva C, Zhang Y, Li B, McFawn LA, Broughton S, Zhang X, Westcott S, Wang P, Tan C, Angessa T, Xu Y, Whitford R, Li C. Uncovering the evolutionary origin of blue anthocyanins in cereal grains. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1057-1074. [PMID: 31571294 DOI: 10.1111/tpj.14557] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/16/2019] [Accepted: 09/24/2019] [Indexed: 05/23/2023]
Abstract
Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.
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Affiliation(s)
- Yong Jia
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Caterina Selva
- School of Agriculture, Food and Wine, Adelaide University, Adelaide, SA, 5064, Australia
| | - Yujuan Zhang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Bo Li
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Lee A McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Xiaoqi Zhang
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Sharon Westcott
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Penghao Wang
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Cong Tan
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
| | - Tefera Angessa
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
| | - Yanhao Xu
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Ryan Whitford
- School of Agriculture, Food and Wine, Adelaide University, Adelaide, SA, 5064, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, 6150, Australia
- State Agricultural Biotechnology Centre (SABC), School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, 6150, Australia
- Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia
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21
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Chao YC, Merritt M, Schaefferkoetter D, Evans TG. High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. BMC Evol Biol 2020; 20:28. [PMID: 32054457 PMCID: PMC7020559 DOI: 10.1186/s12862-020-1593-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background Temperature exerts a strong influence on protein evolution: species living in thermally distinct environments often exhibit adaptive differences in protein structure and function. However, previous research on protein temperature adaptation has focused on small numbers of proteins and on proteins adapted to extreme temperatures. Consequently, less is known about the types and quantity of evolutionary change that occurs to proteins when organisms adapt to small shifts in environmental temperature. In this study, these uncertainties were addressed by developing software that enabled comparison of structural changes associated with temperature adaptation (hydrogen bonding, salt bridge formation, and amino acid use) among large numbers of proteins from warm- and cold-adapted species of marine mussels, Mytilus galloprovincialis and Mytilus trossulus, respectively. Results Small differences in habitat temperature that characterize the evolutionary history of Mytilus mussels were sufficient to cause protein structural changes consistent with temperature adaptation. Hydrogen bonds and salt bridges that increase stability and protect against heat-induced denaturation were more abundant in proteins from warm-adapted M. galloprovincialis compared with proteins from cold-adapted M. trossulus. These structural changes were related to deviations in the use of polar and charged amino acids that facilitate formation of hydrogen bonds and salt bridges within proteins, respectively. Enzymes, in particular those within antioxidant and cell death pathways, were over-represented among proteins with the most hydrogen bonds and salt bridges in warm-adapted M. galloprovincialis. Unlike extremophile proteins, temperature adaptation in Mytilus proteins did not involve substantial changes in the number of hydrophobic or large volume amino acids, nor in the content of glycine or proline. Conclusions Small shifts in organism temperature tolerance, such as that needed to cope with climate warming, may result from structural and functional changes to a small percentage of the proteome. Proteins in which function is dependent on large conformational change, notably enzymes, may be particularly sensitive to temperature perturbation and represent foci for natural selection. Protein temperature adaptation can occur through different types and frequencies of structural change, and adaptive mechanisms used to cope with small shifts in habitat temperature appear different from mechanisms used to retain protein function at temperature extremes.
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Affiliation(s)
- Ying-Chen Chao
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Melanie Merritt
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Devin Schaefferkoetter
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA
| | - Tyler G Evans
- Department of Biological Sciences, California State University East Bay, Hayward, CA, 94542, USA.
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Zhang QF, Hu S, Zhao WR, Huang J, Mei JQ, Mei LH. Parallel Strategy Increases the Thermostability and Activity of Glutamate Decarboxylase. Molecules 2020; 25:molecules25030690. [PMID: 32041144 PMCID: PMC7037157 DOI: 10.3390/molecules25030690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 11/29/2022] Open
Abstract
Glutamate decarboxylase (GAD; EC 4.1.1.15) is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme that specifically catalyzes the decarboxylation of L-glutamic acid to produce γ-aminobutyric acid (GABA), which exhibits several well-known physiological functions. However, glutamate decarboxylase from different sources has the common problem of poor thermostability that affects its application in industry. In this study, a parallel strategy comprising sequential analysis and free energy calculation was applied to identify critical amino acid sites affecting thermostability of GAD and select proper mutation contributing to improve structure rigidity of the enzyme. Two mutant enzymes, D203E and S325A, with higher thermostability were obtained, and their semi-inactivation temperature (T5015) values were 2.3 °C and 1.4 °C higher than the corresponding value of the wild-type enzyme (WT), respectively. Moreover, the mutant, S325A, exhibited enhanced activity compared to the wild type, with a 1.67-fold increase. The parallel strategy presented in this work proved to be an efficient tool for the reinforcement of protein thermostability.
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Affiliation(s)
- Qing-Fei Zhang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China;
| | - Sheng Hu
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
| | - Wei-Rui Zhao
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China;
| | - Jia-Qi Mei
- Hangzhou Zhongmei Huadong Pharmaceutical Co. Ltd., Hangzhou 31011, China;
| | - Le-He Mei
- Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China; (S.H.); (W.-R.Z.)
- Correspondence: ; Tel.: +86-571-879-531-61
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Kohli I, Joshi NC, Mohapatra S, Varma A. Extremophile - An Adaptive Strategy for Extreme Conditions and Applications. Curr Genomics 2020; 21:96-110. [PMID: 32655304 PMCID: PMC7324872 DOI: 10.2174/1389202921666200401105908] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 03/19/2020] [Indexed: 11/22/2022] Open
Abstract
The concurrence of microorganisms in niches that are hostile like extremes of temperature, pH, salt concentration and high pressure depends upon novel molecular mechanisms to enhance the stability of their proteins, nucleic acids, lipids and cell membranes. The structural, physiological and genomic features of extremophiles that make them capable of withstanding extremely selective environmental conditions are particularly fascinating. Highly stable enzymes exhibiting several industrial and biotechnological properties are being isolated and purified from these extremophiles. Successful gene cloning of the purified extremozymes in the mesophilic hosts has already been done. Various extremozymes such as amylase, lipase, xylanase, cellulase and protease from thermophiles, halothermophiles and psychrophiles are of industrial interests due to their enhanced stability at forbidding conditions. In this review, we made an attempt to point out the unique features of extremophiles, particularly thermophiles and psychrophiles, at the structural, genomic and proteomic levels, which allow for functionality at harsh conditions focusing on the temperature tolerance by them.
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Affiliation(s)
- Isha Kohli
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Naveen C. Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University, Noida, India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Noida, India
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In silico Approach to Elucidate Factors Associated with GH1 β-Glucosidase Thermostability. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2019. [DOI: 10.22207/jpam.13.4.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Zou Z, Zhang J. Amino acid exchangeabilities vary across the tree of life. SCIENCE ADVANCES 2019; 5:eaax3124. [PMID: 31840062 PMCID: PMC6892623 DOI: 10.1126/sciadv.aax3124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 09/24/2019] [Indexed: 05/05/2023]
Abstract
Different amino acid pairs have drastically different relative exchangeabilities (REs), and accounting for this variation is an important and common practice in inferring phylogenies, testing selection, and predicting mutational effects, among other analyses. In all such endeavors, REs have been generally considered invariant among species; this assumption, however, has not been scrutinized. Using maximum likelihood to analyze 180 genome sequences, we estimated REs from 90 clades representing all three domains of life, and found numerous instances of substantial between-clade differences in REs. REs show more differences between orthologous proteins of different clades than unrelated proteins of the same clade, suggesting that REs are genome-wide, clade-specific features, probably a result of proteome-wide evolutionary changes in the physicochemical environments of amino acid residues. The discovery of among-clade RE variations cautions against assuming constant REs in various analyses and demonstrates a higher-than-expected complexity in mechanisms of proteome evolution.
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Bundela R, Keown J, Watkin S, Pearce FG. Structure of a hyperthermostable dimeric archaeal Rubisco from Hyperthermus butylicus. Acta Crystallogr D Struct Biol 2019; 75:536-544. [DOI: 10.1107/s2059798319006466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/07/2019] [Indexed: 11/11/2022] Open
Abstract
The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from the hyperthermophilic archaeonHyperthermus butylicusis presented at 1.8 Å resolution. Previous structures of archaeal Rubisco have been found to assemble into decamers, and this oligomerization was thought to be required for a highly thermally stable enzyme. In the current study,H. butylicusRubisco is shown to exist as a dimer in solution, yet has a thermal denaturation midpoint of 114°C, suggesting that high thermal stability can be achieved without an increased oligomeric state. This increased thermal stability appears to be due to an increased number of electrostatic interactions within the monomeric subunit. As such,H. butylicusRubisco presents a well characterized system in which to investigate the role of assembly and thermal stability in enzyme function.
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Disulfide bonds elimination of endoglucanase II from Trichoderma reesei by site-directed mutagenesis to improve enzyme activity and thermal stability: An experimental and theoretical approach. Int J Biol Macromol 2018; 120:1572-1580. [DOI: 10.1016/j.ijbiomac.2018.09.164] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 09/23/2018] [Accepted: 09/25/2018] [Indexed: 01/21/2023]
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Xu L, Wu YH, Zhou P, Cheng H, Liu Q, Xu XW. Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis. BMC Genomics 2018; 19:385. [PMID: 29792177 PMCID: PMC5966882 DOI: 10.1186/s12864-018-4789-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 05/14/2018] [Indexed: 11/10/2022] Open
Abstract
Background Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins. Comparative genomic studies have revealed that different thermal types exist in different taxa, and few studies have been focused on the class Alphaproteobacteria, especially the family Erythrobacteraceae. In this study, eight genomes of Porphyrobacter strains were compared to elucidate how Porphyrobacter thermophiles developed mechanisms to adapt to thermal environments. Results P. cryptus DSM 12079T grew optimally at 50 °C, which was higher than the optimal growth temperature of other Porphyrobacter type strains. Phylogenomic analysis of the genus Porphyrobacter revealed that P. cryptus DSM 12079T formed a distinct and independent clade. Comparative genomic studies uncovered that 1405 single-copy genes were shared by Porphyrobacter type strains. Alignments of single-copy proteins showed that various types of amino acid substitutions existed between P. cryptus DSM 12079T and the other Porphyrobacter strains. The primary substitution types were changes from glycine/serine to alanine. Conclusions P. cryptus DSM 12079T was the sole thermophile within the genus Porphyrobacter. Phylogenomic analysis and amino acid frequencies indicated that amino acid substitutions might play an important role in the thermophily of P. cryptus DSM 12079T. Bioinformatic analysis revealed that major amino acid substitutional types, such as changes from glycine/serine to alanine, increase the frequency of α-helices in proteins, promoting protein thermostability in P. cryptus DSM 12079T. Hence, comparative genomic analysis broadens our understanding of thermophilic mechanisms in the genus Porphyrobacter and may provide a useful insight in the design of thermophilic enzymes for agricultural, industrial and medical applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4789-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lin Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China.,College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, People's Republic of China
| | - Yue-Hong Wu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Qian Liu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography, State Oceanic Administration, 310012, Hangzhou, People's Republic of China. .,Ocean College, Zhejiang University, 316021, Zhoushan, People's Republic of China.
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Gu J, Tong H, Sun L, Lin Z. Molecular dynamics perspective on the thermal stability of mandelate racemase. J Biomol Struct Dyn 2018; 37:383-393. [PMID: 29334318 DOI: 10.1080/07391102.2018.1427631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mandelate racemase from Pseudomonas putida is a promising candidate for the dynamic kinetic resolution of α-hydroxy carboxylic acids. In the present study, the thermal stability of mandelate racemase was investigated through molecular dynamics simulations in the temperature range of 303-363 K, which can guide the design of mandelate racemase with higher stability. The basic features such as radius of gyration, surface accessibility, and secondary structure content suggested the instability of mandelate racemase at high temperatures. With increase in temperature, α-helix content reduced significantly, especially the α-helices exposed to the environment. At the simulation time scale considered, intra-protein hydrogen bonds, hydrogen bonds between protein and water decreased at 363 K, while the number of salt-bridges increased. The long-distance networks remarkably changed at 363 K. A considerable number of long-lived (percentage existence time higher than 90%) hydrogen bonds and Cα contacts were lost. Root mean square fluctuation analysis revealed regions with high fluctuation, which should be helpful in the reengineering of mandelate racemase for enhanced thermal stability.
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Affiliation(s)
- Jiali Gu
- a College of Life Sciences , Huzhou University , Huzhou , Zhejiang , 313000 , China
| | - Hongfei Tong
- a College of Life Sciences , Huzhou University , Huzhou , Zhejiang , 313000 , China
| | - Laiyu Sun
- a College of Life Sciences , Huzhou University , Huzhou , Zhejiang , 313000 , China
| | - Zhijian Lin
- b Novel Search Center , Zhejiang Institute of Scientific and Technological Information , Hangzhou , Zhejiang , 310052 , China
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Yin H, Yang Z, Nie X, Li S, Sun X, Gao C, Wang Z, Zhou G, Xu P, Yang C. Functional and cooperative stabilization of a two-metal (Ca, Zn) center in α-amylase derived from Flavobacteriaceae species. Sci Rep 2017; 7:17933. [PMID: 29263337 PMCID: PMC5738361 DOI: 10.1038/s41598-017-18085-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 12/06/2017] [Indexed: 11/09/2022] Open
Abstract
Mesophilic α-amylase from Flavobacteriaceae (FSA) is evolutionary closely related to thermophilic archaeal Pyrococcus furiosus α-amylase (PWA), but lacks the high thermostability, despite the conservation of most residues involved in the two-metal (Ca, Zn) binding center of PWA. In this study, a disulfide bond was introduced near the two-metal binding center of FSA (designated mutant EH-CC) and this modification resulted in a slight improvement in thermostability. As expected, E204G mutations in FSA and EH-CC led to the recovery of Ca2+-binding site. Interestingly, both Ca2+- and Zn2+-dependent thermostability were significantly enhanced; 153.1% or 50.8% activities was retained after a 30-min incubation period at 50 °C, in the presence of Ca2+ or Zn2+. The C214S mutation, which affects Zn2+-binding, also remarkably enhanced Zn2+- and Ca2+- dependent thermostability, indicating that Ca2+- and Zn2+-binding sites function cooperatively to maintain protein stability. Furthermore, an isothermal titration calorimetry (ITC) analysis revealed a novel Zn2+-binding site in mutant EH-CC-E204G. This metal ion cooperation provides a possible method for the generation of α-amylases with desired thermal properties by in silico rational design and systems engineering, to generate a Zn2+-binding site adjacent to the conserved Ca2+-binding site.
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Affiliation(s)
- Huijia Yin
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Zhou Yang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Xinyu Nie
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Shannan Li
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Xuyang Sun
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Zenghang Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Guangming Zhou
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China
| | - Chunyu Yang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Jinan, 250100, People's Republic of China.
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31
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Zhang X, Zheng QC. Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation. Biopolymers 2017; 109. [DOI: 10.1002/bip.23068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/27/2017] [Accepted: 09/15/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Xue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University; Changchun 130023 People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education; Jilin University; Changchun 130023 People's Republic of China
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Jegousse C, Yang Y, Zhan J, Wang J, Zhou Y. Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA. PLoS One 2017; 12:e0184722. [PMID: 28910383 PMCID: PMC5598986 DOI: 10.1371/journal.pone.0184722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/29/2017] [Indexed: 12/02/2022] Open
Abstract
Temperature adaptation of bacterial RNAs is a subject of both fundamental and practical interest because it will allow a better understanding of molecular mechanism of RNA folding with potential industrial application of functional thermophilic or psychrophilic RNAs. Here, we performed a comprehensive study of rRNA, tRNA, and mRNA of more than 200 bacterial species with optimal growth temperatures (OGT) ranging from 4°C to 95°C. We investigated temperature adaptation at primary, secondary and tertiary structure levels. We showed that unlike mRNA, tRNA and rRNA were optimized for their structures at compositional levels with significant tertiary structural features even for their corresponding randomly permutated sequences. tRNA and rRNA are more exposed to solvent but remain structured for hyperthermophiles with nearly OGT-independent fluctuation of solvent accessible surface area within a single RNA chain. mRNA in hyperthermophiles is essentially the same as random sequences without tertiary structures although many mRNA in mesophiles and psychrophiles have well-defined tertiary structures based on their low overall solvent exposure with clear separation of deeply buried from partly exposed bases as in tRNA and rRNA. These results provide new insight into temperature adaptation of different RNAs.
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MESH Headings
- Bacteria/genetics
- Databases, Genetic
- Models, Molecular
- Nucleic Acid Conformation
- RNA Folding/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/drug effects
- RNA, Transfer/chemistry
- RNA, Transfer/drug effects
- Solvents/pharmacology
- Temperature
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Affiliation(s)
- Clara Jegousse
- UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, Nantes, France
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- * E-mail:
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33
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Geertz-Hansen HM, Kiemer L, Nielsen M, Stanchev K, Blom N, Brunak S, Petersen TN. Protein features as determinants of wild-type glycoside hydrolase thermostability. Proteins 2017; 85:2036-2044. [DOI: 10.1002/prot.25357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/26/2017] [Accepted: 07/21/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Henrik Marcus Geertz-Hansen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Novozymes A/S; DK-2880 Bagsvaerd Denmark
| | | | - Morten Nielsen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin, San Martin, B 1650 HMP; Buenos Aires Argentina
| | - Kiril Stanchev
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Nikolaj Blom
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; DK-2800 Lyngby Denmark
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
- Faculty of Health and Medical Sciences; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen; DK-2200 Copenhagen N Denmark
| | - Thomas Nordahl Petersen
- Department of Bio and Health Informatics; Technical University of Denmark, Kemitorvet; DK-2800 Lyngby Denmark
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Rahban M, Salehi N, Saboury AA, Hosseinkhani S, Karimi-Jafari MH, Firouzi R, Rezaei-Ghaleh N, Moosavi-Movahedi AA. Histidine substitution in the most flexible fragments of firefly luciferase modifies its thermal stability. Arch Biochem Biophys 2017; 629:8-18. [PMID: 28711358 DOI: 10.1016/j.abb.2017.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 11/26/2022]
Abstract
Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C. In line with the common feature of psychrophilic enzymes, the MD data showed that the overall flexibility of H461D was relatively high at low temperature, probably due to a decrease in the number of salt bridges around the mutation site. On the other hand, substitution of His489 by aspartate (H489D) introduced a new salt bridge between the C-terminal and N-terminal domains and increased protein rigidity but only slightly improved its thermal stability. Similar changes were observed for H489K and, to a lesser degree, H489M mutations. Based on our results we conclude that the MD simulation-based rational substitution of histidines by salt-bridge forming residues can modulate conformational dynamics in luciferase and shift its optimal temperature activity.
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Affiliation(s)
- Mahdie Rahban
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Najmeh Salehi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | | | - Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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Engineering and introduction of de novo disulphide bridges in organophosphorus hydrolase enzyme for thermostability improvement. J Biosci 2017; 41:577-588. [PMID: 27966481 DOI: 10.1007/s12038-016-9643-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The organophosphorus hydrolase (OPH) has been used to degrade organophosphorus chemicals, as one of the most frequently used decontamination methods. Under chemical and thermal denaturing conditions, the enzyme has been shown to unfold. To utilize this enzyme in various applications, the thermal stability is of importance. The engineering of de novo disulphide bridges has been explored as a means to increase the thermal stability of enzymes in the rational method of protein engineering. In this study, Disulphide by Design software, homology modelling and molecular dynamics simulations were used to select appropriate amino acid pairs for the introduction of disulphide bridge to improve protein thermostability. The thermostability of the wild-type and three selected mutant enzymes were evaluated by half-life, delta G inactivation (ΔGi) and structural studies (fluorescence and far-UV CD analysis). Data analysis showed that half-life of A204C/T234C and T128C/E153C mutants were increased up to 4 and 24 min, respectively; however, for the G74C/A78C mutant, the half-life was decreased up to 9 min. For the T128C/E124C mutant, both thermal stability and Catalytic efficiency (kcat) were also increased. The half-life and ΔGi results were correlated to the obtained information from structural studies by circular dichroism (CD) spectrometry and extrinsic fluorescence experiments; as rigidity increased in A204C/T2234C and T128C/E153C mutants, half-life and ΔGi also increased. For G74C/A78C mutant, these parameters decreased due to its higher flexibility. The results were submitted a strong evidence for the possibility to improve the thermostability of OPH enzyme by introducing a disulphide bridge after bioinformatics design, even though this design would not be always successful.
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Chakravorty D, Khan MF, Patra S. Multifactorial level of extremostability of proteins: can they be exploited for protein engineering? Extremophiles 2017; 21:419-444. [PMID: 28283770 DOI: 10.1007/s00792-016-0908-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022]
Abstract
Research on extremostable proteins has seen immense growth in the past decade owing to their industrial importance. Basic research of attributes related to extreme-stability requires further exploration. Modern mechanistic approaches to engineer such proteins in vitro will have more impact in industrial biotechnology economy. Developing a priori knowledge about the mechanism behind extreme-stability will nurture better understanding of pathways leading to protein molecular evolution and folding. This review is a vivid compilation about all classes of extremostable proteins and the attributes that lead to myriad of adaptations divulged after an extensive study of 6495 articles belonging to extremostable proteins. Along with detailing on the rationale behind extreme-stability of proteins, emphasis has been put on modern approaches that have been utilized to render proteins extremostable by protein engineering. It was understood that each protein shows different approaches to extreme-stability governed by minute differences in their biophysical properties and the milieu in which they exist. Any general rule has not yet been drawn regarding adaptive mechanisms in extreme environments. This review was further instrumental to understand the drawback of the available 14 stabilizing mutation prediction algorithms. Thus, this review lays the foundation to further explore the biophysical pleiotropy of extreme-stable proteins to deduce a global prediction model for predicting the effect of mutations on protein stability.
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Affiliation(s)
- Debamitra Chakravorty
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Mohd Faheem Khan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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Leng F, Xu C, Xia XY, Pan XM. Establishing knowledge on the sequence arrangement pattern of nucleated protein folding. PLoS One 2017; 12:e0173583. [PMID: 28273143 PMCID: PMC5342263 DOI: 10.1371/journal.pone.0173583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 02/22/2017] [Indexed: 11/21/2022] Open
Abstract
The heat-tolerance mechanisms of (hyper)thermophilic proteins provide a unique opportunity to investigate the unsolved protein folding problem. In an attempt to determine whether the interval between residues in sequence might play a role in determining thermostability, we constructed a sequence interval-dependent value function to calculate the residue pair frequency. Additionally, we identified a new sequence arrangement pattern, where like-charged residues tend to be adjacently assembled, while unlike-charged residues are distributed over longer intervals, using statistical analysis of a large sequence database. This finding indicated that increasing the intervals between unlike-charged residues can increase protein thermostability, with the arrangement patterns of these charged residues serving as thermodynamically favorable nucleation points for protein folding. Additionally, we identified that the residue pairs K-E, R-E, L-V and V-V involving long sequence intervals play important roles involving increased protein thermostability. This work demonstrated a novel approach for considering sequence intervals as keys to understanding protein folding. Our findings of novel relationships between residue arrangement and protein thermostability can be used in industry and academia to aid the design of thermostable proteins.
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Affiliation(s)
- Fei Leng
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chao Xu
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xia-Yu Xia
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xian-Ming Pan
- Key Laboratory of Bioinformatics, Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
- * E-mail:
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38
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Identification of potential inhibitors for oncogenic target of dihydroorotate dehydrogenase using in silico approaches. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Pucci F, Rooman M. Improved insights into protein thermal stability: from the molecular to the structurome scale. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0141. [PMID: 27698032 PMCID: PMC5052726 DOI: 10.1098/rsta.2016.0141] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/09/2016] [Indexed: 05/18/2023]
Abstract
Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability-at the structurome level-contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Fabrizio Pucci
- Department of BioModeling, BioInformatics and BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Avenue 50, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Boulevard, 1050 Brussels, Belgium
| | - Marianne Rooman
- Department of BioModeling, BioInformatics and BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Avenue 50, 1050 Brussels, Belgium Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Boulevard, 1050 Brussels, Belgium
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40
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Kabra A, Fatma F, Shahid S, Pathak PP, Yadav R, Pulavarti SK, Tripathi S, Jain A, Arora A. Structural characterization of peptidyl-tRNA hydrolase from Mycobacterium smegmatis by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1304-14. [DOI: 10.1016/j.bbapap.2016.06.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 10/21/2022]
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41
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You S, Tu T, Zhang L, Wang Y, Huang H, Ma R, Shi P, Bai Y, Su X, Lin Z, Luo H, Yao B. Improvement of the thermostability and catalytic efficiency of a highly active β-glucanase from Talaromyces leycettanus JCM12802 by optimizing residual charge-charge interactions. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:124. [PMID: 27303445 PMCID: PMC4906821 DOI: 10.1186/s13068-016-0544-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/02/2016] [Indexed: 05/31/2023]
Abstract
BACKGROUND β-Glucanase is one of the most extensively used biocatalysts in biofuel, food and animal feed industries. However, the poor thermostability and low catalytic efficiency of most reported β-glucanases limit their applications. Currently, two strategies are used to overcome these bottlenecks, i.e., mining for novel enzymes from extremophiles and engineering existing enzymes. RESULTS A novel endo-β-1,3-1,4-glucanase of GH16 (Tlglu16A) from the thermophilic fungus Talaromyces leycettanus JCM12802 was produced in Pichia pastoris and characterized. For potential industrial applications, recombinant TlGlu16A exhibits favorable enzymatic properties over most reported glucanases, i.e., remarkable stability over a wide pH range from 1.0 to 10.0 and superior activity on glucan substrates (up to 15,197 U/mg). The only weakness of TlGlu16A is the thermolability at 65 °C and higher. To improve the thermostability, the enzyme thermal stability system was then used to engineer TlGlu16A through optimization of residual charge-charge interactions. Eleven mutants were constructed and compared to the wild-type TlGlu16A. Four mutants, H58D, E134R, D235G and D296K, showed longer half-life time at 80 °C (31, 7, 25, 22 vs. 0.5 min), and two mutants, D235G and D296K, had greater specific activities (158.2 and 122.2 %, respectively) and catalytic efficiencies (k cat/K m, 170 and 114 %, respectively). CONCLUSIONS The engineered TlGlu16A has great application potentials from the perspectives of enzyme yield and properties. Its thermostability and activity were apparently improved in the engineered enzymes through charge optimization. This study spans the genetic, functional and structural fields, and provides a combination of gene mining and protein engineering approaches for the systematic improvement of enzyme performance.
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Affiliation(s)
- Shuai You
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Tao Tu
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Lujia Zhang
- />State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 People’s Republic of China
| | - Yuan Wang
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Huoqing Huang
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Rui Ma
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Pengjun Shi
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Yingguo Bai
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Xiaoyun Su
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Zhemin Lin
- />Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou, 571100 People’s Republic of China
| | - Huiying Luo
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
| | - Bin Yao
- />Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing, 100081 People’s Republic of China
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42
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Pucci F, Bourgeas R, Rooman M. Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC. Sci Rep 2016; 6:23257. [PMID: 26988870 PMCID: PMC4796876 DOI: 10.1038/srep23257] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 12/15/2022] Open
Abstract
The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTm values of 4.2 °C that reduces to 2.9 °C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.
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Affiliation(s)
- Fabrizio Pucci
- Department of BioModeling, BioInformatics &BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Bld, 1050 Brussels, Belgium
| | - Raphaël Bourgeas
- Department of BioModeling, BioInformatics &BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Bld, 1050 Brussels, Belgium
| | - Marianne Rooman
- Department of BioModeling, BioInformatics &BioProcesses, Université Libre de Bruxelles, CP 165/61, Roosevelt Ave. 50, 1050 Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, CP 263, Triumph Bld, 1050 Brussels, Belgium
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43
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Craven TW, Cho MK, Traaseth NJ, Bonneau R, Kirshenbaum K. A Miniature Protein Stabilized by a Cation-π Interaction Network. J Am Chem Soc 2016; 138:1543-50. [PMID: 26812069 PMCID: PMC4867217 DOI: 10.1021/jacs.5b10285] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of folded miniature proteins is predicated on establishing noncovalent interactions that direct the self-assembly of discrete thermostable tertiary structures. In this work, we describe how a network of cation-π interactions present in proteins containing "WSXWS motifs" can be emulated to stabilize the core of a miniature protein. This 19-residue protein sequence recapitulates a set of interdigitated arginine and tryptophan residues that stabilize a distinctive β-strand:loop:PPII-helix topology. Validation of the compact fold determined by NMR was carried out by mutagenesis of the cation-π network and by comparison to the corresponding disulfide-bridged structure. These results support the involvement of a coordinated set of cation-π interactions that stabilize the tertiary structure.
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Affiliation(s)
- Timothy W. Craven
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
| | - Min-Kyu Cho
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Nathaniel J. Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY
- Simons Center for Data Analysis, New York, NY
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
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44
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Chen L, Li X, Wang R, Fang F, Yang W, Kan W. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation. J Biomol Struct Dyn 2016; 34:1576-89. [DOI: 10.1080/07391102.2015.1084480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Xue Li
- College of Chemistry and Biology, Beihua Uuniversity, Jilin 132000, P.R. China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Fengqin Fang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wanli Yang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
| | - Wei Kan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, P.R. China
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45
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Tamura K. Origins and Early Evolution of the tRNA Molecule. Life (Basel) 2015; 5:1687-99. [PMID: 26633518 PMCID: PMC4695843 DOI: 10.3390/life5041687] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 11/16/2022] Open
Abstract
Modern transfer RNAs (tRNAs) are composed of ~76 nucleotides and play an important role as "adaptor" molecules that mediate the translation of information from messenger RNAs (mRNAs). Many studies suggest that the contemporary full-length tRNA was formed by the ligation of half-sized hairpin-like RNAs. A minihelix (a coaxial stack of the acceptor stem on the T-stem of tRNA) can function both in aminoacylation by aminoacyl tRNA synthetases and in peptide bond formation on the ribosome, indicating that it may be a vestige of the ancestral tRNA. The universal CCA-3' terminus of tRNA is also a typical characteristic of the molecule. "Why CCA?" is the fundamental unanswered question, but several findings give a comprehensive picture of its origin. Here, the origins and early evolution of tRNA are discussed in terms of various perspectives, including nucleotide ligation, chiral selectivity of amino acids, genetic code evolution, and the organization of the ribosomal peptidyl transferase center (PTC). The proto-tRNA molecules may have evolved not only as adaptors but also as contributors to the composition of the ribosome.
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Affiliation(s)
- Koji Tamura
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
- Research Institute for Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
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46
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Abstract
Protein thermostability has been the focus of growing research interests in the last decades since its understanding and control play important roles in the optimization of a wide series of bioprocesses of academic and industrial importance. The complexity of this issue is rooted in the fact that the mechanisms ensuring thermal resistance are not unique and specific, but rather family- or even protein-dependent. Therefore, and despite the amount of research already accomplished, obtaining fast and precise thermal stability predictions is still a challenge, especially on a large scale. This article deepens the study of protein thermal stability and is focused on the prediction of its best descriptor, the melting temperature Tm. The relations between Tm and a series of factors that are expected to influence the protein stability are analyzed and discussed. Different Tm-prediction methods that utilize these factors, sometimes with additional information about homologous proteins, are introduced, and their individual performances are evaluated. The best methods are based on temperature-dependent statistical potentials, on the environmental temperature of the host organism, on the fraction of charged residues, and on the number of residues. They are combined to build an improved prediction method with significantly increased score. The root mean square deviation between the computed and experimental Tm-values for 45 proteins of known structure from 11 families is about 7°C in cross-validation and decreases to 5°C when 10% outliers are removed. The associated linear correlation coefficients are equal to .91 and .95, respectively.
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Affiliation(s)
- Fabrizio Pucci
- a Department of BioModeling, BioInformatics & BioProcesses , Université Libre de Bruxelles , Roosevelt Ave. 50, 1050 Brussels , Belgium
| | - Marianne Rooman
- a Department of BioModeling, BioInformatics & BioProcesses , Université Libre de Bruxelles , Roosevelt Ave. 50, 1050 Brussels , Belgium
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47
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Improvement in Thermostability of an Achaetomium sp. Strain Xz8 Endopolygalacturonase via the Optimization of Charge-Charge Interactions. Appl Environ Microbiol 2015. [PMID: 26209675 DOI: 10.1128/aem.01363-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Improving enzyme thermostability is of importance for widening the spectrum of application of enzymes. In this study, a structure-based rational design approach was used to improve the thermostability of a highly active, wide-pH-range-adaptable, and stable endopolygalacturonase (PG8fn) from Achaetomium sp. strain Xz8 via the optimization of charge-charge interactions. By using the enzyme thermal stability system (ETSS), two residues--D244 and D299--were inferred to be crucial contributors to thermostability. Single (D244A and D299R) and double (D244A/D299R) mutants were then generated and compared with the wild type. All mutants showed improved thermal properties, in the order D244A < D299R < D244A/D299R. In comparison with PG8fn, D244A/D299R showed the most pronounced shifts in temperature of maximum enzymatic activity (Tmax), temperature at which 50% of the maximal activity of an enzyme is retained (T50), and melting temperature (Tm), of about 10, 17, and 10.2°C upward, respectively, with the half-life (t1/2) extended by 8.4 h at 50°C and 45 min at 55°C. Another distinguishing characteristic of the D244A/D299R mutant was its catalytic activity, which was comparable to that of the wild type (23,000 ± 130 U/mg versus 28,000 ± 293 U/mg); on the other hand, it showed more residual activity (8,400 ± 83 U/mg versus 1,400 ± 57 U/mg) after the feed pelleting process (80°C and 30 min). Molecular dynamics (MD) simulation studies indicated that mutations at sites D244 and D299 lowered the overall root mean square deviation (RMSD) and consequently increased the protein rigidity. This study reveals the importance of charge-charge interactions in protein conformation and provides a viable strategy for enhancing protein stability.
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48
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Pezeshgi Modarres H, Dorokhov BD, Popov VO, Ravin NV, Skryabin KG, Dal Peraro M. Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp. 1519. Biochemistry 2015; 54:3076-85. [DOI: 10.1021/bi501227b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hassan Pezeshgi Modarres
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Boris D. Dorokhov
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Vladimir O. Popov
- Bach
Institute of Biochemistry, Russian Academy of Sciences, Moscow 119071, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Nikolai V. Ravin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
| | - Konstantin G. Skryabin
- Centre
“Bioengineering”, Russian Academy of Sciences, Moscow 117312, Russia
- RSC “Kurchatov Institute”, Moscow 123182, Russia
| | - Matteo Dal Peraro
- Institute
of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
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49
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Yang H, Liu L, Li J, Chen J, Du G. Rational Design to Improve Protein Thermostability: Recent Advances and Prospects. CHEMBIOENG REVIEWS 2015. [DOI: 10.1002/cben.201400032] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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50
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Godin-Roulling A, Schmidpeter PAM, Schmid FX, Feller G. Functional adaptations of the bacterial chaperone trigger factor to extreme environmental temperatures. Environ Microbiol 2015; 17:2407-20. [PMID: 25389111 DOI: 10.1111/1462-2920.12707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 01/26/2023]
Abstract
Trigger factor (TF) is the first molecular chaperone interacting cotranslationally with virtually all nascent polypeptides synthesized by the ribosome in bacteria. Thermal adaptation of chaperone function was investigated in TFs from the Antarctic psychrophile Pseudoalteromonas haloplanktis, the mesophile Escherichia coli and the hyperthermophile Thermotoga maritima. This series covers nearly all temperatures encountered by bacteria. Although structurally homologous, these TFs display strikingly distinct properties that are related to the bacterial environmental temperature. The hyperthermophilic TF strongly binds model proteins during their folding and protects them from heat-induced misfolding and aggregation. It decreases the folding rate and counteracts the fast folding rate imposed by high temperature. It also functions as a carrier of partially folded proteins for delivery to downstream chaperones ensuring final maturation. By contrast, the psychrophilic TF displays weak chaperone activities, showing that these functions are less important in cold conditions because protein folding, misfolding and aggregation are slowed down at low temperature. It efficiently catalyses prolyl isomerization at low temperature as a result of its increased cellular concentration rather than from an improved activity. Some chaperone properties of the mesophilic TF possibly reflect its function as a cold shock protein in E. coli.
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Affiliation(s)
- Amandine Godin-Roulling
- Laboratory of Biochemistry, Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
| | - Philipp A M Schmidpeter
- Laboratorium für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Bayreuth, D-95447, Germany
| | - Franz X Schmid
- Laboratorium für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, Bayreuth, D-95447, Germany
| | - Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, University of Liège, Liège, B-4000, Belgium
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