Comparing the influence of explicit and implicit solvation models on site-specific thermodynamic stability of proteins.

Understanding the molecular basis for protein stability requires a thermodynamic analysis of protein folding. Thermodynamic analysis is often performed by sampling many atomistic conformations using molecular simulations that employ either explicit or implicit water models. However, it remains unclear to what extent thermodynamic results from different solvation models are reliable at the molecular level. In this study, we quantify the influence of both solvation models on folding stability at the individual backbone and side chain resolutions. We assess the residue-specific folding free energy components of a ß-sheet protein and a helical protein using trajectories resulting from TIP3P explicit and generalized Born/surface area implicit solvent simulations of model proteins. We found that the thermodynamic discrepancy due to the implicit solvent mostly originates from charged side chains, followed by the under-stabilized hydrophobic ones. In contrast, the contributions of backbone residue in both proteins were comparable for explicit and implicit water models. Our study lays out the foundation for detailed thermodynamic assessment of solvation models in the context of protein simulation.

In silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils.

α-Synuclein is a presynaptic neuronal protein. The fibril form of α-synuclein is a major constituent of the intraneuronal inclusion called Lewy body, a characteristic hallmark of Parkinson's disease. Recent ssNMR and cryo-EM experiments of wild-type α-synuclein fibrils have shown polymorphism and observed two major polymorphs, rod and twister. To associate the cytotoxicity of α-synuclein fibrils with their structural features, it is essential to understand the origins of their structural stability. In this study, we performed molecular dynamics simulations of the two major polymorphs of wild-type α-synuclein fibrils. The predominance of specific fibril polymorphs was rationalized in terms of relative structural stability in aqueous environments, which was attributed to the cooperative contributions of various stabilizing features. The results of the simulations indicated that highly stable structures in aqueous environments could be maintained by the cooperation of compact sidechain packing in the hydrophobic core, backbone geometry of the maximal ß-sheet content wrapping the hydrophobic core, and solvent-exposed sidechains with large fluctuations maximizing the solvation entropy. The paired structure of the two protofilaments provides additional stability, especially at the interface region, by forming steric zipper interactions and hiding the hydrophobic residues from exposure to water. The sidechain interaction analyses and pulling simulations showed that the rod polymorph has stronger sidechain interactions and exhibits higher dissociation energy than the twister polymorph. It is expected that our study will provide a basis for understanding the pathogenic behaviors of diverse amyloid strains in terms of their structural properties.Communicated by Ramaswamy H. Sarma.

Two-qubit atomic gates: spatio-temporal control of Rydberg interaction.

By controlling the temporal and spatial features of light, we propose a novel protocol to prepare two-qubit entangling gates on atoms trapped at close distance, which could potentially speed up the operation of the gate from the sub-micro to the nanosecond scale. The protocol is robust to variations in the pulse areas and the position of the atoms, by virtue of the coherent properties of a dark state, which is used to drive the population through Rydberg states. From the time-domain perspective, the protocol generalizes the one proposed by Jaksch and coworkers [Jaksch et al., Phys. Rev. Lett., 2000, 85, 2208], with three pulses that operate symmetrically in time, but with different pulse areas. From the spatial-domain perspective, it uses structured light. We analyze the map of the gate fidelity, which forms rotated and distorted lattices in the solution space. Finally, we study the effect of an additional qubit to the gate performance and propose generalizations that operate with multi-pulse sequences.

Selectively Enhanced Electrocatalytic Oxygen Evolution within Nanoscopic Channels Fitting a Specific Reaction Intermediate for Seawater Splitting.

Abundant availability of seawater grants economic and resource-rich benefits to water electrolysis technology requiring high-purity water if undesired reactions such as chlorine evolution reaction (CER) competitive to oxygen evolution reaction (OER) are suppressed. Inspired by a conceptual computational work suggesting that OER is kinetically improved via a double activation within 7 Å-gap nanochannels, RuO2 catalysts are realized to have nanoscopic channels at 7, 11, and 14 Å gap in average (dgap ), and preferential activity improvement of OER over CER in seawater by using nanochanneled RuO2 is demonstrated. When the channels are developed to have 7 Å gap, the OER current is maximized with the overpotential required for triggering OER minimized. The gap value guaranteeing the highest OER activity is identical to the value expected from the computational work. The improved OER activity significantly increases the selectivity of OER over CER in seawater since the double activation by the 7 Å-nanoconfined environments to allow an OER intermediate (*OOH) to be doubly anchored to Ru and O active sites does not work on the CER intermediate (*Cl). Successful operation of direct seawater electrolysis with improved hydrogen production is demonstrated by employing the 7 Å-nanochanneled RuO2 as the OER electrocatalyst.

Mutation effects on FAS1 domain 4 based on structure and solubility.

Mutations in the fasciclin 1 domain 4 (FAS1-4) of transforming growth factor ß-induced protein (TGFBIp) are associated with insoluble extracellular deposits and corneal dystrophies (CDs). The decrease in solubility upon mutation has been implicated in CD; however, the exact molecular mechanisms are not well understood. Here, we performed molecular dynamics simulations followed by solvation thermodynamic analyses of the FAS1-4 domain and its three mutants-R555W, R555Q, and A546T-linked to granular corneal dystrophy type 1, Thiel-Behnke corneal dystrophy and lattice corneal dystrophy, respectively. We found that both R555W and R555Q mutants have less affinity toward solvent water relative to the wild-type protein. In the R555W mutant, a remarkable increase in solvation free energy was observed because of the structural changes near the mutation site. The mutation site W555 is buried in other hydrophobic residues, and R557 simultaneously forms salt bridges with E554 and D561. In the R555Q mutant, the increase in solvation free energy is caused by structural rearrangements far from the mutation site. R558 separately forms salt bridges with D575, E576, and E598. Thus, we thus identified the relationship between the decrease in solubility and conformational changes caused by mutations, which may be useful in designing potential therapeutics and in blocking FAS1 aggregation related to CD.

Dynamics and Entropy of Cyclohexane Rings Control pH-Responsive Reactivity.

Activation entropy (ΔS ‡) is not normally considered the main factor in determining the reactivity of unimolecular reactions. Here, we report that the intramolecular degradation of six-membered ring compounds is mainly determined by the ΔS ‡, which is strongly influenced by the ring-flipping motion and substituent geometry. Starting from the unique difference between the pH-dependent degradation kinetics of geometric isomers of 1,2-cyclohexanecarboxylic acid amide (1,2-CHCAA), where only the cis isomer can readily degrade under weakly acidic conditions (pH < 5.5), we found that the difference originated from the large difference in ΔS ‡ of 16.02 cal·mol-1·K-1. While cis-1,2-CHCAA maintains a preference for the classical chair cyclohexane conformation, trans-1,2-CHCAA shows dynamic interconversion between the chair and twisted boat conformations, which was supported by both MD simulations and VT-NMR analysis. Steric repulsion between the bulky 1,2-substituents of the trans isomer is one of the main reasons for the reduced energy barrier between ring conformations that facilitates dynamic ring inversion motions. Consequently, the more dynamic trans isomer exhibits much a larger loss in entropy during the activation process due to the prepositioning of the reactant than the cis isomer, and the pH-dependent degradation of the trans isomer is effectively suppressed. When the ring inversion motion is inhibited by an additional methyl substituent on the cyclohexane ring, the pH degradability can be dramatically enhanced for even the trans isomer. This study shows a unique example in which spatial arrangement and dynamic properties can strongly influence molecular reactivity in unimolecular reactions, and it will be helpful for the future design of a reactive structure depending on dynamic conformational changes.

Computational Insights into the Aggregation Pathway of Self-Assembled Nanotubules.

We performed molecular dynamics simulations of self-assembled supramolecular nanotubules constructed from amphiphiles with bent-shaped rods. By systematically examining the structure from dimeric aggregates to the fully developed nanotubule, we identified the basic building block of the nanotubule and the optimal dimensions of its stable structure which are consistent with experimental findings. Moreover, we demonstrate that the cooperative interplay of different interactions drives aggregation by selecting and stabilizing the optimal self-assembled structures for various intermediates through a complex pathway. Additionally, contraction of the nanotubule, which accompanies the dehydration process, was observed upon heating. It is suggested that the optimal stability of the self-assembled aggregates is achieved by balancing entropic and enthalpic contributions, of which the ratio is a critical factor that drives the aggregation pathway.

Electron Attachment to the (O2···CO2) van der Waals Complex Results in a Monomeric Anion (O2-CO2)-, a Possible Form of CO4.

We found that electron attachment to the van der Waals complex (O2···CO2) turns the weak intermolecular bond into a pseudochemical bond of significant strength. The resulting monomeric molecular anion (O2-CO2)- may be a form of CO4-, the gaseous anionic species suspected to be present in Earth's ionosphere whose chemical characteristics have not been comprehensively identified since its existence was first predicted by Conway in 1962. The measured vertical detachment energy of CO4- is very large (4.56 ± 0.05 eV), while the known electron affinity of its component species is much smaller (0.448 eV, O2) or even negative (-0.6 eV, CO2). These characteristics are correctly borne out by theoretical calculations that show that electron attachment transforms the van der Waals complex to a single contiguous molecular anion, with the formation of a pseudochemical bond between O2 and CO2 through an extended π-orbital system.

Site-Specific Backbone and Side-Chain Contributions to Thermodynamic Stabilizing Forces of the WW Domain.

The native structure of a protein is stabilized by a number of interactions such as main-chain hydrogen bonds and side-chain hydrophobic contacts. However, it has been challenging to determine how these interactions contribute to protein stability at single amino acid resolution. Here, we quantified site-specific thermodynamic stability at the molecular level to extend our understanding of the stabilizing forces in protein folding. We derived the free energy components of individual amino acid residues separately for the folding of the human Pin WW domain based on simulated structures. A further decomposition of the thermodynamic properties into contributions from backbone and side-chain groups enabled us to identify the critical residues in the secondary structure and hydrophobic core formation, without introducing physical modifications to the system as in site-directed mutagenesis methods. By relating the structural and thermodynamic changes upon folding for each residue, we find that the simultaneous formation of the backbone hydrogen bonds and side-chain contacts cooperatively stabilizes the folded structure. The identification of stabilizing interactions in a folding protein at atomic resolution will provide molecular insights into understanding the origin of the protein structure and into engineering a more stable protein.

Graphene Quantum Dots Alleviate Impaired Functions in Niemann-Pick Disease Type C in Vivo.

While the neuropathological characteristics of Niemann-Pick disease type C (NPC) result in a fatal diagnosis, the development of clinically available therapeutic agent remains a challenge. Here we propose graphene quantum dots (GQDs) as a potential candidate for the impaired functions in NPC in vivo. In addition to the previous findings that GQDs exhibit negligible long-term toxicity and are capable of penetrating the blood-brain barrier, GQD treatment reduces the aggregation of cholesterol in the lysosome through expressed physical interactions. GQDs also promote autophagy and restore defective autophagic flux, which, in turn, decreases the atypical accumulation of autophagic vacuoles. More importantly, the injection of GQDs inhibits the loss of Purkinje cells in the cerebellum while also demonstrating reduced activation of microglia. The ability of GQDs to alleviate impaired functions in NPC proves the promise and potential of the use of GQDs toward resolving NPC and other related disorders.

Control defeasance by anti-alignment in the excited state.

We predict anti-alignment dynamics in the excited state of H2+ or related homonuclear dimers in the presence of a strong field. This effect is a general indirect outcome of the strong transition dipole and large polarizabilities typically used to control or to induce alignment in the ground state. In the excited state, however, the polarizabilities have the opposite sign compared to those in the ground state, generating a torque that aligns the molecule perpendicular to the field, deeming any laser-control strategy impossible.

Computational Study on Structure and Aggregation Pathway of Aß42 Amyloid Protofibril.

Amyloid deposits of Aß protein in neuronal cells are known to be a major symptom of Alzheimer's disease. In particular, Aß42 shows relatively high toxicity among the different Aß isoforms, and its toxicity is thought to be because of its structural features. Recent ssNMR and cryo-EM experiments identified that Aß42 shows an S-shaped triple-ß structure, in contrast to the previously suggested U-shaped ß-arch structure. In order to associate the high toxicity of Aß42 with its structural features, it is essential to explain the conformational stability and aggregation mechanisms of this triple-ß motif. We utilized several different simulation methods, including extensive straight molecular dynamics simulation, steered molecular dynamics simulation, and replica-exchange molecular dynamics simulation. The S-shaped triple-ß motif showed remarkable structural stability because of its complex residual interactions that form stable hydrophobic cores. The triple-ß structure of Aß42 is primarily made up of three ß-sheet regions and two hydrophobic cores formed between ß-sheet regions. Our analysis of ß-sheet rupture patterns between adjacent chains showed that its two hydrophobic cores have different degrees of stability, indicating a lock phase mechanism. Our analysis of the docking pathway of monomeric Aß42 to the fibril motif using REMD simulations showed that each of the three ß-sheet sequences plays a distinct role in the docking process by changing their conformational features. Our results provide an understanding for the stability and consequent high toxicity of the triple-ß structure Aß42.

Grid-Based Ehrenfest Model To Study Electron-Nuclear Processes.

The two-dimensional electron-nuclear Schrödinger equation using soft-core Coulomb potentials has been a cornerstone for modeling and predicting the behavior of one-active-electron diatomic molecules, particularly for processes where both bound and continuum states are important. The model, however, is computationally expensive to extend to more electron or nuclear coordinates. Here we propose use of the Ehrenfest approach to treat the nuclear motion, while the electronic motion is still solved by quantum propagation on a grid. In this work, we present results for a one-dimensional treatment of H2+, where the quantum and semiclassical dynamics can be directly compared, showing remarkably good agreement for a variety of situations. The advantage of the Ehrenfest approach is that it can be easily extended to treat as many nuclear degrees of freedom as needed.

Graphene quantum dots prevent α-synucleinopathy in Parkinson's disease.

Though emerging evidence indicates that the pathogenesis of Parkinson's disease is strongly correlated to the accumulation1,2 and transmission3,4 of α-synuclein (α-syn) aggregates in the midbrain, no anti-aggregation agents have been successful at treating the disease in the clinic. Here, we show that graphene quantum dots (GQDs) inhibit fibrillization of α-syn and interact directly with mature fibrils, triggering their disaggregation. Moreover, GQDs can rescue neuronal death and synaptic loss, reduce Lewy body and Lewy neurite formation, ameliorate mitochondrial dysfunctions, and prevent neuron-to-neuron transmission of α-syn pathology provoked by α-syn preformed fibrils5,6. We observe, in vivo, that GQDs penetrate the blood-brain barrier and protect against dopamine neuron loss induced by α-syn preformed fibrils, Lewy body/Lewy neurite pathology and behavioural deficits.

Geometrical Optimization Approach to Isomerization: Models and Limitations.

We study laser-driven isomerization reactions through an excited electronic state using the recently developed Geometrical Optimization procedure. Our goal is to analyze whether an initial wave packet in the ground state, with optimized amplitudes and phases, can be used to enhance the yield of the reaction at faster rates, driven by a single picosecond pulse or a pair of femtosecond pulses resonant with the electronic transition. We show that the symmetry of the system imposes limitations in the optimization procedure, such that the method rediscovers the pump-dump mechanism.

Site-dependent effects of methylation on the electronic spectra of jet-cooled methylated xanthine compounds.

We obtained the electronic spectra of various methylated xanthine compounds including caffeine in a supersonic jet by resonant two-photon ionization spectroscopy. The methyl group in the tested methylated xanthine compounds has a distinct, site-dependent effect on the electronic spectrum. Methylation at the N3 position causes a significant red shift of the ππ* state, whereas methylation at the N1 position has only minimal effects on the electronic spectrum. The notably broad spectra of theobromine and caffeine result from methyl substitution at the N7 position, which causes a large displacement between the potential energy surfaces of the S0 and S1 states, and a strong vibronic coupling. We also investigated the internal rotation of the methyl group and its effect on the electronic spectrum of the methylated xanthine compounds. We found that the barrier height for the torsional motion in the ground state is significantly affected by a carbonyl or methyl group that lies close to the methyl group of interest. In contrast, the torsional barrier in the excited state is governed by the hyperconjugation interaction in the lowest unoccupied molecular orbital. The agreement between the experimental and simulated spectra of torsional vibronic bands suggested that the low frequency torsional vibrations arising from the tunneling splitting and the coupling between the torsional and molecular motions give theobromine and theophylline the multiplet nature of their origin bands. This study provides a new level of understanding for the methyl substitution effects on the electronically excited states of xanthine compounds, which may very well be applicable to many other methyl substituted biomolecules including DNAs and proteins.

Conformational sampling of metastable states: Tq-REM as a novel replica exchange method.

Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to very large bio-systems is somewhat limited. We propose a new replica exchange scheme (Tq-REM) created by combining the conventional temperature-REM (T-REM) and one of the Hamiltonian-REMs, q-REM, using the effective potential with reduced barriers. In the proposed Tq-REM scheme, high temperature replicas in T-REM are substituted with q-replicas. This combined scheme is expected to exploit advantages of the T-REM and q-REM resulting in improved sampling efficiency while minimizing the drawbacks of both approaches. We investigated the performance of Tq-REM compared with T-REM by performing all-atom MD simulations on Met-enkephalin, (AAQAA)3, and Trpzip2. It was found that convergence of the free energy surfaces was improved by Tq-REM over the conventional T-REM. In particular, the trajectories of Tq-REM were able to sample the relevant conformations for all of the metastable folding intermediates, while some of the local minimum structures are poorly represented by T-REM. The results of the present study suggest that Tq-REM can provide useful tools to investigate systems where metastable states play important roles.

The role of the acidic domain of α-synuclein in amyloid fibril formation: a molecular dynamics study.

The detailed mechanism of the pathology of α-synuclein in the Parkinson's disease has not been clearly elucidated. Recent studies suggested a possible chaperone-like role of the acidic C-terminal region of α-synuclein in the formation of amyloid fibrils. It was also previously demonstrated that the α-synuclein amyloid fibril formation is accelerated by mutations of proline residues to alanine in the acidic region. We performed replica exchange molecular dynamics simulations of the acidic and nonamyloid component (NAC) domains of the wild type and proline-to-alanine mutants of α-synuclein under various conditions. Our results showed that structural changes induced by a change in pH or an introduction of mutations lead to a reduction in mutual contacts between the NAC and acidic regions. Our data suggest that the highly charged acidic region of α-synuclein may act as an intramolecular chaperone by protecting the hydrophobic domain from aggregation. Understanding the function of such chaperone-like parts of fibril-forming proteins may provide novel insights into the mechanism of amyloid formation.

State-Selective Excitation of Quantum Systems via Geometrical Optimization.

We lay out the foundations of a general method of quantum control via geometrical optimization. We apply the method to state-selective population transfer using ultrashort transform-limited pulses between manifolds of levels that may represent, e.g., state-selective transitions in molecules. Assuming that certain states can be prepared, we develop three implementations: (i) preoptimization, which implies engineering the initial state within the ground manifold or electronic state before the pulse is applied; (ii) postoptimization, which implies engineering the final state within the excited manifold or target electronic state, after the pulse; and (iii) double-time optimization, which uses both types of time-ordered manipulations. We apply the schemes to two important dynamical problems: To prepare arbitrary vibrational superposition states on the target electronic state and to select weakly coupled vibrational states. Whereas full population inversion between the electronic states only requires control at initial time in all of the ground vibrational levels, only very specific superposition states can be prepared with high fidelity by either pre- or postoptimization mechanisms. Full state-selective population inversion requires manipulating the vibrational coherences in the ground electronic state before the optical pulse is applied and in the excited electronic state afterward, but not during all times.

"Stirred, Not Shaken": Vibrational Coherence Can Speed Up Electronic Absorption.

We have recently proposed a laser control scheme for ultrafast absorption in multilevel systems by parallel transfer (J. Phys. Chem. Lett. 2015, 6, 1724). In this work we develop an analytical model that better takes into account the main features of electronic absorption in molecules. We show that the initial vibrational coherence in the ground electronic state can be used to greatly enhance the rate and yield of absorption when ultrashort pulses are used, provided that the phases of the coherences are taken into account. On the contrary, the initial coherence plays no role in the opposite limit, when a single long pulse drives the optical transition. The theory is tested by numerical simulations in the first absorption band of Na2.