TY - JOUR
T1 - Normal mode analysis of protein dynamics in a non-Eckart frame
AU - Fuchigami, Sotaro
AU - Omori, Satoshi
AU - Ikeguchi, Mitsunori
AU - Kidera, Akinori
PY - 2010
Y1 - 2010
N2 - Normal mode analysis, with the all-atom or coarse-grained elastic network model, represents the equilibrium fluctuation of protein molecule in the Eckart frame, where contributions from external motions (translation and rotation) of the entire protein molecule are eliminated. On the other hand, domain motion is frequently exhibited by the relative motion of one domain to the other. Such a representation of fluctuations in the non-Eckart frame cannot be achieved by conventional normal mode analysis. Here, we propose normal mode analysis in a non-Eckart frame, where the external degrees of freedom are fixed for any portion of the system. In this analysis, the covariance matrix in the Eckart frame is transformed into one in the non-Eckart frame. Using a molecular dynamics simulation, we have confirmed the validity of the transformation formula and discussed the physical implication of the formula.
AB - Normal mode analysis, with the all-atom or coarse-grained elastic network model, represents the equilibrium fluctuation of protein molecule in the Eckart frame, where contributions from external motions (translation and rotation) of the entire protein molecule are eliminated. On the other hand, domain motion is frequently exhibited by the relative motion of one domain to the other. Such a representation of fluctuations in the non-Eckart frame cannot be achieved by conventional normal mode analysis. Here, we propose normal mode analysis in a non-Eckart frame, where the external degrees of freedom are fixed for any portion of the system. In this analysis, the covariance matrix in the Eckart frame is transformed into one in the non-Eckart frame. Using a molecular dynamics simulation, we have confirmed the validity of the transformation formula and discussed the physical implication of the formula.
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U2 - 10.1063/1.3352566
DO - 10.1063/1.3352566
M3 - Article
C2 - 20232949
AN - SCOPUS:77949634162
SN - 0021-9606
VL - 132
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 10
M1 - 104109
ER -