Takashi Amisaki

MOLECULAR DYNAMICS STUDY OF CONFORMATIONAL CHANGES IN HUMAN SERUM ALBUMIN BY BINDING OF FATTY ACIDS

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.

Fatty acid binding to serum albumin: molecular simulation approaches.

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.

Congenital mirror movement: a study of functional MRI and transcranial magnetic stimulation

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 andthe 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.

Prognostic impact of preoperative hematological disorders and a risk stratification model in bladder cancer patients treated with radical cystectomy.

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.

Development of hardware accelerator for molecular dynamics simulations: a computation board that calculates nonbonded interactions in cooperation with fast multipole method.

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.

Topographic MN-SSEPs (N18, N20 and N30) might characterize underlying CNS involvements in representative types of cerebral palsy

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.

Fas expression in nephrectomized, non-cancerous specimens predicts post-nephrectomy chronic kidney disease progression in patients with renal and upper urinary tract malignancies

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.

Molecular dynamics study on conformational differences between dGMP and 8-oxo-dGMP: Effects of metal ions.

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.

Grid-enabled applications in molecular dynamics simulations using a cluster of dedicated computers

A parallel platform for molecular dynamics simulations and its grid-enabled use are reported. The platform is a cluster of PCs, each of which mounts dedicated computation boards that calculate nonbonded pair interactions. On this dedicated cluster, a parallel fast multipole method is used in cooperation with the special hardware to calculate Coulombic interactions, which is the most problematic part of protein simulations. Regarding a simulation of a protein-water system, the cluster (4 PCs with 2 boards each) was about 47 times faster than a PC without the special hardware support. In addition, we examined two approaches for grid-enabling molecular dynamics calculation using the dedicated cluster. This paper describes the designs and benchmark tests regarding these grid-enabled simulations as well as those on the dedicated cluster.