ABSTRACT
The Spike protein's structure of the SARS-CoV-2 provides a unique opportunity to consider perturbations at the atomic level. We used the cryo-electron microscopy structure of the open conformation of the Spike protein to assess the impact of the mutations observed in the variants of concern at the molecular level. Molecular dynamics were subsequently performed with both the wt and the mutated forms to compare the flexibility and variation data for each residue of the three-dimensional fluctuations in the region associated with each alpha carbon. Additionally, protein-protein docking was used to investigate the interaction of each mutated profile with the ACE-2 receptor. After the molecular dynamics, the results show that the mutations increased the stability of the trimeric protein, with greater stability observed in the Gamma variant harboring the 10 characteristic mutations. The results of molecular dynamics, as shown by RMSF demonstrated for the residues that comprise the binding domain receptor (RBD), exhibited a reduction in flexibility, which was more pronounced in the Gamma variant. Finally, protein-protein docking experiments revealed an increase in the number of hydrophobic interactions and hydrogen bonds in the Gamma variant against the ACE-2 receptor, as opposed to the other variants. Taken together, these in silico experiments suggest that the evolution of the mutations favored the increased stability of Spike protein while potentially improving its interaction with the ACE-2 receptor, which in turn may indicate putative structural outcomes of the selection of these mutations in the convergent adaptive evolution as it has been observed for SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Humans , Spike Glycoprotein, Coronavirus/genetics , Molecular Dynamics Simulation , COVID-19/genetics , Cryoelectron Microscopy , SARS-CoV-2/genetics , Mutation , Protein BindingABSTRACT
Neste trabalho apresentamos um panorama do armazenamento de reativos para diagnóstico in vitro distribuídos pelo Ministério da Saúde aos Laboratórios Centrais de Saúde Pública LACEN, e da Central Nacional de Distribuição de Insumos Estratégicos CENADI. Foi realizada avaliação normativa considerando-se os componentes de estrutura e processo, destacando-se a importância da adoção das Boas Práticas de Armazenamento - BPA, no aprimoramento dos processos de trabalho. Foram avaliados quinze LACEN nas cinco regiões brasileiras. Foram verificados itens de BPA adotados em cada unidade avaliada. Foi evidenciado que os setores de armazenamento das unidades laboratoriais e do nível central carecem de maiores investimentos em capacitação e, em alguns casos, em estrutura física. O planejamento das aquisições também foi abordado e mostrou-se insatisfatório, conforme evidenciado pelo indicador de desabastecimento. Acreditamos que os desafios e pontos positivos destacados neste estudo possam contribuir para a melhoria dos processos de planejamento, aquisição e armazenamento de reativos para diagnóstico in vitro no âmbito do MS.