kernel density estimation (kde)  (CH Instruments)

Journal: Computational and Structural Biotechnology Journal

Article Title: Electro-detachment of kinesin motor domain from microtubule in silico

doi: 10.1016/j.csbj.2023.01.018

Figure Lengend Snippet: Effects of 100 MV/m EF on kinesin (solid line) and β -tubulin C-terminus (dotted line) for various EF directions. a) Kinetics of the dipole moment magnitude and c) angle projection (see Eqs. and ). b) translational and d) rotational work carried out by the EF on the protein. Color coding: X (blue), -X (cyan), Z (red), and -Z (violet) EF directions and gray is the trajectory with no EF. The colored lines are the mean from N = 40 for X, N = 10 for -X, N = 10 for Z, N = 10 for -Z trajectories. In c), the gray lines are the reference (no EF) trajectories: solid dark gray and solid light gray for kinesin and β -tubulin C-terminus respectively, in X and -X EF direction (from Eq. ), dashed dark gray and dashed light gray for kinesin and β -tubulin C-terminus respectively, in Z and -Z EF direction (from Eq. ). Distributions on the right display relative probability of the occurrence and the mean of the value for each quantity at the time when zero number of contacts between kinesin and tubulin (see e) was reached. For example, in a), for the trajectories with X EF direction, the value of the kinesin dipole moment magnitude at the time when zero number of contacts was reached was between 1400 D and 1750 D and the mean value was 1575 D. The probability density functions were obtained by fitting with kernel density estimation utilizing MATLAB 2021a histfit function with five bins.

Article Snippet: For example, in a), for the trajectories with X EF direction, the value of the kinesin dipole moment magnitude at the time when zero number of contacts was reached was between 1400 D and 1750 D and the mean value was 1575 D. The probability density functions were obtained by fitting with kernel density estimation utilizing MATLAB 2021a histfit function with five bins.

Techniques:

Journal: Computational and Structural Biotechnology Journal

Article Title: Electro-detachment of kinesin motor domain from microtubule in silico

doi: 10.1016/j.csbj.2023.01.018

Figure Lengend Snippet: Dependence of the electric field effects on the kinesin (solid lines) and β -tubulin C-terminus (dotted lines) on the EF strength for the X EF direction. Kinetics of a) the number of contacts between kinesin and tubulin, b) the kinesin displacement. c) the kinesin and β -tubulin C-terminus dipole moment magnitude d) the dipole angle projection, e) rotational, and f) translational work carried out by the EF on the kinesin and β -tubulin C-terminus. Color coding: 100 MV/m (blue), 75 MV/m (cyan), 50 MV/m (red), and 30 MV/m (violet) electric field strength and gray is the trajectory with no EF. The colored lines are the mean from N = 40 for 100 MV/m, N = 30 for 75 MV/m, N = 20 for 50 MV/m, N = 10 for 30 MV/m trajectories. The density functions were obtained from kernel density estimation utilizing MATLAB 2021a histfit function with five bins.

Article Snippet: For example, in a), for the trajectories with X EF direction, the value of the kinesin dipole moment magnitude at the time when zero number of contacts was reached was between 1400 D and 1750 D and the mean value was 1575 D. The probability density functions were obtained by fitting with kernel density estimation utilizing MATLAB 2021a histfit function with five bins.

Techniques: