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【Background】 Atrial fibrillation (AF) is an arrhythmia commonly encountered in clinical practice. There is a high risk of thromboembolism in patients with AF. Nonlinear analyses such as electroencephalogram (EEG), electrocardiogram (ECG), and respiratory movement have been used to quantify biological signals, and sample entropy (SampEn) has been employed as a statistical measure to evaluate complex systems. In this study, we examined the values of SampEn in ECG signals for patients with and without AF to measure the regularity and complexity. 【Methods】 ECG signals of lead II were recorded from 34 subjects without arrhythmia and 15 patients with chronic AF in a supine position. The ECG signals were converted into time-series data and SampEn was calculated. 【Results】 The SampEn values for the group without arrhythmia were 0.252 ± 0.114 [time lag (τ) = 1] and 0.533 ± 0.163 (τ = 5), and those for the chronic AF group were 0.392 ± 0.158 (τ = 1) and 0.759 ± 0.246 (τ = 5). The values of SampEn were significantly higher in the group with chronic AF than in the group without arrhythmia (P < 0.01 for τ = 1, P < 0.004 for τ = 5). The constructed three-dimensional vectors were plotted in time-delayed three-dimensional space. We used time lags of τ = 5 and τ = 1. The shape of the loops of the three-dimensional space was better for τ = 5. 【Conclusion】 The values of SampEn from ECG for chronic AF patients were higher than for subjects without arrhythmia, suggesting greater complexity for the time-series from chronic AF patients. SampEn is considered a new index for evaluating complex systems in ECG.

Pulse oximeters are used to noninvasively measure oxygen saturation in arterial blood (SaO2). Although arterial oxygen saturation measured by pulse oximeter (SpO2) is usually indicated in 1% increments, the value of SaO2 from arterial blood gas analysis is not an integer. We have developed a new pulse oximeter that can measure SpO2 to one digit after the decimal point. The values of SpO2 from the newly developed pulse oximeter are highly correlated with the values of SaO2 from arterial blood gas analysis (SpO2 = 0.899 × SaO2 + 9.944, r = 0.887, P < 0.0001). This device may help improve the evaluation of pathological conditions in patients.

The modified nucleotide base 7,8-dihydro-8-oxo-guanine (8-oxo-G) is one of the major sources of spontaneous mutagenesis. Nucleotide-sanitizing enzymes, such as the MutT homolog-1 (MTH1) and nudix-type motif 5 (NUDT5), selectively remove 8-oxo-G from the cellular pool of nucleotides. Previous studies showed that, although the syn conformation generally predominates in purine nucleotides with a bulky substituent at the 8-position, 8-oxo-dGMP binds to both MTH1 and NUDT5 in the anti conformation. This study was initiated to investigate the possibility that 8-oxo-dGMP itself may adopt the anti conformation. Molecular dynamics simulations of mononucleotides (dGMP, 8-oxo-dGMP) in aqueous solution were performed. 8-oxo-dGMP adopted the anti conformation as well as the syn conformation, and the proportion of adopting the anti conformation increased in the presence of metal ions. When 8-oxo-dGMP was in the anti conformation, a metal ion was located between the oxygen atom of phosphate and the oxygen atom at the 8-position of 8-oxo-G. The types of stable anti conformations of 8-oxo-dGMP differed, depending on the ionic radii and charges of coexisting ions. These data suggested a role for metal ions, other than as cofactors for the hydrolysis of the di- and tri-phosphate forms of mononucleotides; that the metal ions help retain the anti conformation of the N-glycosidic torsion angle of 8-oxo-dGMP to promote the binding between the 8-oxo-G deoxynucleotide and the nucleotide-sanitizing enzymes.

Background Binding affinity for human serum albumin (HSA) is one of the most important factors affecting the distribution and free blood concentration of many ligands. The effect of fatty acids (FAs) on HSA-ligand binding has long been studied. Since the elucidation of the 3-dimensional structure of HSA, molecular simulation approaches have been applied to studies of the structure–function relationship of HSA–FA binding. Scope of review We review current insights into the effects of FA binding on HSA, focusing on the biophysical insights obtained using molecular simulation approaches such as docking, molecular dynamics (MD), and binding free energy calculations. Major conclusions Possible conformational changes on binding of FA molecules to HSA have been observed through MD simulations. High- and low-affinity FA-binding sites on HSA have been identified based on binding free energy calculations. The relationship between the warfarin binding affinity of HSA and FA molecules has been clarified based on the results of simulations of multi-site FA binding that cannot be experimentally observed. General significance Molecular simulation approaches have great potentials to provide detailed biophysical insights into HSA as well as the effects of the binding of FAs or other ligands to HSA. This article is part of a Special Issue entitled Serum Albumin.

Objectives The present study investigated prognostic indicators, including clinicopathological and preoperative hematological factors, and developed a prognostic factor-based risk stratification model in bladder cancer patients treated with radical cystectomy. Methods Data were collected from 249 consecutive bladder cancer patients treated with radical cystectomy without neoadjuvant therapy. Prognostic values of the preoperative hematological parameters, along with the patients' clinicopathological parameters were evaluated. A risk stratification model was developed to predict disease-specific survival after radical cystectomy using the regression coefficients of multivariate analysis. Results In the multivariate analysis, preoperative hemoglobin and C-reactive protein levels, as well as the pathological factors of T stage, positive surgical margin and lymph node metastasis, were independently predictive of disease-specific survival. Low hemoglobin ( 0.5 mg/dL), extravesical T stage (≥pT3a) and positive surgical margin were independent predictors of poor disease-specific survival. The risk stratification model showed significant differences in disease-specific survival between the three subgroups. Conclusions This is the first report to show the significance of combining preoperative hemoglobin with the pathology of radical cystectomy specimens as an independent predictor for disease-specific survival, and it also represents the largest contemporary series to date demonstrating that two types of preoperative hematological disorders, assessed by hemoglobin and C-reactive protein, are independent predictors in bladder cancer patients treated with radical cystectomy. Our risk stratification model could provide physicians with useful prognostic information for identifying patients who might be candidates for multimodal treatments.

Pulse oximeters are used to noninvasively measure oxygen saturation in arterial blood (SaO2). Although arterial oxygen saturation measured by pulse oximeter (SpO2) is usually indicated in 1% increments, the value of SaO2 from arterial blood gas analysis is not an integer. We have developed a new pulse oximeter that can measure SpO2 to one digit after the decimal point. The values of SpO2 from the newly developed pulse oximeter are highly correlated with the values of SaO2 from arterial blood gas analysis (SpO2 = 0.899 × SaO2 + 9.944, r = 0.887, P < 0.0001). This device may help improve the evaluation of pathological conditions in patients.

Human serum albumin (HSA) binds with drugs and fatty acids (FAs). This study was initiated to elucidate the relationship between the warfarin binding affinity of HSA and the positions of bound FA molecules. Molecular dynamics simulations of 11 HSA-warfarin-myristate complexes were performed. HSA-warfarin binding free energy was then calculated for each of the complexes by the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method. The results indicated that the magnitude of the binding free energy was smaller in HSA-warfarin complexes that had 4 or more myristate molecules than in complexes with no myristate molecules. The unfavorable effect on the HSA-warfarin binding affinity was caused sterically by the binding of a myristate molecule to the FA binding site closest to the warfarin binding site. On the other hand, the magnitude of HSA-warfarin binding free energy was largest when 3 myristate molecules were bound to the high-affinity sites. The strongest HSA-warfarin binding was attributable to favorable entropic contribution related to larger atomic fluctuations of the amino acid residues at the warfarin binding site. In the binding of 2 myristate molecules to the sites with the highest and second-highest affinities, allosteric modulation that enhanced electrostatic interactions between warfarin and some of the amino acid residues around the warfarin binding site was observed. This study clarified the structural and energetic properties of steric/allosteric effects of FAs on the HSA-warfarin binding affinity and illustrated the approach to analyze protein-ligand interactions in situations such that multiple ligands bind to the other sites of the protein.

Human serum albumin (HSA) has seven common fatty acid (FA) binding sites. In this study, we used the molecular mechanics Poisson-Boltzmann surface area method to identify high affinity FA binding sites on HSA in terms of binding free energy. Using multiple HSA-FA (myristate, palmitate) complex models constructed by molecular dynamics simulations, two methods were performed in molecular mechanics Poisson-Boltzmann surface area, the "three-trajectory method" and the "single-trajectory method". The former, which is less precise than the latter but may be more accurate as it includes the effects of conformational change upon binding, was used to classify high and low affinity sites. As a result, Sites 2, 4, and 5 were identified as high affinity sites for both FAs. The latter method, which is precise because energies are calculated from snapshots of the same trajectory for HSA-FAcomplex, was performed to compare the magnitude of binding free energy for these sites. The order of magnitude was 5>4>2, identical to that of a previous publication by others. In this way, a combination of the two methods was effectively used to identify high affinity sites. This study therefore provides an insight into the quantitative identification of high affinity FA binding sites on HSA.

Previous studies have reported that the respiratory cycle of healthy newborns is more irregular during active sleep. This study aimed to apply non-linear analysis to examine the irregularity of respiratory movement in newborns at different sleep states. The respiratory movement signals from an abdominal band during quiet and active sleep were analyzed using approximate entropy (ApEn). The breathing interval of active sleep was significantly shorter than that of quiet sleep [1.30 (0.17) s vs. 1.58 (0.11) s; (P < 0.03)]. The ApEn of respiratory movements during active sleep were significantly larger than that during quiet sleep [0.785 (0.135) s vs. 0.678 (0.083) s; (P < 0.05)]. We found that the ApEn of respiratory movement in healthy newborns could detect irregularities in respiration during sleep.

This study is aimed at constructing the neurophysiological basis for determining the characteristic features of cerebral motor disturbance in representative cerebral palsy (CP) types using topographical S-SEPs technology. Median-nerve stimulated S-SEPs (MN-SSEPs) were examined for 23 patients with four representative types of cerebral palsy: 6 athetotic (including 3 patients due to hypoxic-ischemic encephalopathy (HIE) and 3 to kernicterus), 7 hemiplegic, 5 diplegic and 5 tetraplegic types, and 13 normal controls. In HIE group of athetotic CP, frontal N30 specifically showed severe amplitude reduction or abolishment. In hemiplegic CP, both N20 and N30 on the affected cerebral side tended either to disappear or to be normally evoked at the same time, and their mean amplitudes declined severely. In diplegic CP, the amplitudes of subcortical N18 and parietal N20 were not small but significantly enlarged. N30 amplitude stayed within normal. The reason for this unexpected enlargement of N18 and N20 is unclear, but may be partly due to premature birth which caused abnormally abundant dendritic spine due to absence from perinatal normal spine elimination in the brainstem. In several quadriplegic patients, both N20 and N30 disappeared. The mean amplitude of N30 severely decreased. In conclusion, topographical results of N18, N20 and N30 may basically suggest the underlying involvement of nervous structures in CP according to their representative type.

Human serum albumin (HSA) binds with fatty acids under normal physiologic conditions. To date, there is little published information on the tertiary structure of HSA-fatty acid complex in aqueous solution. In the present study, we used molecular dynamics (MD) simulations to elucidate possible structural changes of HSA brought about by the binding of fatty acids. Both unliganded HSA and HSA-fatty acid complex models for MD calculations were constructed based on the X‐ray crystal structures. Five myristates (MYRs) were bound in the HSA-fatty acid complex model. In the present MD study, the motion of domains I and III caused by the binding of MYR molecules increased the radius of gyration of HSA. Root‐mean‐square fluctuations from the MD simulations revealed that the atomic fluctuations of the specific amino acids at drug‐binding site I that can regulate the drug‐binding affinity were increased by the binding of MYR molecules. Primary internal motions, characterized by the first three principal components, were observed mainly at domains I and III in the principal component analysis for trajectory data. The directional motion projected on the first principal component of unliganded HSA was conserved in HSA-MYR complex as the third principal directional motion with higher frequency. However, the third principal directional motion in unliganded HSA turned into the first principal directional motion with lower frequency in the HSA-MYR complex. Thus, the present MD study provides insights into the possible conformational changes of HSA caused by the binding of fatty acids. Proteins 2006. © 2006 Wiley‐Liss, Inc.

This paper reports a protein-simulation grid that uses grid remote procedure calls (GridRPCs)to a special-purpose cluster machine for molecular dynamics simulations. The grid was implemented using Ninf-G, Torque, LAM, and the Globus Toolkit. To avoid the inefficiency of a single GridRPC session using all the nodes of the cluster, we designed the grid so that it works efficiently when multiple GridRPC sessions share the cluster. This was done by putting the dedicated nodes(PCs with special computation boards)under the management of the Torque system, thus enabling the manager to dynamically configure a cluster with the requested number of dedicated nodes. In addition, a new job type was added to the Globus toolkit and new backend procedure was added to Ninf-G. The Ninf-G stub was separated from processes that actually perform the force evaluation on the dedicated nodes. Simulations for two proteins gave promising results. Simulations performed using a four-node cluster and a 100-Mbps LAN for GridRPC sessions were 4.6-17.0 times faster than the same simulation performed on the local client PC, while their communication overhead was less than 20% of total execution time. Even when the the four-node cluster machine was shared between two distinct simulations of proteins, the two GridRPC communications did not interfere with each other. This showed the efficacy of multiple GridRPC sessions.

Large-scale SCF calculations require more accurate numerical results. We investigated numerical accuracy on various Fm(z) evaluation methods. We found that the polynomial of z, which are often used for the Taylor series expansion and the Chebyshev approximation in molecular orbital programs, contains unexpectedly large numerical errors even if a polynomial degree is cubic. The numerical accuracy is allowable for small molecules, but may be insufficient for large molecules. On the other hand, the polynomial of δ, which requires only one more calculation step than that of z, maintains sufficient numerical accuracy because round-off errors are hardly propagated in the polynomial of δ.

This article deals with the Ewald summation method for efficiently handling contributions from periodic images in the framework of the fast multipole method (FMM). Although there have already been several reports regarding this method, the given formulas have been slightly different, thus leading to possible confusion. In this study, the summation formula for arbitrary lattice vectors is derived independently to show that this formula is identical to that of the cubic cell of Figueirido et al. (J Chem Phys 1997, 106, 9835 and J Chem Phys 107, 7002). The correctness of the formula is confirmed by numerical tests carefully designed for the verification. In addition, a precise numerical method is proposed for subtracting the contributions of neighbor cells, which is a necessary operation in periodic FMM. Furthermore, an optimal choice is given for the parameters that control the convergence behavior of the summation formula. It is shown by numerical tests for a 50,000-particle system that a method with double-precision numbers gives force accuracies of 7, 11, and 14 digits when the degrees of expansion are 8, 16, and 32, respectively. These results indicate not only the correctness of the summation formula but also the effectiveness of the careful subtraction method. It is also shown that, at most, only 0.1% of the total cost of the force evaluation can be attributed to the summation. As a result, using the choice for parameters, the contributions from distant images can be taken into account with great precision at extremely low computational costs. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1075–1087, 2000

ABSTRACT: Application of molecular dynamics MD simulations to large systems, such as biological macromolecules, is severely limited by the availability of computer resources. As the size of the system increases, the number of . nonbonded forces Coulombic and van der Waals interactions to be evaluated 2 . increases as O N , where N is the number of particles in the system. The force evaluation consumes more than 99% of the CPU time in an MD simulation involving over 10,000 particles. Hence, the major target for reduction of the CPU time should be acceleration of the calculation of nonbonded forces. For this purpose, we developed a custom processor for calculating nonbonded . interactions and a scalable plug-in machine to a workstation , the MD Engine, in which numbers of the custom processors work in parallel. The processor has a pipeline architecture to calculate the total nonbonded force using the coordinates, electric charge, and species of each particle broadcast by the host

Characteristics of the methods for estimating individual pharmacokinetic parameters are compared both theoretically and numerically. The methods examined represent the range of most of modern methods and include the ordinary least squares, iteratively reweighted least squares, extended least squares, generalized least squares, maximum quasi-likelihood and its extended scheme, and minimum relative entropy methods. When the function representing the mean itself is used as a variance function, which may be then related to a Poisson distribution, the iteratively reweighted least squares estimator and maximum quasi-likelihood estimator are both identical to that of the minimum relative entropy method. These methods work by minimizing a kind of relative entropy between observed data and corresponding theoretical values. Furthermore, these methods guarantee agreement between the sum of the observed values and the estimate of the sum. This relation does not hold in general for the other estimators. The sum can, in a sense, be viewed as an approximation of the area under the curve. In addition, it is shown by numerical study that these methods are robust against the misspecification of the variance model and work as effectively as such sophisticated methods as the extended least squares, generalized least squares, and maximum extended quasi-likelihood methods. These sophisticated methods require complicated numerical optimization techniques and should be used only in cases where the estimation of the variance function is demanded. In the other cases, the method of minimum relative entropy or its equivalent is sufficient or even preferable for estimating individual pharmacokinetic parameters.

The 6-min walk test (6MWT) has been used to examine subjective dyspnea, predict mortality and measure clinical outcomes in studies of patients with chronic pulmonary or heart disease. Although the 6MWT is useful to assess the general ability to perform daily physical activity, it is difficult to evaluate time-dependent responses. To improve the 6MWT, we devised a new index, which is the number of steps walked per second (NSPS). We performed the 6MWT in 11 healthy subjects and 7 patients with chronic obstructive pulmonary disease (COPD) and calculated the NSPS. The mean NSPS was significantly higher in the healthy subjects than in the COPD patients, while the coefficient of variation of the NSPS was significantly smaller in healthy subjects compared with COPD patients. Calculation of the NSPS was useful to evaluate the walking pattern. This modified 6MWT may be helpful for assessing the efficacy of rehabilitation and drug therapy for COPD.

For estimating pharmacokinetic parameters, we introduce the minimum relative entropy (MRE) method and compare its performance with least squares methods. There are several variants of least squares, such as ordinary least squares (OLS), weighted least squares, and iteratively reweighted least squares. In addition to these traditional methods, even extended least squares (ELS), a relatively new approach to nonlinear regression analysis, can be regarded as a variant of least squares. These methods are different from each other in their manner of handling weights. It has been recognized that least squares methods with an inadequate weighting scheme may cause misleading results (the "choice of weights" problem). Although least squares with uniform weights, i.e., OLS, is rarely used in pharmacokinetic analysis, it offers the principle of least squares. The objective function of OLS can be regarded as a distance between observed and theoretical pharmacokinetic values on the Euclidean space RN, where N is the number of observations. Thus OLS produces its estimates by minimizing the Euclidean distance. On the other hand, MRE works by minimizing the relative entropy which expresses discrepancy between two probability densities. Because pharmacokinetic functions are not density function in general, we use a particular form of the relative entropy whose domain is extended to the space of all positive functions. MRE never assumes any distribution of errors involved in observations. Thus, it can be a possible solution to the choice of weights problem. Moreover, since the mathematical form of the relative entropy, i.e., an expectation of the log-ratio of two probability density functions, is different from that of a usual Euclidean distance, the behavior of MRE may be different from those of least squares methods. To clarify the behavior of MRE, we have compared the performance of MRE with those of ELS and OLS by carrying out an intensive simulation study, where four pharmaco-kinetic models (mono- or biexponential, Bateman, Michaelis-Menten) and several variance models for distribution of observation errors are employed. The relative precision of each method was investigated by examining the absolute deviation of each individual parameter estimate from the known value. OLS is the best method and MRE is not a good one when the actual observation error magnitude conforms to the assumption of OLS, that is, error variance is constant, but OLS always behaves poorly with the other variance models. On the other hand, MRE performs better than ELS and OLS when the variance of observation is proportional to its mean. In contrast, ELS is superior to MRE and OLS when the standard deviation of observation is proportional to its mean. In either case the difference between MRE and ELS is relatively small. Generally, the performance of MRE is comparable to that of ELS. Thus MRE provides as reliable a method as ELS for estimating pharmacokinetic parameters.

Special-purpose parallel machines that are plugged into a workstation to accelerate molecular dynamics (MD) simulations are attracting a considerable amount of interest. These machines comprise scalable homogeneous multiprocessors for calculating nonbonded forces (Coulombic and van der Waals forces), which consume more than 99% of the central processing unit (CPU) time in standard MD simulations. Each processor element in the machine has a pipeline architecture to calculate the total nonbonded force exerted on a particle by all of the other particles using information regarding the coordinates, the electric charge, and the species of each particle broadcast by the host computer. The processor then sends the calculated force back to the host computer. This article addresses the precision of the calculated nonbonded forces in the design of a processor LSI with minimal complexity. The precision of the arithmetic inside the processor that is required to calculate forces for MD simulations using Verlet's procedure was critically evaluated. Forward and backward error analysis, coupled with numerical MD experiments on one-dimensional systems, was performed, and the following results were obtained: (1) Each element of the position vector which the processor receives from the host computer should have a precision of at least 25 bits; and (2) the pairwise forces should be calculated using floating point numbers with at least 29 bits of mantissa in the processor. Calculation of a pairwise force, which involves second-order polynomial interpolation using a table-driven algorithm, requires a key which contains a duplicate of at least 11 most significant bits of mantissa of the squared pairwise distance. The final result was that (3) the total force that acts on a particle, which is obtained by summing the forces exerted by all of the other particles, should be calculated using an accumulator that has a mantissa of at least 48 bits. © 1995 by John Wiley & Sons, Inc.

The present study investigated prognostic indicators, including clinicopathological and preoperative hematological factors, and developed a prognostic factor-based risk stratification model in bladder cancer patients treated with radical cystectomy.Data were collected from 249 consecutive bladder cancer patients treated with radical cystectomy without neoadjuvant therapy. Prognostic values of the preoperative hematological parameters, along with the patients' clinicopathological parameters were evaluated. A risk stratification model was developed to predict disease-specific survival after radical cystectomy using the regression coefficients of multivariate analysis.In the multivariate analysis, preoperative hemoglobin and C-reactive protein levels, as well as the pathological factors of T stage, positive surgical margin and lymph node metastasis, were independently predictive of disease-specific survival. Low hemoglobin (10.5 g/dL), a high C-reactive protein (0.5 mg/dL), extravesical T stage (≥pT3a) and positive surgical margin were independent predictors of poor disease-specific survival. The risk stratification model showed significant differences in disease-specific survival between the three subgroups.This is the first report to show the significance of combining preoperative hemoglobin with the pathology of radical cystectomy specimens as an independent predictor for disease-specific survival, and it also represents the largest contemporary series to date demonstrating that two types of preoperative hematological disorders, assessed by hemoglobin and C-reactive protein, are independent predictors in bladder cancer patients treated with radical cystectomy. Our risk stratification model could provide physicians with useful prognostic information for identifying patients who might be candidates for multimodal treatments.

Objectives Despite the surgical curability of renal cell carcinoma (RCC) and upper urinary tract urothelial carcinoma (UUT-UC), post-nephrectomy chronic kidney disease (CKD) continues to be a cause of concern. We investigated the correlation between the expression of apoptotic regulatory molecules in the nephrectomized, noncancerous cortex, as well as CKD progression and CKD-related mortality. Materials and methods Fas and Bcl-2 mRNA and protein expression in surgically resected specimens from 100 patients with RCC and UUT-UC were determined. The estimated glomerular filtration rates (eGFR) were determined sequentially before surgery and up to 5 years after surgery. The relationships between CKD progression, the expression of these molecules in the renal cortex, and the clinical characteristics were analyzed. Results The mean 1-year postoperative percent eGFR decrease was 30.2 (Standard deviation [SD]: 15.2). The 1-year postoperative percent eGFR decrease greater than the approximate value of mean ± SD (45) was categorized as severe renal functional deterioration (SRFD). Glomerular Fas protein expression and a Fas/β-actin mRNA ratio >0.3 were independent predictors for SRFD. Significantly increased mortality rates due to cardiovascular events were indicated by glomerular Fas protein expression, Fas mRNA levels >0.3, and SRFD. No significant change in Bcl-2 levels was observed. Conclusions This study is the first report to demonstrate the significance of Fas expression in the nephrectomized normal cortex as a predictor of post-nephrectomy CKD progression. The results from nephrectomized kidney showed that the natural course of renal function in the remaining kidney may be affected not only by Fas-induced glomerular cell apoptosis but also by the total amount of Fas mRNA in cortical cells.

The crystal structure of a mutant ribonuclease T1 (Y45W) complexed with a specific inhibitor, 2'GMP, has been determined by X-ray diffraction and refined at 1.9 A resolution to a conventional R-factor of 0.164. The mode of recognition of the guanine base by the enzyme is similar to that found for the wild-type ribonuclease T1 complexed with 2'GMP. The binding of the guanine base is clearly enhanced by maximum overlapping of the indole ring of Trp45 and the base. The glycosyl torsion angle of the inhibitor is in the syn conformation and the sugar exhibits a C3'-endo type pucker, which differs from that observed in the crystal of the complex between the wild-type ribonuclease T1 and 2'GMP. Analysis of 500-MHZ NMR spectra has also indicated that the 2'GMP molecule as bound to the mutant enzyme in solution exhibits a C3'-endo type pucker, similar to that bound to the wild-type enzyme in solution [Inagaki, Shimada, & Miyazawa (1985) Biochemistry 24, 1013-1020].

We are constructing the computing system, molecular orbital calculation engine (MOE), which realizes super high-performance and cost-down of molecular orbital calculations by developing the special purpose computer for high-performance molecular orbital calculations. This report describes the summary of the MOE.

Evaluation of long-range Coulombic interactions still represents a bottleneck in the molecular dynamics (MD) simulations of biological macromolecules. Despite the advent of sophisticated fast algorithms, such as the fast multipole method (FMM), accurate simulations still demand a great amount of computation time due to the accuracy/speed trade-off inherently involved in these algorithms. Unless higher order multipole expansions, which are extremely expensive to evaluate, are employed, a large amount of the execution time is still spent in directly calculating particle–particle interactions within the nearby region of each particle. To reduce this execution time for pair interactions, we developed a computation unit (board), called MD-Engine II, that calculates nonbonded pairwise interactions using a specially designed hardware. Four custom arithmetic-processors and a processor for memory manipulation (“particle processor”) are mounted on the computation board. The arithmetic processors are responsible for calculation of the pair interactions. The particle processor plays a central role in realizing efficient cooperation with the FMM. The results of a series of 50-ps MD simulations of a protein–water system (50,764 atoms) indicated that a more stringent setting of accuracy in FMM computation, compared with those previously reported, was required for accurate simulations over long time periods. Such a level of accuracy was efficiently achieved using the cooperative calculations of the FMM and MD-Engine II. On an Alpha 21264 PC, the FMM computation at a moderate but tolerable level of accuracy was accelerated by a factor of 16.0 using three boards. At a high level of accuracy, the cooperative calculation achieved a 22.7-fold acceleration over the corresponding conventional FMM calculation. In the cooperative calculations of the FMM and MD-Engine II, it was possible to achieve more accurate computation at a comparable execution time by incorporating larger nearby regions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 582–592, 2003

Two male patients (a child and an adult) with congenital mirror movement were studied using functional MRI (fMRI) and transcranial magnetic stimulation (TMS). Bilateral primary sensorimotor cortices were activated during unilateral hand gripping on fMRI when the child patient was 8 years old and the adult was 37 years old. Bilateral motor evoked potentials were induced from the hand and forearm muscles after TMS of each hemisphere. Bilateral motor responses were also induced from the arm muscles in the adult patient. Bilateral motor responses had short and similar latencies. Contralateral motor responses to TMS were smaller than ipsilateral ones in the hand muscles, while contralateral responses were larger than ipsilateral ones in the arm muscles. Contralateral hand motor responses reduced in amplitude or disappeared with increasing age while in the child patient, mirror movements decreased gradually. Our results suggest that bilateral activation of the primary sensorimotor cortices during intended unilateral hand movement and bilateral motor responses to TMS account, at least in part, for the pathophysiology of congenital mirror movement. Reduction of contralateral hand motor responses may be related to the decrease in mirror movements during development.

The method of maximum extended quasi-likelihood (MEQL) can be viewed as an estimation method in the framework of generalized linear models. The method was applied to a pharmacokinetic problem in which the pharmacokinetic model was a nonlinear function of its parameters. The behavior of the method toward the estimation of a variance function was numerically compared with those of the generalized least squares (GLS) and extended least squares methods. In general, the MEQL and GLS methods were equally better. However, the MEQL estimator often showed smaller mean squared errors for the scaling parameter than the other two estimators. Such a generally comparable but partially distinct property of the MEQL method, as compared with the GLS method, is useful to pharmacokinetic analysis.

We are constructing a high-performance, special-purpose parallel machine for ab initio Molecular Orbital calculations, called MOE (Molecular Orbital calculation Engine). The sequential execution time is O(N4) where N is the number of basis functions, and most of time is spent to the calculations of electron repulsion integrals (ERIs). The calculation of ERIs have a lot of parallelism of O(N4), and therefore MOE tries to exploit the parallelism. This paper discuss the MOE architecture and examines important aspects of architecture design, which is required to calculate ERIs according to the "Obara method". We conclude that n-way parallelization is the most cost-effective, hence we designed the MOE prototype system with a host computer and many processing nodes. The processing node includes a 76 bit oating-point MULTIPLY-and-ADD unit and internal memory, etc., and it performs ERI computations efficiently. We estimate that the prototype system with 100 processing nodes calculate the energy of proteins in a few days.

A branched alpha-cyclodextrin is a derivative of an alpha-cyclodextrin with a branch consisting of an extra glucose unit. Its water solubility is considerably higher than that of the unbranched one. We have studied the high solubility of the molecule in aqueous solution by molecular dynamics simulations. Trajectories of the molecule at 293 K were calculated using GROMOS programs in three different environments, i.e., in vacuo, in the crystalline state, and in aqueous solution. A simulation in vacuo was carried out to explore stable conformations of the molecule in the isolated system. The quality of the simulations were examined by comparing the X-ray and the simulated crystal structures. The results of the simulations show three remarkable structural features of the molecule: self-inclusion with its branched portion, twist-boat conformation of a glucose ring, and wobbling of its macrocycle. Among these, the last feature is closely related to the water solubility of the molecule. The solubility of cyclodextrin appears to be mainly governed by its intramolecular interglucose hydrogen bonds, which inhibit hydration by solvent water molecules. The results of our simulations indicate that the capability to form hydrogen bonds in branched alpha-cyclodextrin decreased as the macrocycle of the molecule lost its regular circular shape. Such wobbling of the macrocycle was observed on a relatively short time scale (several picoseconds). An extra glucose unit introduced to alpha-cyclodextrin may cause the improved water solubility of the molecule through the greater wobbling motion of its macrocycle.

The three-dimensional X-ray structure of the RNase T1[EC 3.1.27.3]-2'GMP complex crystallized at low pH value (4.0) was determined, and refined to 1.9 A resolution to give a final R value of 0.203. The refined model includes 781 protein atoms, 24 inhibitor atoms, and 43 solvent molecules. The imidazole rings of His27 and His40 interact with the carboxyl side chains of Glu82 and Glu58, respectively, whereas that of His92 is in contact with the main chain carbonyl oxygen of Ala75. In the complex, the ribose ring of the 2'GMP molecule adopts a C2'-endo puckering, and the exocyclic conformation is gauche(-)-gauche(+). The glycosyl torsion angle is in the syn range with an intramolecular hydrogen bond between N3 and O5', and the 2'-phosphate orientation is trans-gauche(-). The guanine base of the inhibitor is tightly bound to the base recognition site with five hydrogen bonds (N1--Glu46O epsilon 2, N2---Asn98O,O6---Asn44N, and N7 ---Asn43N delta 2/Asn43N) and is sandwiched between the phenolic ring portions of Tyr42 and Tyr45 by stacking interactions. The 2'-phosphate group interacts with Arg77N eta 2, Glu58O episilon 2, and Tyr 38O eta but not with any of the histidine residues. Arg77N eta 2 also interacts with Tyr38O eta. There is no interaction between the ribose moiety of the inhibitor and the enzyme.

There has been a considerable increase in popularity of the NONMEM method as a technique for estimating population pharmacokinetic parameters. The authors present another approach to population pharmacokinetic analysis, the alternative two stage method (ATS). ATS uses the EM-algorithm for maximizing the likelihood of variance components. The performance of ATS was compared with the NONMEM method on a microcomputer. Simulation studies showed that the precision and accuracy of estimates obtained with ATS were comparable to the NONMEM method, however, the computation time, dependences on initial estimates and convergence properties were somewhat different. ATS could be a valuable alternative to the NONMEM method for estimating population pharmacokinetic parameters in some cases.

The kinetics and metabolic disposition of valproic acid following a single oral administration of two preparations of sodium valproate (sustained-release tablets, KW-6066 N ;and standard tablets, Depakene) were investigated by a Latin square cross-over method insix subjects. Determination of valproic acid and its metabolites in the serum and urinewas performed by GC/MS method.The mean elimination constants (ke), apparent volumes of distribution (Vd), areas underthe serum concentration-time curve (AUC) of the parent drug, and the sum of valproicacid and its metabolites excreted in urine showed no significant differences in the twopreparations. Therefore the extent of bioavailability of Depakene and KW-6066 N seemedto be equivalent.The pharmacokinetic parameters were estimated according to one-compartment openmodel by simultaneous least squares curve fitting method. KW-6066 N exhibited a moreprolonged absorption of valproic acid, showed a more delayed peak time (tmax), and yieldeda longer mean residence time (MRT). Maximum serum concentration (Cmax) obtained afteradministration of KW-6066 N was lower than those following the standard tablets of Depakene. These results indicate that KW-6066 N provides slow release of valproic acid.Using the pharmacokinetic parameters of valproic acid obtained in the study, serumconcentrations of valproic acid after repeated oral administration of Depakene or KW-6066N were simulated. KW-6066 N was expected to be effective even when administeredonce a day.

At pH 4.0, the RNase T 1 -2'GMP complex ( 1 ) crystallizes isomorphously with the isoenzyme complex ( 2 ) (Heinemann, U. and Saenger, W., 1982, Nature 299, 27-31). The X-ray structure of 1 was refined with 1.9 A data to R = 0.195. Polypeptide folding is similar in 1 and 2 . However, the sugar pucker of 2'-GMP is 2'- endo (3' endo in 2 ), and guanine binding involves four hydrogen bonds in 1 , which all differ from the two bonds in 2 . Phosphate contacts Glu58, Arg77, Tyr38 in 1 , but His40 in 2 . These changes are not due to differences in sequence between the mother- and isoenzyme (Gln25-Lys) but are associated with pH changes leadingto an inactive enzyme structure.

A linear relationship in each of the torsion angle pairs, α-β, β-ϵ, ϵ-ζ, and α-γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 A between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers6, 223–242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.