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Biomedical subjects

Hiroaki Yamada

Publications and source records attributed to Hiroaki Yamada.

15 recordsLinked to original sources

Morphine can produce analgesia via spinal kappa opioid receptors in the absence of mu opioid receptors.

Previous studies have demonstrated the virtual lack of analgesia in mu opioid receptor knockout mice after systemic administration of morphine. Thus, it has been suggested that analgesic actions of morphine are produced via the mu opioid receptor, despite its ability to bind to kappa and delta receptors in vitro. However, it is not clear whether the results of these studies reflect the effect of morphine in the spinal cord. In the present study, we report study of the analgesic actions of spinally-administered morphine and other opioid receptor agonists in mu opioid receptor knockout and wild type mice. Morphine produced a dose-dependent antinociceptive effect in the tail flick test in the knockout mice, although higher doses were needed to produce antinociception than in wild type mice. The antinociceptive effect of morphine was completely blocked by naloxone (a non-selective opioid antagonist) and nor-binaltorphimine (nor-BNI, a selective kappa-opioid receptor antagonist), but not by naltrindole (a selective delta-opioid receptor antagonist). U-50,488H (a selective kappa-opioid receptor agonist) also produced a dose-dependent antinociceptive effect in knockout mice but presented lower analgesic potency in knockout mice than in wild type mice. Analgesic effects of [d-Pen2,d-Pen5]enkephalin (DPDPE, a selective delta-opioid receptor agonist) were observed in wild type mice but abolished in knockout mice. SNC80 (a selective delta-opioid receptor agonist) was not antinociceptive even in wild type mice. The present study demonstrated that morphine can produce thermal antinociception via the kappa opioid receptor in the spinal cord in the absence of the mu opioid receptor. Lower potency of U50,488H in mu opioid receptor knockout mice suggests interaction between kappa and mu opioid receptors at the spinal level.

Analgesics, Opioid↗

Rugged fitness landscapes of Kauffman models with a scale-free network.

We study the nature of the fitness landscapes of a "quenched" Kauffman's Boolean model with a scale-free network. We have numerically calculated the rugged fitness landscapes, the distributions, their tails, and the correlation between the fitness of local optima and their Hamming distance from the highest optimum found, respectively. We have found that (a) there is an interesting difference between random and scale-free networks such that the statistics of the rugged fitness landscapes is Gaussian for the random network while it is non-Gaussian with a tail for the scale-free network; (b) as the average degree [k] increases, there is a phase transition at the critical value of [k]=[k]c=2, below which there is a global order and above which the order goes away.

Algorithms↗

Exactly solvable scale-free network model.

We study a deterministic scale-free network recently proposed by Barabási, Ravasz, and Vicsek. We find that there are two types of nodes: the hub and rim nodes, which form a bipartite structure of the network. We first derive the exact numbers P (k) of nodes with degree k for the hub and rim nodes in each generation of the network, respectively. Using this, we obtain the exact exponents of the distribution function P (k) of nodes with k degree in the asymptotic limit of k-->infinity . We show that the degree distribution for the hub nodes exhibits the scale-free nature, P (k) proportional to k(-gamma) with gamma=ln 3/ln 2=1.584 962 , while the degree distribution for the rim nodes is given by P(k) proportional to e(-gamma'k) with gamma' =ln (3/2) =0.405 465 . Second, we analytically calculate the second-order average degree of nodes, d(-) . Third, we numerically as well as analytically calculate the spectra of the adjacency matrix A for representing topology of the network. We also analytically obtain the exact number of degeneracies at each eigenvalue in the network. The density of states (i.e., the distribution function of eigenvalues) exhibits the fractal nature with respect to the degeneracy. Fourth, we study the mathematical structure of the determinant of the eigenequation for the adjacency matrix. Fifth, we study hidden symmetry, zero modes, and its index theorem in the deterministic scale-free network. Finally, we study the nature of the maximum eigenvalue in the spectrum of the deterministic scale-free network. We will prove several theorems for it, using some mathematical theorems. Thus, we show that most of all important quantities in the network theory can be analytically obtained in the deterministic scale-free network model of Barabási, Ravasz, and Vicsek. Therefore, we may call this network model the exactly solvable scale-free network.

Journal Article↗

Vibrational modes and spectrum of oscillators on a scale-free network.

We study vibrational modes and spectrum of a model system of atoms and springs on a scale-free network where we assume that the atoms and springs are distributed as nodes and links of a scale-free network. To understand the nature of excitations with many degrees of freedom on the scale-free network, we adopt a particular model that we assign the mass M(i) and the specific oscillation frequency omega(i) of the ith atom and the spring constant K(ij) between the ith and jth atoms. We show that the density of states of the spectrum follows a scaling law P (omega(2)) proportional, variant (omega(2))(-gamma), where gamma = 3 and that as the number of nodes N is increasing, the maximum eigenvalue grows as fast as sqrt[N].

Journal Article↗

Intact glycation end products containing carboxymethyl-lysine and glyoxal lysine dimer obtained from synthetic collagen model peptide.

Advanced glycation end products (AGE) are accumulated in human tissues when long-lived proteins are glycated due to hyperglycemia and/or aging. In this study, we synthesized a collagen model peptide, Ac-(Pro-Hyp-Gly)(5)-Pro-Lys-Gly-(Pro-Hyp-Gly)(5)-Ala-NH(2) to investigate intact AGEs in peptides. The peptide formed a stable triple helix structure, and was subjected to glycation reactions with glucose, ribose and glyoxal. Besides carboxymethyl-lysine in the peptide, a conjugated form linked with glyoxal lysine dimer (GOLD) was detected upon treatment with glyoxal. This is the first example of intact glycation-derived dimers of peptides retaining intrinsic protein structures.

Amino Acid Sequence↗

Pressure-dissociable reversible assembly of intrinsically denatured lysozyme is a precursor for amyloid fibrils.

Although a diversity of proteins is known to form amyloid fibers, their common mechanisms are not clear. Here, we show that an intrinsically unfolded protein (U), represented by a disulfide-deficient variant of hen lysozyme with no tertiary structure, forms an amyloid-like fibril after prolonged incubation. Using variable pressure NMR along with sedimentation velocity, circular dichroism, and fluorescence measurements, we show that, before the fibril formation, the protein forms a pressure-dissociable, soluble assemblage (U'(n)) with a sedimentation coefficient of 17 S and a rich intermolecular beta-sheet structure. The reversible assemblage is characterized with a Gibbs energy for association of -23.3 +/- 0.8 kJ.mol(-1) and a volume increase of 52.7 +/- 11.3 ml.mol(-1) per monomer unit, and involves preferential interaction of hydrophobic residues in the initial association step. These results indicate that amyloid fibril formation can proceed from an intrinsically denatured protein and suggest a scheme N <==>U <==>U'(n)-->fibril as a common mechanism of fibril formation in amyloidogenic proteins, where two-way arrows represent reversible processes, one-way arrow represents an irreversible process, and N, U, and U'(n)represent, respectively, the native conformer, the unfolded monomeric conformer, and the soluble assemblage of unfolded conformers.

Amyloid↗

Inhibitory actions of endothelin-1 on pain processing.

Endothelin-1 (ET-1) in the central nervous system has been suggested to produce suppressive effects on pain transmission. We investigated the manner by which ET-1 exerts this action. ET-1 administered intracerebroventricularly produced a dose-dependent antinociceptive effect in a thermal pain test that utilized a spinal reflex to determine nociceptive thresholds. This suggested that the antinociceptive effect of ET-1 involved a descending pain inhibitory system. The antinociceptive effect was blocked by an ETA receptor antagonist but not by an ETB receptor antagonist, indicating that the action was mediated through the ETA receptor. Antagonists of opioid receptors, serotonin receptors, alpha-2 adrenergic receptors, oxytocin receptors, and dopamine receptors did not block the antinociceptive effect of ET-1. Thus, major descending inhibitory systems were probably not involved. The antinociceptive effect was blocked by intracerebroventricular administration of an alpha-1 adrenergic receptor antagonist. This indicated that the antinociceptive effect involved the activation of a supraspinal noradrenergic pathway, which in turn may activate a still unknown descending pain inhibitory system.

Adrenergic alpha-1 Receptor Antagonists↗

Infrequent cavity-forming fluctuations in HPr from Staphylococcus carnosus revealed by pressure- and temperature-dependent tyrosine ring flips.

Infrequent structural fluctuations of a globular protein is seldom detected and studied in detail. One tyrosine ring of HPr from Staphylococcus carnosus, an 88-residue phosphocarrier protein with no disulfide bonds, undergoes a very slow ring flip, the pressure and temperature dependence of which is studied in detail using the on-line cell high-pressure nuclear magnetic resonance technique in the pressure range from 3 MPa to 200 MPa and in the temperature range from 257 K to 313 K. The ring of Tyr6 is buried sandwiched between a beta-sheet and alpha-helices (the water-accessible area is less than 0.26 nm2), its hydroxyl proton being involved in an internal hydrogen bond. The ring flip rates 10(1)-10(5) s(-1) were determined from the line shape analysis of H(delta1, delta2) and H(epsilon1,epsilon2) of Tyr6, giving an activation volume DeltaV++ of 0.044 +/- 0.008 nm3 (27 mL mol(-1)), an activation enthalpy DeltaH++ of 89 +/- 10 kJ mol(-1), and an activation entropy DeltaS++ of 16 +/- 2 JK(-1) mol(-1). The DeltaV++) and DeltaH++ values for HPr found previously for Tyr and Phe ring flips of BPTI and cytochrome c fall within the range of DeltaV(double dagger) of 28 to 51 mL mol(-1) and DeltaH++ of 71 to 155 kJ mol(-1). The fairly common DeltaV++ and DeltaH++ values are considered to represent the extra space or cavity required for the ring flip and the extra energy required to create a cavity, respectively, in the core part of a globular protein. Nearly complete cold denaturation was found to take place at 200 MPa and 257 K independently from the ring reorientation process.

Bacterial Proteins↗

Pressure-induced unfolding of the molten globule of all-Ala alpha-lactalbumin.

Pressure-induced unfolding of a molten globule (MG) was studied in a residue-specific manner with (1)H-(15)N two-dimensional NMR spectroscopy using a variant of human alpha-lactalbumin (alpha-LA), in which all eight cysteines had been replaced with alanines (all-Ala alpha-LA). The NMR spectrum underwent a series of changes from 30 to 2000 bar at 20 degrees C and from -18 degrees C to 36 degrees C at 2000 bar, showing a highly heterogeneous unfolding pattern according to the secondary structural elements of the native structure. Unfolding began in the loop part of the beta-domain, and then extended to the remainder of the beta-domain, after which the alpha-domain began to unfold. Within the alpha-domain, the pressure stability decreased in the order: D-helix approximately 3(10)-helix > C-helix approximately B-helix > A-helix. The D-helix, C-terminal 3(10)-helix and a large part of B- and C-helices did not unfold at 2000 bar, even at 36 degrees C or at -18 degrees C. The results verify that the MG state consists of a mixture of variously unfolded conformers from the mostly folded to the nearly totally unfolded that differ in stability and partial molar volume. Not only heat but also cold denaturation was observed, supporting the view that the MG state is stabilized by hydrophobic interactions.

Alanine↗

Locally disordered conformer of the hamster prion protein: a crucial intermediate to PrPSc?

A crucial step for transformation of the normal cellular isoform of the prion protein (PrP(C)) to the infectious prion protein (PrP(Sc)) is thought to entail a previously uncharacterized intermediate conformer, PrP*, which interacts with a template PrP(Sc) molecule in the conversion process. By carrying out (15)N-(1)H two-dimensional NMR measurements under variable pressure on Syrian hamster prion protein rPrP(90-231), we found a metastable conformer of PrP(C) coexisting at a population of approximately 1% at pH 5.2 and 30 degrees C, in which helices B and C are preferentially disordered. While the identity is still unproven, this observed metastable conformer is most logically PrP* or a closely related precursor. The structural characteristics of this metastable conformer are consistent with available immunological and pathological information about the prion protein.

Animals↗

Equilibrium and pressure-jump relaxation studies of the conformational transitions of P13MTCP1.

The conformational transitions of a small oncogene product, p13(MTCP1), have been studied by high-pressure fluorescence of the intrinsic tryptophan emission and high-pressure 1D and 2D 1H-15N NMR. While the unfolding transition monitored by fluorescence is cooperative, two kinds of NMR spectral changes were observed, depending on the pressure range. Below approximately 200 MPa, pressure caused continuous, non-linear shifts of many of the 15N and 1H signals, suggesting the presence of an alternate folded conformer(s) in rapid equilibrium (tau<<ms) with the basic native structure. Above approximately 200 MPa, pressure caused a sharp decrease in the intensity of the folded proteins signals, while the peaks corresponding to disordered structures increased, yielding a free energy of unfolding change of 6.0 kcal/mol and associated volume change of -100 ml/mol, in agreement with the fluorescence result. Differential scanning calorimetry also reveals two transitions between 21 and 65 degrees C, confirming the existence of an additional species under mildly denaturing conditions. We report here a real-time observation of pressure-jump unfolding kinetics by 2D NMR spectroscopy on P13MTCP1 made possible due to its very long relaxation times at high pressure revealed by fluorescence studies. Within the dead-time after the pressure-jump, the NMR spectra of the native conformer changed to those of the transient conformational species, identified in the equilibrium studies, demonstrating the equivalence between a transient species and an equilibrium excited state. After these rapid spectral changes, the intensities of all of the individual 15N-1H cross-peaks decreased gradually, and those of the disordered structure increased, consistent with the slow relaxation to the unfolded form at this pressure. Rate constants of unfolding monitored at individual amide sites within the beta-barrel were similar to those obtained from fluorescence and from side-chain protons in the hydrophobic core region, consistent with nearly cooperative unfolding. However, some heterogeneity in the apparent unfolding rate constants is apparent across the sequence and can be understood as non-uniform effects of pressure on the unfolding rate constant due to non-uniform hydration.

Humans↗

Decreased thermodynamic stability as a crucial factor for familial amyloidotic polyneuropathy.

A single mutation in the wild-type transthyretin (WT TTR) such as V30M causes a familial amyloidotic polyneuropathy disease. Comparison of the three-dimensional crystal structures of WT and V30M does not tell much about the reason. High-pressure NMR revealed that at neutral pH both WT and V30M exist as equilibrium between the native tetramer and the dissociated/unfolded monomer. The native tetramer is highly stable in WT (deltaG(0)=104 kJ/mol at 37 degrees C, pH 7.1), but the stability is significantly reduced in V30M (deltadeltaG(0)=-18 kJ/mol), increasing the fraction of the unfolded monomer by a 1000-fold. Significant reduction of thermodynamic stability of WT TTR by mutation could be a crucial factor for familial amyloidotic polyneuropathy.

Amyloid Neuropathies, Familial↗

High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded.

Pressure-induced reversible conformational changes of sperm whale apomyoglobin have been studied between 30 bar and 3000 bar on individual residue basis by utilizing 1H/15N hetero nuclear single-quantum coherence two-dimensional NMR spectroscopy at pH 6.0 and 35 degrees C. Apomyoglobin showed a series of pressure-dependent NMR spectra as a function of pressure, assignable to the native (N), intermediates (I), molten globule (MG) and unfolded (U) conformers. At 30 bar, the native fold (N) shows disorder only in the F helix. Between 500 bar and 1200 bar, a series of locally disordered conformers I are produced, in which local disorder occurs in the C helix, the CD loop, the G helix and part of the H helix. At 2000 bar, most cross-peaks exhibit severe line-broadening, suggesting the formation of a molten globule, but at 3000 bar all the cross-peaks reappear, showing that the molten globule turns into a well-hydrated, mobile unfolded conformation U. Since all the spectral changes were reversible with pressure, apomyoglobin is considered to exist as an equilibrium mixture of the N, I, MG and U conformers at all pressures. MG is situated at 2.4+/-(0.1) kcal/mol above N at 1 bar and the unfolding transition from the combined N-I state to MG is accompanied by a loss of partial molar volume by 75+/-(3) ml/mol. On the basis of these observations, we postulate a theorem that the partial molar volume of a protein decreases in parallel with the loss of its conformational order.

Apoproteins↗

Anderson localized state as a predissipative state: irreversible emission of thermalized quanta from a dynamically delocalized state.

It was shown that localization in one-dimensional disordered (quantum) electronic system is destroyed against coherent harmonic perturbations and the delocalized electron exhibits an unlimited diffusive motion [Yamada and Ikeda, Phys. Rev. E 59, 5214 (1999)]. The appearance of diffusion implies that the system has potential for irreversibility and dissipation. In the present paper, we investigate dissipative property of the dynamically delocalized state, and we show that an irreversible quasistationary energy flow indeed appears in the form of a "heat" flow when we couple the system with another dynamical degree of freedom. In the concrete we numerically investigate dissipative properties of a one-dimensional tight-binding electronic system perturbed by time-dependent harmonic forces, by coupling it with a quantum harmonic oscillator or a quantum anharmonic oscillator. It is demonstrated that if the on-site potential is spatially irregular an irreversible energy transfer from the scattered electron to the test oscillator occurs. Moreover, the test oscillator promptly approaches a thermalized state characterized by a well-defined time-dependent temperature. On the contrary, such a relaxation process cannot be observed at all for periodic potential systems. Our system is one of the minimal quantum systems in which a distinct nonequilibrium statistical behavior is self-induced.

Journal Article↗

[Contribution of pharmacology for new drug application in Japan].

The Organization for Pharmaceutical Safety and Research (OPSR), Pharmaceuticals and Medical Devices Evaluation Center (PMDEC), National Institute of Health Sciences and Ministry of Health, Labour, and Welfare (MHLW) are working together on the new pharmaceutical approval process in Japan for appropriate scientific approaches. The Consultation Division of OPSR helps the pharmaceutical companies to answer find solutions to their concerns about non-clinical and clinical trials in the new pharmaceutical development process. After a new pharmaceutical application, PMDEC evaluates the quality, efficacy, and safety of each pharmaceutical compound in the review process. Final judgment for approval is made by MHLW. Pharmacological mechanisms examined in non-clinical trials would be useful for selection of the appropriate end-point in the clinical trials. For safety assessment, International Conference of Harmonization (ICH) Guideline on Safety Pharmacology Studies was officially notified. According to pharmacological data on safety, clinical investigators can better design clinical trials to prevent patients from suffering serious adverse events. To development new epoch pharmaceuticals, continuous progress on pharmacological research will be indispensable. Further discussion among all interested parties such as pharmacological researchers, medical doctors, companies, and regulatory sites will be necessary and useful to develop more appropriate approaches in the pharmaceutical development process.

Animals↗