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Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme

Mammalian purine nucleoside phosphorylase (PNP) is biologically active as a homotrimer, in which each monomer catalyzes a reaction independently of the others. To answer the question of why the native PNP forms a trimeric structure, we constructed, in silico and in vitro, the monomeric form of the e...

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Autores principales: Dyzma, Alicja, Wielgus-Kutrowska, Beata, Girstun, Agnieszka, Matošević, Zoe Jelić, Staroń, Krzysztof, Bertoša, Branimir, Trylska, Joanna, Bzowska, Agnieszka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9916683/
https://www.ncbi.nlm.nih.gov/pubmed/36768477
http://dx.doi.org/10.3390/ijms24032157
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author Dyzma, Alicja
Wielgus-Kutrowska, Beata
Girstun, Agnieszka
Matošević, Zoe Jelić
Staroń, Krzysztof
Bertoša, Branimir
Trylska, Joanna
Bzowska, Agnieszka
author_facet Dyzma, Alicja
Wielgus-Kutrowska, Beata
Girstun, Agnieszka
Matošević, Zoe Jelić
Staroń, Krzysztof
Bertoša, Branimir
Trylska, Joanna
Bzowska, Agnieszka
author_sort Dyzma, Alicja
collection PubMed
description Mammalian purine nucleoside phosphorylase (PNP) is biologically active as a homotrimer, in which each monomer catalyzes a reaction independently of the others. To answer the question of why the native PNP forms a trimeric structure, we constructed, in silico and in vitro, the monomeric form of the enzyme. Molecular dynamics simulations showed different geometries of the active site in the non-mutated trimeric and monomeric PNP forms, which suggested that the active site in the isolated monomer could be non-functional. To confirm this hypothesis, six amino acids located at the interface of the subunits were selected and mutated to alanines to disrupt the trimer and obtain a monomer (6Ala PNP). The effects of these mutations on the enzyme structure, stability, conformational dynamics, and activity were examined. The solution experiments confirmed that the 6Ala PNP mutant occurs mainly as a monomer, with a secondary structure almost identical to the wild type, WT PNP, and importantly, it shows no enzymatic activity. Simulations confirmed that, although the secondary structure of the 6Ala monomer is similar to the WT PNP, the positions of the amino acids building the 6Ala PNP active site significantly differ. These data suggest that a trimeric structure is necessary to stabilize the geometry of the active site of this enzyme.
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spelling pubmed-99166832023-02-11 Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme Dyzma, Alicja Wielgus-Kutrowska, Beata Girstun, Agnieszka Matošević, Zoe Jelić Staroń, Krzysztof Bertoša, Branimir Trylska, Joanna Bzowska, Agnieszka Int J Mol Sci Article Mammalian purine nucleoside phosphorylase (PNP) is biologically active as a homotrimer, in which each monomer catalyzes a reaction independently of the others. To answer the question of why the native PNP forms a trimeric structure, we constructed, in silico and in vitro, the monomeric form of the enzyme. Molecular dynamics simulations showed different geometries of the active site in the non-mutated trimeric and monomeric PNP forms, which suggested that the active site in the isolated monomer could be non-functional. To confirm this hypothesis, six amino acids located at the interface of the subunits were selected and mutated to alanines to disrupt the trimer and obtain a monomer (6Ala PNP). The effects of these mutations on the enzyme structure, stability, conformational dynamics, and activity were examined. The solution experiments confirmed that the 6Ala PNP mutant occurs mainly as a monomer, with a secondary structure almost identical to the wild type, WT PNP, and importantly, it shows no enzymatic activity. Simulations confirmed that, although the secondary structure of the 6Ala monomer is similar to the WT PNP, the positions of the amino acids building the 6Ala PNP active site significantly differ. These data suggest that a trimeric structure is necessary to stabilize the geometry of the active site of this enzyme. MDPI 2023-01-21 /pmc/articles/PMC9916683/ /pubmed/36768477 http://dx.doi.org/10.3390/ijms24032157 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Dyzma, Alicja
Wielgus-Kutrowska, Beata
Girstun, Agnieszka
Matošević, Zoe Jelić
Staroń, Krzysztof
Bertoša, Branimir
Trylska, Joanna
Bzowska, Agnieszka
Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title_full Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title_fullStr Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title_full_unstemmed Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title_short Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme
title_sort trimeric architecture ensures the stability and biological activity of the calf purine nucleoside phosphorylase: in silico and in vitro studies of monomeric and trimeric forms of the enzyme
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9916683/
https://www.ncbi.nlm.nih.gov/pubmed/36768477
http://dx.doi.org/10.3390/ijms24032157
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