Study of pH-dependent misfolding of surfactant protein C using state-of-the-art...

• Author(s): Santos, Catarina Azevedo Carvalheda dos
• Date: 2011
• Persistent ID: http://hdl.handle.net/10451/8054
• Origin: Repositório da Universidade de Lisboa
• Subject(s): SP-C; Misfolding; Dinâmica molecular a pH constante; Misturas de solvent orgânico; pH; Teses de mestrado - 2011
• Document Type: Master Thesis
• Language: English
• Advisor(s): Baptista, António M.; Machuqueiro, Miguel Ângelo dos Santos

Description

Tese de mestrado em Bioquímica, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2011 SP-C is a highly hydrophobic protein with two covalently linked fatty acyl chains that adopts a mainly helix structure while associated with the membrane. However, it misfolds into a β-rich structure under certain environmental conditions, which suggests that SP-C is in a metastable state. The slow α→β transitions are likely to be caused by the membrane-dissociation, deacylation and exposure to the neutral pH of the alveolar subphase, leading to the formation of amyloid aggregates associated with Pulmonary Alveolar Proteinosis (PAP). Here, we present the first study of the pH-dependent conformational behaviour of the deacylated SP-C (dSP-C) in a chloroform/methanol/water mixture using state-of-the-art molecular modelling methods, with the aim of getting insight into several structural properties of dSP-C that might be relevant for the formation of amyloid fibrils in PAP. We performed 60 simulations of 100 ns each, considering 6 different pH conditions and using the GROMOS 43A1 and the recently released GROMOS 54A7 force fields. Although the results for both force fields are contradictory and neither of them reproduces the experimental results for the dSP-C under similar conditions, they identify the increase of pH as a promoter of protein-protein interactions, in this type of organic mixtures. The possibility of undergoing inter-protein interactions due to the presence of other dSP-C molecules may be the principal contributor factor for the α→β transitions observed at pH 8 in the experimental results and that were not captured in our simulations. Our simulations show that the loss of structure is more prone to begin at the C-terminal region and that the β motifs start to form simultaneously in both N and C-terminal regions of the dSP-C with their approximation. These observations reinforce the necessity of using more than one force field to address a scientific question and validate the newest GROMOS 96 version, the 54A7.