RISMiCal: A software package to perform fast RISM/3D-RISM calculations.

Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.

Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.

Proteins that do not fold into their functional native state have been linked to diseases. In this study, the influence of the main and side chains of individual amino acids on the folding of the tryptophan cage (Trp-cage), a designed 20-residue miniprotein, was analyzed. For this purpose, we calculated the solvation free energy (SFE) contributions of individual atoms by using the 3D-reference interaction site model with the atomic decomposition method. The mechanism by which the Trp-cage is stabilized during the folding process was examined by calculating the total energy, which is the sum of the conformational energy and SFE. The folding process of the Trp-cage resulted in a stable native state, with a total energy that was 62.4 kcal/mol lower than that of the unfolded state. The solvation entropy, which is considered to be responsible for the hydrophobic effect, contributed 31.3 kcal/mol to structural stabilization. In other words, the contribution of the solvation entropy accounted for approximately half of the total contribution to Trp-cage folding. The hydrophobic core centered on Trp6 contributed 15.6 kcal/mol to the total energy, whereas the solvation entropy contribution was 6.3 kcal/mol. The salt bridge formed by the hydrophilic side chains of Asp9 and Arg16 contributed 10.9 and 5.0 kcal/mol, respectively. This indicates that not only the hydrophobic core but also the salt bridge of the hydrophilic side chains gain solvation entropy and contribute to stabilizing the native structure of the Trp-cage.

Volatile Short-Chain Aliphatic Aldehydes Act as Taste Modulators through the Orally Expressed Calcium-Sensing Receptor CaSR.

Aldehydes are natural volatile aroma compounds generated by the Maillard reaction of sugars and amino acids in food and affect the flavor of food. They have been reported to exert taste-modifying effects, such as increases in taste intensity at concentrations below the odor detection threshold. The present study examined the taste-enhancing effects of short-chain aliphatic aldehydes, such as isovaleraldehyde (IVAH) and 2-methylbutyraldehyde, thus attempting to identify the taste receptors involved. The results obtained revealed that IVAH enhanced the taste intensity of taste solutions even under the condition of olfactory deprivation by a noseclip. Furthermore, IVAH activated the calcium-sensing receptor CaSR in vitro. Receptor assays on aldehyde analogues showed that C3-C6 aliphatic aldehydes and methional, a C4 sulfur aldehyde, activated CaSR. These aldehydes functioned as a positive allosteric modulator for CaSR. The relationship between the activation of CaSR and taste-modifying effects was investigated by a sensory evaluation. Taste-modifying effects were found to be dependent on the activation state of CaSR. Collectively, these results suggest that short-chain aliphatic aldehydes function as taste modulators that modify sensations by activating orally expressed CaSR. We propose that volatile aroma aldehydes may also partially contribute to the taste-modifying effect via the same molecular mechanism as kokumi substances.

Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.

We apply moving root-mean-square deviation (mRMSD), which does not require a reference structure, as a method for analyzing protein dynamics. This method can be used to calculate the root-mean-square deviation (RMSD) of structure between two specified time points and to analyze protein dynamics behavior through time series analysis. We applied this method to the Trp-cage trajectory calculated by the Anton supercomputer and found that it shows regions of stable states as well as the conventional RMSD. In addition, we extracted a characteristic structure in which the side chains of Asp1 and Arg16 form hydrogen bonds near the most stable structure of the Trp-cage. We also determined that ≥20 ns is an appropriate time interval to investigate protein dynamics using mRMSD. Applying this method to NuG2 protein, we found that mRMSD can be used to detect regions of metastable states in addition to the stable state. This method can be applied to molecular dynamics simulations of proteins whose stable structures are unknown.

Increases in the pungency of allyl isothiocyanate and piperine by CaSR agonists, glutathione and γ-glutamyl-valyl-glycine.

γ-Glutamyl peptides, including glutathione (γ-Glu-Cys-Gly, GSH) and γ-glutamyl-valyl-glycine (γ-Glu-Val-Gly), have been shown to increase the intensity of basic tastes, such as salty, sweet, and umami, and flavor, including mouthfulness, but had no taste themselves at the concentrations tested. Although the mechanisms of action of γ-glutamyl peptides currently remain unclear, the involvement of the calcium sensing receptor (CaSR) has been suggested. Since GSH and γ-Glu-Val-Gly increase the pungency of some spices, the present study investigated their effects on the pungency of allyl isothiocyanate (AITC) using a sensory evaluation. GSH and γ-Glu-Val-Gly both significantly increased the pungency of AITC, while anserine, a peptide without CaSR activity, did not. GSH-induced increases in pungency were suppressed by NPS-2143, a CaSR inhibitor. Further, γ-Glu-Val-Gly significantly increased the pungency of piperine. The present results suggest that GSH and γ-Glu-Val-Gly increased the pungency by activating CaSR.

Lipocalin 15 in the olfactory mucus is a biomarker for Bowman's gland activity.

Olfactory mucus contributes to the specific functions of the olfactory mucosa, but the composition and source of mucus proteins have not been fully elucidated. In this study, we used comprehensive proteome analysis and identified lipocalin 15 (LCN15), a human-specific lipocalin family protein, as an abundant component of the olfactory mucus. Western blot analysis and enzyme-linked immunosorbent assay (ELISA) using a newly generated anti-LCN15 antibody showed that LCN15 was concentrated in olfactory mucus samples, but not in respiratory mucus samples. Immunohistochemical staining using anti-LCN15 antibody revealed that LCN15 localized to the cytokeratin 18-positive Bowman's glands of the olfactory cleft mucosa. Quantitative image analysis revealed that the area of LCN15 immunoreactivity along the olfactory cleft mucosa significantly correlated with the area of neuron-specific Protein-Gene Product 9.5 (PGP9.5) immunoreactivity, suggesting that LCN15 is produced in non-degenerated areas of the olfactory neuroepithelium. ELISA demonstrated that the concentration of LCN15 in the mucus was lower in participants with normal olfaction (≥ 50 years) and also tended to be lower in patients with idiopathic olfactory loss (≥ 50 years) than in participants with normal olfaction (< 50 years). Thus, LCN15 may serve as a biomarker for the activity of the Bowman's glands.

Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory.

The binding process of angiotensin-converting enzyme 2 (ACE2) to the receptor-binding domain (RBD) of the severe acute respiratory syndrome-like coronavirus 2 spike protein was investigated using molecular dynamics simulation and the three-dimensional reference interaction-site model theory. The results suggested that the protein-binding process consists of a protein-protein approaching step, followed by a local structural rearrangement step. In the approaching step, the interprotein interaction energy decreased as the proteins approached each other, whereas the solvation free energy increased. As the proteins approached, the glycan of ACE2 first established a hydrogen bond with the RBD. Thereafter, the number of interprotein hydrogen bonds increased rapidly. The solvation free energy increased because of the desolvation of the protein as it approached its partner. The spatial distribution function of the solvent revealed the presence of hydrogen bonds bridged by water molecules on the RBD-ACE2 interface. Finally, principal component analysis revealed that ACE2 showed a pronounced conformational change, whereas there was no significant change in RBD.

Microplastic pollution of commercial fishes from coastal and offshore waters in southwestern Japan.

Microplastic (MP) pollution in the marine environment is a worldwide issue. There is growing concern of consuming MPs through fish, yet the contamination status of fish collected from deeper waters surrounding Japan remains limited. Here, we presented baseline data on MPs in commercially important fishes from the coastal and offshore waters near Kyushu, Japan (East China Sea). We examined the MPs in the digestive tracts of two pelagic (n = 150) and five demersal species (n = 235). The fish were caught by pole and line, and bottom trawl at different geographical positions. The MPs in pelagic fish (39.1%) were more than in demersal fish (10.3%) and were of larger sizes. Moreover, the MPs correlated with habitat depth and type and species variation in the shape and polymer composition of MPs was observed. The results increase our understanding of the heterogeneous uptake of MPs by fishes.

GPR120 agonists enhance the fatty orosensation when added to fat-containing system, but do not evoke it by themselves in humans.

Dietary fat, an important macronutrient, has been considered to be perceived by texture and olfaction. Recently, fatty acid transporter, CD36, and fatty acid receptor, GPR120 are considered to be involved in human gustatory fatty acids perception in humans. However, limited information is currently available to show that agonists of CD36 and GPR120 evoke fatty oral sensations regarding to dietary fat in humans. Therefore, the role of GPR120 agonists in dietary fat perception in humans was investigated herein. An emulsion prepared from vegetable oil had a stronger fatty orosensation, an orosensation similar to an oily mouth-coating sensed 5 - 10 s after tasting, than that prepared from mineral oil; however, the physical properties of both emulsions, such as viscosity, particle distribution, interfacial tension, contact angle, frictional load, and ζ-electric potential were similar. The potent GPR120 agonist, TUG-891 enhanced the fatty orosensation when added to the emulsion prepared from vegetable oil, but not to that from mineral oil. All GPR120 agonists tested enhanced the fatty orosensation when added to a low-fat food system whereas they did not evoke any fatty sensation in aqueous solution at the concentrations tested in food system, and sensory activity positively correlated with GPR120 activity. These results suggest that GPR120 agonists enhance the fatty orosensation in humans when added to vegetable oil or a low-fat food system, but do not evoke it by themselves.

Evaluation of a Novel Boron-Containing α-D-Mannopyranoside for BNCT.

Boron neutron capture therapy (BNCT) is a unique anticancer technology that has demonstrated its efficacy in numerous phase I/II clinical trials with boronophenylalanine (BPA) and sodium borocaptate (BSH) used as 10B delivery agents. However, continuous drug administration at high concentrations is needed to maintain sufficient 10B concentration within tumors. To address the issue of 10B accumulation and retention in tumor tissue, we developed MMT1242, a novel boron-containing α-d-mannopyranoside. We evaluated the uptake, intracellular distribution, and retention of MMT1242 in cultured cells and analyzed biodistribution, tumor-to-normal tissue ratio and toxicity in vivo. Fluorescence imaging using nitrobenzoxadiazole (NBD)-labeled MMT1242 and inductively coupled mass spectrometry (ICP-MS) were performed. The effectiveness of BNCT using MMT1242 was assessed in animal irradiation studies at the Kyoto University Research Reactor. MMT1242 showed a high uptake and broad intracellular distribution in vitro, longer tumor retention compared to BSH and BPA, and adequate tumor-to-normal tissue accumulation ratio and low toxicity in vivo. A neutron irradiation study with MMT1242 in a subcutaneous murine tumor model revealed a significant tumor inhibiting effect if injected 24 h before irradiation. We therefore report that 10B-MMT1242 is a candidate for further clinical BNCT studies.

Mycelial biomass estimation and metabolic quotient of Lentinula edodes using species-specific qPCR.

Lentinula edodes, commonly known as shiitake, is an edible mushroom that is cultivated and consumed around the globe, especially in Asia. Monitoring mycelial growth inside a woody substrate is difficult, but it is essential for effective management of mushroom cultivation. Mycelial biomass also affects the rate of wood decomposition under natural conditions and must be known to determine the metabolic quotient, an important ecophysiological parameter of fungal growth. Therefore, developing a method to measure it inside a substrate would be very useful. In this study, as the first step in understanding species-specific rates of fungal decomposition of wood, we developed species-specific primers and qPCR procedures for L. edodes. We tested primer specificity using strains of L. edodes from Japan and Southeast Asia, as well as related species of fungi and plant species for cultivation of L. edodes, and generated a calibration curve for quantification of mycelial biomass in wood dust inoculated with L. edodes. The qPCR procedure we developed can specifically detect L. edodes and allowed us to quantify the increase in L. edodes biomass in wood dust substrate and calculate the metabolic quotient based on the mycelial biomass and respiration rate. Development of a species-specific method for biomass quantification will be useful for both estimation of mycelial biomass and determining the kinetics of fungal growth in decomposition processes.

Random walk to describe diffusion phenomena in three-dimensional discontinuous media: Extension to anisotropic phases and nonplane interfaces.

We extend the step-balanced random walk [Y. Maruyama, Phys. Rev. E 96, 032135 (2017)2470-004510.1103/PhysRevE.96.032135], which was proposed for diffusion phenomena in three-dimensional discontinuous media, to systems that contain anisotropic phase zones with nonplane interfaces. What is key is threefold: For each interstep transition at discontinuous interfaces to be equilibrated by its reverse transition, incident and penetration steps are in one-to-one correspondence; at each incidence, penetration probability is determined by the normal components of an incident step and the corresponding penetration step with respect to an incident tangential plane, and for reflection, the reverse of an incident step, which satisfies the conditions for time reversibility at any interface, is used as a reflection step.

Mutation-induced change in chignolin stability from π-turn to α-turn.

Chignolin, which consists of 10 amino acids, adopts two stable states in simulations at room temperature at 1 atm: the native and misfolded states. The sequence of chignolin is optimized to form a stable π-turn and thus the native state has a π-turn from Asp3 to Thr8. On the other hand, the misfolded state adopts an α-turn from Asp3 to Gly7. We previously investigated the differences in the stability mechanism of the two states using computational techniques. Our previous detailed energy analysis implied that the native state was stabilized by hydrogen bonding between the side chain atoms of Thr6 and Thr8, and Thr8 was not involved in stabilization of the misfolded state. Thus, we predicted that mutation of Thr8 to a neutral amino acid could stabilize the misfolded structure over the native structure. In the present work, we performed 4 µs molecular dynamics simulations for 19 mutants of the 8th residue. Among them, the T8I, T8F, T8P, T8N, and T8Y mutants, in which the 8th residue was changed to a neutral residue, formed only the misfolded structure at room temperature. Even at high temperature, for the T8P mutant, the native structure was not observed, as the T8P mutant cannot form the native structure because of steric hindrance caused by the distinctive cyclic structure of proline. Interestingly, the T8P mutant at high temperature has trans and cis conformations in the Gly7-Pro8 sequence, with the trans conformation corresponding to the misfolded state. NMR analysis of the T8P mutant supported our results.

Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory.

Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.

Analysis of Structural Stability of Chignolin.

We discuss the stability of an entire protein and the influence of main chains and side chains of individual amino acids to investigate the protein-folding mechanism. For this purpose, we calculated the solvation free-energy contribution of individual atoms using the three-dimensional reference interaction site model with the atomic decomposition method. We generated structures of chignolin miniprotein by a molecular dynamics simulation and classified them into six types: native 1, native 2, misfolded 1, misfolded 2, intermediate, and unfolded states. The total energies of the native (-171.1 kcal/mol) and misfolded (-171.2 kcal/mol) states were almost the same and lower than those of the intermediate (-158.5 kcal/mol) and unfolded (-148.1 kcal/mol) states; however, their components were different. In the native state, the side-chain interaction between Thr6 and Thr8 is important for the formation of π-turn. On the other hand, the hydrogen bonds between the atoms of the main chains in the misfolded state become stronger than those in the intermediate state.

Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy.

Recently, we proposed a reference-modified density functional theory (RMDFT) to calculate solvation free energy (SFE), in which a hard-sphere fluid was introduced as the reference system instead of an ideal molecular gas. Through the RMDFT, using an optimal diameter for the hard-sphere reference system, the values of the SFE calculated at room temperature and normal pressure were in good agreement with those for more than 500 small organic molecules in water as determined by experiments. In this study, we present an application of the RMDFT for calculating the temperature and pressure dependences of the SFE for solute molecules in water. We demonstrate that the RMDFT has high predictive ability for the temperature and pressure dependences of the SFE for small solute molecules in water when the optimal reference hard-sphere diameter determined for each thermodynamic condition is used. We also apply the RMDFT to investigate the temperature and pressure dependences of the thermodynamic stability of an artificial small protein, chignolin, and discuss the mechanism of high-temperature and high-pressure unfolding of the protein. © 2017 Wiley Periodicals, Inc.

Stability of Unfolded and Folded Protein Structures Using a 3D-RISM with the RMDFT.

Protein stability is determined by the characteristics of the protein itself as well as the surrounding solvent. Herein, we discuss the stability of the folded and unfolded structures of proteins obtained from Anton's long simulations (Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Shaw, D.E. Science, 2011, 334, 517-520). Specifically, the stabilities of CLN025, the WW domain variant GTT, the triple mutant of the redesigned protein G variant NuG2, and the de novo-designed three-helix bundle protein are investigated. The solvation free energy of the structures is calculated using the three-dimensional reference interaction site model with the reference-modified density functional theory. The total energy is given by the sum of the conformational energy and the solvation free energy, and their balance results in the stabilization of protein structure, as demonstrated by the correspondence between structures with the lowest total energy of all proteins to their native structures. Overall, these findings indicate that the total energy function is appropriate for evaluating the stability of protein folding systems. Moreover, decomposing the energy terms reveals that proteins achieve their stabilities from the balance between the conformational energy and the solvation free energy. In particular, the solvation entropy is the main contributor to the process of folding from more extended structures to compact structures. The native structure is more stable than the compact structure owing to competition between intramolecular and intermolecular interactions.

Random walk to describe diffusion phenomena in three-dimensional discontinuous media: Step-balance and fictitious-velocity corrections.

In this paper, we show that diffusion phenomena in three-dimensional discontinuous media can be described as a random walk by two simple interface-correction methods, namely step-balance and fictitious-velocity corrections, which are completely different in a physical picture but equivalent in that the continuity of the random walk at interfaces is considered. In both corrections, asymmetric interface permeability of a random walker, which comes from ensuring the continuity, causes apparent confinement of the walker in higher-diffusivity layers for benchmark tests on heat diffusion in two-phase multilayered systems. Effective thermal conductivities (walker diffusivities) computed from the trajectories are in excellent agreement with the series and parallel conduction formulas, indicating the equivalence of the two corrections and the importance of ensuring the continuity of a random walk at interfaces.

Structure-CaSR-Activity Relation of Kokumi γ-Glutamyl Peptides.

Modulation of the calcium sensing receptor (CaSR) is one of the physiological activities of γ-glutamyl peptides such as glutathione (γ-glutamylcysteinylglycine). γ-Glutamyl peptides also possess a flavoring effect, i.e., sensory activity of kokumi substances, which modifies the five basic tastes when added to food. These activities have been shown to be positively correlated, suggesting that kokumi γ-glutamyl peptides are perceived through CaSRs in humans. Our research is based on the hypothesis that the discovery of highly active CaSR agonist peptides will lead to the creation of practical kokumi peptides. Through continuous study of the structure-CaSR-activity relation of a large number of γ-glutamyl peptides, we have determined that the structural requirements for intense CaSR activity of γ-glutamyl peptides are as follows: existence of an N-terminal γ-L-glutamyl residue; existence of a moderately sized, aliphatic, neutral substituent at the second residue in an L-configuration; and existence of a C-terminal carboxylic acid, preferably with the existence of glycine as the third constituent. By the sensory analysis of γ-glutamyl peptides selected by screening using the CaSR activity assay, γ-glutamylvalylglycine was found to be a potent kokumi peptide. Furthermore, norvaline-containing γ-glutamyl peptides, i.e., γ-glutamylnorvalylglycine and γ-glutamylnorvaline, possessed excellent sensory activity of kokumi substances. A novel, practical industrial synthesis of regiospecific γ-glutamyl peptides is also required for their commercialization, which was achieved through the ring opening reaction of N-α-carbobenzoxy-L-glutamic anhydride and amino acids or peptides in the presence of N-hydroxysuccinimide.

A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution.

In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.