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Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using 12 different Mg2+ parameter sets that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygens on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes. [ABSTRACT FROM AUTHOR]

Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on the water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+–water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and the ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations. [ABSTRACT FROM AUTHOR]

Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg2+ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg2+, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations. [ABSTRACT FROM AUTHOR]

Secondary nucleation pathways in which existing amyloid fibrils catalyze the formation of new aggregates and neurotoxic oligomers are of immediate importance for the onset and progression of Alzheimer's disease. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to study surface-activated secondary nucleation pathways at the extended lateral β-sheet surface of a preformed Aβ9-40 filament. Calculation of free-energy profiles allows us to determine binding free energies and conformational intermediates for nucleation complexes consisting of 1-4 Aβ peptides. In addition, we combine the free-energy profiles with position-dependent diffusion profiles to extract complementary kinetic information and macroscopic growth rates. Single monomers bind to the β-sheet surface in a disordered, hydrophobically collapsed conformation, whereas dimers and larger oligomers can retain a cross-β conformation resembling a more ordered fibril structure. The association processes during secondary nucleation follow a dock/lock mechanism consisting of a fast initial encounter phase (docking) and a slow structural rearrangement phase (locking). The major driving forces for surface-activated secondary nucleation are the release of a large number of hydration water molecules and the formation of hydrophobic interface contacts, the latter being in contrast to the elongation process at filament tips, which is dominated by the formation of stable and highly specific interface hydrogen bonds. The calculated binding free energies and the association rates for the attachment of Aβ monomers and oligomers to the extended lateral β-sheet surface of the filament seed are higher compared to those for elongation at the filament tips, indicating that secondary nucleation pathways can become important once a critical concentration of filaments has formed. [ABSTRACT FROM AUTHOR]

In this work, we characterize the nucleation and elongation mechanisms of the "diseased" polymorph of the amyloid-β 40 (Aβ40) fibril using an off-lattice coarse-grained (CG) protein model. After determining the nucleation size and subsequent stable protofibrillar structure from the CG model, validated with all-atom simulations, we consider the "lock and dock" and "activated monomer" fibril elongation mechanisms for the protofibril by statistical additions of a monomer drawn from four different ensembles of the free Aβ40 peptide to grow the fibril. Our CG model shows that the dominant mechanism for fibril elongation is the lock and dock mechanism across all monomer ensembles, even when the monomer is in the activated form. Although our CG model finds no thermodynamic difference between the two fibril elongation mechanisms, the activated monomer is found to be kinetically faster by a factor of 2 for the "locking" step compared with all other structured or unstructured monomer ensembles. [ABSTRACT FROM AUTHOR]

Magnesium and calcium play an essential role in the folding and function of nucleic acids. To correctly describe their interactions with DNA and RNA in biomolecular simulations, an accurate parameterization is crucial. In most cases, the ion parameters are optimized based on a set of experimental solution properties such as solvation free energies, radial distribution functions, water exchange rates, and activity coefficient derivatives. However, the transferability of such bulk-optimized ion parameters to quantitatively describe biomolecular systems is limited. Here, we extend the applicability of our previous bulk-optimized parameters by including experimental binding affinities toward the phosphate oxygen on nucleic acids. In particular, we systematically adjust the combination rules that are an integral part of the pairwise interaction potentials of classical force fields. This allows us to quantitatively describe specific ion binding to nucleic acids without changing the solution properties in the most simple and efficient way. We show the advancement of the optimized Lorentz combination rule for two representative nucleic acid systems. For double-stranded DNA, the optimized combination rule for Ca2+ significantly improves the agreement with experiments, while the standard combination rule leads to unrealistically distorted DNA structures. For the add A-riboswitch, the optimized combination rule for Mg2+ improves the structure of two specifically bound Mg2+ ions as judged by the experimental distance to the binding site. Including experimental binding affinities toward specific ion binding sites on biomolecules, therefore, provides a promising perspective to develop a more accurate description of metal cations for biomolecular simulations. [ABSTRACT FROM AUTHOR]

The pH-dependent change in protonation of ionizable lipids is crucial for the success of lipid-based nanoparticles as mRNA delivery systems. Despite their widespread application in vaccines, the structural changes upon acidification are not well understood. Molecular dynamics simulations support structure prediction but require an a priori knowledge of the lipid packing and protonation degree. The presetting of the protonation degree is a challenging task in the case of ionizable lipids since it depends on pH and on the local lipid environment and often lacks experimental validation. Here, we introduce a methodology of combining all-atom molecular dynamics simulations with experimental total-reflection x-ray fluorescence and scattering measurements for the ionizable lipid Dlin-MC3-DMA (MC3) in POPC monolayers. This joint approach allows us to simultaneously determine the lipid packing and the protonation degree of MC3. The consistent parameterization is expected to be useful for further predictive modeling of the action of MC3-based lipid nanoparticles. [ABSTRACT FROM AUTHOR]

Over recent years, the supposedly universal Hofmeister series has been replaced by a diverse spectrum of direct, partially altered and reversed series. This review aims to provide a detailed understanding of the full spectrum by combining results from molecular dynamics simulations, Poisson–Boltzmann theory and AFM experiments. Primary insight into the origin of the Hofmeister series and its reversal is gained from simulation-derived ion–surface interaction potentials at surfaces containing non-polar, polar and charged functional groups for halide anions and alkali cations. In a second step, the detailed microscopic interactions of ions, water and functional surface groups are incorporated into Poisson–Boltzmann theory. This allows us to quantify ion-specific binding affinities to surface groups of varying polarity and charge, and to provide a connection to the experimentally measured long-ranged electrostatic forces that stabilize colloids, proteins and other particles against precipitation. Based on the stabilizing efficiency, the direct Hofmeister series is obtained for negatively charged hydrophobic surfaces. Hofmeister series reversal is induced by changing the sign of the surface charge from negative to positive, by changing the nature of the functional surface groups from hydrophobic to hydrophilic, by increasing the salt concentration, or by changing the pH. The resulting diverse spectrum reflects that alterations of Hofmeister series are the rule rather than the exception and originate from the variation of ion-surface interactions upon changing surface properties. [ABSTRACT FROM AUTHOR]

The binding of peptides and proteins to lipid membrane surfaces is of fundamental importance for many membrane-mediated cellular processes. Using closely matched molecular dynamics simulations and atomic force microscopy experiments, we study the force-induced desorption of single peptide chains from phospholipid bilayers to gain microscopic insight into the mechanism of reversible attachment. This approach allows quantification of desorption forces and decomposition of peptide-membrane interactions into energetic and entropic contributions. In both simulations and experiments, the desorption forces of peptides with charged and polar side chains are much smaller than those for hydrophobic peptides. The adsorption of charged/polar peptides to the membrane surface is disfavored by the energetic components, requires breaking of hydrogen bonds involving the peptides, and is favored only slightly by entropy. By contrast, the stronger adsorption of hydrophobic peptides is favored both by energy and by entropy and the desorption forces increase with increasing side-chain hydrophobicity. Interestingly, the calculated net adsorption free energies per residue correlate with experimental results of single residues, indicating that side-chain free energy contributions are largely additive. This observation can help in the design of peptides with tailored adsorption properties and in the estimation of membrane binding properties of peripheral membrane proteins. [ABSTRACT FROM AUTHOR]

Filamentous β-amyloid aggregates are crucial for the pathology of Alzheimer's disease. Despite the tremendous biomedical importance, the molecular pathway of growth propagation is not completely understood and remains challenging to investigate by simulations due to the long time scales involved. Here, we apply extensive all-atom molecular dynamics simulations in explicit water to obtain free energy profiles and kinetic information from position-dependent diffusion profiles for three different Aβ9-40-growth processes: fibril elongation by single monomers at the structurally unequal filament tips and association of larger filament fragments. Our approach provides insight into the molecular steps of the kinetic pathway and allows close agreement with experimental binding free energies and macroscopic growth rates. Water plays a decisive role, and solvent entropy is identified as the main driving force for assembly. Fibril growth is disfavored energetically due to cancellation of direct peptide--peptide interactions and solvation effects. The kinetics of growth is consistent with the characteristic dock/lock mechanism, and docking is at least 2 orders of magnitude faster. During initial docking, interactions are mediated by transient non-native hydrogen bonds, which efficiently catch the incoming monomer or fragment already at separations of about 3 nm. In subsequent locking, the dynamics is much slower due to formation of kinetically trapped conformations caused by long-lived non-native hydrogen bonds. Fibril growth additionally requires collective motion of water molecules to create a dry binding interface. Fibril growth is further retarded due to reduced mobility of the involved hydration water, evident from a 2-fold reduction of the diffusion coefficient. [ABSTRACT FROM AUTHOR]

Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field parameters for the metal cations Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+ in combination with the TIP3P water model that is frequently used in biomolecular simulations. In progressing toward improved force fields, the approach presented here is an extension of previous efforts and allows us to simultaneously reproduce thermodynamic and kinetic properties of aqueous solutions. We systematically derive the parameters of the 12-6 Lennard-Jones potential which accurately reproduces the experimental solvation free energy, the activity derivative, and the characteristics of water exchange from the first hydration shell of the metal cations. In order to reproduce all experimental properties, a modification of the Lorentz-Berthelot combination rule is required for Mg2+. Using a balanced set of solution properties, the optimized force field parameters aim to capture the fine differences between distinct metal cations including specific ion binding affinities and the kinetics of cation binding to biologically important anionic groups. [ABSTRACT FROM AUTHOR]

Ion binding to acidic groups is acentral mechanism for ion-specificityof macromolecules and surfaces. Depending on pH, acidic groups areeither protonated or deprotonated and thus change not only chargebut also chemical structure with crucial implications for their interactionwith ions. In a two-step modeling approach, we first determine single-ionsurface interaction potentials for a few selected halide and alkaliions at uncharged carboxyl (COOH) and charged carboxylate (COO–) surface groups from atomistic MD simulations withexplicit water. Care is taken to subtract the bare Coulomb contributiondue to the net charge of the carboxylate group and thereby to extractthe nonelectrostatic ion–surface potential. Even at this stage,pronounced ion-specific effects are observed and the ion surface affinitystrongly depends on whether the carboxyl group is protonated or not.In the second step, the ion surface interaction potentials are usedin a Poisson–Boltzmann model to calculate the surface chargeand the potential distribution in the solution depending on salt type,salt concentration, and solution pH in a self-consistent manner. Hofmeisterphase diagrams are derived on the basis of the long-ranged forcesbetween two carboxyl-functionalized surfaces. For cations we predictdirect, reversed, and altered Hofmeister series as a function of thepH, qualitatively similar to recent experimental results for silicasurfaces. The Hofmeister series reversal for cations is rationalizedby a reversal of the single-cation affinity to the carboxyl groupdepending on its protonation state: the deprotonated carboxylate (COO–) surface group interacts most favorably with smallcations such as Li+and Na+, whereas the protonatedcarboxyl (COOH) surface group interacts most favorably with largecations such as Cs+and thus acts similarly to a hydrophobicsurface group. Our results provide a general mechanism for the pH-dependentreversal of the Hofmeister series due to the different specific ionbinding to protonated and deprotonated surface groups. [ABSTRACT FROM AUTHOR]

Using a two-step modeling approach, we address the fullspectrumof direct, reversed, and altered ionic sequences as the charge ofthe ion, the charge of the surface, and the surface polarity are varied.From solvent-explicit molecular dynamics simulations, we extract single-ionsurface interaction potentials for halide and alkali ions at hydrophilicand hydrophobic surfaces. These are used within Poisson–Boltzmanntheory to calculate ion density and electrostatic potential distributionsat mixed polar/unpolar surfaces for varying surface charge. The resultinginterfacial tension increments agree quantitatively with experimentaldata and capture the Hofmeister series, especially the anomaly oflithium, which is difficult to obtain using continuum theory. Phasediagrams that feature different Hofmeister series as a function ofsurface charge, salt concentration, and surface polarity are constructedfrom the long-range force between two surfaces interacting acrosselectrolyte solutions. Large anions such as iodide have a high hydrophobicsurface affinity and increase the effective charge magnitude on negativelycharged unpolar surfaces. Large cations such as cesium also have alarge hydrophobic surface affinity and thereby compensate an externalnegative charge surface charge most efficiently, which explains thewell-known asymmetry between cations and anions. On the hydrophilicsurface, the size-dependence of the ion surface affinity is reversed,explaining the Hofmeister series reversal when comparing hydrophobicwith hydrophilic surfaces. [ABSTRACT FROM AUTHOR]

The force-induced desorption of single peptide chains from mixed OH/CH3-terminated self-assembled monolayers is studied in closely matched molecular dynamics simulations and atomic force microscopy experiments with the goal to gain microscopic understanding of the transition between peptide adsorption and adsorption resistance as the surface contact angle is varied. In both simulations and experiments, the surfaces become adsorption resistant against hydrophilic as well as hydrophobic peptides when their contact angle decreases below θ~ 50°-60°, thus confirming the so-called Berg limit established in the context of protein and cell adsorption. Entropy/enthalpy decomposition of the simulation results reveals that the key discriminator between the adsorption of different residues on a hydrophobic monolayer is of entropic nature and thus is suggested to be linked to the hydrophobic effect. By pushing a polyalanine peptide onto a polar surface, simulations reveal that the peptide adsorption resistance is caused by the strongly bound water hydration layer and characterized by the simultaneous gain of both total entropy in the system and total number of hydrogen bonds between water, peptide, and surface. This mechanistic insight into peptide adsorption resistance might help to refine design principles for anti-fouling surfaces. [ABSTRACT FROM AUTHOR]

Interactions between ions and solutes are key to ion-specificity.A generic model in which ions interact via square well potentialsof finite range with charged plates is solved analytically on thePoisson–Boltzmann level and analyzed globally for varying surfacecharge, salt concentration, and ion–surface affinity. Ion adsorptionas well as depletion can lead to stably bound plates at finite separation,relevant for the equilibrium salting-out of small solutes such asproteins. The interplate pressure at large plate separation, relevantfor aggregation kinetics of large solutes, exhibits direct as wellas indirect Hofmeister ordering, depending on surface charge and saltconcentration. A simple method for mapping explicit ion–surfacepotentials of mean force as obtained from solvent-explicit moleculardynamics simulations onto square-well potential parameters is demonstrated. [ABSTRACT FROM AUTHOR]

[Display omitted] • This study examines the effect of seeding with ex vivo Aβ amyloid fibrils on the fibril morphology in vitro. • Seeded fibrils are right-hand twisted and show a peptide fold that corresponds to the one in the seeds. • The twist and peptide fold of seeded fibrils differ from unseeded fibrils. • Upon multiple rounds of seeding, the propagation of the seed structure loses efficiency and de novo nucleated fibril structures emerge. • These findings imply a competition between seed extension and de novo nucleation in seeded samples. Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can be proliferated by seeding in vitro. The proliferation reaction is only efficient for one of the three abundant ex vivo Aβ fibril morphologies, which consists of two peptide stacks, while the inefficiently proliferated fibril morphologies contain four or six peptide stacks. In addition to the seeded fibril structures, we find that de novo nucleated fibril structures can emerge in seeded samples if the seeding reaction is continued over multiple generations. These data imply a competition between de novo nucleation and seed extension and suggest further that seeding favours the outgrowth of fibril morphologies that contain fewer peptide stacks. [ABSTRACT FROM AUTHOR]

Lipid nanoparticles (LNPs) are advanced core-shell particles for messenger RNA (mRNA) based therapies that are made of polyethylene glycol (PEG) lipid, distearoylphosphatidylcholine (DSPC), cationic ionizable lipid (CIL), cholesterol (chol), and mRNA. Yet the mechanism of pH-dependent response that is believed to cause endosomal release of LNPs is not well understood. Here, we show that eGFP (enhanced green fluorescent protein) protein expression in the mouse liver mediated by the ionizable lipids DLin-MC3-DMA (MC3), DLin-KC2-DMA (KC2), and DLinDMA (DD) ranks MC3 = KC2 > DD despite similar delivery of mRNA per cell in all cell fractions isolated. We hypothesize that the three CIL-LNPs react differently to pH changes and hence study the structure of CIL/chol bulk phases in water. Using synchrotron X-ray scattering a sequence of ordered CIL/chol mesophases with lowering pH values are observed. These phases show isotropic inverse micellar, cubic Fd3m inverse micellar, inverse hexagonal HII and bicontinuous cubic Pn3m symmetry. If polyadenylic acid, as mRNA surrogate, is added to CIL/chol, excess lipid coexists with a condensed nucleic acid lipid Hc II phase. The next-neighbor distance in the excess phase shows a discontinuity at the Fd3m inverse micellar to inverse hexagonal HII transition occurring at pH 6 with distinctly larger spacing and hydration for DD vs. MC3 and KC2. In mRNA LNPs, DD showed larger internal spacing, as well as retarded onset and reduced level of DD-LNP-mediated eGFP expression in vitro compared to MC3 and KC2. Our data suggest that the pH-driven Fd3m-H II transition in bulk phases is a hallmark of CIL-specific differences in mRNA LNP efficacy. [ABSTRACT FROM AUTHOR]

Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers. [ABSTRACT FROM AUTHOR]

[Display omitted] • Mice expressing ApoA-IIF rather than ApoA-IIC are resistant to AApoAII amyloidosis. • Cryo-EM structures of ApoA-IIC-derived fibrils reveal the pathogenic fibril fold. • The mutations in ApoA-IIF destabilise the fold of the fibril proteins. • Our data explain previous observation of the importance of the Asn62Lys mutation. • Our study supports the idea that disease arises from specific fibril morphologies. Amyloid resistance is the inability or the reduced susceptibility of an organism to develop amyloidosis. In this study we have analysed the molecular basis of the resistance to systemic AApoAII amyloidosis, which arises from the formation of amyloid fibrils from apolipoprotein A-II (ApoA-II). The disease affects humans and animals, including SAMR1C mice that express the C allele of ApoA-II protein, whereas other mouse strains are resistant to development of amyloidosis due to the expression of other ApoA-II alleles, such as ApoA-IIF. Using cryo-electron microscopy, molecular dynamics simulations and other methods, we have determined the structures of pathogenic AApoAII amyloid fibrils from SAMR1C mice and analysed the structural effects of ApoA-IIF-specific mutational changes. Our data show that these changes render ApoA-IIF incompatible with the specific fibril morphologies, with which ApoA-II protein can become pathogenic in vivo. [ABSTRACT FROM AUTHOR]

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes in proteins in different salt solutions. We demonstrate the existence of ion-specific attractive double-layer forces between neutral hydrophobic and hydrophilic surfaces in the presence of certain salt solutions. This is performed by solving a generalized Poisson-Boltzmann equation for two unequal surfaces. In the calculations, we utilize parametrized ion-surface potentials and dielectric-constant profiles deduced from recent non-primitive-model molecular dynamics simulations that partially account for molecular structure and hydration effects. [ABSTRACT FROM AUTHOR]

[Display omitted] • The full-length hnRNPA1 fibril structure was resolved at 3.32 Å resolution using cryo-EM. • The fibril core is formed by a 45-residue segment of the low-complexity domain of hnRNPA1. • The remaining parts of the protein form a fuzzy coat around the fibril core. • The fibril core contains several disease-associated mutational sites, but lacks the most aggregation-prone segments of hnRNPA1. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein that is associated with neurodegenerative diseases, such as amyotrophic lateral sclerosis and multisystem proteinopathy. In this study, we have used cryo-electron microscopy to investigate the three-dimensional structure of amyloid fibrils from full-length hnRNPA1 protein. We find that the fibril core is formed by a 45-residue segment of the prion-like low-complexity domain of the protein, whereas the remaining parts of the protein (275 residues) form a fuzzy coat around the fibril core. The fibril consists of two fibril protein stacks that are arranged into a pseudo-2 1 screw symmetry. The ordered core harbors several of the positions that are known to be affected by disease-associated mutations, but does not encompass the most aggregation-prone segments of the protein. These data indicate that the structures of amyloid fibrils from full-length proteins may be more complex than anticipated by current theories on protein misfolding. [ABSTRACT FROM AUTHOR]