TY - JOUR
T1 - MD-SAXS method with nonspherical boundaries
AU - Oroguchi, Tomotaka
AU - Ikeguchi, Mitsunori
N1 - Funding Information:
This work was supported by Grants-in-Aid for Scientific Research on Innovative Areas (No. 21118713) and that on (B) (No. 22300102) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, by the Grand Challenges in Next-Generation Integrated Simulation of Living Matter, a part of the Development and Use of the Next-Generation Supercomputer Project of MEXT.
PY - 2012/7/10
Y1 - 2012/7/10
N2 - Small-angle X-ray solution scattering (SAXS) experiments provide information about protein structures in solution, albeit at low resolution. The molecular dynamics (MD)-SAXS method is capable of linking SAXS data and high-resolution atomic structures of proteins including hydrating water molecules. The MD-SAXS method, which was previously limited to spherical boundary conditions, is here extended to nonspherical boundary conditions while retaining accuracy. The method presented here is computationally effective, particularly for elongated proteins, because a number of water molecules can be eliminated compared to the original formulation.
AB - Small-angle X-ray solution scattering (SAXS) experiments provide information about protein structures in solution, albeit at low resolution. The molecular dynamics (MD)-SAXS method is capable of linking SAXS data and high-resolution atomic structures of proteins including hydrating water molecules. The MD-SAXS method, which was previously limited to spherical boundary conditions, is here extended to nonspherical boundary conditions while retaining accuracy. The method presented here is computationally effective, particularly for elongated proteins, because a number of water molecules can be eliminated compared to the original formulation.
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U2 - 10.1016/j.cplett.2012.05.057
DO - 10.1016/j.cplett.2012.05.057
M3 - Article
AN - SCOPUS:84862871798
VL - 541
SP - 117
EP - 121
JO - Chemical Physics Letters
JF - Chemical Physics Letters
SN - 0009-2614
ER -