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

• Ano de defesa: 2024
• Autor(a) principal: Moraes, João Victor Badaró de
• Tipo de documento: Dissertação
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Universidade Federal de Viçosa; Biologia Celular e Estrutural
• Palavras-chave em Português: Enzimas; Reações químicas; Fosfatos; Biologia Celular e Estrutural
• Link de acesso: https://locus.ufv.br/handle/123456789/32703; https://doi.org/10.47328/ufvbbt.2024.066

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.