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Interfacial Dynamics and Growth Modes of ß2-Microglobulin Dimers.
Oliveira, Nuno F B; Rodrigues, Filipe E P; Vitorino, João N M; Faísca, Patrícia F N; Machuqueiro, Miguel.
Afiliação
  • Oliveira NFB; BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
  • Rodrigues FEP; BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
  • Vitorino JNM; BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
  • Faísca PFN; BioISI: Biosystems and Integrative Sciences Institute, Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
  • Machuqueiro M; BioISI: Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
J Chem Inf Model ; 63(14): 4447-4457, 2023 07 24.
Article em En | MEDLINE | ID: mdl-37132512
ABSTRACT
Protein aggregation is a complex process, strongly dependent on environmental conditions and highly structurally heterogeneous, both at the final level of fibril structure and intermediate level of oligomerization. Since the first step in aggregation is the formation of a dimer, it is important to clarify how certain properties of the latter (e.g., stability or interface geometry) may play a role in self-association. Here, we report a simple model that represents the dimer's interfacial region by two angles and combine it with a simple computational method to investigate how modulations of the interfacial region occurring on the ns-µs time scale change the dimer's growth mode. To illustrate the proposed methodology, we consider 15 different dimer configurations of the ß2m D76N mutant protein equilibrated with long Molecular Dynamics simulations and identify which interfaces lead to limited and unlimited growth modes, having, therefore, different aggregation profiles. We found that despite the highly dynamic nature of the starting configurations, most polymeric growth modes tend to be conserved within the studied time scale. The proposed methodology performs remarkably well taking into consideration the nonspherical morphology of the ß2m dimers, which exhibit unstructured termini detached from the protein's core, and the relatively weak binding affinities of their interfaces, which are stabilized by nonspecific apolar interactions. The proposed methodology is general and can be applied to any protein for which a dimer structure has been experimentally determined or computationally predicted.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação de Dinâmica Molecular / Agregados Proteicos Tipo de estudo: Prognostic_studies Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Portugal

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Simulação de Dinâmica Molecular / Agregados Proteicos Tipo de estudo: Prognostic_studies Idioma: En Revista: J Chem Inf Model Assunto da revista: INFORMATICA MEDICA / QUIMICA Ano de publicação: 2023 Tipo de documento: Article País de afiliação: Portugal