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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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 B delivery agents. However, continuous drug administration at high concentrations is needed to maintain sufficient B concentration within tumors. To address the issue of B accumulation and retention in tumor tissue, we developed MMT1242, a novel boron-containing α-d-mannopyranoside.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Biotic and Abiotic Factors Controlling Respiration Rates of Above- and Belowground Woody Debris of Fagus crenata and Quercus crispula in Japan.

As a large, long-term pool and source of carbon and nutrients, woody litter is an important component of forest ecosystems. The objective of this study was to estimate the effect of the factors that regulate the rate of decomposition of coarse and fine woody debris (CFWD) of dominant tree species in a cool-temperate forest in Japan. Respiration rates of dead stems, branches, and coarse and fine roots of Fagus crenata and Quercus crispula felled 4 years prior obtained in situ ranged from 20.

A solvation-free-energy functional: a reference-modified density functional formulation.

The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids.

Mesophyll conductance in leaves of Japanese white birch (Betula platyphylla var. japonica) seedlings grown under elevated CO2 concentration and low N availability.

To test the hypothesis that mesophyll conductance (gm ) would be reduced by leaf starch accumulation in plants grown under elevated CO2 concentration [CO2 ], we investigated gm in seedlings of Japanese white birch grown under ambient and elevated [CO2 ] with an adequate and limited nitrogen supply using simultaneous gas exchange and chlorophyll fluorescence measurements. Both elevated [CO2 ] and limited nitrogen supply decreased area-based leaf N accompanied with a decrease in the maximum rate of Rubisco carboxylation (Vc,max ) on a CO2 concentration at chloroplast stroma (Cc ) basis. Conversely, only seedlings grown at elevated [CO2 ] under limited nitrogen supply had significantly higher leaf starch content with significantly lower gm among the treatment combinations.

Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT.

A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically.