2022/10/14 更新

写真a

ウラノ リョウ
浦野 諒
URANO Ryo
所属
異分野基礎科学研究所 助教(特任)
職名
助教(特任)
外部リンク

学位

  • 博士(理学) ( 名古屋大学 )

 

論文

  • Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles 査読

    The Journal of Chemical Physics   2018年10月

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  • Cellular prion protein targets amyloid-β fibril ends via its C-terminal domain to prevent elongation 査読

    Erin Bove-Fenderson, Ryo Urano, John E. Straub, David A. Harris

    Journal of Biological Chemistry   292 ( 41 )   16858 - 16871   2017年10月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Society for Biochemistry {\&} Molecular Biology ({ASBMB})  

    DOI: 10.1074/jbc.M117.789990

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  • Observation of helix associations for insertion of a retinal molecule and distortions of helix structures in bacteriorhodopsin 査読

    Ryo Urano, Yuko Okamoto

    Journal of Chemical Physics   143 ( 23 )   12B630\_1   2015年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:American Institute of Physics Inc.  

    We applied a newly proposed prediction method for membrane protein structures to bacteriorhodopsin that has distorted transmembrane helices in the native structure. This method uses an implicit membrane model, which restricts sampling space during folding in a membrane region, and includes helix bending. Replica-exchange simulations were performed with seven transmembrane helices only without a retinal molecule. Obtained structures were classified into clusters of similar structures, which correspond to local-minimum free energy states. The two lowest free energy states corresponded to a native-like structure with the correct empty space for retinal and a structure with this empty space filled with a helix. Previous experiments of bacteriorhodopsin suggested that association of transmembrane helices enables them to make a room for insertion of a retinal. Our results are consistent with these results. Moreover, distortions of helices in the native-like structures were successfully reproduced. In the distortions, whereas the locations of kinks for all helices were similar to those of Protein Data Bank's data, the amount of bends was more similar for helices away from the retinal than for those close to the retinal in the native structure. This suggests a hypothesis that the amino-acid sequence specifies the location of kinks in transmembrane helices and that the amount of distortions depends on the interactions with the surrounding molecules such as neighboring helices, lipids, and retinal.

    DOI: 10.1063/1.4935964

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  • Deterministic replica-exchange method without pseudo random numbers for simulations of complex systems 査読

    Ryo Urano, Yuko Okamoto

    COMPUTER PHYSICS COMMUNICATIONS   197   128 - 135   2015年12月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    We propose a replica-exchange method (REM) which does not use pseudo random numbers. For this purpose, we first give a conditional probability for Gibbs sampling replica-exchange method (GSREM) based on the heat bath method. In GSREM, replica exchange is performed by conditional probability based on the weight of states using pseudo random numbers. From the conditional probability, we propose a new method called deterministic replica-exchange method (DETREM) that produces thermal equilibrium distribution based on a differential equation instead of using pseudo random numbers. This method satisfies the detailed balance condition using a conditional probability of Gibbs heat bath method and thus results can reproduce the Boltzmann distribution within the condition of the probability. We confirmed that the equivalent results were obtained by REM and DETREM with two-dimensional Ising model. DETREM can avoid problems of choice of seeds in pseudo random numbers for parallel computing of REM and gives analytic method for REM using a differential equation. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cpc.2015.08.020

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  • Designed-walk replica-exchange method for simulations of complex systems 査読

    Ryo Urano, Yuko Okamoto

    COMPUTER PHYSICS COMMUNICATIONS   196   380 - 383   2015年11月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:ELSEVIER SCIENCE BV  

    We propose a new implementation of the replica-exchange method (REM) in which replicas follow a pre-planned route in temperature space instead of a random walk. Our method satisfies the detailed balance condition in the proposed route. The method forces tunneling events between the highest and lowest temperatures to happen with an almost constant period. The number of tunneling counts is proportional to that of the random-walk REM multiplied by the square root of moving distance in temperature space. We applied this new implementation to two kinds of REM and compared the results with those of the conventional random-walk REM. The test system was a two-dimensional Ising model, and our new method reproduced the results of the conventional random-walk REM and could adjust the tunneling counts by two times or more than that of the random-walk REM by replica-exchange attempt frequency. (C) 2015 Elsevier B.V. All rights reserved.

    DOI: 10.1016/j.cpc.2015.07.007

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  • Predictions of tertiary structures of $α$-helical membrane proteins by replica-exchange method with consideration of helix deformations 査読

    Urano Ryo, Kokubo Hironori, Okamoto Yuko

    Journal of the Physical Society of Japan   84 ( 8 )   084802   2015年8月

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    記述言語:英語   掲載種別:研究論文(学術雑誌)   出版者・発行元:The Physical Society of Japan  

    DOI: 10.7566/JPSJ.84.084802

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  • New implementations of replica-exchange method for simulations of complex systems: Designed-walk and deterministic replica-exchange methods 査読

    Ryo Urano, Yuko Okamoto

    Proceedings of the 28th Workshop on Computer Simulation Studies in Condensed Matter Physics (CSP2015)   68   100 - 104   2015年

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    記述言語:英語   掲載種別:研究論文(国際会議プロシーディングス)   出版者・発行元:ELSEVIER SCIENCE BV  

    Two new methods of replica-exchange method (REM) are tested for a two-dimensional Ising spin model. The first method is the deterministic replica-exchange method (DETREM) which uses a differential equation based on Gibbs sampling method instead of Metropolis criteria. The other is the designed-walk replica-exchange method (DEWREM) which determines the trajectory of replica in temperature space without random walk. This method gives more number of tunneling events than conventional REM, where the tunneling event is a round-trip of temperature from the lowest to the highest back to the lowest. We examined physical quantities such as magnetization and susceptibility. Our new methods reproduced the results of the conventional random-walk REM. (C) 2015 The Authors. Published by Elsevier B.V.

    DOI: 10.1016/j.phpro.2015.07.116

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  • Computer Simulations for Predicting Membrane Protein Structures with the Replica-Exchange Methods and Implicit Membrane Model of a Restricted Configurational Space 査読

    Ryo Urano, Yuko Okamoto

    Biophysical Journal   106 ( 2 )   655a   2014年1月

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    出版者・発行元:Elsevier {BV}  

    DOI: 10.1016/j.bpj.2013.11.3627

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