Prion versus Doppel Protein Misfolding: New Insights from Replica-Exchange Molecular Dynamics Simulations

The doppel (Dpl) and prion (PrP) proteins share a very similar fold (three helices and two short β-strands), while they differ significantly in sequence (only 25% homologous) and in disease-related β-rich conformations that occur for PrP only. In a previous study [Baillod, P., et al. (2012) <i>Biochemistry</i> <i>51</i>, 9891–9899], we investigated the misfolding and rare, β-rich folds of monomeric PrP with replica-exchange molecular dynamics (REMD) simulations. In the work presented here, we perform analogous simulations for Dpl with the aim of comparing the two systems and characterizing possible specificities of PrP for misfolding and amyloidogenesis. Our extensive simulations, which allow us to overcome high energy barriers via the REMD approach, sample several β-rich folds, some of which are stable at room temperature, for both proteins. Per residue secondary structure propensities reveal that novel β-sheets of Dpl and PrP are formed by amino acids belonging to the helices that are the least stable in the respective native structure, H1 for Dpl and H2 and H3 for PrP, in agreement with experimental data. Using a specific clustering method that allows discrimination against different β-strand arrangements, seven β-rich folds could be characterized for PrP and five for Dpl, which are clearly distinct and share only one single similar fold. A major difference between the two proteins is found in the free energy barriers leading to misfolded structures: they are approximately 3 times higher for Dpl than for PrP. This suggests that the difference in amyloidogenic behavior between PrP and Dpl might be due to kinetic reasons

Study of the Redox Properties of Singlet and Triplet Tris(2,2′-bipyridine)ruthenium(II) ([Ru(bpy)₃]²⁺) in Aqueous Solution by Full Quantum and Mixed Quantum/Classical Molecular Dynamics Simulations

The oxidation of ground-state (singlet) and triplet [Ru­(bpy)₃]²⁺ were studied by full quantum-mechanical (QM) and mixed quantum/classical (QM/MM) molecular dynamics simulations. Both approaches provide reliable results for the redox potentials of the two spin states. The two redox reactions closely obey Marcus theory for electron transfer. The free energy difference between the two [Ru­(bpy)₃]²⁺ states amounts to 1.78 eV from both QM and QM/MM simulations. The two methods also provide similar results for the reorganization free energy associated with the transition from singlet to triplet [Ru­(bpy)₃]²⁺ (0.06 eV for QM and 0.07 eV for QM/MM). On the basis of single-point calculations, we estimate the entropic contribution to the free energy difference between singlet and triplet [Ru­(bpy)₃]²⁺ to be 0.27 eV, which is significantly greater than previously assumed (0.03 eV) and in contradiction with the assumption that the transition between these two states can be accurately described using purely energetic considerations. Employing a thermodynamic cycle involving singlet [Ru­(bpy)₃]²⁺, triplet [Ru­(bpy)₃]²⁺, and [Ru­(bpy)₃]³⁺, we calculated the triplet oxidation potential to be −0.62 V vs the standard hydrogen electrode, which is significantly different from a previous experimental estimate based on energetic considerations only (−0.86 V)

Structure and Dynamics of Liquid Water from ab Initio Molecular DynamicsComparison of BLYP, PBE, and revPBE Density Functionals with and without van der Waals Corrections

We investigate the accuracy provided by different treatments of the exchange and correlation effects, in particular the London dispersion forces, on the properties of liquid water using <i>ab initio</i> molecular dynamics simulations with density functional theory. The lack of London dispersion forces in generalized gradient approximations (GGAs) is remedied by means of dispersion-corrected atom-centered potentials (DCACPs) or damped atom-pairwise dispersion corrections of the <i>C</i>₆<i>R</i>^–6 form. We compare results from simulations using GGA density functionals (BLYP, PBE, and revPBE) with data from their van der Waals (vdW) corrected counterparts. As pointed out previously, all vdW-corrected BLYP simulations give rise to highly mobile water whose softened structure is closer to experimental data than the one predicted by the bare BLYP functional. Including vdW interactions in the PBE functional, on the other hand, has little influence on both structural and dynamical properties of water. Augmenting the revPBE functional with either damped atom-pairwise dispersion corrections or DCACP evokes opposite behaviors. The former further softens the already under-structured revPBE water, whereas the latter makes it more glassy. These results demonstrate the delicacy needed in describing weak interactions in molecular liquids

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of the protein matrix in modulating the absorption of retinal chromophore in rhodopsin, but, while generally agreeing in predicting the correct location of the absorption maximum, they often reached contradicting conclusions on how the environment tunes the spectrum. To address this controversial issue, we combine here a thorough structural and dynamical characterization of rhodopsin with a careful validation of its excited-state properties via the use of a wide range of state-of-the-art quantum chemical approaches including various flavors of time-dependent density functional theory (TDDFT), different multireference perturbative schemes (CASPT2 and NEVPT2), and quantum Monte Carlo (QMC) methods. Through extensive quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, we obtain a comprehensive structural description of the chromophore–protein system and sample a wide range of thermally accessible configurations. We show that, in order to obtain reliable excitation properties, it is crucial to employ a sufficient number of representative configurations of the system. In fact, the common use of a single, ad hoc structure can easily lead to an incorrect model and an agreement with experimental absorption spectra due to cancelation of errors. Finally, we show that, to properly account for polarization effects on the chromophore and to quench the large blue-shift induced by the counterion on the excitation energies, it is necessary to adopt an enhanced description of the protein environment as given by a large quantum region including as many as 250 atoms

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references

Enhanced Sampling Molecular Dynamics Identifies PrP^Sc Structures Harboring a C‑Terminal β‑Core

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 μs total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124–226) of the mouse prion protein (PrP); 1.3% of the conformations sampled display a high level of β-structure (≥19 residues), allowing the assessment of β-propensities along the sequence and highlighting the most structurally labile hot spots. A clustering algorithm is applied to sort the structures of this pool according to their fold. Ten β-rich folds are thus defined and analyzed with regard to their topology, accumulation temperatures, and structural characteristics. In contrast to the so-called spiral and β-helix models suggesting that the β-rich core of the scrapie isoform (PrP^Sc) comprises the N-terminal tail and part of the C-terminal domain up to helix 1 (H1), we present putative structural models for monomeric precursors of PrP^Sc and PrP β-oligomers that are characterized by a C-terminal β-rich core, in agreement with the suggestions of a series of recent experiments

Enhanced Sampling Molecular Dynamics Identifies PrP^Sc Structures Harboring a C‑Terminal β‑Core

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 μs total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124–226) of the mouse prion protein (PrP); 1.3% of the conformations sampled display a high level of β-structure (≥19 residues), allowing the assessment of β-propensities along the sequence and highlighting the most structurally labile hot spots. A clustering algorithm is applied to sort the structures of this pool according to their fold. Ten β-rich folds are thus defined and analyzed with regard to their topology, accumulation temperatures, and structural characteristics. In contrast to the so-called spiral and β-helix models suggesting that the β-rich core of the scrapie isoform (PrP^Sc) comprises the N-terminal tail and part of the C-terminal domain up to helix 1 (H1), we present putative structural models for monomeric precursors of PrP^Sc and PrP β-oligomers that are characterized by a C-terminal β-rich core, in agreement with the suggestions of a series of recent experiments

The Charge Transfer Problem in Density Functional Theory Calculations of Aqueously Solvated Molecules

Recent advances in algorithms and computational hardware have enabled the calculation of excited states with time-dependent density functional theory (TDDFT) for large systems of <i>O</i>(<i>1000</i>) atoms. Unfortunately, the aqueous charge transfer problem in TDDFT (whereby many spuriously low-lying charge transfer excited states are predicted) seems to become more severe as the system size is increased. In this work, we concentrate on the common case where a chromophore is embedded in aqueous solvent. We examine the role of exchange-correlation functionals, basis set effects, ground state geometries, and the treatment of the external environment in order to assess the root cause of this problem. We conclude that the problem rests largely on water molecules at the boundary of a finite cluster model, i.e., “edge waters.” We also demonstrate how the TDDFT problem can be related directly to ground state problems. These findings demand caution in the commonly employed strategy that rests on “snapshot” cutout geometries taken from ground state dynamics with molecular mechanics. We also find that the problem is largely ameliorated when the range-separated hybrid functional LC-ωPBEh is used

Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one correspondence between the structures of the different early intermediates (dark, batho, BSI, lumi) involved in the initial steps of the rhodopsin photoactivation mechanism and their optical spectra. A systematic analysis of the results based on a correlation-based feature selection algorithm shows that the origin of the color shifts among these intermediates can be mainly ascribed to alterations in intrinsic properties of the chromophore structure, which are tuned by several residues located in the protein binding pocket. In addition to the expected electrostatic and dipolar effects caused by the charged residues (Glu113, Glu181) and to strong hydrogen bonding with Glu113, other interactions such as π-stacking with Ala117 and Thr118 backbone atoms, van der Waals contacts with Gly114 and Ala292, and CH/π weak interactions with Tyr268, Ala117, Thr118, and Ser186 side chains are found to make non-negligible contributions to the modulation of the color tuning among the different rhodopsin photointermediates

In Situ Mapping of the Molecular Arrangement of Amphiphilic Dye Molecules at the TiO₂ Surface of Dye-Sensitized Solar Cells

Amphiphilic sensitizers are central to the function of dye-sensitized solar cells. It is known that the cell’s performance depends on the molecular arrangement and the density of the dye on the semiconductor surface, but a molecular-level picture of the cell–electrolyte interface is still lacking. Here, we present subnanometer in situ atomic force microscopy images of the Z907 dye at the surface of TiO₂ in a relevant liquid. Our results reveal changes in the conformation and the lateral arrangement of the dye molecules, depending on their average packing density on the surface. Complementary quantitative measurements on the ensemble of the film are obtained by the quartz-crystal microbalance with dissipation technique. An atomistic picture of the dye coverage-dependent packing, the effectiveness of the hydrophobic alkyl chains as blocking layer, and the solvent accessibility is obtained from molecular dynamics simulations