Molecular dynamics simulations of the adsorption of an intrinsically disordered protein: Force field and water model evaluation in comparison with experiments.

This study investigates possible structural changes of an intrinsically disordered protein (IDP) when it adsorbs to a solid surface. Experiments on IDPs primarily result in ensemble averages due to their high dynamics. Therefore, molecular dynamics (MD) simulations are crucial for obtaining more detailed information on the atomistic and molecular levels. An evaluation of seven different force field and water model combinations have been applied: (A) CHARMM36IDPSFF + CHARMM-modified TIP3P, (B) CHARMM36IDPSFF + TIP4P-D, (C) CHARMM36m + CHARMM-modified TIP3P, (D) AMBER99SB-ILDN + TIP3P, (E) AMBER99SB-ILDN + TIP4P-D, (F) AMBERff03ws + TIP4P/2005, and (G) AMBER99SB-disp + disp-water. The results have been qualitatively compared with those of small-angle X-ray scattering, synchrotron radiation circular dichroism spectroscopy, and attenuated total reflectance Fourier transform infrared spectroscopy. The model IDP corresponds to the first 33 amino acids of the N-terminal of the magnesium transporter A (MgtA) and is denoted as KEIF. With a net charge of +3, KEIF is found to adsorb to the anionic synthetic clay mineral Laponite® due to the increase in entropy from the concomitant release of counterions from the surface. The experimental results show that the peptide is largely disordered with a random coil conformation, whereas the helical content (α- and/or 310-helices) increased upon adsorption. MD simulations corroborate these findings and further reveal an increase in polyproline II helices and an extension of the peptide conformation in the adsorbed state. In addition, the simulations provided atomistic resolution of the adsorbed ensemble of structures, where the arginine residues had a high propensity to form hydrogen bonds with the surface. Simulations B, E, and G showed significantly better agreement with experiments than the other simulations. Particularly noteworthy is the discovery that B and E with TIP4P-D water had superior performance to their corresponding simulations A and D with TIP3P-type water. Thus, this study shows the importance of the water model when simulating IDPs and has also provided an insight into the structural changes of surface-active IDPs induced by adsorption, which may play an important role in their function.

Slow Dissolution Kinetics of Model Peptide Fibrils.

Understanding the kinetics of peptide self-assembly is important because of the involvement of peptide amyloid fibrils in several neurodegenerative diseases. In this paper, we have studied the dissolution kinetics of self-assembled model peptide fibrils after a dilution quench. Due to the low concentrations involved, the experimental method of choice was isothermal titration calorimetry (ITC). We show that the dissolution is a strikingly slow and reaction-limited process, that can be timescale separated from other rapid processes associated with dilution in the ITC experiment. We argue that the rate-limiting step of dissolution involves the breaking up of inter-peptide ß-sheet hydrogen bonds, replacing them with peptide-water hydrogen bonds. Complementary pH experiments revealed that the self-assembly involves partial deprotonation of the peptide molecules.

Stable, metastable and unstable cellulose solutions.

We have characterized the dissolution state of microcrystalline cellulose (MCC) in aqueous tetrabutylammonium hydroxide, TBAH(aq), at different concentrations of TBAH, by means of turbidity and small-angle X-ray scattering. The solubility of cellulose increases with increasing TBAH concentration, which is consistent with solubilization driven by neutralization. When comparing the two polymorphs, the solubility of cellulose I is higher than that of cellulose II. This has the consequence that the dissolution of MCC (cellulose I) may create a supersaturated solution with respect to cellulose II. As for the dissolution state of cellulose, we identify three different regimes. (i) In the stable regime, corresponding to concentrations below the solubility of cellulose II, cellulose is molecularly dissolved and the solutions are thermodynamically stable. (ii) In the metastable regime, corresponding to lower supersaturations with respect to cellulose II, a minor aggregation of cellulose occurs and the solutions are kinetically stable. (iii) In the unstable regime, corresponding to larger supersaturations, there is macroscopic precipitation of cellulose II from solution. Finally, we also discuss strong alkali solvents in general and compare TBAH(aq) with the classical NaOH(aq) solvent.