Biomedical subjects

Yuichi Harano

Publications and source records attributed to Yuichi Harano.

11 recordsLinked to original sources

PubMed2006

Changes in thermodynamic quantities upon contact of two solutes in solvent under isochoric and isobaric conditions.

The changes in excess thermodynamic quantities upon the contact of two solutes immersed in a solvent are analyzed using the radial-symmetric and three-dimensional versions of the integral equation theory. A simple model mimicking a solute in water is employed. The solute-solute interaction energy is not included in the calculations. Under the isochoric condition, the solute contact always leads to a positive entropy change irrespective of the solute solvophobicity or solvophilicity. The energy change is negative for solvophobic solutes while it is positive for solvophilic ones. Under the isobaric condition, the contact of solvophobic solutes results in system-volume compression but that of solvophilic ones gives rise to expansion. Effects of the compression and expansion on the changes in enthalpy and entropy are enlarged with rising temperature. When the solute solvophobicity is sufficiently high, the entropy change (multiplied by the absolute temperature) can become negative due to the compression, except at low temperatures with the result of an even larger, negative enthalpy change. The expansion in the case of solvophilic solutes leads to a large, positive entropy change accompanied by an even larger, positive enthalpy change. The changes in enthalpy and entropy are strongly dependent on the temperature. However, the changes in enthalpy and entropy are largely cancelled out and the temperature dependency of the free-energy change is much weaker. The authors also discuss possible relevance to the enthalpy-entropy compensation experimentally known for a variety of physicochemical processes in aqueous solution such as protein folding.

Journal Article↗

PubMed2006

Morphometric approach to the solvation free energy of complex molecules.

We show that the solvation free energy of a complex molecule such as a protein can be calculated using only four geometrical measures of the molecular structure and corresponding thermodynamical coefficients. We compare results from this morphometric approach to those obtained by an elaborate statistical-mechanical theory in liquid state physics for a large variety of different structures of protein G and find excellent agreement. Since the computational time is drastically reduced, the new approach provides a practical and efficient way for calculating the solvation free energy which can be employed when this quantity has to be calculated for a large number of structures, as in a simulation study of protein folding.

Models, Chemical↗

PubMed2006

A theoretical analysis on hydration thermodynamics of proteins.

The hydration free energy (HFE) of several proteins modeled using the all-atom force field is calculated by employing the three-dimensional reference interaction site model theory, a recently developed integral equation theory of molecular solvation. The HFE is decomposed into the energetic and entropic components under the isochoric condition. The former comprises the protein-water interaction energy and the water reorganization energy arising from the structural changes induced in water. Each component is further decomposed into the nonelectrostatic and electrostatic contributions. It is found that the HFE is governed by the nonelectrostatic hydration entropy and the electrostatic hydration energy. The nonelectrostatic hydration entropy is almost exclusively ascribed to the translational entropy loss of water upon the protein insertion. It asymptotically becomes proportional to the excluded volume (EV) for water molecules as the protein size increases. The hydration energy is determined by the protein-water interaction energy which is half compensated by the water reorganization energy. These energy terms are approximately proportional to the water-accessible surface area (ASA). The energetic and entropic contributions are balanced with each other and the HFE has no apparent linear relation with the EV and ASA.

Biophysics↗

PubMed2006

Crucial importance of translational entropy of water in pressure denaturation of proteins.

We present statistical thermodynamics of pressure denaturation of proteins, in which the three-dimensional integral equation theory is employed. It is applied to a simple model system focusing on the translational entropy of the solvent. The partial molar volume governing the pressure dependence of the structural stability of a protein is expressed for each structure in terms of the excluded volume for the solvent molecules, the solvent-accessible surface area (ASA), and a parameter related to the solvent-density profile formed near the protein surface. It is argued that the entropic effect originating from the translational movement of water molecules plays critical roles in the pressure-induced denaturation. We also show that the exceptionally small size of water molecules among dense liquids in nature is crucial for pressure denaturation. An unfolded structure, which is only moderately less compact than the native structure but has much larger ASA, is shown to turn more stable than the native one at an elevated pressure. The water entropy for the native structure is higher than that for the unfolded structure in the low-pressure region, whereas the opposite is true in the high-pressure region. Such a structure is characterized by the cleft and/or swelling and the water penetration into the interior. In another solvent whose molecular size is 1.5 times larger than that of water, however, the inversion of the stability does not occur any longer. The random coil becomes relatively more destabilized with rising pressure, irrespective of the molecular size of the solvent. These theoretical predictions are in qualitatively good agreement with the experimental observations.

Entropy↗

PubMed2006

Pair-correlation entropy of hydrophobic hydration: decomposition into translational and orientational contributions and analysis of solute-size effects.

We develop an efficient method to evaluate the translational and orientational contributions to the solute-water pair-correlation entropy that is a major component of the hydration entropy. A water molecule is modeled as a hard sphere of diameter dS=0.28 nm in which a point dipole and a point quadrupole of tetrahedral symmetry are embedded. A hard sphere of diameter dM, a hydrophobic solute, is immersed at infinite dilution in the model water. The pair-correlation entropy is decomposed into the translational and orientational contributions in an analytical manner using the angle-dependent Ornstein-Zernike integral equation theory. The two contributions are calculated for solutes with a variety of sizes (0.6<or=dM/dS<or=30). The effects of the solute-water attractive interaction are also studied. As dM becomes larger, the percentage of the orientational contribution first increases, takes a maximum value at dM=DM (DM/dS depends on the strength of the solute-water attractive interaction and is in the range of 1.4-2), and then decreases toward a limiting value. The percentage of the orientational contribution reduces progressively as the solute-water attractive interaction becomes stronger. The physical origin of the maximum orientational restriction at dM=DM is discussed in detail.

Chemistry, Physical↗

PubMed2006

Fenofibrate, a peroxisome proliferator-activated receptor alpha agonist, reduces hepatic steatosis and lipid peroxidation in fatty liver Shionogi mice with hereditary fatty liver.

BACKGROUND AND AIMS: The fatty liver Shionogi (FLS) mouse, a unique model for nonalcoholic fatty liver disease (NAFLD), is an inbred strain that develops spontaneous hepatic steatosis without obesity or diabetes mellitus. Peroxisome proliferator-activated receptor (PPAR) alpha controls fatty acid metabolism. In the present study, we investigated the effect of fenofibrate, a PPARalpha agonist, on hepatic steatosis in FLS mice. METHODS: Thirteen-week-old FLS mice were fed a diet with 0.1% fenofibrate (w/w) for 12 days. The degree of hepatic steatosis was estimated by histological examination and hepatic triglyceride levels. Expression levels of genes involved in fatty acid turnover, including Acox1, Cpt1a, Fabp1, Acadl, and Acadm, were determined by Northern blot analyses. We measured levels of lipid peroxidation, glutathione, and anti-oxidative enzymes, such as superoxide dismutase, catalase, and glutathione peroxidase, in the liver. RESULT: Treatment of FLS mice with fenofibrate improved hepatic steatosis by activating expression of genes involved in fatty acid turnover and decreased hepatic lipid peroxidation. Fenofibrate increased the activity of catalase by upregulating its mRNA levels. CONCLUSION: Fenofibrate, which is currently used in therapy of hyperlipidemia, might also be useful for treating patients with NAFLD even in cases where NAFLD is not associated with obesity or diabetes mellitus.

Animals↗

PubMed2005

Translational-entropy gain of solvent upon protein folding.

We show that even in the complete absence of potential energies among the atoms in a protein-aqueous solution system, there is a physical factor that favors the folded state of the protein. It is a gain in the translational entropy (TE) of water originating from the translational movement of water molecules. An elaborate statistical-mechanical theory is employed to analyze the TE of water in which a protein or peptide with a prescribed conformation is immersed. It is shown that if the number of residues is sufficiently large, the TE gain is powerful enough to compete with the conformational-entropy loss upon folding. For protein G we have tested over 100 compact conformations generated by a computer simulation with the all-atom potentials as well as the native structure. A significant finding is that the largest TE is attained in the native structure. The translational movement of water molecules is quite effective in achieving the tight packing in the interior of a natural protein. These results are true only when the solvent is water whose molecular size is the smallest among the ordinary liquids in nature.

Computer Simulation↗

PubMed2004

PPARalpha ligands activate antioxidant enzymes and suppress hepatic fibrosis in rats.

Oxidative stress is a major pathogenetic factor in hepatic fibrosis. Peroxisome proliferator-activated receptor alpha (PPARalpha) is a nuclear receptor which is known to affect oxidative stress and PPARalpha ligands may have rescue effects on hepatic fibrosis. We tested this hypothesis using rat thioacetamide (TAA) models of liver cirrhosis. Rats were given intraperitoneal injection of TAA and treated with a diet containing one of the two PPARalpha ligands, Wy-14,643 (WY) or fenofibrate. WY treatment dramatically reduced hepatic fibrosis and also prevented the inhibition catalase of mRNA expression caused by TAA. Correspondingly, catalase activity increased in the TAA+WY group but decreased in the control TAA group. The antifibrotic action of fenofibrate in the TAA model was comparable with that of WY. PPARalpha ligands have an antifibrotic action in the rat TAA model of liver cirrhosis, probably due to an antioxidant effect of enhanced catalase expression and activity in the liver.

Animals↗

PubMed2004

Chemokine CCL20 enhances the growth of HuH7 cells via phosphorylation of p44/42 MAPK in vitro.

CCR6 is the receptor of chemokine CCL20. In the present study, we demonstrated that the surface expression of CCR6 was enhanced on the human HCC cell lines (HuH7, PLC/PRF/5, and HepG2) especially on HuH7 cells, but not on HLE or HLF cells. These HCC cell lines (HuH7, PLC/PRF/5, and HepG2) especially the HuH7 cells secreted a significant amount of CCL20 spontaneously, whereas HLE or HLF did not. Stimulation by CCL20 up-regulated the mRNA expression of CCR6 in HuH7 cells and significantly enhanced the growth of HuH7 cells. CCL20-stimulated growth of HuH7 cells was abrogated by the inhibition of downstream signal transduction pathway mediated by p44/42 MAPK, but not by p38 MAPK or SAPK/JNK. CCR6 expression in human HCC tissues was confirmed by RT-PCR. These results indicate that the growth of a proportion of human HCC cells may be mediated by CCL20-CCR6 axis, like HuH7 cells, in an autocrine or paracrine manner.

Base Sequence↗

PubMed2004

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.

We have studied the potential of mean force of two peptides, one known to adopt a beta-hairpin and the other an alpha-helical conformation in solution. These peptides are, respectively, residues 41-56 of the C-terminus (GEWTYDDATKTFTVTE) of the B1 domain of protein G and the 13 residue C-peptide (KETAAAKFERQHM) of ribonuclease A. Extensive canonical ensemble sampling has been performed using a parallel replica exchange method. The effective potential employed in this work consists of the OPLS all-atom force field (OPLS-AA) and an analytical generalized Born (AGB) implicit solvent model including a novel nonpolar solvation free energy estimator (NP). An additional dielectric screening parameter has been incorporated into the AGBNP model. In the case of the beta-hairpin, the nonpolar solvation free energy estimator provides the necessary effective interactions for the collapse of the hydrophobic core (W43, Y45, F52, and V54), which the more commonly used surface-area-dependent nonpolar model does not provide. For both the beta-hairpin and the alpha-helix, increased dielectric screening reduces the stability of incorrectly formed salt bridges, which tend to disrupt the formation of the hairpin and helix, respectively. The fraction of beta-hairpin and alpha-helix content we obtained using the AGBNP model agrees well with experimental results. The thermodynamic stability of the beta-hairpin from protein G and the alpha-helical C-peptide from ribonuclease A as modeled with the OPLS-AA/AGBNP effective potential reflects the balance between the nonpolar effective potential terms, which drive compaction, and the polar and hydrogen bonding terms, which promote secondary structure formation.

Amino Acid Sequence↗

PubMed2002

Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Residual dipolar couplings provide significant structural information for proteins in the solution state, which makes them attractive for the rapid determination of protein structures. While dipolar couplings contain inherent structural ambiguities, these can be reduced via an overlap similarity measure that insists that protein fragments assigned to overlapping regions of the sequence must have self-consistent structures. This allows us to determine a backbone fold (including the correct Calpha-Cbeta bond orientations) using only residual dipolar coupling data from one ordering medium. The resulting backbone structures are of sufficient quality to allow for modeling of sidechain rotamer states using a rotamer prediction algorithm and a force field employing the Surface Generalized Born continuum solvation model. We demonstrate the applicability of the method using experimental data for ubiquitin. These results illustrate the synergies that are possible between protein structural database and molecular modeling methods and NMR spectroscopy, and we expect that the further development of these methods will lead to the extraction of high resolution structural information from minimal NMR data.

Computer Simulation↗