Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.

In the replica-permutation method, an advanced version of the replica-exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid-ß(16-22) peptides using RPST with the "randomly assigned" list (RPST-RA) and RPST with the "sequentially assigned" list (RPST-SA). The results show the decreases in the transition probabilities in RPST-SA are eliminated, and the sampling efficiency is improved in RPST-RA.

Energetics and kinetics of substrate analog-coupled staphylococcal nuclease folding revealed by a statistical mechanical approach.

Protein conformational changes associated with ligand binding, especially those involving intrinsically disordered proteins, are mediated by tightly coupled intra- and intermolecular events. Such reactions are often discussed in terms of two limiting kinetic mechanisms, conformational selection (CS), where folding precedes binding, and induced fit (IF), where binding precedes folding. It has been shown that coupled folding/binding reactions can proceed along both CS and IF pathways with the flux ratio depending on conditions such as ligand concentration. However, the structural and energetic basis of such complex reactions remains poorly understood. Therefore, we used experimental, theoretical, and computational approaches to explore structural and energetic aspects of the coupled-folding/binding reaction of staphylococcal nuclease in the presence of the substrate analog adenosine-3',5'-diphosphate. Optically monitored equilibrium and kinetic data, combined with a statistical mechanical model, gave deeper insight into the relative importance of specific and Coulombic protein-ligand interactions in governing the reaction mechanism. We also investigated structural aspects of the reaction at the residue level using NMR and all-atom replica-permutation molecular dynamics simulations. Both approaches yielded clear evidence for accumulation of a transient protein-ligand encounter complex early in the reaction under IF-dominant conditions. Quantitative analysis of the equilibrium/kinetic folding revealed that the ligand-dependent CS-to-IF shift resulted from stabilization of the compact transition state primarily by weakly ligand-dependent Coulombic interactions with smaller contributions from specific binding energies. At a more macroscopic level, the CS-to-IF shift was represented as a displacement of the reaction "route" on the free energy surface, which was consistent with a flux analysis.

Replica permutation with solute tempering for molecular dynamics simulation and its application to the dimerization of amyloid-ß fragments.

We propose the replica permutation with solute tempering (RPST) by combining the replica-permutation method (RPM) and the replica exchange with solute tempering (REST). Temperature permutations are performed among more than two replicas in RPM, whereas temperature exchanges are performed between two replicas in the replica-exchange method (REM). The temperature transition in RPM occurs more efficiently than in REM. In REST, only the temperatures of the solute region, the solute temperatures, are exchanged to reduce the number of replicas compared to REM. Therefore, RPST is expected to be an improved method taking advantage of these methods. For comparison, we applied RPST, REST, RPM, and REM to two amyloid-ß(16-22) peptides in explicit water. We calculated the transition ratio and the number of tunneling events in the temperature space and the number of dimerization events of amyloid-ß(16-22) peptides. The results indicate that, in RPST, the number of replicas necessary for frequent random walks in the temperature and conformational spaces is reduced compared to the other three methods. In addition, we focused on the dimerization process of amyloid-ß(16-22) peptides. The RPST simulation with a relatively small number of replicas shows that the two amyloid-ß(16-22) peptides form the intermolecular antiparallel ß-bridges due to the hydrophilic side-chain contact between Lys and Glu and hydrophobic side-chain contact between Leu, Val, and Phe, which stabilizes the dimer of the peptides.

State-of-the-Art Molecular Dynamics Simulation Studies of RNA-Dependent RNA Polymerase of SARS-CoV-2.

Molecular dynamics (MD) simulations are powerful theoretical methods that can reveal biomolecular properties, such as structure, fluctuations, and ligand binding, at the level of atomic detail. In this review article, recent MD simulation studies on these biomolecular properties of the RNA-dependent RNA polymerase (RdRp), which is a multidomain protein, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are presented. Although the tertiary structures of RdRps in SARS-CoV-2 and SARS-CoV are almost identical, the RNA synthesis activity of RdRp of SARS-CoV is higher than SARS-CoV-2. Recent MD simulations observed a difference in the dynamic properties of the two RdRps, which may cause activity differences. RdRp is also a drug target for Coronavirus disease 2019 (COVID-19). Nucleotide analogs, such as remdesivir and favipiravir, are considered to be taken up by RdRp and inhibit RNA replication. Recent MD simulations revealed the recognition mechanism of RdRp for these drug molecules and adenosine triphosphate (ATP). The ligand-recognition ability of RdRp decreases in the order of remdesivir, favipiravir, and ATP. As a typical recognition process, it was found that several lysine residues of RdRp transfer these ligand molecules to the binding site such as a "bucket brigade." This finding will contribute to understanding the mechanism of the efficient ligand recognition by RdRp. In addition, various simulation studies on the complexes of SARS-CoV-2 RdRp with several nucleotide analogs are reviewed, and the molecular mechanisms by which these compounds inhibit the function of RdRp are discussed. The simulation studies presented in this review will provide useful insights into how nucleotide analogs are recognized by RdRp and inhibit the RNA replication.

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-ß Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.

Alzheimer's disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-ß (Aß) peptides. This review article presents molecular dynamics (MD) simulation studies of Aß peptides and Aß fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aß, a ß-hairpin structure promotes the formation of intermolecular ß-sheet structures. Aß peptides tend to exist at hydrophilic/hydrophobic interfaces and form more ß-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aß peptides, interact with Aß. An MD simulation study of the Aß amyloid fibrils in equilibrium is also presented: the Aß amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer's disease using MD simulations.

"Bucket brigade" using lysine residues in RNA-dependent RNA polymerase of SARS-CoV-2.

The RNA-dependent RNA polymerase (RdRp) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a promising drug target for coronavirus disease 2019 (COVID-19) because it plays the most important role in the replication of the RNA genome. Nucleotide analogs such as remdesivir and favipiravir are thought to interfere with the RNA replication by RdRp. More specifically, they are expected to compete with nucleoside triphosphates, such as ATP. However, the process in which these drug molecules and nucleoside triphosphates are taken up by RdRp remains unknown. In this study, we performed all-atom molecular dynamics simulations to clarify the recognition mechanism of RdRp for these drug molecules and ATP that were at a distance. The ligand recognition ability of RdRp decreased in the order of remdesivir, favipiravir, and ATP. We also identified six recognition paths. Three of them were commonly found in all ligands, and the remaining three paths were ligand-dependent ones. In the common two paths, it was observed that the multiple lysine residues of RdRp carried the ligands to the binding site like a "bucket brigade." In the remaining common path, the ligands directly reached the binding site. Our findings contribute to the understanding of the efficient ligand recognition by RdRp at the atomic level.

Dynamic properties of SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases studied by molecular dynamics simulations.

One of the promising drug targets against COVID-19 is an RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. The tertiary structures of the SARS-CoV-2 and SARS-CoV RdRps are almost the same. However, the RNA-synthesizing activity of the SARS-CoV RdRp is higher than that of the SARS-CoV-2 RdRp. We performed molecular dynamics simulations and found differences in their dynamic properties. In the SARS-CoV RdRp, motifs A-G, which form the active site, are up to 63% closer to each other. We also observed cooperative domain motion in the SARS-CoV RdRp. Such dynamic differences may cause the activity differences between the two RdRps.

Promotion and Inhibition of Amyloid-ß Peptide Aggregation: Molecular Dynamics Studies.

Aggregates of amyloid-ß (Aß) peptides are known to be related to Alzheimer's disease. Their aggregation is enhanced at hydrophilic-hydrophobic interfaces, such as a cell membrane surface and air-water interface, and is inhibited by polyphenols, such as myricetin and rosmarinic acid. We review molecular dynamics (MD) simulation approaches of a full-length Aß peptide, Aß40, and Aß(16-22) fragments in these environments. Since these peptides have both hydrophilic and hydrophobic amino acid residues, they tend to exist at the interfaces. The high concentration of the peptides accelerates the aggregation there. In addition, Aß40 forms a ß-hairpin structure, and this structure accelerates the aggregation. We also describe the inhibition mechanism of the Aß(16-22) aggregation by polyphenols. The aggregation of Aß(16-22) fragments is caused mainly by the electrostatic attraction between charged amino acid residues known as Lys16 and Glu22. Since polyphenols form hydrogen bonds between their hydroxy and carboxyl groups and these charged amino acid residues, they inhibit the aggregation.

Molecular dynamics simulations of amyloid-ß(16-22) peptide aggregation at air-water interfaces.

Oligomers of amyloid-ß (Aß) peptides are known to be related to Alzheimer's disease, and their formation is accelerated at hydrophilic-hydrophobic interfaces, such as the cell membrane surface and air-water interface. Here, we report molecular dynamics simulations of aggregation of Aß(16-22) peptides at air-water interfaces. First, 100 randomly distributed Aß(16-22) peptides moved to the interface. The high concentration of peptides then accelerated their aggregation and formation of antiparallel ß-sheets. Two layers of oligomers were observed near the interface. In the first layer from the interface, the oligomer with less ß-bridges exposed the hydrophobic residues to the air. The second layer consisted of oligomers with more ß-bridges that protruded into water. They are more soluble in water because the hydrophobic residues are covered by N- and C-terminal hydrophilic residues that are aligned well along the oligomer edge. These results indicate that amyloid protofibril formation mainly occurs in the second layer.

Clinical Outcomes of Off-Label Dosing of Direct Oral Anticoagulant Therapy Among Japanese Patients With Atrial Fibrillation Identified From the SAKURA AF Registry.

BACKGROUND: Off-label dosing of direct oral anticoagulants (DOACs) is encountered clinically among patients with atrial fibrillation (AF), although data on the clinical outcomes of over- and under-dosing are lacking in Japan. Methods and Results: We examined the clinical outcomes of off-label DOAC dosing using the SAKURA AF Registry, a prospective multicenter registry in Japan. Among 3,237 enrollees, 1,676 under any of the 4 DOAC regimens were followed up for a median of 39.3 months: 746 (45.0%), appropriate standard-dose; 477 (28.7%), appropriate low-dose; 66 (4.0%), over-dose; and 369 (22.2%) under-dose. Compared with the standard-dose group, patients in the under- and over-dose groups were significantly older and had a higher stroke risk. After multivariate adjustment, stroke/systemic embolism (SE) and death events were equivalent between the standard- and under-dose groups, but major bleeding events tended to be lower in the under-dose group (hazard ratio [HR] 0.474, P=0.0739). Composite events (stroke/SE, major bleeding, or death) were higher in the over-dose than in the standard-dose group (HR 2.714, P=0.0081). CONCLUSIONS: Clinical outcomes were not worse for under-dose than for standard-dose users among patients with different backgrounds. Over-dose users, however, were at higher risk for all clinical events and required careful follow-up. Further studies are needed to clarify the safety and effectiveness of off-label DOAC dosing in Japan.

Amyloid fibril disruption by ultrasonic cavitation: nonequilibrium molecular dynamics simulations.

We describe the disruption of amyloid fibrils of Alzheimer's amyloid-ß peptides by ultrasonic cavitation. For this purpose, we performed nonequilibrium all-atom molecular dynamics simulations with sinusoidal pressure and visualized the process with movies. When the pressure is negative, a bubble is formed, usually at hydrophobic residues in the transmembrane region. Most ß-strands maintain their secondary structures in the bubble. When the pressure becomes positive, the bubble collapses, and water molecules crash against the hydrophilic residues in the nontransmembrane region to disrupt the amyloid. Shorter amyloids require longer sonication times for disruption because they do not have enough hydrophobic residues to serve as a nucleus to form a bubble. These results agree with experiments in which monodispersed amyloid fibrils were obtained by ultrasonication.

Coulomb replica-exchange method: handling electrostatic attractive and repulsive forces for biomolecules.

We propose a new type of the Hamiltonian replica-exchange method (REM) for molecular dynamics (MD) and Monte Carlo simulations, which we refer to as the Coulomb REM (CREM). In this method, electrostatic charge parameters in the Coulomb interactions are exchanged among replicas while temperatures are exchanged in the usual REM. By varying the atom charges, the CREM overcomes free-energy barriers and realizes more efficient sampling in the conformational space than the REM. Furthermore, this method requires only a smaller number of replicas because only the atom charges of solute molecules are used as exchanged parameters. We performed Coulomb replica-exchange MD simulations of an alanine dipeptide in explicit water solvent and compared the results with those of the conventional canonical, replica exchange, and van der Waals REMs. Two force fields of AMBER parm99 and AMBER parm99SB were used. As a result, the CREM sampled all local-minimum free-energy states more frequently than the other methods for both force fields. Moreover, the Coulomb, van der Waals, and usual REMs were applied to a fragment of an amyloid-ß peptide (Aß) in explicit water solvent to compare the sampling efficiency of these methods for a larger system. The CREM sampled structures of the Aß fragment more efficiently than the other methods. We obtained ß-helix, α-helix, 3(10)-helix, ß-hairpin, and ß-sheet structures as stable structures and deduced pathways of conformational transitions among these structures from a free-energy landscape.

Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-ß(29-42) peptides.

We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-ß(29-42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-ß(29-42) and reveal its dimerization pathways.

On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics.

Mean-force dynamics (MFD), which is a fictitious dynamics for a set of collective variables on a potential of mean-force, is a powerful algorithm to efficiently explore free-energy landscapes. Recently, we have introduced logarithmic MFD (LogMFD) (Morishita et al., Phys. Rev. E 2012, 85, 066702) which overcomes difficulties encounterd in free-energy calculations using standard approaches such as thermodynamic integration. Here, we present a guide to implementing LogMFD calculations paying attention to the practical issues in choosing the parameters in LogMFD. A primary focus is given to the effect of the parameters on the accuracy of the reconstructed free-energy profiles. A recipe for reducing the errors due to energy dissipation is presented. We also demonstrate that multidimensional free-energy landscapes can be reconstructed on-the-fly using LogMFD, which cannot be accomplished using any other free-energy calculation techniques.

Transformation of a design peptide between the α-helix and ß-hairpin structures using a helix-strand replica-exchange molecular dynamics simulation.

We investigated the transformation between the α-helix and ß-hairpin structures of an 18-residue design peptide, whose sequence is INYWLAHAKAGYIVHWTA. This peptide has both α-helix and ß-hairpin structures in aqueous solution. For this purpose, we proposed the helix-strand replica-exchange method. This is one of the Hamiltonian replica-exchange methods in which we exchange parameters for umbrella potentials to enhance the α-helix or ß-strand structure formation. We performed an all-atom helix-strand replica-exchange molecular dynamics (MD) simulation of this peptide in explicit water solvent with five replicas. Because the suitable umbrella potential was applied, the helix-strand replica-exchange MD simulation reproduced conformations closer to experimental conformations than a temperature replica-exchange MD simulation when the same numbers of the replicas were used, while the temperature replica-exchange MD simulation does not require bias along any specific order parameter. We calculated its free-energy landscape and revealed the transformation pathways between the α-helix and ß-hairpin structures and the folding pathways from an extended structure. Although the fractions of the α-helix and ß-hairpin structures are less than those obtained by the experiment, the free-energy difference between the two structures is calculated to be almost zero, which agrees with the experimental results.

Interlaboratory trial of the rat Pig-a mutation assay using an erythroid marker HIS49 antibody.

The peripheral blood Pig-a assay has shown promise as a tool for evaluating in vivo mutagenicity. In this study five laboratories participated in a collaborative trial that evaluated the transferability and reproducibility of a rat Pig-a assay that uses a HIS49 antibody reacts with an antigen found on erythrocytes and erythroid progenitors. In preliminary work, flow cytometry methods were established that enabled all laboratories to detect CD59-negative erythrocyte frequencies (Pig-a mutant frequencies) of <10×10(-6) in control rats. Four of the laboratories (the in-life labs) then treated male rats with a single oral dose of N-nitroso-N-ethylurea, 7,12-dimethylbenz[a]anthracene (DMBA), or 4-nitroquinoline-1-oxide (4NQO). Blood samples were collected up to 4 weeks after the treatments and analyzed by flow cytometry for the frequency of CD59-negative cells among total red blood cells (RBCs; RBC Pig-a assay). RBC Pig-a assays were conducted in the four in-life laboratories, plus a fifth laboratory that received blood samples from the other laboratories. In addition, three of the five laboratories performed a Pig-a assay on reticulocytes (RETs; PIGRET assay), using blood from the rats treated with DMBA and 4NQO. The four in-life laboratories detected consistent, time- and dose-related increases in RBC Pig-a mutant frequency (MF) for all three test articles. Furthermore, comparable results were obtained in the fifth laboratory that received blood samples from other laboratories. The three laboratories conducting the PIGRET assay also detected consistent, time- and dose-related increases in Pig-a MF, with the RET MFs increasing more rapidly with time than RBC MFs. These results indicate that rat Pig-a assays using a HIS49 antibody were transferable between laboratories and that data generated by the assays were reproducible. The findings also suggest that the PIGRET assay may detect the in vivo mutagenicity of test compounds earlier than the RBC Pig-a assay.

Decomposition-order effects of time integrator on ensemble averages for the Nosé-Hoover thermostat.

Decomposition-order dependence of time development integrator on ensemble averages for the Nosé-Hoover dynamics is discussed. Six integrators were employed for comparison, which were extensions of the velocity-Verlet or position-Verlet algorithm. Molecular dynamics simulations by these integrators were performed for liquid-argon systems with several different time steps and system sizes. The obtained ensemble averages of temperature and potential energy were shifted from correct values depending on the integrators. These shifts increased in proportion to the square of the time step. Furthermore, the shifts could not be removed by increasing the number of argon atoms. We show the origin of these ensemble-average shifts analytically. Our discussion can be applied not only to the liquid-argon system but also to all MD simulations with the Nosé-Hoover thermostat. Our recommended integrators among the six integrators are presented to obtain correct ensemble averages.

Dissociation process of polyalanine aggregates by free electron laser irradiation.

Polyalanine (polyA) disease-causative proteins with an expansion of alanine repeats can be aggregated. Although curative treatments for polyA diseases have not been explored, the dissociation of polyA aggregates likely reduces the cytotoxicity of polyA. Mid-infrared free electron laser (FEL) successfully dissociated multiple aggregates. However, whether the FEL dissociates polyA aggregates like other aggregates has not been tested. Here, we show that FEL at 6.1 µm experimentally weakened the extent of aggregation of a peptide with 13 alanine repeats (13A), and the irradiated 13A exerted lesser cytotoxicity to neuron-like cells than non-irradiated 13A. Then, we applied molecular dynamics (MD) simulation to follow the dissociation process by FEL. We successfully observed how the intermolecular ß-sheet of polyA aggregates was dissociated and separated into monomers with helix structures upon FEL irradiation. After the dissociation by FEL, water molecules inhibited the reformation of polyA aggregates. We recently verified the same dissociation process using FEL-treated amyloid-ß aggregates. Thus, a common mechanism underlies the dissociation of different protein aggregates that cause different diseases, polyA disease and Alzheimer's disease. However, MD simulation indicated that polyA aggregates are less easily dissociated than amyloid-ß aggregates and require longer laser irradiation due to hydrophobic alanine repeats.

Inhibition of amyloid-ß(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.

Aggregates of amyloid-ß (Aß) peptides are thought to cause Alzheimer's disease. Polyphenolic compounds are known to inhibit Aß aggregation. We applied replica permutation with solute tempering (RPST) to the system of Aß fragments, Aß(16-22), and polyphenols to elucidate the mechanism of inhibition of Aß aggregation. The RPST molecular dynamics simulations were performed for two polyphenols, myricetin (MYC) and rosmarinic acid (ROA). Two Aß fragments were distant, and the number of residues forming the intermolecular ß-sheet was reduced in the presence of MYC and ROA compared with that in the absence of polyphenols. MYC was found to interact with glutamic acid and phenylalanine of Aß fragments. These interactions induce helix structure formation of Aß fragments, making it difficult to form ß-sheet. ROA interacted with glutamic acid and lysine, which reduced the hydrophilic interaction between Aß fragments. These results indicate that these polyphenols inhibit the aggregation of Aß fragments with different mechanisms.