TY - JOUR
T1 - A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method
AU - Yoshida, Norio
N1 - Funding Information:
This work was supported by Grants-in-Aid [ 16H00842 , 16 16 16 ] from MEXT , Japan. The author is grateful to Dr. Daniel J. Sindhikara (Schrodinger Inc.), Prof. Shigehiko Hayashi ( Kyoto University ), and Prof. Haruyuki Nakano, ( Kyushu University ) for invaluable discussions. The original program of the string method was taken from Dr. Weiqing Ren’s website ( http://www.math.nus.edu.sg/~matrw/string/index.html ). Molecular graphics and analyses were performed with the UCSF Chimera package [33] .
Funding Information:
This work was supported by Grants-in-Aid [16H00842, 161616] from MEXT, Japan. The author is grateful to Dr. Daniel J. Sindhikara (Schrodinger Inc.), Prof. Shigehiko Hayashi (Kyoto University), and Prof. Haruyuki Nakano, (Kyushu University) for invaluable discussions. The original program of the string method was taken from Dr. Weiqing Ren's website (http://www.math.nus.edu.sg/~matrw/string/index.html). Molecular graphics and analyses were performed with the UCSF Chimera package [33].
Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2018/5
Y1 - 2018/5
N2 - A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example.
AB - A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has been proposed. The 3D-RISM theory produces the distribution function, or the potential of mean force (PMF), for transporting substances around the given protein structures. By applying the string method to the PMF surface, one can readily determine the MFEP on the PMF surface. The method has been applied to consider the Na+ conduction pathway of channelrhodopsin as an example.
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U2 - 10.1016/j.cplett.2018.03.034
DO - 10.1016/j.cplett.2018.03.034
M3 - Article
AN - SCOPUS:85044164571
SN - 0009-2614
VL - 699
SP - 22
EP - 27
JO - Chemical Physics Letters
JF - Chemical Physics Letters
ER -