Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations
ABSTRACT Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins...
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Published in | Proteins, structure, function, and bioinformatics Vol. 82; no. 10; pp. 2353 - 2363 |
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Main Authors | , , , |
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Language | English |
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01.10.2014
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Abstract | ABSTRACT
Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification. Proteins 2014; 82:2353–2363. © 2014 Wiley Periodicals, Inc. |
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AbstractList | Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification. ABSTRACT Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification. Proteins 2014; 82:2353–2363. © 2014 Wiley Periodicals, Inc. Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification. Proteins 2014; 82:2353-2363. © 2014 Wiley Periodicals, Inc. [PUBLICATION ABSTRACT] Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells, has relatively short operational lifetimes. Several recent studies (both experimental and theoretical), carried out on small proteins (or small fractions of large proteins), show that a detailed knowledge of how the breakdown process starts and proceeds on molecular level could be of significant help to artificially improve the stability of fragile proteins. We have performed extended molecular dynamics (MD) simulations to study the denaturation of GOx (a protein dimer containing nearly 1200 amino acids) to identify weak points in its structure and in this way gather information to later make it more stable, for example, by mutations. A denaturation of a protein can be simulated by increasing the temperature far above physiological temperature. We have performed a series of MD simulations at different temperatures (300, 400, 500, and 600 K). The exit from the protein's native state has been successfully identified with the clustering method and supported by other methods used to analyze the simulation data. A common set of amino acids is regularly found to initiate the denaturation, suggesting a moiety where the enzyme could be strengthened by a suitable amino acid based modification. Proteins 2014; 82:2353-2363. copyright 2014 Wiley Periodicals, Inc. |
Author | Todde, Guido Laaksonen, Aatto Hovmöller, Sven Mocci, Francesca |
Author_xml | – sequence: 1 givenname: Guido surname: Todde fullname: Todde, Guido organization: Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden – sequence: 2 givenname: Sven surname: Hovmöller fullname: Hovmöller, Sven organization: Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden – sequence: 3 givenname: Aatto surname: Laaksonen fullname: Laaksonen, Aatto organization: Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden – sequence: 4 givenname: Francesca surname: Mocci fullname: Mocci, Francesca email: fmocci@unica.it organization: Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden |
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CitedBy_id | crossref_primary_10_1021_acscatal_7b01575 crossref_primary_10_3390_ijms17111796 crossref_primary_10_1016_j_ijbiomac_2018_03_083 crossref_primary_10_3389_fmicb_2017_01032 crossref_primary_10_1007_s00894_015_2696_z crossref_primary_10_1016_j_molcatb_2016_09_008 crossref_primary_10_1002_pro_4689 crossref_primary_10_1016_j_foodhyd_2019_105450 crossref_primary_10_1007_s42995_022_00128_z crossref_primary_10_1016_j_ijbiomac_2017_08_018 crossref_primary_10_3390_ijms22116028 |
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Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the... Glucose oxidase (GOx) is a flavoenzyme having applications in food and medical industries. However, GOx, as many other enzymes when extracted from the cells,... |
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SubjectTerms | cluster analysis fysikalisk kemi Glucose Oxidase - chemistry Hot Temperature MD simulation Models, Molecular Molecular Dynamics Simulation mutation Penicillium - enzymology Penicillium amagasakiense Physical Chemistry Protein Conformation Protein Denaturation Protein Folding unfolding |
Title | Glucose oxidase from Penicillium amagasakiense: Characterization of the transition state of its denaturation from molecular dynamics simulations |
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