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Liu Y, Zhang N, Ma J, Zhou Y, Wei Q, Tian C, Fang Y, Zhong R, Chen G, Zhang S. Advances in cold-adapted enzymes derived from microorganisms. Front Microbiol 2023; 14:1152847. [PMID: 37180232 PMCID: PMC10169661 DOI: 10.3389/fmicb.2023.1152847] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
Cold-adapted enzymes, produced in cold-adapted organisms, are a class of enzyme with catalytic activity at low temperatures, high temperature sensitivity, and the ability to adapt to cold stimulation. These enzymes are largely derived from animals, plants, and microorganisms in polar areas, mountains, and the deep sea. With the rapid development of modern biotechnology, cold-adapted enzymes have been implemented in human and other animal food production, the protection and restoration of environments, and fundamental biological research, among other areas. Cold-adapted enzymes derived from microorganisms have attracted much attention because of their short production cycles, high yield, and simple separation and purification, compared with cold-adapted enzymes derived from plants and animals. In this review we discuss various types of cold-adapted enzyme from cold-adapted microorganisms, along with associated applications, catalytic mechanisms, and molecular modification methods, to establish foundation for the theoretical research and application of cold-adapted enzymes.
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Affiliation(s)
- Yehui Liu
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Na Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Jie Ma
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Yuqi Zhou
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Qiang Wei
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yi Fang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Rongzhen Zhong
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
| | - Sitong Zhang
- College of Life Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, Changchun, China
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Radhakrishnan G, Silva MS, Lock EJ, Belghit I, Philip AJP. Assessing amino acid solubility of black soldier fly larvae meal in Atlantic salmon ( Salmo salar) in vivo and in vitro. Front Physiol 2022; 13:1028992. [PMID: 36505052 PMCID: PMC9727232 DOI: 10.3389/fphys.2022.1028992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
In vitro and in vivo methods were used to evaluate amino acids solubility of black soldier fly (BSF) larvae meal and two experimental diets (reference and test diets) for Atlantic salmon. The current study used in vitro method such as pH stat to compare and standardise the salmon extracted enzyme (SE), and commercial enzyme (CE) based on their hydrolytic capacity on a purified protein substrate. Further, an in vitro amino acid solubility of feed ingredients and diets were measured using the standardised enzyme volume from SE and CE. Results showed that SE and CE exhibit similar protein hydrolytic capacity upon standardisation on purified substrates. However, when using the two-stage hydrolysis (acidic and alkaline steps), significantly higher amino acid solubility was observed with CE except for glycine, and proline which were equally solubilised by both SE, and CE. No significant difference was observed between reference and test diet using the SE except for tyrosine, valine, leucine, and phenylalanine, which were significantly higher solubilised in reference diet than test diet. Whereas higher solubility of valine, isoleucine, aspartic acid, and glutamic acid was observed in test diet using CE than SE. Similarly, the solubility of valine, isoleucine, and glutamic acid were higher in BSF larvae meal when CE was used. The in vivo true protein digestibility of BSF larvae meal was 99%, and 81% for the test diet containing BSF larvae meal. The results demonstrated a positive correlation (r = 0.91; p < 0.01) between salmon and commercial enzymes but overall, no significant correlation was observed for amino acid solubility between in vivo and in vitro. However, there was a strong positive correlation for protein solubility using SE (r = 0.98) than CE (r = 0.74) with the in vivo true protein digestibility. The efficiency of SE, and CE can be compared, and standardised based on DH%, and hence correlates better with the in vivo protein digestibility but not with amino acid solubilities.
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Affiliation(s)
- Gopika Radhakrishnan
- Institute of Marine Research, Bergen, Norway,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Erik-Jan Lock
- Institute of Marine Research, Bergen, Norway,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ikram Belghit
- Institute of Marine Research, Bergen, Norway,*Correspondence: Ikram Belghit,
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3
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Cold-active enzymes in the dairy industry: Insight into cold adaption mechanisms and their applications. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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4
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Chen Q, Wu Y, Huang Z, Zhang W, Mu W. Molecular Characterization of a Mesophilic Cellobiose 2-Epimerase That Maintains a High Catalytic Efficiency at Low Temperatures. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8268-8275. [PMID: 34231359 DOI: 10.1021/acs.jafc.1c02025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cellobiose 2-epimerase (CE) can catalyze bioconversion of lactose to its prebiotic derivative epilactose. The catalytic property of a novel CE from Treponema brennaborense (Trbr-CE) was investigated. Trbr-CE showed the highest catalytic efficiency of epimerization toward lactose among all of the previously reported CEs. This enzyme's specific activity could reach as high as 208.5 ± 5.3 U/mg at its optimum temperature, which is 45 °C. More importantly, this enzyme demonstrated a considerably high activity at low temperatures, suggesting Trbr-CE as a promising enzyme for industrial low-temperature production of epilactose. This structurally flexible enzyme exhibited a comparatively high binding affinity toward substrates, which was confirmed by both experimental verification and computational analysis. Molecular dynamics (MD) simulations and binding free energy calculations were applied to provide insights into molecular recognition upon temperature changes. Compared with thermophilic CEs, Trbr-CE presents a more negative enthalpy change and a higher entropy change when the temperature drops.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Yanchang Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Zhaolin Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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5
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Nicholls RA, Wojdyr M, Joosten RP, Catapano L, Long F, Fischer M, Emsley P, Murshudov GN. The missing link: covalent linkages in structural models. Acta Crystallogr D Struct Biol 2021; 77:727-745. [PMID: 34076588 PMCID: PMC8171067 DOI: 10.1107/s2059798321003934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
Covalent linkages between constituent blocks of macromolecules and ligands have been subject to inconsistent treatment during the model-building, refinement and deposition process. This may stem from a number of sources, including difficulties with initially detecting the covalent linkage, identifying the correct chemistry, obtaining an appropriate restraint dictionary and ensuring its correct application. The analysis presented herein assesses the extent of problems involving covalent linkages in the Protein Data Bank (PDB). Not only will this facilitate the remediation of existing models, but also, more importantly, it will inform and thus improve the quality of future linkages. By considering linkages of known type in the CCP4 Monomer Library (CCP4-ML), failure to model a covalent linkage is identified to result in inaccurate (systematically longer) interatomic distances. Scanning the PDB for proximal atom pairs that do not have a corresponding type in the CCP4-ML reveals a large number of commonly occurring types of unannotated potential linkages; in general, these may or may not be covalently linked. Manual consideration of the most commonly occurring cases identifies a number of genuine classes of covalent linkages. The recent expansion of the CCP4-ML is discussed, which has involved the addition of over 16 000 and the replacement of over 11 000 component dictionaries using AceDRG. As part of this effort, the CCP4-ML has also been extended using AceDRG link dictionaries for the aforementioned linkage types identified in this analysis. This will facilitate the identification of such linkage types in future modelling efforts, whilst concurrently easing the process involved in their application. The need for a universal standard for maintaining link records corresponding to covalent linkages, and references to the associated dictionaries used during modelling and refinement, following deposition to the PDB is emphasized. The importance of correctly modelling covalent linkages is demonstrated using a case study, which involves the covalent linkage of an inhibitor to the main protease in various viral species, including SARS-CoV-2. This example demonstrates the importance of properly modelling covalent linkages using a comprehensive restraint dictionary, as opposed to just using a single interatomic distance restraint or failing to model the covalent linkage at all.
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Affiliation(s)
- Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marcin Wojdyr
- Global Phasing Limited, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Robbie P. Joosten
- Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Lucrezia Catapano
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Marcus Fischer
- Chemical Biology and Therapeutics and Structural Biology, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105-3678, USA
| | - Paul Emsley
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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Hjörleifsson JG, Helland R, Magnúsdóttir M, Ásgeirsson B. The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop. FEBS Open Bio 2020; 11:173-184. [PMID: 33197282 PMCID: PMC7780099 DOI: 10.1002/2211-5463.13041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
The role of surface loops in mediating communication through residue networks is still a relatively poorly understood part in the study of cold adaptation of enzymes, especially in terms of their quaternary interactions. Alkaline phosphatase (AP) from the psychrophilic marine bacterium Vibrio splendidus (VAP) is characterized by an analogous large surface loop in each monomer, referred to as the large loop, that hovers over the active site of the other monomer. It presumably has a role in the high catalytic efficiency of VAP which accompanies its extremely low thermal stability. Here, we designed several different variants of VAP with the aim of removing intersubunit interactions at the dimer interface. Breaking the intersubunit contacts from one residue in particular (Arg336) reduced the temperature stability of the catalytically potent conformation and caused a 40% drop in catalytic rate. The high catalytic rates of enzymes from cold‐adapted organisms are often associated with increased dynamic flexibility. Comparison of the relative B‐factors of the R336L crystal structure to that of the wild‐type confirmed surface flexibility was increased in a loop on the opposite monomer, but not in the large loop. The increase in flexibility resulted in a reduced catalytic rate. The large loop increases the area of the interface between the subunits through its contacts and may facilitate an alternating structural cycle demanded by a half‐of‐sites reaction mechanism through stronger ties, as the dimer oscillates between high affinity (active) or low phosphoryl group affinity (inactive).
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Affiliation(s)
| | - Ronny Helland
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT, The Arctic University of Tromsø, Norway
| | - Manuela Magnúsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
| | - Bjarni Ásgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavik, Iceland
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7
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Structural features of cold-adapted dimeric GH2 β-D-galactosidase from Arthrobacter sp. 32cB. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:776-786. [PMID: 31195142 DOI: 10.1016/j.bbapap.2019.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 05/12/2019] [Accepted: 06/06/2019] [Indexed: 12/21/2022]
Abstract
Crystal structures of cold-adapted β-d-galactosidase (EC 3.2.1.23) from the Antarctic bacterium Arthrobacter sp. 32cB (ArthβDG) have been determined in an unliganded form resulting from diffraction experiments conducted at 100 K (at resolution 1.8 Å) and at room temperature (at resolution 3.0 Å). A detailed comparison of those two structures of the same enzyme was performed in order to estimate differences in their molecular flexibility and rigidity and to study structural rationalization for the cold-adaptation of the investigated enzyme. Furthermore, a comparative analysis with structures of homologous enzymes from psychrophilic, mesophilic, and thermophilic sources has been discussed to elucidate the relationship between structure and cold-adaptation in a wider context. The performed studies confirm that the structure of cold-adapted ArthβDG maintains balance between molecular stability and structural flexibility, which can be observed independently on the temperature of conducted X-ray diffraction experiments. Obtained information about proper protein function under given conditions provide a guideline for rational engineering of proteins in terms of their temperature optimum and thermal stability.
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Gilannejad N, Paykan Heyrati F, Dorafshan S, Martos-Sitcha JA, Yúfera M, Martínez-Rodríguez G. Molecular basis of the digestive functionality in developing Persian sturgeon (Acipenser persicus) larvae: additional clues for its phylogenetic status. J Comp Physiol B 2019; 189:367-383. [DOI: 10.1007/s00360-019-01215-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 03/10/2019] [Accepted: 03/20/2019] [Indexed: 12/11/2022]
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9
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Jesús-de la Cruz K, Álvarez-González CA, Peña E, Morales-Contreras JA, Ávila-Fernández Á. Fish trypsins: potential applications in biomedicine and prospects for production. 3 Biotech 2018; 8:186. [PMID: 29556440 DOI: 10.1007/s13205-018-1208-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/09/2018] [Indexed: 11/28/2022] Open
Abstract
In fishes, trypsins are adapted to different environmental conditions, and the biochemical and kinetic properties of a broad variety of native isoforms have been studied. Proteolytic enzymes remain in high demand in the detergent, food, and feed industries; however, our analysis of the literature showed that, in the last decade, some fish trypsins have been studied for the synthesis of industrial peptides and for specific biomedical uses as antipathogenic agents against viruses and bacteria, which have been recently patented. In addition, innovative strategies of trypsin administration have been studied to ensure that trypsins retain their properties until they exert their action. Biomedical uses require the production of high-quality enzymes. In this context, the production of recombinant trypsins is an alternative. For this purpose, E. coli-based systems have been tested for the production of fish trypsins; however, P. pastoris-based systems also seem to show great potential in the production of fish trypsins with higher production quality. On the other hand, there is a lack of information regarding the specific structures, biochemical and kinetic properties, and characteristics of trypsins produced using heterologous systems. This review describes the potential uses of fish trypsins in biomedicine and the enzymatic and structural properties of native and recombinant fish trypsins obtained to date, outlining some prospects for their study.
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Affiliation(s)
- Kristal Jesús-de la Cruz
- Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco México
| | | | - Emyr Peña
- Laboratorio de Acuacultura, DACBiol-UJAT, Carr. Villahermosa-Cárdenas Km 0.5, 86139 Villahermosa, Tabasco México
- Cátedra Consejo Nacional de Ciencia y Tecnología-UJAT, Villahermosa, Tabasco México
| | - José Antonio Morales-Contreras
- 2Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulté, 86150 Villahermosa, Tabasco México
| | - Ángela Ávila-Fernández
- 2Centro de Investigación, DACS-Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez No. 2838-A. Col. Tamulté, 86150 Villahermosa, Tabasco México
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10
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Crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase from a psychrophilic bacterium, Colwellia psychrerythraea 34H. Biochem Biophys Res Commun 2017; 492:500-506. [PMID: 28830812 DOI: 10.1016/j.bbrc.2017.08.063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/18/2017] [Indexed: 11/21/2022]
Abstract
To survive at low temperatures, psychrophiles seem to produce cold-adapted enzymes with a high flexibility around active sites for high catalytic efficiency. To gain insights into the cold-adaptation of psychrophilic enzymes in atomic detail, we determined the crystal structure of 5-enolpyruvylshikimate-3-phosphate synthase (CpsEPSPS) from Colwellia psychrerythraea, a psychrophilic bacterium. EPSPS is the primary target for the broad-spectrum herbicide, glyphosate, and a promising target for the development of antimicrobial and antiparasitic agents since it is absent in animals. The crystal structure of unliganded, open CpsEPSPS was determined at 2.2 Å resolution in space group P21 with two protomers per asymmetric unit. Superposition of separate domain I and II of CpsEPSPS structure with those of Escherichia coli EPSPS (EcoEPSPS) structure showed relatively small differences of RMSD values of 0.423 Å and 0.693 Å for domains I and II, respectively, implying the residues in ligand binding and catalysis of cold-adapted CpsEPSPS showed no significant flexibility. This result is conflicting to other cases of cold-adapted proteins. We also observed that hydrogen-bond forming residues in the surface of EcoEPSPS was mutated to non- or lesser hydrogen-bond forming one in CpsEPSPS, which makes the protein surface softer and eventually makes the protein more active at low temperature. In addition, domain rotation angle between open and closed states of CpsEPSPS was smaller than those of any EPSPSs whose structures are known. The restriction of the domain closure, which reduces the entropy cost of ligand binding and catalysis, may be a novel molecular adaptations of cold-adapted enzymes.
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12
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Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
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Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
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13
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Crystal Structures of Two Isozymes of Citrate Synthase from Sulfolobus tokodaii Strain 7. Biochem Res Int 2016; 2016:7560919. [PMID: 27656296 PMCID: PMC5021468 DOI: 10.1155/2016/7560919] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/17/2016] [Indexed: 11/17/2022] Open
Abstract
Thermoacidophilic archaeon Sulfolobus tokodaii strain 7 has two citrate synthase genes (ST1805-CS and ST0587-CS) in the genome with 45% sequence identity. Because they exhibit similar optimal temperatures of catalytic activity and thermal inactivation profiles, we performed structural comparisons between these isozymes to elucidate adaptation mechanisms to high temperatures in thermophilic CSs. The crystal structures of ST1805-CS and ST0587-CS were determined at 2.0 Å and 2.7 Å resolutions, respectively. Structural comparison reveals that both of them are dimeric enzymes composed of two identical subunits, and these dimeric structures are quite similar to those of citrate synthases from archaea and eubacteria. ST0587-CS has, however, 55 ion pairs within whole dimer structure, while having only 36 in ST1805-CS. Although the number and distributions of ion pairs are distinct from each other, intersubunit ion pairs between two domains of each isozyme are identical especially in interterminal region. Because the location and number of ion pairs are in a trend with other CSs from thermophilic microorganisms, the factors responsible for thermal adaptation of ST-CS isozymes are characterized by ion pairs in interterminal region.
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14
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Enzyme surface rigidity tunes the temperature dependence of catalytic rates. Proc Natl Acad Sci U S A 2016; 113:7822-7. [PMID: 27354533 DOI: 10.1073/pnas.1605237113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural origin of enzyme adaptation to low temperature, allowing efficient catalysis of chemical reactions even near the freezing point of water, remains a fundamental puzzle in biocatalysis. A remarkable universal fingerprint shared by all cold-active enzymes is a reduction of the activation enthalpy accompanied by a more negative entropy, which alleviates the exponential decrease in chemical reaction rates caused by lowering of the temperature. Herein, we explore the role of protein surface mobility in determining this enthalpy-entropy balance. The effects of modifying surface rigidity in cold- and warm-active trypsins are demonstrated here by calculation of high-precision Arrhenius plots and thermodynamic activation parameters for the peptide hydrolysis reaction, using extensive computer simulations. The protein surface flexibility is systematically varied by applying positional restraints, causing the remarkable effect of turning the cold-active trypsin into a variant with mesophilic characteristics without changing the amino acid sequence. Furthermore, we show that just restraining a key surface loop causes the same effect as a point mutation in that loop between the cold- and warm-active trypsin. Importantly, changes in the activation enthalpy-entropy balance of up to 10 kcal/mol are almost perfectly balanced at room temperature, whereas they yield significantly higher rates at low temperatures for the cold-adapted enzyme.
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15
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Papot C, Cascella K, Toullec JY, Jollivet D. Divergent ecological histories of two sister Antarctic krill species led to contrasted patterns of genetic diversity in their heat-shock protein (hsp70) arsenal. Ecol Evol 2016; 6:1555-75. [PMID: 27087928 PMCID: PMC4775515 DOI: 10.1002/ece3.1989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/28/2015] [Accepted: 01/03/2016] [Indexed: 11/12/2022] Open
Abstract
The Arctic and the Antarctic Peninsula are currently experiencing some of the most rapid rates of ocean warming on the planet. This raises the question of how the initial adaptation to extreme cold temperatures was put in place and whether or not directional selection has led to the loss of genetic variation at key adaptive systems, and thus polar species’ (re)adaptability to higher temperatures. In the Southern Ocean, krill represents the most abundant fauna and is a critical member at the base of the Antarctic food web. To better understand the role of selection in shaping current patterns of polymorphisms, we examined genetic diversity of the cox‐1 and hsp70 genes by comparing two closely related species of Euphausiid that differ in ecology. Results on mtcox‐1 agreed with previous studies, indicating high and similar effective population sizes. However, a coalescent‐based approach on hsp70 genes highlighted the role of positive selection and past demographic changes in their recent evolution. Firstly, some form of balancing selection was acting on the inducible isoform C, which reflected the maintenance of an ancestral adaptive polymorphism in both species. Secondly, E. crystallorophias seems to have lost most of its hsp70 diversity because of a population crash and/or directional selection to cold. Nonsynonymous diversities were always greater in E. superba, suggesting that it might have evolved under more heterogeneous conditions. This can be linked to species’ ecology with E. superba living in more variable pelagic conditions, while E. crystallorophias is strictly associated with continental shelves and sea ice.
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Affiliation(s)
- Claire Papot
- Université de Lille 1 CNRS UMR 8198 Groupe 'Ecoimmunology of Marine Annelids' Bât SN2, 1er étage porte 113 59655 Villeneuve d'Ascq France
| | - Kévin Cascella
- CNRS UMR 7144 Equipe ABICE Station Biologique de Roscoff 29682 Roscoff France; Laboratoire 'Adaptation et Diversité en Milieu Marin' UPMC Station Biologique 29682 Roscoff France
| | - Jean-Yves Toullec
- CNRS UMR 7144 Equipe ABICE Station Biologique de Roscoff 29682 Roscoff France; Laboratoire 'Adaptation et Diversité en Milieu Marin' UPMC Station Biologique 29682 Roscoff France
| | - Didier Jollivet
- CNRS UMR 7144 Equipe ABICE Station Biologique de Roscoff 29682 Roscoff France; Laboratoire 'Adaptation et Diversité en Milieu Marin' UPMC Station Biologique 29682 Roscoff France
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16
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Isaksen GV, Åqvist J, Brandsdal BO. Protein surface softness is the origin of enzyme cold-adaptation of trypsin. PLoS Comput Biol 2014; 10:e1003813. [PMID: 25165981 PMCID: PMC4148182 DOI: 10.1371/journal.pcbi.1003813] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/10/2014] [Indexed: 11/19/2022] Open
Abstract
Life has effectively colonized most of our planet and extremophilic organisms require specialized enzymes to survive under harsh conditions. Cold-loving organisms (psychrophiles) express heat-labile enzymes that possess a high specific activity and catalytic efficiency at low temperatures. A remarkable universal characteristic of cold-active enzymes is that they show a reduction both in activation enthalpy and entropy, compared to mesophilic orthologs, which makes their reaction rates less sensitive to falling temperature. Despite significant efforts since the early 1970s, the important question of the origin of this effect still largely remains unanswered. Here we use cold- and warm-active trypsins as model systems to investigate the temperature dependence of the reaction rates with extensive molecular dynamics free energy simulations. The calculations quantitatively reproduce the catalytic rates of the two enzymes and further yield high-precision Arrhenius plots, which show the characteristic trends in activation enthalpy and entropy. Detailed structural analysis indicates that the relationship between these parameters and the 3D structure is reflected by significantly different internal protein energy changes during the reaction. The origin of this effect is not localized to the active site, but is found in the outer regions of the protein, where the cold-active enzyme has a higher degree of softness. Several structural mechanisms for softening the protein surface are identified, together with key mutations responsible for this effect. Our simulations further show that single point-mutations can significantly affect the thermodynamic activation parameters, indicating how these can be optimized by evolution.
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Affiliation(s)
- Geir Villy Isaksen
- The Norwegian Structural Biology Center and the Center for Theoretical Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, Tromsø, Norway
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Bjørn Olav Brandsdal
- The Norwegian Structural Biology Center and the Center for Theoretical Computational Chemistry, Department of Chemistry, Faculty of Science and Technology, University of Tromsø, Tromsø, Norway
- * E-mail:
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17
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Hiteshi K, Gupta R. Thermal adaptation of α-amylases: a review. Extremophiles 2014; 18:937-44. [DOI: 10.1007/s00792-014-0674-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/06/2014] [Indexed: 11/24/2022]
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18
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Kumar V, Yedavalli P, Gupta V, Rao NM. Engineering lipase A from mesophilic Bacillus subtilis for activity at low temperatures. Protein Eng Des Sel 2014; 27:73-82. [PMID: 24402332 DOI: 10.1093/protein/gzt064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Loops or unordered regions of a protein are structurally dynamic and are strongly implicated in activity, stability and proteolytic susceptibility of proteins. Diminished activity of proteins at lower temperatures is considered to be due to compromised dynamics of the protein at lower temperatures. To evolve an active mesophilic lipase (Bacillus subtilis) at low temperatures, we subjected all the loop residues (n = 88) to site saturation mutagenesis (SSM). Based on a three-level screening protocol, we identified 14 substitutions, among 16,000 mutant population, which contributed to a substantial increase in activity at 5 °C. Based on the preliminary activity of recombinants at several temperatures, 5 substitutions among the 14 were found to be beneficial. A recombinant of these five mutations, named as 5CR, exhibited 7-fold higher catalytic efficiency than wild-type (WT) lipase at 10 °C. All the mutants, individually and in a recombinant (5CR), were characterized by substrate-binding parameters, melting temperatures and secondary structure. 5CR was similar to WT in substrate preferences and showed a significant improvement in activity at both lower and higher temperatures compared with the WT. To establish the contribution of mutations on the dynamics of the protein, we performed 100-ns molecular dynamics (MD) simulations on the WT and mutant lipase at 10 and 37 °C. The root mean square fluctuations (RMSFs) indeed showed that the mutations enhance the protein dynamics locally in the loop region having a catalytic residue, which may help in improved activities at lower temperatures.
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Affiliation(s)
- Virender Kumar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
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19
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Zhang XL, Tibbits GF, Paetzel M. The structure of cardiac troponin C regulatory domain with bound Cd2+ reveals a closed conformation and unique ion coordination. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:722-34. [PMID: 23633581 DOI: 10.1107/s0907444913001182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/11/2013] [Indexed: 12/22/2022]
Abstract
The amino-terminal domain of cardiac troponin C (cNTnC) is an essential Ca(2+) sensor found in cardiomyocytes. It undergoes a conformational change upon Ca(2+) binding and transduces the signal to the rest of the troponin complex to initiate cardiac muscle contraction. Two classical EF-hand motifs (EF1 and EF2) are present in cNTnC. Under physiological conditions, only EF2 binds Ca(2+); EF1 is a vestigial site that has lost its function in binding Ca(2+) owing to amino-acid sequence changes during evolution. Proteins with EF-hand motifs are capable of binding divalent cations other than calcium. Here, the crystal structure of wild-type (WT) human cNTnC in complex with Cd(2+) is presented. The structure of Cd(2+)-bound cNTnC with the disease-related mutation L29Q, as well as a structure with the residue differences D2N, V28I, L29Q and G30D (NIQD), which have been shown to have functional importance in Ca(2+) sensing at lower temperatures in ectothermic species, have also been determined. The structures resemble the overall conformation of NMR structures of Ca(2+)-bound cNTnC, but differ significantly from a previous crystal structure of Cd(2+)-bound cNTnC in complex with deoxycholic acid. The subtle structural changes observed in the region near the mutations may play a role in the increased Ca(2+) affinity. The 1.4 Å resolution WT cNTnC structure, which is the highest resolution structure yet obtained for cardiac troponin C, reveals a Cd(2+) ion coordinated in the canonical pentagonal bipyramidal geometry in EF2 despite three residues in the loop being disordered. A Cd(2+) ion found in the vestigial ion-binding site of EF1 is coordinated in a noncanonical `distorted' octahedral geometry. A comparison of the ion coordination observed within EF-hand-containing proteins for which structures have been solved in the presence of Cd(2+) is presented. A refolded WT cNTnC structure is also presented.
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Affiliation(s)
- Xiaolu Linda Zhang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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20
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Potential use of Atlantic cod trypsin in biomedicine. BIOMED RESEARCH INTERNATIONAL 2013; 2013:749078. [PMID: 23555095 PMCID: PMC3600245 DOI: 10.1155/2013/749078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/09/2013] [Accepted: 01/27/2013] [Indexed: 12/01/2022]
Abstract
Surface proteins of viruses and bacteria used for cell attachment and invasion are candidates for degradation by proteases. Trypsin from Atlantic cod (Gadus morhua) was previously demonstrated to have efficacy against influenza viruses in vitro and on skin. In this paper, cod trypsin is shown to be 3–12 times more effective in degrading large native proteins than its mesophilic analogue, bovine trypsin. This is in agreement with previous findings where cod trypsin was found to be the most active among twelve different proteases in cleaving various cytokines and pathological proteins. Furthermore, our results show that cod trypsin has high efficacy against herpes simplex virus type 1 (HSV-1) and the respiratory syncytial virus (RSV) in vitro. The results on the antipathogenic properties of cod trypsin are important because rhinovirus, RSV, and influenza are the most predominant pathogenic viruses in upper respiratory tract infections. Results from a clinical study presented in this paper show that a specific formulation containing cod trypsin was preferred for wound healing over other methods used in the study. Apparently, the high digestive ability of the cold-adapted cod trypsin towards large native proteins plays a role in its efficacy against pathogens and its positive effects on wounds.
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21
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Rojo L, García-Carreño F, de Los Angeles Navarrete del Toro M. Cold-adapted digestive aspartic protease of the clawed lobsters Homarus americanus and Homarus gammarus: biochemical characterization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:87-96. [PMID: 22648335 DOI: 10.1007/s10126-012-9461-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 04/23/2012] [Indexed: 06/01/2023]
Abstract
Aspartic proteinases in the gastric fluid of clawed lobsters Homarus americanus and Homarus gammarus were isolated to homogeneity by single-step pepstatin-A affinity chromatography; such enzymes have been previously identified as cathepsin D-like enzymes based on their deduced amino acid sequence. Here, we describe their biochemical characteristics; the properties of the lobster enzymes were compared with those of its homolog, bovine cathepsin D, and found to be unique in a number of ways. The lobster enzymes demonstrated hydrolytic activity against synthetic and natural substrates at a wider range of pH; they were more temperature-sensitive, showed no changes in the K(M) value at 4°C, 10°C, and 25°C, and had 20-fold higher k(cat)/K(M) values than bovine enzyme. The bovine enzyme was temperature-dependent. We propose that both properties arose from an increase in molecular flexibility required to compensate for the reduction of reaction rates at low habitat temperatures. This is supported by the fast denaturation rates induced by temperature.
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Affiliation(s)
- Liliana Rojo
- Centro de Investigaciones Biológicas del Noroeste-CIBNOR, Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, B.C.S. 23096, Mexico
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22
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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23
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Pasi M, Lavery R, Ceres N. PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties. J Chem Theory Comput 2012; 9:785-93. [DOI: 10.1021/ct3007925] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Marco Pasi
- Bases Moléculaires
et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors,
69367 Lyon, France
| | - Richard Lavery
- Bases Moléculaires
et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors,
69367 Lyon, France
| | - Nicoletta Ceres
- Bases Moléculaires
et Structurales des Systèmes
Infectieux, Univ. Lyon I/CNRS UMR 5086, IBCP, 7 Passage du Vercors,
69367 Lyon, France
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24
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Kim M, Jeong Y. Purification and Characterization of a Trypsin-Like Protease from Flatfish (Paralichthys olivaceus) Intestine. J Food Biochem 2012. [DOI: 10.1111/j.1745-4514.2012.00672.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Misook Kim
- Department of Food Science and Nutrition; Dankook University; 126 Jukjeon-Ro, Suji-gu Yongin Gyeonggi-Do 448-701 Korea
| | - Yoonhwa Jeong
- Department of Food Science and Nutrition; Dankook University; 126 Jukjeon-Ro, Suji-gu Yongin Gyeonggi-Do 448-701 Korea
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25
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Lam SY, Yeung RCY, Yu TH, Sze KH, Wong KB. A rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity. PLoS Biol 2011; 9:e1001027. [PMID: 21423654 PMCID: PMC3057955 DOI: 10.1371/journal.pbio.1001027] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/01/2011] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. Here we employed a thermophilic acylphosphatase from Pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity. METHODS AND FINDINGS Acylphosphatases have a unique structural feature that its conserved active-site arginine residue forms a salt-bridge with the C-terminal carboxyl group only in thermophilic acylphosphatases, but not in mesophilic acylphosphatases. We perturbed the local rigidity of this active-site residue by removing the salt-bridge in the thermophilic acylphosphatase and by introducing the salt-bridge in the mesophilic homologue. The mutagenesis design was confirmed by x-ray crystallography. Removing the salt-bridge in the thermophilic enzyme lowered the activation energy that decreased the activation enthalpy and entropy. Conversely, the introduction of the salt-bridge to the mesophilic homologue increased the activation energy and resulted in increases in both activation enthalpy and entropy. Revealed by molecular dynamics simulations, the unrestrained arginine residue can populate more rotamer conformations, and the loss of this conformational freedom upon the formation of transition state justified the observed reduction in activation entropy. CONCLUSIONS Our results support the conclusion that restricting the active-site flexibility entropically favors the enzymatic activity at high temperatures. However, the accompanying enthalpy-entropy compensation leads to a stronger temperature-dependency of the enzymatic activity, which explains the less active nature of the thermophilic enzymes at low temperatures.
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Affiliation(s)
- Sonia Y. Lam
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Rachel C. Y. Yeung
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Tsz-Ha Yu
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kong-Hung Sze
- Department of Chemistry, University of Hong Kong, Hong Kong SAR, China
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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26
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Structural properties of trypsin from cold-adapted fish, arabesque greenling (Pleurogrammus azonus). Eur Food Res Technol 2010. [DOI: 10.1007/s00217-010-1404-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Rojo L, Muhlia-Almazan A, Saborowski R, García-Carreño F. Aspartic cathepsin D endopeptidase contributes to extracellular digestion in clawed lobsters Homarus americanus and Homarus gammarus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2010; 12:696-707. [PMID: 20169386 DOI: 10.1007/s10126-010-9257-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 01/18/2010] [Indexed: 05/28/2023]
Abstract
Acid digestive proteinases were studied in the gastric fluids of two species of clawed lobster (Homarus americanus and Homarus gammarus). An active protein was identified in both species as aspartic proteinase by specific inhibition with pepstatin A. It was confirmed as cathepsin D by mass mapping, N-terminal, and full-length cDNA sequencing. Both lobster species transcribed two cathepsin D mRNAs: cathepsin D1 and cathepsin D2. Cathepsin D1 mRNA was detected only in the midgut gland, suggesting its function as a digestive enzyme. Cathepsin D2 mRNA was found in the midgut gland, gonads, and muscle. The deduced amino acid sequence of cathepsin D1 and cathepsin D2 possesses two catalytic DTG active-site motifs, the hallmark of aspartic proteinases. The putatively active cathepsin D1 has a molecular mass of 36.4 kDa and a calculated pI of 4.14 and possesses three potential glycosylation sites. The sequences showed highest similarities with cathepsin D from insects but also with another crustacean cathepsin D. Cathepsin D1 transcripts were quantified during a starvation period using real-time qPCR. In H. americanus, 15 days of starvation did not cause significant changes, but subsequent feeding caused a 2.5-fold increase. In H. gammarus, starvation caused a 40% reduction in cathepsin D1 mRNA, and no effect was observed with subsequent feeding.
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Affiliation(s)
- Liliana Rojo
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Col. Playa Palo de Santa Rita, La Paz, BCS 23096, Mexico
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28
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KISHIMURA HIDEKI, KLOMKLAO SAPPASITH, NALINANON SITTHIPONG, BENJAKUL SOOTTAWAT, CHUN BYUNGSOO, ADACHI KOHSUKE. COMPARATIVE STUDY ON THERMAL STABILITY OF TRYPSIN FROM THE PYLORIC CECA OF THREADFIN HAKELING (LAEMONEMA LONGIPES). J Food Biochem 2010. [DOI: 10.1111/j.1745-4514.2009.00263.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk. PLoS One 2009; 4:e7009. [PMID: 19759914 PMCID: PMC2740865 DOI: 10.1371/journal.pone.0007009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 08/03/2009] [Indexed: 11/19/2022] Open
Abstract
The cestode Echinococcus granulosus, the agent of hydatidosis/echinococcosis, is remarkably well adapted to its definitive host. However, the molecular mechanisms underlying the successful establishment of larval worms (protoscoleces) in the dog duodenum are unknown. With the aim of identifying molecules participating in the E. granulosus-dog cross-talk, we surveyed the transcriptomes of protoscoleces and protoscoleces treated with pepsin at pH 2. This analysis identified a multigene family of secreted monodomain Kunitz proteins associated mostly with pepsin/H(+)-treated worms, suggesting that they play a role at the onset of infection. We present the relevant molecular features of eight members of the E. granulosus Kunitz family (EgKU-1 - EgKU-8). Although diverse, the family includes three pairs of close paralogs (EgKU-1/EgKU-4; EgKU-3/EgKU-8; EgKU-6/EgKU-7), which would be the products of recent gene duplications. In addition, we describe the purification of EgKU-1 and EgKU-8 from larval worms, and provide data indicating that some members of the family (notably, EgKU-3 and EgKU-8) are secreted by protoscoleces. Detailed kinetic studies with native EgKU-1 and EgKU-8 highlighted their functional diversity. Like most monodomain Kunitz proteins, EgKU-8 behaved as a slow, tight-binding inhibitor of serine proteases, with global inhibition constants (K(I) (*)) versus trypsins in the picomolar range. In sharp contrast, EgKU-1 did not inhibit any of the assayed peptidases. Interestingly, molecular modeling revealed structural elements associated with activity in Kunitz cation-channel blockers. We propose that this family of inhibitors has the potential to act at the E. granulosus-dog interface and interfere with host physiological processes at the initial stages of infection.
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Sigurdardóttir AG, Arnórsdóttir J, Thorbjarnardóttir SH, Eggertsson G, Suhre K, Kristjánsson MM. Characteristics of mutants designed to incorporate a new ion pair into the structure of a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1794:512-8. [PMID: 19100869 DOI: 10.1016/j.bbapap.2008.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 10/31/2008] [Accepted: 11/19/2008] [Indexed: 12/01/2022]
Abstract
Structural comparisons of VPR, a subtilisin-like serine proteinase from a psychrotrophic Vibrio species and a thermophilic homologue, aqualysin I, have led us to hypothesize about the roles of different residues in the temperature adaptation of the enzymes. Some of these hypotheses are now being examined by analysis of mutants of the enzymes. The selected substitutions are believed to increase the stability of the cold adapted enzyme based on structural analysis of the thermostable structure. We report here on mutants, which were designed to incorporate an ion pair into the structure of VPR. The residues Asp17 and Arg259 are assumed to form an ion pair in aqualysin I. The cold adapted VPR contains Asn (Asn15) and Lys (Lys257) at corresponding sites in its structure. In VPR, Asn 15 is located on a surface loop with its side group pointing towards the side chain of Lys257. By substituting Asn15 by Asp (N15D) it was considered feasible that a salt bridge would form between the oppositely charged groups. To mimic further the putative salt bridge from the thermophile enzyme the corresponding double mutant (N15D/K257R) was also produced. The N15D mutation increased the thermal stability of VPR by approximately 3 degrees C, both in T(50%) and T(m). Addition of the K257R mutation did not however, increase the stability of the double mutant any further. Despite this stabilization of the VPR mutants the catalytic activity (k(cat)) against the substrate Suc-AAPF-NH-Np was increased in the mutants. Molecular dynamics simulations on wild type and the two mutant proteins suggested that indeed a salt bridge was formed in both cases. Furthermore, a truncated form of the N15D mutant (N15DDeltaC) was produced, lacking a 15 residue long C-terminal extended sequence not present in the thermophilic enzyme. In wild type VPR this supposedly moveable, negatively charged arm on the protein molecule might interfere with the new salt bridge introduced as a result of the N15D mutation. Removal of the C-terminal arm improved the thermal stability (T(m) approximately +1.5 degrees C) of the truncated enzyme (VPRDeltaC) as compared to the wild type VPR. Introduction of the N15D substitution into VPRDeltaC improved the thermal stability further by about 3 degrees C, or to about the same extent as in the wild type. However, contrary to what was observed for the wild type, the introduction of the putative salt bridge did not affect the catalytic properties (k(cat)) of the C-terminal truncated enzyme.
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Affiliation(s)
- Anna Gudný Sigurdardóttir
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
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31
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Papisova AI, Semenova SA, Kislitsyn IA, Rudenskaia GN. [Characteristics of substrate hydrolysis by endopeptidases from the hepatopancreas of the king crab]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2008; 34:479-86. [PMID: 18695720 DOI: 10.1134/s1068162008040067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Kinetic parameters of hydrolysis of peptide and protein substrates by psychrophilic endopeptidases from hepatopancreas of the king crab Paralithodes camtschaticus (PC), in particular, by trypsin, collagenolytic protease, and metalloprotease, were measured at different temperatures. The PC trypsin was shown to hydrolyze Bz-Arg-pNA in the temperature range studied (4-37 degrees C) 19 times more effectively than bovine trypsin. The rate constants of hydrolysis of Glp-Ala-Ala-Leu-pNA by the PC collagenolytic protease increased approximately by one order of magnitude along with temperature decrease, while Km decreased by 3.5 times. The effective values of Km for the hydrolysis of azocasein by the metalloprotease insignificantly depend on temperature. We proposed that electrostatic interactions of negative charges around the cavity of active site are critical for the effective hydrolysis of substrates by endopeptidases of the PC hepatopancreas.
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32
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Ræder ILU, Leiros I, Willassen NP, Smalås AO, Moe E. Uracil-DNA N-glycosylase (UNG) from the marine, psychrophilic bacterium Vibrio salmonicida shows cold adapted features. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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33
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Invertebrate trypsins: a review. J Comp Physiol B 2008; 178:655-72. [DOI: 10.1007/s00360-008-0263-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 03/18/2008] [Accepted: 03/25/2008] [Indexed: 11/26/2022]
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34
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Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases. FEBS Lett 2008; 582:1008-18. [DOI: 10.1016/j.febslet.2008.02.048] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 01/29/2008] [Accepted: 02/19/2008] [Indexed: 11/17/2022]
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Olufsen M, Smalås AO, Brandsdal BO. Electrostatic interactions play an essential role in DNA repair and cold-adaptation of uracil DNA glycosylase. J Mol Model 2008; 14:201-13. [PMID: 18196298 DOI: 10.1007/s00894-007-0261-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Accepted: 12/03/2007] [Indexed: 01/01/2023]
Abstract
Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k(cat) and reduced K(m) relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K(m)) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation.
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Affiliation(s)
- Magne Olufsen
- The Norwegian Structural Biology Centre, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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36
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Gillis TE, Marshall CR, Tibbits GF. Functional and evolutionary relationships of troponin C. Physiol Genomics 2007; 32:16-27. [PMID: 17940202 DOI: 10.1152/physiolgenomics.00197.2007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Striated muscle contraction is initiated when, following membrane depolarization, Ca(2+) binds to the low-affinity Ca(2+) binding sites of troponin C (TnC). The Ca(2+) activation of this protein results in a rearrangement of the components (troponin I, troponin T, and tropomyosin) of the thin filament, resulting in increased interaction between actin and myosin and the formation of cross bridges. The functional properties of this protein are therefore critical in determining the active properties of striated muscle. To date there are 61 known TnCs that have been cloned from 41 vertebrate and invertebrate species. In vertebrate species there are also distinct fast skeletal muscle and cardiac TnC proteins. While there is relatively high conservation of the amino acid sequence of TnC homologs between species and tissue types, there is wide variation in the functional properties of these proteins. To date there has been extensive study of the structure and function of this protein and how differences in these translate into the functional properties of muscles. The purpose of this work is to integrate these studies of TnC with phylogenetic analysis to investigate how changes in the sequence and function of this protein, integrate with the evolution of striated muscle.
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Affiliation(s)
- Todd E Gillis
- Department of Integrative Biology, University of Guelph, Guelph, Canada.
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37
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Arnórsdóttir J, Helgadóttir S, Thorbjarnardóttir SH, Eggertsson G, Kristjánsson MM. Effect of selected Ser/Ala and Xaa/Pro mutations on the stability and catalytic properties of a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:749-55. [PMID: 17490920 DOI: 10.1016/j.bbapap.2007.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 03/29/2007] [Accepted: 03/29/2007] [Indexed: 11/22/2022]
Abstract
A subtilisin-like serine proteinase from a psychrotrophic Vibrio species (VPR) shows distinct cold adapted traits regarding stability and catalytic properties, while sharing high sequence homology with enzymes adapted to higher temperatures. Based on comparisons of sequences and examination of 3D structural models of VPR and related enzymes of higher temperature origin, five sites were chosen to be subject to site directed mutagenesis. Three serine residues were substituted with alanine and two residues in loops were substituted with proline. The single mutations were combined to make double and triple mutants. The single Ser/Ala mutations had a moderately stabilizing effect and concomitantly decreased catalytic efficiency. Introducing a second Ser/Ala mutation did not have additive effect on stability; on the contrary a double Ser/Ala mutant had reduced stability with regard to both wild type and single mutants. The Xaa/Pro mutations stabilized the enzyme and did also tend to decrease the catalytic efficiency more than the Ser/Ala mutations.
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Affiliation(s)
- Jóhanna Arnórsdóttir
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107, Reykjavík, Iceland
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38
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Abstract
The three dimensional model of cold-adapted Alaskan psychrotroph Pseudomonas species (Strain B11-1) lipase has been constructed by homology modeling based on the crystal structure of acetyl esterase from Rhodococcus species and refined by molecular dynamics methods. Our model locates the substrate-binding cavity and further suggests that Ser-155, Asp-250, and His-280 are the members of the catalytic triad. Substrate specificity of the modeled lipase has been examined by docking experiments, which indicates that the ester of C(6) fatty acid has the highest affinity for the enzyme. Our model also identifies the oxyanion hole that plays an important role in the stabilization of the tetrahedral intermediate during catalysis. Comparison of this cold-adapted lipase with the crystal structure of a thermophilic Bacillus stearothermophilus P1 lipase supported the assumption that cold-adapted enzymes have a more flexible three-dimensional structure than their thermophilic counterparts. The conformational flexibility of this modeled cold-adapted lipase at low temperature probably originates from a combination of factors compared to its thermophilic counterpart, i.e., lower number of salt bridges and cation-pi interactions, increase in the non-polar surface area exposed to solvent. Our study may help in understanding the structural features of a cold-adapted lipase and can further be used in engineering lipase that can function at or near extreme temperatures with considerable biotechnological potential.
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Affiliation(s)
- D Roy
- Bioinformatics Centre, Bose Institute, Acharya J.C Bose Centenary Building, Kolkata, India.
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39
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Srimathi S, Jayaraman G, Feller G, Danielsson B, Narayanan PR. Intrinsic halotolerance of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis. Extremophiles 2007; 11:505-15. [PMID: 17310272 DOI: 10.1007/s00792-007-0062-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 12/27/2006] [Indexed: 10/23/2022]
Abstract
The halotolerance of a cold adapted alpha-amylase from the psychrophilic bacterium Pseudoalteromonas haloplanktis (AHA) was investigated. AHA exhibited hydrolytic activity over a broad range of NaCl concentrations (0.01-4.5 M). AHA showed 28% increased activity in 0.5-2.0 M NaCl compared to that in 0.01 M NaCl. In contrast, the corresponding mesophilic (Bacillus amyloliquefaciens) and thermostable (B. licheniformis) alpha-amylases showed a 39 and 46% decrease in activity respectively. Even at 4.5 M NaCl, 80% of the initial activity was detected for AHA, whereas the mesophilic and thermostable enzymes were inactive. Besides an unaltered fluorescence emission and secondary structure, a 10 degrees C positive shift in the temperature optimum, a stabilization factor of >5 for thermal inactivation and a Delta T(m) of 8.3 degrees C for the secondary structure melting were estimated in 2.7 M NaCl. The higher activation energy, half-life time and T(m) indicated reduced conformational dynamics and increased rigidity in the presence of higher NaCl concentrations. A comparison with the sequences of other halophilic alpha-amylases revealed that AHA also contains higher proportion of small hydrophobic residues and acidic residues resulting in a higher negative surface potential. Thus, with some compromise in cold activity, psychrophilic adaptation has also manifested halotolerance to AHA that is comparable to the halophilic enzymes.
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Affiliation(s)
- Soundararajan Srimathi
- Department of Microbiology, Tuberculosis Research Centre, Mayor Ramanathan Road, Chetput, Chennai, 600 031, India.
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40
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Abstract
By far the largest proportion of the Earth's biosphere is comprised of organisms that thrive in cold environments (psychrophiles). Their ability to proliferate in the cold is predicated on a capacity to synthesize cold-adapted enzymes. These enzymes have evolved a range of structural features that confer a high level of flexibility compared to thermostable homologs. High flexibility, particularly around the active site, is translated into low-activation enthalpy, low-substrate affinity, and high specific activity at low temperatures. High flexibility is also accompanied by a trade-off in stability, resulting in heat lability and, in the few cases studied, cold lability. This review addresses the structure, function, and stability of cold-adapted enzymes, highlighting the challenges for immediate and future consideration. Because of the unique properties of cold-adapted enzymes, they are not only an important focus in extremophile biology, but also represent a valuable model for fundamental research into protein folding and catalysis.
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Affiliation(s)
- Khawar Sohail Siddiqui
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
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41
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Papaleo E, Riccardi L, Villa C, Fantucci P, De Gioia L. Flexibility and enzymatic cold-adaptation: A comparative molecular dynamics investigation of the elastase family. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1397-406. [PMID: 16920043 DOI: 10.1016/j.bbapap.2006.06.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 06/14/2006] [Accepted: 06/26/2006] [Indexed: 11/21/2022]
Abstract
Molecular dynamics simulations of representative mesophilic and psycrophilic elastases have been carried out at different temperatures to explore the molecular basis of cold adaptation inside a specific enzymatic family. The molecular dynamics trajectories have been compared and analyzed in terms of secondary structure, molecular flexibility, intramolecular and protein-solvent interactions, unravelling molecular features relevant to rationalize the efficient catalytic activity of psychrophilic elastases at low temperature. The comparative molecular dynamics investigation reveals that modulation of the number of protein-solvent interactions is not the evolutionary strategy followed by the psycrophilic elastase to enhance catalytic activity at low temperature. In addition, flexibility and solvent accessibility of the residues forming the catalytic triad and the specificity pocket are comparable in the cold- and warm-adapted enzymes. Instead, loop regions with different amino acid composition in the two enzymes, and clustered around the active site or the specificity pocket, are characterized by enhanced flexibility in the cold-adapted enzyme. Remarkably, the psycrophilic elastase is characterized by reduced flexibility, when compared to the mesophilic counterpart, in some scattered regions distant from the functional sites, in agreement with hypothesis suggesting that local rigidity in regions far from functional sites can be beneficial for the catalytic activity of psychrophilic enzymes.
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Affiliation(s)
- Elena Papaleo
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, P.za della Scienza 2, 20126, Milan, Italy
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42
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Asgeirsson B, Cekan P. Microscopic rate-constants for substrate binding and acylation in cold-adaptation of trypsin I from Atlantic cod. FEBS Lett 2006; 580:4639-44. [PMID: 16879823 DOI: 10.1016/j.febslet.2006.07.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 07/07/2006] [Indexed: 10/24/2022]
Abstract
Temperature imposes limits on where life can thrive and this is evident in the evolution of the basic structural properties of proteins. Cold-adaptation of enzymes is one example, where the catalytic rate constant (k(cat)) is increased compared with hot-acclimated homologous under identical assay conditions. Trypsin I from Atlantic cod (Gadus morhua) has catalytic efficiency (k(cat)/K(m)) for amide hydrolysis that is 17-fold larger than observed for bovine trypsin. Here, the individual rate-constants for association of substrate (k(1)), dissociation of substrate (k(-1)), and acylation of the enzyme (k(2)) have been determined using benzoyl-Arg-p-nitroanilide or benzyloxycarbonyl-Gly-Pro-Arg-p-nitroanilide as substrates. Rather unexpectedly, by far the largest difference (37-fold increase) was observed in k(1), the rate constant for binding of substrate. The cold-adaptation of the dissociation and catalytic steps were not as prominent (increased by 3.7-fold). The length of substrate did have an effect by increasing the reaction rate by 70-fold, and again, the step most affected was the initial binding-step.
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Affiliation(s)
- Bjarni Asgeirsson
- Department of Biochemistry, Science Institute, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland.
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43
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Jayaraman G, Srimathi S, Bjarnason JB. Conformation and stability of elastase from Atlantic cod, Gadus morhua. Biochim Biophys Acta Gen Subj 2006; 1760:47-54. [PMID: 16213098 DOI: 10.1016/j.bbagen.2005.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 08/24/2005] [Accepted: 09/02/2005] [Indexed: 11/29/2022]
Abstract
Metal binding and conformational stability characteristics of psychrophilic elastase (ACE) from Atlantic cod (Gadus morhua) has been investigated. Chelation to Ca(2+) was found to be important for maintaining the biologically active conformation and for the thermal stability of the enzyme. However, presence of metal ions such as Zn(2+), Fe(3+) and Cu(2+) was found to inhibit its hydrolytic activity and so did the chelating agent EDTA. Both pH and guanidinium chloride induced denaturation of the enzyme was followed by monitoring the changes in the tryptophan fluorescence. ACE exhibited a simple two-state unfolding pattern in both acidic and basic conditions with the midpoint of transition at pH values 4.08 and 10.29, respectively. Guanidinium chloride and heat induced denaturation of the enzyme was investigated at two pH values, 5.50 and 8.00, wherein the enzyme possesses similar tertiary structure but differ in its hydrolytic activity. Guanidinium chloride induced denaturation indicated that the enzyme unfolds with a C(m) of 1.53 M at pH 8.0 and a DeltaG(H2O) of 6.91 kJ mol(-1) (28.65 J mol(-1) residue(-1)) which is the lowest reported for psychrophilic enzymes investigated till-date. However, at pH 5.50, DeltaG(H2O) value is slightly lowered by 0.65 kJ mol(-1) consistent with the observed increase in the apparent quenching constant obtained with acrylamide. On the other hand, increase in T(m) by 38.45 degrees C was observed for the enzyme at acid pH (5.50) in comparison to the heat induced unfolding at pH 8.0. The increase in the apparent T(m) has been attributed to the possible weak intermolecular association of the enzyme molecules at moderately high temperatures that is favoured by the increase in the accessible surface area / dynamics under acidic conditions. The stability characteristics of ACE have been compared with the available data for mesophilic porcine pancreatic elastase and possible mechanism for the low temperature adaptation of ACE has been proposed.
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Affiliation(s)
- G Jayaraman
- Centre for Protein Engineering and Biomedical Research, The Voluntary Health Services, Adyar, Chennai 600 113, India.
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44
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Adekoya OA, Helland R, Willassen NP, Sylte I. Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family. Proteins 2005; 62:435-49. [PMID: 16294337 DOI: 10.1002/prot.20773] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Knowledge about the structural features underlying cold adaptation is important for designing enzymes of different industrial relevance. Vibriolysin from Antarctic bacterium strain 643 (VAB) is at present the only enzyme of the thermolysin family from an organism that thrive in extremely cold climate. In this study comparative sequence-structure analysis and molecular dynamics (MD) simulations were used to reveal the molecular features of cold adaptation of VAB. Amino acid sequence analysis of 44 thermolysin enzymes showed that VAB compared to the other enzymes has: (1) fewer arginines, (2) a lower Arg/(Lys + Arg) ratio, (3) a lower fraction of large aliphatic side chains, expressed by the (Ile + Leu)/(Ile + Leu + Val) ratio, (4) more methionines, (5) more serines, and (6) more of the thermolabile amino acid asparagine. A model of the catalytic domain of VAB was constructed based on homology with pseudolysin. MD simulations for 3 ns of VAB, pseudolysin, and thermolysin supported the assumption that cold-adapted enzymes have a more flexible three-dimensional (3D) structure than their thermophilic and mesophilic counterparts, especially in some loop regions. The structural analysis indicated that VAB has fewer intramolecular cation-pi electron interactions and fewer hydrogen bonds than its mesophilic (pseudolysin) and thermophilic (thermolysin) counterparts. Lysine is the dominating cationic amino acids involved in salt bridges in VAB, while arginine is dominating in thermolysin and pseudolysin. VAB has a greater volume of inaccessible cavities than pseudolysin and thermolysin. The electrostatic potentials on the surface of the catalytic domain were also more negative for VAB than for thermolysin and pseudolysin. Thus, the MD simulations, the structural patterns, and the amino acid composition of VAB relative to other enzymes of the thermolysin family suggest that VAB possesses the biophysical properties generally following adaptation to cold climate.
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Affiliation(s)
- Olayiwola A Adekoya
- Department of Pharmacology, Institute of Medical Biology, Faculty of Medicine, University of Tromsø, Tromsø, Norway
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45
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Papaleo E, Fantucci P, De Gioia L. Effects of Calcium Binding on Structure and Autolysis Regulation in Trypsins. A Molecular Dynamics Investigation. J Chem Theory Comput 2005; 1:1286-97. [DOI: 10.1021/ct050092o] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Piercarlo Fantucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
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46
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Skálová T, Dohnálek J, Spiwok V, Lipovová P, Vondrácková E, Petroková H, Dusková J, Strnad H, Králová B, Hasek J. Cold-active β-Galactosidase from Arthrobacter sp. C2-2 Forms Compact 660kDa Hexamers: Crystal Structure at 1.9Å Resolution. J Mol Biol 2005; 353:282-94. [PMID: 16171818 DOI: 10.1016/j.jmb.2005.08.028] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/15/2005] [Accepted: 08/16/2005] [Indexed: 11/20/2022]
Abstract
The X-ray structure of cold-active beta-galactosidase (isoenzyme C-2-2-1) from an Antarctic bacterium Arthrobacter sp. C2-2 was solved at 1.9A resolution. The enzyme forms 660 kDa hexamers with active sites opened to the central cavity of the hexamer and connected by eight channels with exterior solvent. To our best knowledge, this is the first cold-active beta-galactosidase with known structure and also the first known beta-galactosidase structure in the form of compact hexamers. The hexamer organization regulates access of substrates and ligands to six active sites and this unique packing, present also in solution, raises questions about its purpose and function. This enzyme belongs to glycosyl hydrolase family 2, similarly to Escherichia coli beta-galactosidase, forming tetramers necessary for its enzymatic function. However, we discovered significant differences between these two enzymes affecting the ability of tetramer/hexamer formation and complementation of the active site. This structure reveals new insights into the cold-adaptation mechanisms of enzymatic pathways of extremophiles.
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Affiliation(s)
- Tereza Skálová
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 1606 Praha 6, Czech Republic.
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47
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Gudmundsdóttir A, Pálsdóttir HM. Atlantic cod trypsins: from basic research to practical applications. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2005; 7:77-88. [PMID: 15759084 DOI: 10.1007/s10126-004-0061-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Accepted: 06/24/2004] [Indexed: 05/24/2023]
Abstract
Atlantic cod trypsin I is an appropriate representative of the traditionally classified cold-adapted group I trypsins, and the recombinant form of cod trypsin Y is the only biochemically characterized member of the novel group III trypsins. Trypsin Y is adapted to lower temperatures than all other presently known trypsins. This review describes the basic characteristics of and practical uses for trypsins of Atlantic cod, as well as those of other organisms. Overexpression of the recombinant forms of cod trypsins I and Y in microorganisms is explained as well as the advantages of using site-directed mutagenesis to increase their stability toward autolysis and thermal inactivation. Trypsins appear to play a key role in the nutrition and development of marine fish. We discuss the potential use of cod trypsins as biomarkers to evaluate the nutritional status of cod larvae and describe the industrial applications of cod trypsin I and other trypsins.
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Affiliation(s)
- Agústa Gudmundsdóttir
- Science Institute, University of Iceland, Laeknagardi, Vatnsmýrarvegi 16, Reykjavík, IS-101, Iceland.
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48
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Arnórsdóttir J, Kristjánsson MM, Ficner R. Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation. FEBS J 2005; 272:832-45. [PMID: 15670163 DOI: 10.1111/j.1742-4658.2005.04523.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of a subtilisin-like serine proteinase from the psychrotrophic marine bacterium, Vibrio sp. PA-44, was solved by means of molecular replacement and refined at 1.84 A. This is the first structure of a cold-adapted subtilase to be determined and its elucidation facilitates examination of the molecular principles underlying temperature adaptation in enzymes. The cold-adapted Vibrio proteinase was compared with known three-dimensional structures of homologous enzymes of meso- and thermophilic origin, proteinase K and thermitase, to which it has high structural resemblance. The main structural features emerging as plausible determinants of temperature adaptation in the enzymes compared involve the character of their exposed and buried surfaces, which may be related to temperature-dependent variation in the physical properties of water. Thus, the hydrophobic effect is found to play a significant role in the structural stability of the meso- and thermophile enzymes, whereas the cold-adapted enzyme has more of its apolar surface exposed. In addition, the cold-adapted Vibrio proteinase is distinguished from the more stable enzymes by its strong anionic character arising from the high occurrence of uncompensated negatively charged residues at its surface. Interestingly, both the cold-adapted and thermophile proteinases differ from the mesophile enzyme in having more extensive hydrogen- and ion pair interactions in their structures; this supports suggestions of a dual role of electrostatic interactions in the adaptation of enzymes to both high and low temperatures. The Vibrio proteinase has three calcium ions associated with its structure, one of which is in a calcium-binding site not described in other subtilases.
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Affiliation(s)
- Jóhanna Arnórsdóttir
- Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August Universität Göttingen, Germany
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49
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Leiros HKS, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalås AO. Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements. Protein Sci 2004; 13:1056-70. [PMID: 15044735 PMCID: PMC2280040 DOI: 10.1110/ps.03498604] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.
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50
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Recombinant Trypsin Y from Atlantic Cod—Properties for Commercial Use. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2004. [DOI: 10.1300/j030v13n02_08] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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