Eritoran inhibits S100A8-mediated TLR4/MD-2 activation and tumor growth by changing the immune microenvironment.

S100A8/A9 is a major component of the acute phase of inflammation, and appears to regulate cell proliferation, redox regulation and chemotaxis. We previously reported that S100A8/S100A9 are upregulated in the premetastatic lung. However, the detailed mechanisms by which S100A8 contributes to tumor progression have not been elucidated. In this study, we investigated the TLR4/MD-2 dependency by S100A8 on tumor progression. We found that S100A8 (2-89) peptide stimulated cell migration in a manner dependent on TLR4, MD-2 and MyD88. The S100A8 (2-89) peptide also activated p38 and NF-κB in TLR4-dependent manner. The peptide induced the upregulation of both IL-6 and Ccl2 in peritoneal macrophages obtained from wild-type mice, but not TLR4-deficient mice. We then investigated the responsible region of S100A8 for TLR4/MD-2 binding by a binding assay, and found that C-terminal region of S100A8 binds to TLR4/MD-2 complex. To further evaluate the TLR4 dependency on tumor microenvironment, Lewis lung carcinoma-bearing mice were treated with Eritoran, an antagonist of TLR4/MD-2 complex. We found that both tumor volume and pulmonary recruitment of myeloid-derived suppressor cells were reduced with the treatment of Eritoran for five consecutive days. Eritoran reduced the development of tumor vasculature, and increased tumor-infiltration of CD8(+) T-cells. Taken together, S100A8 appears to play a crucial role in the activation of the TLR4/MD-2 pathway and the promotion of a tumor growth-enhancing immune microenvironment.

A randomised, placebo-controlled, double-blind study of aprepitant in nondrinking women younger than 70 years receiving moderately emetogenic chemotherapy.

BACKGROUND: We evaluated the efficacy of aprepitant plus granisetron and an increased dose of dexamethasone in selected patients undergoing moderately emetogenic chemotherapy (MEC). METHODS: Nondrinking women <70 years undergoing MEC were randomly assigned to aprepitant (day 1, 125 mg; days 2 and 3, 80 mg) or placebo. Dexamethasone on days 1-3 was 12, 4, and 4 mg with aprepitant and 20, 8, and 8 mg with placebo. The primary end point was complete response (CR; no emesis or rescue therapy) during 120 h of the first cycle. Logistic regression analysis was performed to identify predictors of overall CR. RESULTS: Of the 94 patients enrolled, 91 were assessable. Most received carboplatin-based chemotherapy. In the aprepitant (n=45) and placebo (n=46) groups, the overall, acute (day 1), and delayed (days 2-5) CR rates were 62% and 52%, 98% and 96%, and 62% and 52%, respectively. Although not statistically significant, the overall CR rate was 10% higher in the aprepitant group. Both regimens were well tolerated. On multivariate analysis, advanced ovarian cancer (OR, 0.26 (0.10-0.72)) was independently associated with a lower CR. CONCLUSION: Even with an increased dose of dexamethasone, aprepitant seemed more effective than placebo in these selected patients undergoing MEC; however, delayed phase management remains a significant problem.

Hydration affects both harmonic and anharmonic nature of protein dynamics.

To understand the effect of hydration on protein dynamics, inelastic neutron-scattering experiments were performed on staphylococcal nuclease samples at differing hydration levels: dehydrated, partially hydrated, and hydrated. At cryogenic temperatures, hydration affected the collective motions with energies lower than 5 meV, whereas the high-energy localized motions were independent of hydration. The prominent change was a shift of boson peak toward higher energy by hydration, suggesting a hardening of harmonic potential at local minima on the energy landscape. The 240 K transition was observed only for the hydrated protein. Significant quasielastic scattering at 300 K was observed only for the hydrated sample, indicating that the origin of the transition is the motion activated by hydration water. The neutron-scattering profile of the partially hydrated sample was quite similar to that of the hydrated sample at 100 K and 200 K, whereas it was close to the dehydrated sample at 300 K, indicating that partial hydration is sufficient to affect the harmonic nature of protein dynamics, and that there is a threshold hydration level to activate anharmonic motions. Thus, hydration water controls both harmonic and anharmonic protein dynamics by differing means.

Persistent urticaria--urticarial reaction caused by late phase reaction?

In ordinary urticaria, individual lesions disappear within 24 hours. We encountered 3 patients who showed urticarial reactions lasting more than 24 hours. In all patients, skin biopsy revealed interstitial dermal edema and a perivascular infiltration predominated by eosinophils, without immunoglobulins or complement deposition, or endothelial fibrinoid degeneration. Their eosinophil counts and serum complement levels were within normal range. No proteinurea or joint pain was observed. They could not be controlled by any medications except for glucocorticoid. These findings indicate our cases are not ordinary urticaria, urticarial reaction accompanied by eosinophilia, urticarial vasculitis or delayed pressure urticaria. We recognize such urticarial reaction as a different clinical entity from the usual urticaria, and we speculate that this condition is caused by late phase reaction because of the clinical course and eosinophil infiltrations.

The effects of fatty acyl CoA esters on the formation of prostaglandin and arachidonoyl-CoA formed from arachidonic acid in rabbit kidney medulla microsomes.

Under physiological conditions, small amounts of free arachidonic acid (AA) are released from membrane phospholipids, and cyclooxygenase (COX) and acyl CoA synthetase (ACS) competitively act on this fatty acid to form prostaglandins (PGs) and arachidonoyl-CoA (AA-CoA). We have previously shown that palmitoyl-CoA (PA-CoA) shifts AA away from the COX pathway into the ACS pathway in rabbit kidney medulla at a low concentration of AA (5 microM, close to the physiological concentration of substrate). In the present study, we investigated the effects of stearoyl (SA)-, oleoyl (OA)- and linoleoyl (LA)- CoAs on the formation of PG and AA-CoA from 5microM AA in rabbit kidney medulla microsomes. The kidney medulla microsomes were incubated with 5microM [(14)C]-AA in 0.1 M-Tris/HCl buffer (pH 8.0) containing cofactors of COX (reduced glutathione and hydroquinone) and cofactors of ACS (ATP, MgCl(2)and CoA). After incubation, PG (as total PGs), AA-CoA and residual AA were separated by selective extraction using petroleum ether and ethyl acetate. SA- and OA-CoAs increased AA-CoA formation with a reduction of PG formation, as well as PA-CoA. On the other hand, LA-CoA decreased formation of both PG and AA-CoA. These results suggest that fatty acyl CoA esters can be regulators of PG and AA-CoA formation in kidney medulla under physiological conditions.

The regulation of prostaglandin and arachidonoyl-CoA formation from arachidonic acid in rabbit kidney medulla microsomes by palmitoyl-CoA.

Under physiological conditions, small amounts of free arachidonic acid (AA) are released from membrane phospholipids, and cyclooxygenase (COX) and acyl-CoA synthetase (ACS) competitively act on this fatty acid to form prostaglandins (PGs) and arachidonoyl-CoA (AA-CoA). In the present study, we investigated the effects of palmitic acid (PA) and palmitoyl-CoA (PA-CoA) on the PG and AA-CoA formation from high and low concentrations of AA (60 and 5 microM) in rabbit kidney medulla microsomes. The kidney medulla microsomes were incubated with 60 or 5 microM [14C]-AA in 0.1 M-Tris/HCl buffer (pH 8.0) containing cofactors of COX (reduced glutathione and hydroquinone) and cofactors of ACS (ATP, MgCl2 and CoA). After incubation, PG (as total PGs), AA-CoA and residual AA were separated by selective extraction using petroleum ether and ethyl acetate. PA (10-100 microM) had no effect on the PG and AA-CoA formation from either 60 or 5 microM AA. PA-CoA (10-100 microM) was without effect on the PG and AA-CoA formation from 60 microM AA, whereas it markedly decreased the PG formation (6-40%) and increased the AA-CoA formation (1.1-2.3-fold) from 5 microM AA, showing that the effects of PA-CoA on the PG and AA-CoA formation change depending on the AA concentration. These results suggest that PA-CoA, but not PA, may regulate the PG and AA-CoA formation at low substrate concentrations (close to the physiological concentration of AA), and that this in-vitro method using 5 microM AA may be useful for clarifying the homeostatic control of the metabolic fate of AA into these two enzymatic pathways.

A space-time structure determination of human CD2 reveals the CD58-binding mode.

We describe a procedure for a space-time description of protein structures. The method is capable of determining populations of conformational substates, and amplitudes and directions of internal protein motions. This is achieved by fitting static and dynamic NMR data. The approach is based on the jumping-among-minima concept. First, a wide conformational space compatible with structural NMR data is sampled to find a large set of substates. Subsequently, intrasubstate motions are sampled by using molecular dynamics calculations with force field energy terms. Next, the populations of substates are fitted to NMR relaxation data. By diagonalizing a second moment matrix, directions and amplitudes of motions are identified. The method was applied to the adhesion domain of human CD2. We found that very few substates can account for most of the experimental data. Furthermore, only two types of collective motions have high amplitudes. They represent transitions between a concave (closed) and flat (open) binding face and resemble the change upon counter-receptor (CD58) binding.

Molecular dynamics simulation shows large volume fluctuations of proteins.

In this paper we present a new approach to study the volume fluctuations of proteins. From a 1 ns molecular dynamics simulation, the volume fluctuation of human lysozyme has been calculated. We used two different ways for the calculation. In the first one, the volume fluctuation is extracted directly from the trajectory. For the second one, a newly developed formalism based on principal component analysis is used. The r.m.s. volume fluctuations obtained from the two analyses agree well with each other. The isothermal intrinsic compressibility was found to be larger than the one reported by experiment. The difference is discussed and suggested to exist in the assumed uncertainty of the compressibility of hydrated water to deduce the isothermal intrinsic compressibility from the experimental value. Spectral analysis shows that low-frequency dynamics dominate the total volume fluctuation. The same aspect is found in the study using principal component analysis. This low-frequency region is related to large and slow motions of proteins. Therefore a long time dynamics simulation is necessary to describe the volume fluctuations of proteins.

Simultaneous measurement of prostaglandin and arachidonoyl CoA formed from arachidonic acid in rabbit kidney medulla microsomes: the roles of Zn2+ and Cu2+ as modulators of formation of the two products.

Under physiological conditions, small amounts of free arachidonic acid (AA) is released from membrane phospholipids, and cyclooxygenase (COX) and acyl-CoA synthetase (ACS) act competitively on this fatty acid to form prostaglandins (PGs) and arachidonoyl-CoA (AA-CoA). To date, there is no information about the factors deciding the metabolic fate of free AA into these two pathways. In this study, we tried to establish a method for the simultaneous measurement of PG and AA-CoA synthesis from exogenous AA in microsomes from rabbit kidney medulla. The kidney medulla microsomes were incubated with [14C]-AA in 0.1 M-Tris/HCI buffer (pH 8.0) containing cofactors of COX (reduced glutathione and hydroquinone) and cofactors of ACS (ATP, MgCl2 and CoA). After incubation, PG (as total PGs), AA-CoA and residual AA were separated by selective extraction using petroleum ether and ethyl acetate. When 60 microM AA was used as the substrate, indomethacin (an inhibitor of COX) and triacsin C (an inhibitor of ACS) reduced only PG and AA-CoA formation, respectively. On the other hand, when 5 microM AA was used as the substrate, indomethacin and triacsin C came to increase significantly the AA-CoA and PG formation, respectively. Thus, the experiments utilizing indomethacin and triacsin C revealed that the incubation using 60 microM AA can simultaneously detect the changes in the activities of COX and ACS caused by drugs, while the incubation using 5 microM AA can detect the changes in the product formation elicited by the resulting shunt of AA. Further, using these incubation conditions, the effects of Zn2+ and Cu2+ on the PG and AA-CoA formation were examined. Zn2+ inhibited the AA-CoA synthesis from 60 microM AA without affecting the PG synthesis. In contrast, when 5 microM AA was used as the substrate, a significant increase in the PG formation was observed in the presence of this ion, indicating that drug actions on the PG formation from AA by the kidney medulla microsomes may change depending on the substrate concentration. On the other hand, Cu2+ increased PG synthesis and inhibited AA-CoA synthesis from both 60 and 5 microM AA. These results suggest that the simultaneous measurements of PG and AA-CoA formation by the kidney medulla microsomes under high (60 microM) and low (5 microM) substrate concentrations can investigate the direct and indirect actions of drugs on the COX and ACS activities, and are useful for clarifying the haemostatic control of the metabolic fate of AA into the two enzymatic pathways. Furthermore, this study showed that Zn2+ and Cu2+ can modulate PG and AA-CoA formation by affecting COX activity, ACS activity, and/or the AA flow into the two enzymatic pathways.

Investigating protein dynamics in collective coordinate space.

Currently, collective coordinates are commonly employed in order to examine protein dynamics. In recent studies, they have been successfully applied to finding functionally relevant motions, to investigating the physical nature of protein dynamics, to sampling of the conformational space and to the analysis of experimental data. Collective coordinates also have other possible applications.

Energy landscape of a native protein: jumping-among-minima model.

We have investigated energy landscape of human lysozyme in its native state by using principal component analysis and a model, jumping-among-minima (JAM) model. These analyses are applied to 1 nsec molecular dynamics trajectory of the protein in water. An assumption embodied in the JAM model allows us to divide protein motions into intra-substate and inter-substate motions. By examining intra-substate motions, it is shown that energy surfaces of individual conformational substates are nearly harmonic and mutually similar. As a result of principal component analysis and JAM model analysis, protein motions are shown to consist of three types of collective modes, multiply hierarchical modes, singly hierarchical modes, and harmonic modes. Multiply hierarchical modes, the number of which accounts only for 0.5% of all modes, dominate contributions to total mean-square atomic fluctuation. Inter-substate motions are observed only in a small-dimensional subspace spanned by the axes of multiplyhierarchical and singly hierarchical modes. Inter-substate motions have two notable time components: faster component seen within 200 psec and slower component. The former involves transitions among the conformational substates of the low-level hierarchy, whereas the latter involves transitions of the higher level substates observed along the first four multiply hierarchical modes. We also discuss dependence of the subspace, which contains conformational substates, on time duration of simulation.

Dependence of protein stability on the structure of the denatured state: free energy calculations of I56V mutation in human lysozyme.

Free energy calculations were carried out to understand the effect of the I56V mutation of human lysozyme on its thermal stability. In the simulation of the denatured state, a short peptide including the mutation site in the middle is employed. To study the dependence of the stability on the denatured-state structure, five different initial conformations, native-like, extended, and three random-coil-like conformations, were examined. We found that the calculated free energy difference, DeltaDeltaGcal, depends significantly on the structure of the denatured state. When native-like structure is employed, DeltaDeltaGcal is in good agreement with the experimental free energy difference, DeltaDeltaGexp, whereas in the other four models, DeltaDeltaGcal differs sharply from DeltaDeltaGexp. It is therefore strongly suggested that the structure around the mutation site takes a native-like conformation rather than an extended or random-coil conformation. From the free energy component analysis, it has been shown that free energy components originating from Lennard-Jones and covalent interactions dominantly determine DeltaDeltaGcal. The contribution of protein-protein interactions to the nonbonded component of DeltaDeltaGcal is about the same as that from protein-water interactions. The residues that are located in a hydrophobic core (F3, L8, Y38, N39, T40, and I89) contribute significantly to the nonbonded free energy component of DeltaDeltaGcal. We also propose a general computational strategy for the study of protein stability that is equally conscious of the denatured and native states.

Computational analysis of thermal stability: effect of Ile-->Val mutations in human lysozyme.

BACKGROUND: Free energy calculations are carried out to study the change of thermal stability caused by Ile23-->Val, Ile56-->Val, Ile89-->Val and Ile106-->Val mutations in human lysozyme. In order to examine the dependence of the free energy difference, DeltaDeltaG, on the denatured-state structure, extended and native-like conformations are employed as initial conformations in the denatured-state simulations. RESULTS: Calculated values of DeltaDeltaG for the mutations, Ile56-->Val, Ile89-->Val and Ile106-->Val, were in good agreement with experimental values when the native-like structure was employed in the respective denatured-state simulations. In the case of Ile23-->Val, a considerable difference between the calculated and experimental values of DeltaDeltaG was observed. CONCLUSIONS: The physical nature of Ile56-->Val, Ile89-->Val and Ile106-->Val mutations was rationally characterized by a free energy component analysis. It is suggested that the alpha domain in which Ile23 is included is considerably structured even in the denatured state.

Improved protein free energy calculation by more accurate treatment of nonbonded energy: application to chymotrypsin inhibitor 2, V57A.

We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nosé-Hoover equation are employed. The performance of the developed software package is demonstrated in the case of valine to alanine mutation of the 57th residue in chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable to experimental results. By the free energy component analysis, it is shown that leucine 51, arginine 65, arginine 67, and phenylalanine 69 residues contribute significantly to the total free energy shift, deltadeltaG. Among them, contribution from the hydrophilic arginine 67 residue, which is in close contact with the mutation site, is the largest. Structure around the mutation site is largely changed by the mutation. The structure change is caused mainly by two effects, hydrophobic interaction and short-range interaction along the sequence. Effects of Nosé-Hoover algorithm and Kirkwood reaction field are also discussed.

Transient damage to the axonal transport system without Wallerian degeneration by acute nerve compression.

The aim of this study was to examine whether acute nerve compression damages an axonal transport system based on microtubules and how the fibers recover after the compression. A 5-mm segment of the tibial nerve of male wistar rat was compressed with a specially designed clip. Functional recovery was assessed using Tibial Nerve Functional Index (TFI). Rats were sacrificed each day from Day 0 to Day 2 and every 2 days between Day 4 and Day 10. For immunohistochemical analysis of the tibial nerve, the proximal uncompressed, the middle compressed, and the distal uncompressed segments of each section were assessed under immunofluoroscent microscopy for anti-dynein, anti-tubulin, and anti-neurofilament antibodies staining. In rats whose tibial nerve was compressed by 25 g/mm2 of pressure for 5 min, staining of dynein and mirotubules in the compressed portion were obscure on Days 4-8, suggesting that the microtubules based axonal transport system was temporarily damaged, while neurofilaments were retained. In contrast, in the distal portion, anti-neurofilament staining showed no abnormality throughout the experimental period, indicating that Wallerian degeneration did not occur. We conclude that acute nerve compression can cause transient damage to the axonal transport system in nerve fibers without Wallerian degeneration.

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme.

Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations. For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by modes of motion external to the domains. To analyze the molecular dynamics trajectory, a principal component analysis tailored specifically to analyze interdomain motions is applied. A method based on the curl of the atomic displacements is described, which yields a sharp discrimination of domains, and which defines a unique interdomain screw-axis. Hinge axes are defined and classified as twist or closure axes depending on their direction. The methods have been tested on lysozyme. A remarkable correspondence was found between the first normal mode axis and the first principal mode axis, with both axes passing within 3 A of the alpha-carbon atoms of residues 2, 39, and 56 of human lysozyme, and near the interdomain helix. The axes of the first modes are overwhelmingly closure axes. A lesser degree of correspondence is found for the second modes, but in both cases they are more twist axes than closure axes. Both analyses reveal that the interdomain connections allow only these two degrees of freedom, one more than provided by a pure mechanical hinge.

Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis.

A comparison of a normal mode analysis and principal component analysis of a 200-ps molecular dynamics trajectory of bovine pancreatic trypsin inhibitor in vacuum has been made in order to further elucidate the harmonic and anharmonic aspects in the dynamics of proteins. An anharmonicity factor is defined which measures the degree of anharmonicity in the modes, be they principal modes or normal modes, and it is shown that the principal mode system naturally divides into anharmonic modes with peak frequencies below 80 cm-1, and harmonic modes with frequencies above this value. In general the larger the mean-square fluctuation of a principal mode, the greater the degree of anharmonicity in its motion. The anharmonic modes represent only 12% of the total number of variables, but account for 98% of the total mean-square fluctuation. The transitional nature of the anharmonic motion is demonstrated. The results strongly suggest that in a large subspace, the free energy surface, as probed by the simulation, is approximated by a multi-dimensional parabola which is just a rescaled version of the parabola corresponding to the harmonic approximation to the conformational energy surface at a single minimum. After 200 ps, the rescaling factor, termed the "normal mode rescaling factor," has apparently converged to a value whereby the mean-square fluctuation within the subspace is about twice that predicted by the normal mode analysis.

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space.

Normal mode analyses on the protein, bovine pancreatic trypsin inhibitor, in dihedral angle space and Cartesian coordinate space are compared. In Cartesian coordinate space it is found that modes of frequencies lower than 30 cm(-1) contribute 80% of the total mean-square fluctuation and are represented almost completely by motions in the dihedral angles. Bond angle and length fluctuations dominate in modes above 200 cm(-1), but contribute less than 2% to the total mean-square fluctuation. In the low-frequency modes a good correspondence between patterns of atomic displacements was found, but on average the root-mean-square fluctuations of the Cartesian coordinate modes are 13% greater than their dihedral angle counterparts. The main effect of fluctuations in the bond angles and lengths, therefore, is to allow the dihedral angles to become more flexible. As the important subspaces determined from the two methods overlap considerably, dihedral angle space analysis can be applied to proteins too large for Cartesian coordinate space analysis.

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.

A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.

Effect of solvent on collective motions in globular protein.

Two molecular dynamics simulations on bovine pancreatic trypsin inhibitor (BPTI), have been made, one in vacuum, the other in water, in order to assess the effect of the solvent water on collective motions. Principal component analysis has been performed to determine collective modes, the principal components, which are assumed to behave as effectively independent harmonic oscillators. Projection of the protein's motion in water onto the plane defined by the first two principal components shows a clustering effect in the trajectory, absent in the vacuum trajectory. This is thought to be due to many local minima in the free energy surface caused by solute-solvent interactions. In order to assess the viscous effect of the solvent, friction coefficients for the principal components were determined by analyzing their velocity correlation functions in terms of the Langevin equation for an independent damped oscillator. Consistent with this analysis is that all modes have friction coefficients centered on the value of 47 cm-1 in a range of +/- 10 cm-1. With this friction coefficient, all modes of effective frequencies below 23.5 cm-1 display overdamped motion. By assuming the harmonic approximation for the conformational energy surface for BPTI in vacuum to be valid for BPTI in water, and treating each mode as an independent damped oscillator with a friction coefficient of 47 cm-1, the shift to higher frequencies in the water spectrum relative to the vacuum spectrum could be almost exactly reproduced, indicating this shift is due solely to the viscous effect of the solvent. By analyzing the time correlation functions of the first four principal components it is found that they can be very well described as independent damped oscillators each with a friction coefficient of 47 cm-1.