Biology subjects

Kubo, S.

Publications and source records attributed to Kubo, S..

21 records · Page 2Linked to original sources

bioRxiv2019

Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor

The FO motor in FOF1 ATP synthase rotates its rotor driven by the proton motive force. While earlier studies elucidated basic mechanisms therein, recent advances in high-resolution cryo-electron microscopy enabled to investigate proton-transfer coupled FO rotary dynamics at structural details. Here, developing a hybrid Monte Carlo/molecular dynamics simulation method, we studied reversible dynamics of a yeast mitochondrial FO. We obtained the 36{degrees}-stepwise rotations of FO per one proton transfer in the ATP synthesis mode and the proton pumping in the ATP hydrolysis mode. In both modes, the most prominent path alternatively sampled states with two and three deprotonated glutamates in c-ring, by which the c-ring rotates one step. The free energy transduction efficiency in the model FO motor reaches ~ 90% in optimal conditions. Moreover, mutations in key glutamate and a highly conserved arginine increased proton leakage and markedly decreased the coupling, in harmony with previous experiments.

biophysics↗

bioRxiv2019

Diverse stepping motions of cytoplasmic dynein revealed by kinetic modeling

Cytoplasmic dynein is a two-headed molecular motor that moves to the minus end of microtubule (MT) using ATP hydrolysis free energy. By employing its two heads (motor domains), cytoplasmic dynein shows various bipedal stepping motions; the inchworm and hand-over-hand motions, as well as non-alternate steps of one head. However, the molecular basis to achieve such diverse stepping manners remains obscure. Here, we propose a kinetic model for bipedal motions of cytoplasmic dynein and performed Gillespie Monte Carlo simulations that reproduces most experimental data obtained to date. The model represents status of each motor domain as five states according to conformations, nucleotide- and MT-binding conditions of the domain. Also, the relative positions of the two domains were approximated by three discrete states. Accompanied by ATP hydrolysis cycles, the model dynein stochastically and processively moved forward in multiple steps via diverse pathways, including inchworm and hand-over-hand motions, same as experimental data. The model reproduced key experimental motility-related parameters including velocity and run-length as functions of ATP concentration and external force. Our model reveals that, in a typical inchworm motion, the leading domain moves via the ATP-dependent power-stroke of the linker coupled with a small change in the stalk angle, whereas the lagging domain moves via diffusion dragged by the leading domain. Moreover, the hand-over-hand motion in the model dynein clearly differs from that of kinesin by the usage of the power-stroke.\n\nAuthor SummaryCytoplasmic dynein is a two-headed molecular motor, which moves linearly and transports intra-cellar organelles along microtubules driven by ATP hydrolysis free energy. In contrast to other better-known molecular motors, such as kinesin, dynein is known to take various stepping motions including motions akin to human walking and inchworm-like motions. However, molecular mechanisms underpinning the diverse stepping motions are unclear. Here, based on recent high-resolution structure information and single-molecule motility assay data, we designed a kinetic model that explicitly include two heads, each of which makes ATP hydrolysis cycles and moves along the microtubules. Using the model, we performed Monte Carlo simulations. The simulation reproduced most of currently available experimental results. More importantly, the simulation suggested molecular mechanisms of various stepping motions. While stepping motions apparently resemble to those proposed before, once looking into details, we found the resulting mechanisms distinct from previously proposed ones in the usage of ATP and protein conformation changes coupled with stepping motions.

biophysics↗

bioRxiv2018

National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB): Outline and Patient-Matching Technique

BackgroundThe National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB) is a comprehensive database of health insurance claims data under Japans National Health Insurance system. The NDB uses two types of personal identification variables (referred to in the database as \"ID1\" and \"ID2\") to link the insurance claims of individual patients. However, the information entered against these ID variables is prone to change for several reasons, such as when claimants find or change employment, or due to variations in the spelling of their name. In the present study, we developed a new patient-matching technique that improves upon the existing system of using ID1 and ID2 variables. We also sought to validate a new personal ID variable (ID0) that we propose in order to enhance the efficiency of patient matching in the NDB database.\n\nMethodsOur study targeted data from health insurance claims filed between April 2013 and March 2016 for hospitalization, combined diagnostic procedures, outpatient treatment, and dispensing of prescription medication. We developed a new patient-matching algorithm based on the ID1 and ID2 variables, as well as variables for treatment date and clinical outcome. We then attempted to validate our algorithm by comparing the number of patients identified by patient matching with the current ID1 variable and our proposed ID0 variable against the estimated patient population as of 1 October 2015.\n\nResultsThe numbers of patients in each sex and age group that were identified with the ID0 variable were lower than those identified using the ID1 variable. By using the ID0 variable, we were able to reduce the number of duplicate records for male and female patients by 5.8% and 6.4%, respectively. The numbers of children, adults older than 75 years, and women of reproductive age identified using the ID1 patient-matching variable were all higher than their corresponding estimates. Conversely, the numbers of these patients identified with the ID0 patient-matching variable were all within their corresponding estimates.\n\nConclusionOur findings show that the proposed ID0 variable delivers more precise patient-matching results than the existing ID1 variable. The ID0 variable is currently the best available technique for patient matching in the NDB database. Future patient population estimates should therefore rely on the ID0 variable instead of the ID1 variable.

epidemiology↗