start-ver=1.4
cd-journal=joma
no-vol=161
cd-vols=
no-issue=21
article-no=
start-page=214501
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20241202
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=The nature of the hydrophobic interaction varies as the solute size increases from methane�fs to C60�fs
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The hydrophobic interaction, often combined with the hydrophilic or ionic interactions, makes the behavior of aqueous solutions very rich and plays an important role in biological systems. Theoretical and computer simulation studies have shown that the water-mediated force depends strongly on the size and other chemical properties of the solute, but how it changes with these factors remains unclear. We report here a computer simulation study that illustrates how the hydrophobic pair interaction and the entropic and enthalpic terms change with the solute size when the solute?solvent weak attractive interaction is unchanged with the solute size. The nature of the hydrophobic interaction changes qualitatively as the solute size increases from that of methane to that of fullerene. The potential of mean force between small solutes has several well-defined extrema, including the third minimum, whereas the potential of mean force between large solutes has the deep contact minimum and the large free-energy barrier between the contact and the water-bilayer separated configurations. The difference in the potential of mean force is related to the differences in the water density, energy, and hydrogen bond number distributions in the vicinity of the pairs of hydrophobic solutes.
en-copyright=
kn-copyright=

en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=15
cd-vols=
no-issue=
article-no=
start-page=1329162
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240809
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Vaccine and antiviral drug promise for preventing post-acute sequelae of COVID-19, and their combination for its treatment
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Introduction: Most healthy individuals recover from acute SARS-CoV-2 infection, whereas a remarkable number continues to suffer from unexplained symptoms, known as Long COVID or post-acute COVID-19 syndrome (PACS). It is therefore imperative that methods for preventing and treating the onset of PASC be investigated with the utmost urgency.<br>
Methods: A mathematical model of the immune response to vaccination and viral infection with SARS-CoV-2, incorporating immune memory cells, was developed.<br>
Results and discussion: Similar to our previous model, persistent infection was observed by the residual virus in the host, implying the possibility of chronic inflammation and delayed recovery from tissue injury. Pre-infectious vaccination and antiviral medication administered during onset can reduce the acute viral load; however, they show no beneficial effects in preventing persistent infection. Therefore, the impact of these treatments on the PASC, which has been clinically observed, is mainly attributed to their role in preventing severe tissue damage caused by acute viral infections. For PASC patients with persistent infection, vaccination was observed to cause an immediate rapid increase in viral load, followed by a temporary decrease over approximately one year. The former was effectively suppressed by the coadministration of antiviral medications, indicating that this combination is a promising treatment for PASC.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HaradaKouji
en-aut-sei=Harada
en-aut-mei=Kouji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
en-keyword=post-acute sequelae of SARS-CoV-2 infection
kn-keyword=post-acute sequelae of SARS-CoV-2 infection
en-keyword=PASC
kn-keyword=PASC
en-keyword=long Covid
kn-keyword=long Covid
en-keyword=persistent viruses
kn-keyword=persistent viruses
en-keyword=vaccine
kn-keyword=vaccine
en-keyword=antiviral drug
kn-keyword=antiviral drug
en-keyword=mathematical model
kn-keyword=mathematical model
en-keyword=immune response
kn-keyword=immune response
END

start-ver=1.4
cd-journal=joma
no-vol=32
cd-vols=
no-issue=10
article-no=
start-page=e4763
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=20230925
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2?M TFE and urea. As 2?M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.
en-copyright=
kn-copyright=

en-aut-name=NakataNoa
en-aut-sei=Nakata
en-aut-mei=Noa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Information Science, University of Hyogo
kn-affil=

affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=5
en-affil=Department of Chemistry, Graduate School of Science, Chiba University
kn-affil=

affil-num=6
en-affil=Department of Bio-Science, Nagahama Institute of Bio-Science and Technology
kn-affil=
en-keyword=2,2,2-trifluoroethanol
kn-keyword=2,2,2-trifluoroethanol
en-keyword=cosolvent effects
kn-keyword=cosolvent effects
en-keyword=preferential binding parameter
kn-keyword=preferential binding parameter
en-keyword=protein folding stability
kn-keyword=protein folding stability
en-keyword=urea
kn-keyword=urea
END

start-ver=1.4
cd-journal=joma
no-vol=249
cd-vols=
no-issue=
article-no=
start-page=440
end-page=452
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=2024
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=How do water-mediated interactions and osmotic second virial coefficients vary with particle size?
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=We examine quantitatively the solute-size dependences of the effective interactions between nonpolar solutes in water and in a simple liquid. The potential w(r) of mean force and the osmotic second virial coefficients B are calculated with high accuracy from molecular dynamics simulations. As the solute diameter increases from methane's to C60's with the solute?solute and solute?solvent attractive interaction parameters fixed to those for the methane?methane and methane?water interactions, the first minimum of w(r) lowers from ?1.1 to ?4.7 in units of the thermal energy kT. Correspondingly, the magnitude of B (<0) increases proportional to �Ѓ� with some power close to 6 or 7, which reinforces the solute-size dependence of B found earlier for a smaller range of �� [H. Naito, R. Okamoto, T. Sumi and K. Koga, J. Chem. Phys., 2022, 156, 221104]. We also demonstrate that the strength of the attractive interactions between solute and solvent molecules can qualitatively change the characteristics of the effective pair interaction between solute particles, both in water and in a simple liquid. If the solute?solvent attractive force is set to be weaker (stronger) than a threshold, the effective interaction becomes increasingly attractive (repulsive) with increasing solute size.
en-copyright=
kn-copyright=

en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=25
cd-vols=
no-issue=45
article-no=
start-page=31107
end-page=31117
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2023
dt-pub=2023
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Solvation free energies of alcohols in water: temperature and pressure dependences
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Solvation free energies ��* of amphiphilic species, methanol and 1,2-hexanediol, are obtained as a function of temperature or pressure based on molecular dynamics simulations combined with efficient free-energy calculation methods. In general, ��* of an amphiphile can be divided into Image ID:d3cp03799a-t1.gif and Image ID:d3cp03799a-t2.gif, the nonpolar and electrostatic contributions, and the former is further divided into Image ID:d3cp03799a-t3.gif and Image ID:d3cp03799a-t4.gif which are the work of cavity formation process and the free energy change due to weak, attractive interactions between the solute molecule and surrounding solvent molecules. We demonstrate that ��* of the two amphiphilic solutes can be obtained accurately using a perturbation combining method, which relies on the exact expressions for Image ID:d3cp03799a-t5.gif and Image ID:d3cp03799a-t6.gif and requires no simulations of intermediate systems between the solute with strong, repulsive interactions and the solute with the van der Waals and electrostatic interactions. The decomposition of ��* gives us several physical insights including that ��* is an increasing function of T due to Image ID:d3cp03799a-t7.gif, that the contributions of hydrophilic groups to the temperature dependence of ��* are additive, and that the contribution of the van der Waals attraction to the solvation volume is greater than that of the electrostatic interactions.
en-copyright=
kn-copyright=

en-aut-name=TairaAoi
en-aut-sei=Taira
en-aut-mei=Aoi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Information Science, University of Hyogo
kn-affil=

affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=25
cd-vols=
no-issue=8
article-no=
start-page=104723
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220819
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Immune response to SARS-CoV-2 in severe disease and long COVID-19
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=COVID-19 is mild to moderate in otherwise healthy individuals but may nonetheless cause life-threatening disease and/or a wide range of persistent symptoms. The general determinant of disease severity is age mainly because the immune response declines in aging patients. Here, we developed a mathematical model of the immune response to SARS-CoV-2 and revealed that typical age-related risk factors such as only a several 10% decrease in innate immune cell activity and inhibition of type-I interferon signaling by autoantibodies drastil ally increased the viral load. It was reported that the numbers of certain dendritic cell subsets remained less than half those in healthy donors even seven months after infection. Hence, the inflammatory response was ongoing. Our model predicted the persistent DC reduction and showed that certain patients with severe and even mild symptoms could not effectively eliminate the virus and could potentially develop long COVID.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HaradaKouji
en-aut-sei=Harada
en-aut-mei=Kouji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=156
cd-vols=
no-issue=22
article-no=
start-page=221104
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220614
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Osmotic second virial coefficients for hydrophobic interactions as a function of solute size
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=To gain quantitative insight into how the overall strength of the hydrophobic interaction varies with the molecular size, we calculate osmotic second virial coefficients B for hydrophobic spherical molecules of different diameters �� in water based on molecular simulation with corrections to the finite-size and finite-concentration effects. It is shown that B?(&lt;0) changes by two orders of magnitude greater as �� increases twofold and its solute-size dependence is best fit by a power law B �� ��<jats:sup> ��</jats:sup> with the exponent �� ? 6, which contrasts with the cubic power law that the second virial coefficients of gases obey. It is also found that values of B for the solutes in a nonpolar solvent are positive but they obey the same power law as in water. A thermodynamic identity for B derived earlier [K. Koga, V. Holten, and B. Widom, J. Phys. Chem. B 119, 13391 (2015)] indicates that if B is asymptotically proportional to a power of ��, the exponent �� must be equal to or greater than 6. 
en-copyright=
kn-copyright=

en-aut-name=NaitoHidefumi
en-aut-sei=Naito
en-aut-mei=Hidefumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=3
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=4
cd-vols=
no-issue=1
article-no=
start-page=149
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20211022
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor. 
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HaradaKouji
en-aut-sei=Harada
en-aut-mei=Kouji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=125
cd-vols=
no-issue=23
article-no=
start-page=6296
end-page=6305
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=202168
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Ion Size Dependences of the Salting-Out Effect: Reversed Order of Sodium and Lithium Ions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=A general trend of the salting-out effect on hydrophobic solutes in aqueous solution is that the smaller the size of a dissolved ion, the larger the effect of reducing the solubility of a hydrophobe. An exception is that Li+, the smallest in alkali metal ions, has a notably weaker effect than Na+. To understand the reversed order in the cation series, we performed molecular dynamics simulations of aqueous solutions of salt ions and calculated the Setschenow coefficient of methane with the ionic radius of either a cation or an anion varied in a wide range. It is confirmed that the Setschenow coefficient is correlated with the packing fraction of salt solution, as observed in earlier studies, and also correlated with the partial molar volume of an ion. Analyses of correlation function integrals, packing fractions of solvation spheres, and orientations of water molecules surrounding an ion reveal the key differences in microscopic properties between the cation and anion series, which give rise to the reversed order in the cation series of the partial molar volumes of ions and ultimately that of the Setschenow coefficients.
en-copyright=
kn-copyright=

en-aut-name=KatsutoHiroyuki
en-aut-sei=Katsuto
en-aut-mei=Hiroyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkamotoRyuichi
en-aut-sei=Okamoto
en-aut-mei=Ryuichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=4
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=23
cd-vols=
no-issue=10
article-no=
start-page=5760
end-page=5772
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210323
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Two different regimes in alcohol-induced coil?helix transition: effects of 2,2,2-trifluoroethanol on proteins being either independent of or enhanced by solvent structural fluctuations
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Inhomogeneous distribution of constituent molecules in a mixed solvent has been known to give remarkable effects on the solute, e.g., conformational changes of biomolecules in an alcohol-water mixture. We investigated the general effects of 2,2,2-trifiuoroethanoE (TFE) on proteins/peptides in a mixture of water and TFE using melittin as a model protein. Fluctuations and Kirkwood-Buff integrals (KBIs) in the TFE-H2O mixture, quantitative descriptions of inhomogeneity, were determined by smallangle X-ray scattering investigation and compared with those in the aqueous solutions of other alcohols. The concentration fluctuation for the mixtures ranks as methanol < ethanol << TFE < tert-butanol < 1-propanol, indicating that the inhomogeneity of molecular distribution in the TFE-H2O mixture is unexpectedly comparable to those in the series of mono-ok. On the basis of the concentration dependence of KBIs between the TFE molecules, it was found that a strong attraction between the TFE molecules is not necessarily important to induce helix conformation, which is inconsistent with the previously proposed mechanism. To address this issue, by combining the KBIs and the helix contents reported by the experimental spectroscopic studies, we quantitatively evaluated the change in the preferential binding parameter of TFE to melittin attributed to the coil-helix transition. As a result, we found two different regimes on TFE-induced helix formation. In the dilute concentration region of TFE below similar to 2 M, where the TFE molecules are not aggregated among themselves, the excess preferential binding of TFE to the helix occurs due to the direct interaction between them, namely independent of the solvent fluctuation. In the higher concentration region above similar to 2 M, in addition to the former effect, the excess preferential binding is significantly enhanced by the solvent fluctuation. This scheme should be held as general cosoEvent effects of TFE on proteins/peptides.
en-copyright=
kn-copyright=

en-aut-name=OhgiHiroyo
en-aut-sei=Ohgi
en-aut-mei=Hiroyo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=NishikawaKeiko
en-aut-sei=Nishikawa
en-aut-mei=Keiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KogaYoshikata
en-aut-sei=Koga
en-aut-mei=Yoshikata
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=WesthPeter
en-aut-sei=Westh
en-aut-mei=Peter
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

affil-num=1
en-affil=Department of Chemistry, Graduate School of Science, Chiba University
kn-affil=

affil-num=2
en-affil=Department of Applied Chemistry, College of Life Sciences, Ritsumeikan University
kn-affil=

affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Graduate School of Science, Chiba University
kn-affil=

affil-num=5
en-affil=Department of Chemistry, The University of British Columbia
kn-affil=

affil-num=6
en-affil=Department of Biotechnology and Biomedicine, Technical University of Denmark
kn-affil=

affil-num=7
en-affil=Department of Chemistry, Graduate School of Science, Chiba University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=21
cd-vols=
no-issue=3
article-no=
start-page=1303
end-page=1310 
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210122
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Unveiling the Interaction Potential Surface between Drug-Entrapped Polymeric Micelles Clarifying the High Drug Nanocarrier Efficiency
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Polymeric micelles are invaluable media as drug nanocarriers. Although knowledge of an interaction between the micelles is a key to understanding the mechanisms and developing the superior functions, the interaction potential surface between drug-incorporated polymeric micelles has not yet been quantitatively evaluated due to the extremely complex structure. Here, the interaction potential surface between drug-entrapped polymeric micelles was unveiled by combining a small-angle scattering experiment and a model-potential-free liquid-state theory. Triblock copolymer composed of poly(ethylene oxide) and poly(propylene oxide) was investigated over a wide concentration range (0.5?10.0 wt %). Effects of the entrapment of a water-insoluble hydrophobic drug, cyclosporin A, on the interaction were explored by comparing the interactions with and without the drug. The results directly clarified the high drug carrier efficiency in terms of the interaction between the micelles. In addition, an investigation based on density functional theory provided a deeper insight into the monomer contribution to the extremely stable dispersion of the nanocarrier.
en-copyright=
kn-copyright=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MukaideSayaka
en-aut-sei=Mukaide
en-aut-mei=Sayaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=ChenZiqiao
en-aut-sei=Chen
en-aut-mei=Ziqiao
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=HigashiKenjirou
en-aut-sei=Higashi
en-aut-mei=Kenjirou
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

en-aut-name=MoribeKunikazu
en-aut-sei=Moribe
en-aut-mei=Kunikazu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=

affil-num=1
en-affil=Graduate School of Science, Chiba University
kn-affil=

affil-num=2
en-affil=Graduate School of Pharmaceutical Sciences, Chiba University
kn-affil=

affil-num=3
en-affil=Graduate School of Pharmaceutical Sciences, Chiba University
kn-affil=

affil-num=4
en-affil=Graduate School of Pharmaceutical Sciences, Chiba University
kn-affil=

affil-num=5
en-affil=College of Life Sciences, Ritsumeikan University
kn-affil=

affil-num=6
en-affil=Graduate School of Pharmaceutical Sciences, Chiba University
kn-affil=

affil-num=7
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=polymeric micelle
kn-keyword=polymeric micelle
en-keyword=drug entrapment
kn-keyword=drug entrapment
en-keyword=nanocarrier
kn-keyword=nanocarrier
en-keyword=interaction potential surface
kn-keyword=interaction potential surface
en-keyword=small-angle X-ray scattering
kn-keyword=small-angle X-ray scattering
en-keyword=model-potential-free liquid-state theory 
kn-keyword=model-potential-free liquid-state theory 
END

start-ver=1.4
cd-journal=joma
no-vol=10
cd-vols=
no-issue=1
article-no=
start-page=14711
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200907
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP) and long-term depression (LTD) of signal transmission form neural circuits and thus are thought to underlie learning and memory. These mechanisms are mediated by AMPA receptor (AMPAR) trafficking in postsynaptic neurons. However, the regulatory mechanism of bidirectional plasticity at excitatory synapses remains unclear. We present a network model of AMPAR trafficking for adult hippocampal pyramidal neurons, which reproduces both LTP and LTD. We show that the induction of both LTP and LTD is regulated by the competition between exocytosis and endocytosis of AMPARs, which are mediated by the calcium-sensors synaptotagmin 1/7 (Syt1/7) and protein interacting with C-kinase 1 (PICK1), respectively. Our result indicates that recycling endosomes containing AMPAR are always ready for Syt1/7-dependent exocytosis of AMPAR at peri-synaptic/synaptic membranes. This is because molecular motor myosin V-b constitutively transports the recycling endosome toward the membrane in a Ca2+-independent manner.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=HaradaKouji
en-aut-sei=Harada
en-aut-mei=Kouji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
en-keyword=Biophysical models
kn-keyword=Biophysical models
en-keyword=Long-term depression
kn-keyword=Long-term depression
en-keyword=Long-term potentiation
kn-keyword=Long-term potentiation
END

start-ver=1.4
cd-journal=joma
no-vol=9
cd-vols=
no-issue=
article-no=
start-page=5186
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=2019326
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Theoretical analysis on thermodynamic stability of chignolin
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil= Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=39
cd-vols=
no-issue=4
article-no=
start-page=202
end-page=217
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=20171108
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Application of reference-modified density functional theory: Temperature and pressure dependences of solvation free energy
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= 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.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=Mochizuki Kenji
en-aut-sei=Mochizuki 
en-aut-mei=Kenji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=2
en-affil=Co-Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=3
en-affil= Department of Physics, Keio University
kn-affil=

affil-num=4
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=

affil-num=5
en-affil= Division of Superconducting and Functional Materials, Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
en-keyword=3D-RISM theory
kn-keyword=3D-RISM theory
en-keyword=chignolin
kn-keyword=chignolin
en-keyword=classical density functional theory
kn-keyword=classical density functional theory
en-keyword=high-pressure unfolding
kn-keyword=high-pressure unfolding
en-keyword=hydrophobic solute
kn-keyword=hydrophobic solute
en-keyword=protein
kn-keyword=protein
en-keyword=temperature and pressure dependences of solvation free energy
kn-keyword=temperature and pressure dependences of solvation free energy
en-keyword=thermal denaturation
kn-keyword=thermal denaturation
END

start-ver=1.4
cd-journal=joma
no-vol=36
cd-vols=
no-issue=18
article-no=
start-page=1359
end-page=1369
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150531
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A solvation-free-energy functional: A reference-modified density functional formulation
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= 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. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules. 
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University,
kn-affil=

affil-num=2
en-affil=Department of Physics, Keio University,
kn-affil=

affil-num=3
en-affil=Department of Physics, Keio University,
kn-affil=
en-keyword=salvation-free-energy
kn-keyword=salvation-free-energy
en-keyword=classical density functional theory
kn-keyword=classical density functional theory
en-keyword=3D-RISM theory
kn-keyword=3D-RISM theory
en-keyword= water
kn-keyword= water
en-keyword=amino acid side-chain
kn-keyword=amino acid side-chain
en-keyword=chignolin
kn-keyword=chignolin
END

start-ver=1.4
cd-journal=joma
no-vol=144
cd-vols=
no-issue=22
article-no=
start-page=224104
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2016
dt-pub=20160610
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= 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.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=MaruyamaYutaka
en-aut-sei=Maruyama
en-aut-mei=Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MitsutakeAyori
en-aut-sei=Mitsutake
en-aut-mei=Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=KogaKenichiro
en-aut-sei=Koga
en-aut-mei=Kenichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=3
en-affil=Co-Design Team, Exascale Computing Project, RIKEN Advanced Institute for Computational Science
kn-affil=

affil-num=4
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=16
cd-vols=
no-issue=46
article-no=
start-page=25492
end-page=25497
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2014
dt-pub=20141017
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Model-potential-free analysis of small angle scattering of proteins in solution: insights into solvent effects on protein-protein interaction
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= To extract protein-protein interaction from experimental small-angle scattering of proteins in solutions using liquid state theory, a model potential consisting of a hard-sphere repulsive potential and the excess interaction potential has been introduced. In the present study, we propose a model-potential-free integral equation method that extracts the excess interaction potential by using the experimental small-angle scattering data without specific model potential such as the Derjaguin-Landau-Verwey-Overbeek (DLVO)-type model. Our analysis of experimental small-angle X-ray scattering data for lysozyme solution shows both the stabilization of contact configurations of protein molecules and a large activation barrier against the formation of the contact configurations in addition to the screened Coulomb repulsion. These characteristic features, which are not well-described by the DLVO-type model, are interpreted as solvent effects.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=IsogaiYasuhiro
en-aut-sei=Isogai
en-aut-mei=Yasuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

en-aut-name=NishikawaKeiko
en-aut-sei=Nishikawa
en-aut-mei=Keiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=

affil-num=3
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=

affil-num=4
en-affil=Department of Biotechnology, Toyama Prefectural University
kn-affil=

affil-num=5
en-affil=Graduate School of Advanced Integration Science, Chiba University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=200
cd-vols=
no-issue=Part.A
article-no=
start-page=42
end-page=46
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2014
dt-pub=20140401
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=A model-free method for extracting interaction potential between protein molecules using small-angle X-ray
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A small-angle X-ray scattering has been used to probe protein?protein interaction in solution. Conventional methods need to input modeled potentials with variable/invariable parameters to reproduce the experimental structure factor. In the present study, a model-free method for extracting the excess part of effective interaction potential between protein molecules in solutions over an introduced hard-sphere potential by using experimental data of small-angle X-ray scattering is presented on the basis of liquid-state integral equation theory. The reliability of the model-free method is tested by the application to experimentally derived structure factors for dense lysozyme solutions with different solution conditions [Javid et al., Phys. Rev. Lett. 99, 028101 (2007), Schroer et al., Phys. Rev. Lett. 106, 178102 (2011)]. The structure factors calculated from the model-free method agree well with the experimental ones. The model-free method provides the following picture of the lysozyme solution: these are the stabilization of contact-pair configurations, large activation barrier against their formations, and screened Coulomb repulsion between the charged proteins. In addition, the model-free method will be useful to verify whether or not a model for colloidal system is acceptable to describing protein?protein interaction.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=ImamuraHiroshi
en-aut-sei=Imamura
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=MoritaTakeshi
en-aut-sei=Morita
en-aut-mei=Takeshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=NishikawaKeiko
en-aut-sei=Nishikawa
en-aut-mei=Keiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=

affil-num=3
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=

affil-num=4
en-affil=Graduate School of Advanced integration Science, Chiba University
kn-affil=
en-keyword=Protein solutions
kn-keyword=Protein solutions
en-keyword=Lysozyme
kn-keyword=Lysozyme
en-keyword=Protein-protein interaction
kn-keyword=Protein-protein interaction
en-keyword=Liquid state theory
kn-keyword=Liquid state theory
en-keyword=Integral equation
kn-keyword=Integral equation
en-keyword=DLVO model
kn-keyword=DLVO model
END

start-ver=1.4
cd-journal=joma
no-vol=96
cd-vols=
no-issue=4-1
article-no=
start-page=042410
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=20171019
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Numerical calculation on a two-step subdiffusion behavior of lateral protein movement in plasma membranes
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A two-step subdiffusion behavior of lateral movement of transmembrane proteins in plasma membranes has been observed by using single-molecule experiments. A nested double-compartment model where large compartments are divided into several smaller ones has been proposed in order to explain this observation. These compartments are considered to be delimited by membrane-skeleton "fences" and membrane-protein "pickets" bound to the fences. We perform numerical simulations of a master equation using a simple two-dimensional lattice model to investigate the heterogeneous diffusion dynamics behavior of transmembrane proteins within plasma membranes. We show that the experimentally observed two-step subdiffusion process can be described using fence and picket models combined with decreased local diffusivity of transmembrane proteins in the vicinity of the pickets. This allows us to explain the two-step subdiffusion behavior without explicitly introducing nested double compartments.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=OkumotoAtsushi
en-aut-sei=Okumoto
en-aut-mei=Atsushi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=GotoHitoshi
en-aut-sei=Goto
en-aut-mei=Hitoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

en-aut-name=SekinoHideo
en-aut-sei=Sekino
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=

affil-num=3
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=

affil-num=4
en-affil= Department of Computer Science and Engineering, Graduate School of Engineering, Toyohashi University of Technology
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=19
cd-vols=
no-issue=5
article-no=
start-page=3370
end-page=3378
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=20190424
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Is F-1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= We present a chemomechanical network model of the rotary molecular motor F1-ATPase which quantitatively describes not only the rotary motor dynamics driven by ATP hydrolysis but also the ATP synthesis caused by forced reverse rotations. We observe a high reversibility of F1-ATPase, that is, the main cycle of ATP synthesis corresponds to the reversal of the main cycle in the hydrolysis-driven motor rotation. However, our quantitative analysis indicates that torque-induced mechanical slip without chemomechanical coupling occurs under high external torque and reduces the maximal efficiency of the free energy transduction to 40?80% below the optimal efficiency. Heat irreversibly dissipates not only through the viscous friction of the probe but also directly from the motor due to torque-induced mechanical slip. Such irreversible heat dissipation is a crucial limitation for achieving a 100% free-energy transduction efficiency with biological nanomachines because biomolecules are easily deformed by external torque.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=KlumppStefan
en-aut-sei=Klumpp
en-aut-mei=Stefan
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces
kn-affil=
en-keyword=F-1-ATPase
kn-keyword=F-1-ATPase
en-keyword=rotary molecular motor
kn-keyword=rotary molecular motor
en-keyword=chemomechanical network model
kn-keyword=chemomechanical network model
en-keyword=free-energy transduction efficiency
kn-keyword=free-energy transduction efficiency
en-keyword=ATP synthesis
kn-keyword=ATP synthesis
en-keyword=torque-induced mechanical slip
kn-keyword=torque-induced mechanical slip
END

start-ver=1.4
cd-journal=joma
no-vol=36
cd-vols=
no-issue=26
article-no=
start-page=2009
end-page=2011
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150731
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Erratum: "A solvation-free-energy functional: A reference-modified density functional formulation" [J. Comput. Chem. 2015, 36, 1359-1369].
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=Mitsutake Ayori
en-aut-sei=Mitsutake
en-aut-mei= Ayori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

en-aut-name=Maruyama  Yutaka
en-aut-sei=Maruyama
en-aut-mei=  Yutaka
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=

affil-num=1
en-affil= Department of Chemistry, Faculty of Science, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Physics, Keio University
kn-affil=

affil-num=3
en-affil=Department of Physics, Keio University
kn-affil=
END

start-ver=1.4
cd-journal=joma
no-vol=3
cd-vols=
no-issue=31
article-no=
start-page=12743
end-page=12750
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2013
dt-pub=20130507
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Effects of hydrophobic hydration on polymer chains immersed in supercooled water
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= A multiscale simulation of a hydrophobic polymer chain immersed in water including the supercooled region is presented. Solvent effects on the polymer conformation were taken into account via liquid?state density functional theory in which a free-energy functional model was constructed using a density response function of bulk water, determined from a molecular dynamics (MD) simulation. This approach overcomes sampling problems in simulations of high-viscosity polymer solutions in the deeply supercooled region. Isobars determined from the MD simulations of 4000 water molecules suggest a liquid?liquid transition in the deeply supercooled region. The multiscale simulation reveals that a hydrophobic polymer chain exhibits swelling upon cooling along isobars below a hypothesized second critical pressure; no remarkable swelling is observed at higher pressures. These observations agree with the behavior of a polymer chain in a Jagla solvent model that qualitatively reproduces the thermodynamics and dynamics of liquid water. A theoretical analysis of the results obtained from the multiscale simulation show that a decrease in entropy due to the swelling arises from the formation of a tetrahedral hydrogen bond network in the hydration shell.
en-copyright=
kn-copyright=

en-aut-name=SumiTomonari
en-aut-sei=Sumi
en-aut-mei=Tomonari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=

en-aut-name=SekinoHideo
en-aut-sei=Sekino
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=

affil-num=1
en-affil=Department of Chemistry, Okayama University
kn-affil=

affil-num=2
en-affil=Department of Computer Science and Engineering, Toyohashi University of Technology
kn-affil=
END