Structural modeling of E-NTPDase-substrate complexes preserving catalytic experimental features

Detalhes bibliográficos
Ano de defesa: 2024
Autor(a) principal: Moraes, João Victor Badaró de
Orientador(a): Não Informado pela instituição
Banca de defesa: Não Informado pela instituição
Tipo de documento: Dissertação
Tipo de acesso: Acesso aberto
Idioma: eng
Instituição de defesa: Universidade Federal de Viçosa
Biologia Celular e Estrutural
Programa de Pós-Graduação: Não Informado pela instituição
Departamento: Não Informado pela instituição
País: Não Informado pela instituição
Palavras-chave em Português:
Link de acesso: https://locus.ufv.br/handle/123456789/32703
https://doi.org/10.47328/ufvbbt.2024.066
Resumo: The Ecto-Nucleoside Triphosphate Diphosphohydrolase (E-NTPDase or NTPDase) family, essential for converting tri- and diphosphate nucleotides to monophosphates, significantly influences purinergic/pyrimidinergic signaling. However, detailed structural insights, particularly for NTPDase-nucleotide complexes, are scarce. The limited structural information leads to challenges in rationally optimizing and exploring the therapeutic potential of these enzymes. Addressing this limitation, this study introduces a computational strategy for assembling NTPDase-substrate complexes. While Molecular Docking may serve this purpose, limitations such as the inability to precisely reproduce experimentally characterized ligand conformations can undermine the complexes' reliability and further computational studies relying on them. Leveraging the active site's high conservation across NTPDases, we hypothesized a consistent substrate binding conformation. Pursuing that, we structurally aligned the available experimental structures in substrate-bound productive states and identified a canonical substrate conformation prevalent in the majority of experimentally resolved complexes. We also observed other general features of the complexes, which were conserved in all the characterized experimental structures. In light of these conserved features, we proposed a method for modeling NTPDase-nucleotide complexes that are compliant with the available experimental data. These complexes can be modeled by transferring crystallized substrate structures to well-modeled NTPDase structures, also carrying their cofactors and relevant water molecules. Subsequent energy minimization and equilibration through Molecular Dynamics simulations yield a final structure that closely resembles the conserved features characterized in experimental structures. We demonstrated this approach's utility by modeling complexes for each human NTPDase with ATP, ADP, GTP, GDP, UTP, and UDP, presenting a novel methodological avenue for future research. Keywords: E-NTPDase; Computational Modeling; Enzyme-Substrate Complex.