Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study

Abstract

The pulmonary surfactant protein C (SP-C) is a small highly hydrophobic protein that adopts a mainly helical structure while associated with the membrane but misfolds into a β-rich metastable structure upon deacylation, membrane dissociation, and exposure to the neutral pH of the aqueous alveolar subphase, eventually leading to the formation of amyloid aggregates associated with pulmonary alveolar proteinosis. The present constant-pH MD study of the acylated and deacylated isoforms of SP-C in a chloroform/methanol/water mixture, often used to mimic the membrane environment, shows that the loss of the acyl groups has a structural destabilizing effect and that the increase of pH promotes intraprotein contacts which contribute to the loss of helical structure in solution. These contacts result from the poor solvation of charged groups by the solvent mixture, which exhibits a limited membrane-mimetic character. Although a single SP-C molecule was used in the simulations, we propose that analogous intermolecular interactions may play a role in the early stages of the protein misfolding and aggregation in this mixture.

Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

“…The MEAD package 38 version 2.2.9 was used to calculate the PB-derived energy terms, using atomic charges and radii derived from the GROMOS 54A7 force field 39 , and the p K a values of model compounds described in Table 1 of reference 40 . The molecular surface was computed by considering a rolling probe of radius 1.4 Å, and the Stern layer was 2 Å.…”

The role of electrostatics in TrxR electron transfer mechanism: A computational approach

“…For the model compound, a two step focusing is done with the first having 61 grid points spaced by 1.0 Å and the second with 61 grid points spaced by 0.25 Å and both centered on the site of interest. The pK mod values used in this work were taken from Carvalheda et al . for the normal residues (8.58 for Cys) and a value of 5.43 was used for selenocysteine …”

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations

“…The first block is a PB/MC calculation (see section 2.4) whose last-generated protonation states are assigned to the protein (simply assigning to each site the state closer to its average protonation would ignore site-site correlations and would break the underlying Markov chain [29]). The second block is a short MM/MD simulation of the system with a frozen protein and membrane, here taken as 0.1 ps long [39,55], intended to allow the solvent to adapt to the new protonation states (longer relaxation times result in abnormal water penetration into the membrane, leading to its destabilization or even rupture [39]). The third block is an MM/MD simulation of the completely unconstrained system, here taken as 10 ps long, which samples the system configurations for a fixed set of protonation states; the last snapshot of this simulation is then used for the first block of the next cycle.…”

“…The dielectric constant was 2 for the protein/lipids and 80 for the solvent, the temperature was 310 K and the ionic strength 0.1 M. The finite-difference linear PB calculations used a three-step focusing [62] procedure employing consecutive grid spacings of 3.0, 1.0 and 0.25 Å. The pK a values of the model compounds were the ones listed in Table 1 of [63], 13.65 for the arginine residues (the pK a of guanidine and alkylated derivatives [64,65]) and 9.11 for the cross-linked Y288 I [66].…”