A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a "first-principles" DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

The "Hot-Solvent/Cold-Solute" Problem Revisited

The temperature steers the equilibrium and nonequilibrium conformational dynamics of macromolecules in solution. Therefore, corresponding molecular dynamics simulations require a strategy for temperature control which should guarantee that the experimental statistical ensemble is also sampled in silico. Several algorithms for temperature control have been proposed. All these thermostats interfere with the macromolecule's "natural" dynamics as given by the Newtonian mechanics. Furthermore, using a single thermostat for an inhomogeneous solute-solvent system can lead to stationary temperature gradients. To avoid this "hot solvent/cold solute" problem, two separate thermostats are frequently applied, one to the solute and one to the solvent. However, such a separate temperature control will perturb the dynamics of the macromolecule much more strongly than a global one and, therefore, can introduce large artifacts into its conformational dynamics. Based on the concept that an explicit solvent environment represents an ideal thermostat concerning the magnitude and time correlation of temperature fluctuations of the solute, we propose a temperature control strategy that, on the one hand, provides a homogeneous temperature distribution throughout the system together with the correct statistical ensemble for the solute molecule while, on the other hand, minimally perturbing its dynamics.

Simulated Solute Tempering

For the enhanced conformational sampling in molecular dynamics (MD) simulations, we present "simulated solute tempering" (SST) which is an easy to implement variant of simulated tempering. SST extends conventional simulated tempering (CST) by key concepts of "replica exchange with solute tempering" (REST, Liu et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 13749). We have applied SST, CST, and REST to molecular dynamics (MD) simulations of an alanine octapeptide in explicit water. The weight parameters required for CST and SST are determined by two different formulas whose performance is compared. For SST only one of them yields a uniform sampling of the temperature space. Compared to CST and REST, SST provides the highest exchange probabilities between neighboring rungs in the temperature ladder. Concomitantly, SST leads to the fastest diffusion of the simulation system through the temperature space, in particular, if the "even-odd" exchange scheme is employed in SST. As a result, SST exhibits the highest sampling speed of the investigated tempering methods.

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved-up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

Electrostatics of proteins in dielectric solvent continua. I. An accurate and efficient reaction field description

We present a reaction field (RF) method which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of an electrostatics calculation with polarizable molecular mechanics (MM) force fields. The method combines an approach originally suggested by Egwolf and Tavan [J. Chem. Phys. 118, 2039 (2003)] with concepts generalizing the Born solution [Z. Phys. 1, 45 (1920)] for a solvated ion. First, we derive an exact representation according to which the sources of the RF potential and energy are inducible atomic anti-polarization densities and atomic shielding charge distributions. Modeling these atomic densities by Gaussians leads to an approximate representation. Here, the strengths of the Gaussian shielding charge distributions are directly given in terms of the static partial charges as defined, e.g., by standard MM force fields for the various atom types, whereas the strengths of the Gaussian anti-polarization densities are calculated by a self-consistency iteration. The atomic volumes are also described by Gaussians. To account for covalently overlapping atoms, their effective volumes are calculated by another self-consistency procedure, which guarantees that the dielectric function ε(r) is close to one everywhere inside the protein. The Gaussian widths σ(i) of the atoms i are parameters of the RF approximation. The remarkable accuracy of the method is demonstrated by comparison with Kirkwood's analytical solution for a spherical protein [J. Chem. Phys. 2, 351 (1934)] and with computationally expensive grid-based numerical solutions for simple model systems in dielectric continua including a di-peptide (Ac-Ala-NHMe) as modeled by a standard MM force field. The latter example shows how weakly the RF conformational free energy landscape depends on the parameters σ(i). A summarizing discussion highlights the achievements of the new theory and of its approximate solution particularly by comparison with so-called generalized Born methods. A follow-up paper describes how the method enables Hamiltonian, efficient, and accurate MM molecular dynamics simulations of proteins in dielectric solvent continua.

Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics

In Paper I of this work [S. Bauer, G. Mathias, and P. Tavan, J. Chem. Phys. 140, 104102 (2014)] we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfilled by RF quantities introduced in Paper I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e., energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Paper I by scanning of configurations and with one obtained from an explicit solvent simulation.

Coupling density functional theory to polarizable force fields for efficient and accurate Hamiltonian molecular dynamics simulations

Hybrid molecular dynamics (MD) simulations, in which the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 10(3)-10(5) molecules, pose a challenge. A corresponding computational approach should guarantee energy conservation, exclude artificial distortions of the electron density at the interface between the DFT and PMM fragments, and should treat the long-range electrostatic interactions within the hybrid simulation system in a linearly scaling fashion. Here we describe a corresponding Hamiltonian DFT/(P)MM implementation, which accounts for inducible atomic dipoles of a PMM environment in a joint DFT/PMM self-consistency iteration. The long-range parts of the electrostatics are treated by hierarchically nested fast multipole expansions up to a maximum distance dictated by the minimum image convention of toroidal boundary conditions and, beyond that distance, by a reaction field approach such that the computation scales linearly with the number of PMM atoms. Short-range over-polarization artifacts are excluded by using Gaussian inducible dipoles throughout the system and Gaussian partial charges in the PMM region close to the DFT fragment. The Hamiltonian character, the stability, and efficiency of the implementation are investigated by hybrid DFT/PMM-MD simulations treating one molecule of the water dimer and of bulk water by DFT and the respective remainder by PMM.

Piperazine derivatives inhibit PrP/PrP(res) propagation in vitro and in vivo

Prion diseases are fatal neurodegenerative disorders, which are not curable and no effective treatment exists so far. The major neuropathological change in diseased brains is the conversion of the normal cellular form of the prion protein PrPc(C) into a disease-associated isoform PrP(Sc). PrP(Sc) accumulates into multimeres and fibrillar aggregates, which leads to the formation of amyloid plaques. Increasing evidence indicates a fundamental role of PrP(Sc) species and its aggregation in the pathogenesis of prion diseases, which initiates the pathological cascade and leads to neurodegeneration accompanied by spongiform changes. In search of compounds that have the potential to interfere with PrP(Sc) formation and propagation, we used a cell based assay for the screening of potential aggregation inhibitors. The assay deals with a permanently prion infected cell line that was adapted for a high-throughput screening of a compound library composed of 10,000 compounds (DIVERset 2, ChemBridge). We could detect six different classes of highly potent inhibitors of PrP(Sc) propagation in vitro and identified piperazine derivatives as a new inhibitory lead structure, which increased incubation time of scrapie infected mice.

Polarizable six-point water models from computational and empirical optimization

Tröster et al. (J. Phys. Chem B 2013, 117, 9486-9500) recently suggested a mixed computational and empirical approach to the optimization of polarizable molecular mechanics (PMM) water models. In the empirical part the parameters of Buckingham potentials are optimized by PMM molecular dynamics (MD) simulations. The computational part applies hybrid calculations, which combine the quantum mechanical description of a H2O molecule by density functional theory (DFT) with a PMM model of its liquid phase environment generated by MD. While the static dipole moments and polarizabilities of the PMM water models are fixed at the experimental gas phase values, the DFT/PMM calculations are employed to optimize the remaining electrostatic properties. These properties cover the width of a Gaussian inducible dipole positioned at the oxygen and the locations of massless negative charge points within the molecule (the positive charges are attached to the hydrogens). The authors considered the cases of one and two negative charges rendering the PMM four- and five-point models TL4P and TL5P. Here we extend their approach to three negative charges, thus suggesting the PMM six-point model TL6P. As compared to the predecessors and to other PMM models, which also exhibit partial charges at fixed positions, TL6P turned out to predict all studied properties of liquid water at p0 = 1 bar and T0 = 300 K with a remarkable accuracy. These properties cover, for instance, the diffusion constant, viscosity, isobaric heat capacity, isothermal compressibility, dielectric constant, density, and the isobaric thermal expansion coefficient. This success concurrently provides a microscopic physical explanation of corresponding shortcomings of previous models. It uniquely assigns the failures of previous models to substantial inaccuracies in the description of the higher electrostatic multipole moments of liquid phase water molecules. Resulting favorable properties concerning the transferability to other temperatures and conditions like the melting of ice are also discussed.

The Microscopic Physical Cause for the Density Maximum of Liquid Water

The existence of a density maximum at 277 K is probably the most prominent anomaly among the many very special thermodynamic properties of liquid water. While usually attributed to so-called hydrogen bonding, the microscopic physical cause of this prominent anomaly is still elusive. Here we show that the density anomaly is caused by those short-range electrostatic forces, which are generated by the quadrupole and higher moments of the charge distributions present in liquid-phase water molecules. This conclusion derives from 20 ns replica exchange molecular-dynamics simulations with closely related polarizable four-, five-, and six-point water models. As soon as the model complexity suffices to represent the higher electrostatic moments with sufficient accuracy, the density temperature profile n(T) calculated for T ∈ [250,320] K at the standard pressure 1 bar locks in to the experimental observation. The corresponding six-point model is, therefore, the most simple available cartoon for liquid-phase water molecules.

Polarizable water models from mixed computational and empirical optimization

Here we suggest a mixed computational and empirical approach serving to optimize the parameters of complex and polarizable molecular mechanics (PMM) models for complicated liquids. The computational part of the parameter optimization relies on hybrid calculations combining density functional theory (DFT) for a solute molecule with a PMM treatment of its solvent environment at well-defined thermodynamic conditions. As an application we have developed PMM models for water featuring ν = 3, 4, and 5 points of force action, a Gaussian inducible dipole and a Buckingham potential at the oxygen, the experimental liquid phase geometry, the experimental gas phase polarizability α(exp)(g) = 1.47 ų, and, for ν = 4 and 5, the gas phase value μ(exp)(g) = 1.855 D for the static dipole moment. The widths of the Gaussian dipoles and, for ν = 4 and 5, also the electrostatic geometries of these so-called TLνP models are derived from self-consistent DFT/PMM calculations, and the parameters of the Buckingham potentials (and the static TL3P dipole moment) are estimated from molecular dynamics (MD) simulations. The high quality of the resulting models is demonstrated for the observables targeted during optimization (potential energy per molecule, pressure, radial distribution functions) and a series of predicted properties (quadrupole moments, density at constant pressure, dielectric constant, diffusivity, viscosity, compressibility, heat capacity) at certain standard conditions. Remaining deficiencies and possible ways for their removal are discussed.

Anle138b: a novel oligomer modulator for disease-modifying therapy of neurodegenerative diseases such as prion and Parkinson's disease

In neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and prion diseases, deposits of aggregated disease-specific proteins are found. Oligomeric aggregates are presumed to be the key neurotoxic agent. Here we describe the novel oligomer modulator anle138b [3-(1,3-benzodioxol-5-yl)-5-(3-bromophenyl)-1H-pyrazole], an aggregation inhibitor we developed based on a systematic high-throughput screening campaign combined with medicinal chemistry optimization. In vitro, anle138b blocked the formation of pathological aggregates of prion protein (PrP^Sc) and of α-synuclein (α-syn), which is deposited in PD and other synucleinopathies such as dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). Notably, anle138b strongly inhibited all prion strains tested including BSE-derived and human prions. Anle138b showed structure-dependent binding to pathological aggregates and strongly inhibited formation of pathological oligomers in vitro and in vivo both for prion protein and α-synuclein. Both in mouse models of prion disease and in three different PD mouse models, anle138b strongly inhibited oligomer accumulation, neuronal degeneration, and disease progression in vivo. Anle138b had no detectable toxicity at therapeutic doses and an excellent oral bioavailability and blood–brain-barrier penetration. Our findings indicate that oligomer modulators provide a new approach for disease-modifying therapy in these diseases, for which only symptomatic treatment is available so far. Moreover, our findings suggest that pathological oligomers in neurodegenerative diseases share structural features, although the main protein component is disease-specific, indicating that compounds such as anle138b that modulate oligomer formation by targeting structure-dependent epitopes can have a broad spectrum of activity in the treatment of different protein aggregation diseases.

Electronic excitations in long polyenes revisited

We apply the valence shell model OM2 [W. Weber and W. Thiel, Theor. Chem. Acc. 103, 495, (2000)] combined with multireference configuration interaction (MRCI) to compute the vertical excitation energies and transition dipole moments of the low-energy singlet excitations in the polyenes with 4 ≤ N ≤ 22π-electrons. We find that the OM2/MRCI descriptions closely resemble those of Pariser-Parr-Pople (PPP) π-electron models [P. Tavan and K. Schulten, Phys. Rev. B 36, 4337, (1987)], if equivalent MRCI procedures and regularly alternating model geometries are used. OM2/MRCI optimized geometries are shown to entail improved descriptions particularly for smaller polyenes (N ≤ 12), for which sizeable deviations from the regular model geometries are found. With configuration interaction active spaces covering also the σ- in addition to the π-electrons, OM2/MRCI excitation energies turn out to become smaller by at most 0.35 eV for the ionic and 0.15 eV for the covalent excitations. The particle-hole (ph) symmetry, which in Pariser-Parr-Pople models arises from the zero-differential overlap approximation, is demonstrated to be only weakly broken in OM2 such that the oscillator strengths of the covalent 1B(u)(-) states, which artificially vanish in ph-symmetric models, are predicted to be very small. According to OM2/MRCI and experimental data the 1B(u)(-) state is the third excited singlet state for N < 12 and becomes the second for N ≥ 14. By comparisons with results of other theoretical approaches and experimental evidence we argue that deficiencies of the particular MRCI method employed by us, which show up in a poor size consistency of the covalent excitations for N > 12, are caused by its restriction to at most doubly excited references.

Optimizing the Accuracy and Efficiency of Fast Hierarchical Multipole Expansions for MD Simulations

Based on p'th order Cartesian Taylor expansions of Coulomb interactions and on hierarchical decompositions of macromolecular simulation systems into hierarchies of nested, structure-adapted, and adaptively formed clusters of increasing size, fast multipole methods are constructed for rapid and accurate calculations of electrostatic interactions. These so-called SAMMp algorithms are formulated through totally symmetric and traceless tensors describing the multipole moments and the coefficients of local Taylor expansions. Simple recursions for the efficient evaluation and shifting of multipole moments are given. The required tensors are explicitly given up to order p = 4. The SAMMp algorithms are shown to guarantee the reaction principle. For systems with periodic boundaries, a reaction field (RF) correction is applied, which introduces at distances beyond the "minimum image convention" boundary a dielectric continuum surrounding each cluster at the top level of coarse graining. The correctness of the present SAMMp implementation is demonstrated by analyzing the scaling of the residuals and by checking the numerical accuracy of the reaction principle for a pair of distant molecular ions in vacuum. Molecular dynamics simulations of pure water and aqueous solutions containing artificial ions, which are enclosed by periodic boundaries, demonstrate the stability and low-noise behavior of SAMMp/RF.

Diphenylpyrazole-derived compounds increase survival time of mice after prion infection

Transmissible spongiform encephalopathies (TSEs) represent a group of fatal neurodegenerative disorders that can be transmitted by natural infection or inoculation. TSEs include scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, and Creutzfeldt-Jakob disease (CJD) in humans. The emergence of a variant form of CJD (vCJD), which has been associated with BSE, produced strong pressure to search for effective treatments with new drugs. Up to now, however, TSEs have proved incurable, although many efforts have been made both in vitro and in vivo to search for potent therapeutic and prophylactic compounds. For this purpose, we analyzed a compound library consisting of 10,000 compounds with a cell-based high-throughput screening assay dealing with scrapie-infected scrapie mouse brain and ScN(2)A cells and identified a new class of inhibitors consisting of 3,5-diphenylpyrazole (DPP) derivatives. The most effective DPP derivative showed half-maximal inhibition of PrP(Sc) formation at concentrations (IC(50)) of 0.6 and 1.2 μM, respectively. This compound was subsequently subjected to a number of animal experiments using scrapie-infected wild-type C57BL/6 and transgenic Tga20 mice. The DPP derivative induced a significant increase of incubation time both in therapeutic and prophylactic experiments. The onset of the prion disease was delayed by 37 days after intraperitoneal and 42 days after oral application, respectively. In summary, we demonstrate a high in vitro efficiency of DPP derivatives against prion infections that was substantiated in vivo for one of these compounds. These results indicate that the novel class of DPP compounds should comprise excellent candidates for future therapeutic studies.

DFT/MM description of flavin IR spectra in BLUF domains

A class of photoreceptors occurring in various organisms consists of domains that are blue light sensing using flavin (BLUF). The vibrational spectra of the flavin chromophore are spectroscopically well characterized for the dark-adapted resting states and for the light-adapted signaling states of BLUF domains in solution. Here we present a theoretical analysis of such spectra by applying density functional theory (DFT) to the flavin embedded in molecular mechanics (MM) models of its protein and solvent environment. By DFT/MM we calculate flavin spectra for seven different X-ray and NMR structures of BLUF domains occurring in the transcriptional antirepressor AppA and in the blue light receptor B (BlrB) of the purple bacterium Rb. Sphaeroides as well as in the phototaxis photoreceptor Slr1694 of the cyanobacterium Synechocystis. By considering the dynamical stabilities of associated all-atom simulation models and by comparing calculated with observed vibrational spectra, we show that two of the considered structures (both AppA) are obviously erroneous and that specific features of two further crystal structures (BlrB and Slr1694) cannot represent the states of the respective BLUF domains in solution. Thereby, the conformational transitions elicited by solvation are identified. In this context we demonstrate how hydrogen bonds of varying strengths can tune in BLUF domains the C═O stretching frequencies of the flavin chromophore. Furthermore we show that the DFT/MM spectra of the flavin calculated for two different AppA BLUF conformations, which are called Trp(in) and Met(in), fit very well to the spectroscopic data observed for the dark and light states, respectively, if (i) polarized MM force fields, which are calculated by an iterative DFT/MM procedure, are employed for the flavin binding pockets and (ii) the calculated frequencies are properly scaled. Although the associated analysis indicates that the Trp(in) conformation belongs to the dark state, no clear light vs dark distinction emerges for the Met(in) conformation. In this connection, a number of methodological issues relevant for such complex computations are thoroughly discussed showing, in particular, why our current descriptions could not decide the light vs dark question for Met(in).

From high-throughput cell culture screening to mouse model: identification of new inhibitor classes against prion disease

Transmissible spongiform encephalopathies (TSE) or prion diseases belong to a category of fatal and so far untreatable neurodegenerative conditions. All prion diseases are characterized by both degeneration in the central nervous system (CNS) in humans and animals and the deposition and accumulation of Proteinase K-resistant prion protein (PrP(res)). Until now, no pharmaceutical product has been available to cure these diseases or to alleviate their associated symptoms. Here, a cell-culture screening system is described that allows for the large-scale analysis of the PrP(res) inhibitory potential of a library of compounds and the identification of structural motifs leading potent compounds able to cause PrP(res) clearance at the cellular level. Based on different scrapie-infected cell lines, 10,000 substances were tested, out of which 530 potential inhibitors were identified. After re-screening and validation using a series of dilutions, 14 compounds were identified as the most effective. These 14 compounds were then used for therapeutic studies in a mouse bioassay to test and verify their in vivo potency. Two compounds exhibited therapeutic potential in the mouse model by significantly extending the survival time of intracerebrally infected mice, when treated 90 days after infection with scrapie.

Quasiparticle Excitations in Polyenes and Polyacetylene

We apply the Pariser-Parr-Pople Hamiltonian to study many-electron excitations in polyenes and polyacetylene. The excited singlet states of polyenes, calculated by a multireference double excitation expansion, are classified as quasi-particle excitations, namely as triplet-triplet magnons and particle-hole excitons. From finite polyene spectra we derive approximate dispersion relations for these quasi-particles in the infinite polyene, i.e. polyacetylene.

Highly polar environments catalyze the unfolding of PrP C helix 1

The first alpha-helix (H1) likely plays an important role in the conversion of the cellular prion protein (PrP(C)) into its pathogenic isoform (PrP(Sc)). In this conversion, H1 may either have to unfold or may represent a site of intermolecular contact. A recent molecular dynamics simulation suggested that H1 can unfold if it is detached from the protein core (Hirschberger et al. in Biophys J 90:3908, 2006). It has been hypothesized that the high dielectric constant epsilon (S) of the bulk water environment facilitates the unfolding of H1. To check this hypothesis, we performed a number of replica exchange molecular dynamics simulations of an H1 peptide in solvents of different epsilon (S). We found that the equilibrium helix fraction in water is less than 40%, in agreement with previous experimental findings, and that the helix unfolds much faster in water than in less polar solvents. The kinetically stabilizing effect of the organic solvents is largely unspecific and correlates well with their dielectric constant epsilon (S).

Substituents at the c(13) position of retinal and their influence on the function of bacteriorhodopsin

Retinal analogues in which the 13-methyl group is replaced by H, C(2)H(5), CF(3), and OCH(3) residues are studied by means of quantumchemical modified neglect of diatomic overlap-correlated version (MNDOC) calculations. The analogues are suitable to test the stereochemical mechanism of proton pumping in bacteriorhodopsin. The results explain the proton-pumping activities of bacterio-opsin reconstituted with these analogues and elucidate the decisive role of retinal's ground-state intramolecular properties in the pump cycle of bacteriorhodopsin.

Structural investigation of bacteriorhodopsin and some of its photoproducts by polarized Fourier transform infrared spectroscopic methods-difference spectroscopy and photoselection

The direction of selected IR-transition moments of the retinal chromophore of bacteriorhodopsin (BR) and functional active amino acid residues are determined for light- and dark-adapted BR and for the intermediates K and L of the photocycle. Torsions around single bonds of the chromophore are found to be present in all the investigated BR states. The number of twisted single bonds and the magnitude of these torsions decreases in the order K, L, light-adapted BR, dark-adapted BR. In the last, only the C(14)-C(15) single bond is twisted. The orientation of molecular planes and chemical bonds of such protein side chains, which are perturbed during the transition of light-adapted BR to the respective intermediates, are deduced and the results compared with the current three dimensional model of BR. Trp 86 and Trp 185 are found to form a rigid part of the protein, whereas Asp 96 and Asp 115 perform molecular rearrangements upon formation of the L-intermediate.

Evidence for a 13,14-cis cycle in bacteriorhodopsin

We discuss to what extent the vibrational spectra of bacteriorhodopsin that have been observed and assigned by Smith et al. (1, 2) by means of resonance Raman and by Gerwert and Siebert (EMBO (Eur. Mol. Biol. Organ.) J. In press) by means of infrared absorption experiments are in agreement with a photo-cycle of bacteriorhodopsin that involves the sequence BR, IO(all-trans) --> K(13,14-cis) --> L(13,14-cis) --> M(13-cis) --> N(13-cis) --> O(all-trans). Our discussion is based on a quantumchemical modified neglect of diatomic overlap [MNDO] calculation of the vibrational spectra of the relevant isomers of the protonated retinal Schiff base. In particular, we investigated in these calculations the effects of different charge environments on the frequencies of the relevant C-C single bond stretching vibrations of these isomers.

A polarizable force field for computing the infrared spectra of the polypeptide backbone

The shapes of the amide bands in the infrared (IR) spectra of proteins and peptides are caused by electrostatically coupled vibrations within the polypeptide backbone and code the structures of these biopolymers. A structural decoding of the amide bands has to resort to simplified models because the huge size of these macromolecules prevents the application of accurate quantum mechanical methods such as density functional theory (DFT). Previous models employed transition-dipole coupling methods that are of limited accuracy. Here we propose a concept for the computation of protein IR spectra, which describes the molecular mechanics (MM) of polypeptide backbones by a polarizable force field of "type II". By extending the concepts of conventional polarizable MM force fields, such a PMM/II approach employs field-dependent parameters not only for the electrostatic signatures of the molecular components but also for the local potentials modeling the stiffness of chemical bonds with respect to elongations, angle deformations, and torsions. Using a PMM/II force field, the IR spectra of the polypeptide backbone can be efficiently calculated from the time dependence of the backbone's dipole moment during a short (e.g., 100 ps) MD simulation by Fourier transformation. PMM/II parameters are derived for harmonic bonding potentials of amide groups in polypeptides from a series of DFT calculations on the model molecule N-methylacetamide (NMA) exposed to homogeneous external electric fields. The amide force constants are shown to vary by as much as 20% for relevant field strengths. As a proof of principle, it is shown that the large solvatochromic effects observed in the IR spectra of NMA upon transfer from the gas phase into aqueous solution are not only excellently reproduced by DFT/MM simulations but are also nicely modeled by the PMM/II approach. The tasks remaining for a proof of practice are specified.

Light-triggered beta-hairpin folding and unfolding

A light-switchable peptide is transformed with ultrashort pulses from a beta-hairpin to an unfolded hydrophobic cluster and vice versa. The structural changes are monitored by mid-IR probing. Instantaneous normal mode analysis with a Hamiltonian combining density functional theory with molecular mechanics is used to interpret the absorption transients. Illumination of the beta-hairpin state triggers an unfolding reaction that visits several intermediates and reaches the unfolded state within a few nanoseconds. In this unfolding reaction to the equilibrium hydrophobic cluster conformation, the system does not meet significant barriers on the free-energy surface. The reverse folding process takes much longer because it occurs on the time scale of 30 micros. The folded state has a defined structure, and its formation requires an extended search for the correct hydrogen-bond pattern of the beta-strand.

Electrostatics of proteins in dielectric solvent continua. II. First applications in molecular dynamics simulations

In the preceding paper by Stork and Tavan, [J. Chem. Phys. 126, 165105 (2007)], the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)]. The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential, which are generated within the protein by the polarization of the surrounding continuum. Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms. Quite like in a polarizable force field, also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms. Based on the reformulated theory, the authors have suggested expressions for the RF forces, which obey Newton's third law. Previous continuum approaches, which were also built on solutions of the Poisson equation, used to violate the reactio principle required by this law, and thus were inapplicable to molecular dynamics (MD) simulations. In this paper, the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides. These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities. Using the well-studied conformational dynamics of alanine dipeptide as the simplest example, the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach.

Electrostatics of proteins in dielectric solvent continua. I. Newton’s third law marries qE forces

The authors reformulate and revise an electrostatic theory treating proteins surrounded by dielectric solvent continua [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)] to make the resulting reaction field (RF) forces compatible with Newton's third law. Such a compatibility is required for their use in molecular dynamics (MD) simulations, in which the proteins are modeled by all-atom molecular mechanics force fields. According to the original theory the RF forces, which are due to the electric field generated by the solvent polarization and act on the partial charges of a protein, i.e., the so-called qE forces, can be quite accurately computed from Gaussian RF dipoles localized at the protein atoms. Using a slightly different approximation scheme also the RF energies of given protein configurations are obtained. However, because the qE forces do not account for the dielectric boundary pressure exerted by the solvent continuum on the protein, they do not obey the principle that actio equals reactio as required by Newton's third law. Therefore, their use in MD simulations is severely hampered. An analysis of the original theory has led the authors now to a reformulation removing the main difficulties. By considering the RF energy, which represents the dominant electrostatic contribution to the free energy of solvation for a given protein configuration, they show that its negative configurational gradient yields mean RF forces obeying the reactio principle. Because the evaluation of these mean forces is computationally much more demanding than that of the qE forces, they derive a suggestion how the qE forces can be modified to obey Newton's third law. Various properties of the thus established theory, particularly issues of accuracy and of computational efficiency, are discussed. A sample application to a MD simulation of a peptide in solution is described in the following paper [M. Stork and P. Tavan, J. Chem. Phys., 126, 165106 (2007).

Identification of anti-prion compounds as efficient inhibitors of polyglutamine protein aggregation in a zebrafish model

Several neurodegenerative diseases, including Huntington disease (HD), are associated with aberrant folding and aggregation of polyglutamine (polyQ) expansion proteins. Here we established the zebrafish, Danio rerio, as a vertebrate HD model permitting the screening for chemical suppressors of polyQ aggregation and toxicity. Upon expression in zebrafish embryos, polyQ-expanded fragments of huntingtin (htt) accumulated in large SDS-insoluble inclusions, reproducing a key feature of HD pathology. Real time monitoring of inclusion formation in the living zebrafish indicated that inclusions grow by rapid incorporation of soluble htt species. Expression of mutant htt increased the frequency of embryos with abnormal morphology and the occurrence of apoptosis. Strikingly, apoptotic cells were largely devoid of visible aggregates, suggesting that soluble oligomeric precursors may instead be responsible for toxicity. As in nonvertebrate polyQ disease models, the molecular chaperones, Hsp40 and Hsp70, suppressed both polyQ aggregation and toxicity. Using the newly established zebrafish model, two compounds of the N'-benzylidene-benzohydrazide class directed against mammalian prion proved to be potent inhibitors of polyQ aggregation, consistent with a common structural mechanism of aggregation for prion and polyQ disease proteins.

Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution

The midinfrared (MIR) spectra of molecules in polar solvents exhibit inhomogeneously broadened bands whose spectral positions are shifted as compared to the gas phase. The shifts are caused by interactions with structured solvation shells and the broadenings by fluctuations of these interactions. The MIR spectra can be calculated from hybrid molecular dynamics (MD) simulations, which treat the solute molecule by density functional theory and the solvent by molecular mechanics by the so-called instantaneous normal mode analysis (INMA) or by Fourier transforming the time correlation function (FTTCF) of the molecular dipole moment. In Paper I of this work [M. Schmitz and P. Tavan, J. Chem. Phys. 121, 12233 (2004)] we explored an alternative method based on generalized virial (GV) frequencies noting, however, that GV systematically underestimates frequencies. As shown by us these artifacts are caused by solvent-induced fluctuations of the (i) equilibrium geometry, (ii) force constants, and (iii) normal mode directions as well as by (iv) diagonal and (v) off-diagonal anharmonicities. Here we now show, by analyzing the time scales of fluctuations and sample MD trajectories of formaldehyde in the gas phase and in water, that all these sources of computational artifacts can be made visible by a Fourier analysis of the normal coordinates. Correspondingly, the error sources (i) and (iii)-(v) can be removed by bandpass filtering, as long as the spectral signatures of the respective effects are well separated from the fundamental band. Furthermore, the artifacts arising from effect (ii) can be strongly diminished by a time-resolved version of the GV approach (TF-GV). The TF-GV method then yields for each mode j a trajectory of the vibrational frequency omega(j)(tmid R:tau) at a time resolution tau>tau(j), which is only limited by the corresponding oscillation time tau(j)=2pi/omega(j) and, thus, is in the femtosecond range. A correlation analysis of these trajectories clearly separates the librational motions from the conformational dynamics of the solvation shells and yields the inhomogeneously broadened MIR spectra, if the theory of motional narrowing is properly included. The MIR spectrum of formaldehyde in solution obtained by TF-GV agrees very well with the FTTCF result, if one applies the so-called "harmonic approximation" quantum correction factor and a temperature scaling to the FTTCF intensities. Also for INMA an excellent agreement is achieved if one disregards a slight INMA overestimate of linewidths.

Structural instability of the prion protein upon M205S/R mutations revealed by molecular dynamics simulations

The point mutations M205S and M205R have been demonstrated to severely disturb the folding and maturation process of the cellular prion protein (PrP(C)). These disturbances have been interpreted as consequences of mutation-induced structural changes in PrP, which are suggested to involve helix 1 and its attachment to helix 3, because the mutated residue M205 of helix 3 is located at the interface of these two helices. Furthermore, current models of the prion protein scrapie (PrP(Sc)), which is the pathogenic isoform of PrP(C) in prion diseases, imply that helix 1 disappears during refolding of PrP(C) into PrP(Sc). Based on molecular-dynamics simulations of wild-type and mutant PrP(C) in aqueous solution, we show here that the native PrP(C) structure becomes strongly distorted within a few nanoseconds, once the point mutations M205S and M205R have been applied. In the case of M205R, this distortion is characterized by a motion of helix 1 away from the hydrophobic core into the aqueous environment and a subsequent structural decay. Together with experimental evidence on model peptides, this decay suggests that the hydrophobic attachment of helix 1 to helix 3 at M205 is required for its correct folding into its stable native structure.

Systematic identification of antiprion drugs by high-throughput screening based on scanning for intensely fluorescent targets

Conformational changes and aggregation of specific proteins are hallmarks of a number of diseases, like Alzheimer's disease, Parkinson's disease, and prion diseases. In the case of prion diseases, the prion protein (PrP), a neuronal glycoprotein, undergoes a conformational change from the normal, mainly alpha-helical conformation to a disease-associated, mainly beta-sheeted scrapie isoform (PrP(Sc)), which forms amyloid aggregates. This conversion, which is crucial for disease progression, depends on direct PrP(C)/PrP(Sc) interaction. We developed a high-throughput assay based on scanning for intensely fluorescent targets (SIFT) for the identification of drugs which interfere with this interaction at the molecular level. Screening of a library of 10,000 drug-like compounds yielded 256 primary hits, 80 of which were confirmed by dose response curves with half-maximal inhibitory effects ranging from 0.3 to 60 microM. Among these, six compounds displayed an inhibitory effect on PrP(Sc) propagation in scrapie-infected N2a cells. Four of these candidate drugs share an N'-benzylidene-benzohydrazide core structure. Thus, the combination of high-throughput in vitro assay with the established cell culture system provides a rapid and efficient method to identify new antiprion drugs, which corroborates that interaction of PrP(C) and PrP(Sc) is a crucial molecular step in the propagation of prions. Moreover, SIFT-based screening may facilitate the search for drugs against other diseases linked to protein aggregation.