Root mean squared fluctuation (RMSF) of protein residues was obtained by g_rmsf.
Root mean squared fluctuation (RMSF) was carried out to analyze the fluctuation of residues on ApoE4 protein.
The root mean squared fluctuation (RMSF) is a commonly used measure of variability across multiple structure alignments.
Thirdly, we further calculate root mean squared fluctuation (RMSF) for each protein residue by commands of g_rmsf.
We using root mean squared fluctuation (RMSF) to analyze the fluctuation of residues on protein binding site; the binding region (GLN60, GLY61, ASP80, ILE158, ILE166, ASP276, GLY278, and THR279) shows small flexibility.
The atomicfluct command in the cpptraj module of AMBER12 (Case et al. 2012) was used to generate root mean squared fluctuation (RMSF) plots from 5,000 snapshots taken at regularly spaced intervals from the MD simulation.
CCG, computational carbohydrate grafting; CFG, Consortium for Functional Glycomics; GalNAcα, α-galactosamine; GBP, glycan-binding protein; GlcNAcβ, β-glucosamine; MD, Molecular Dynamics QMM, quantum mechanical; RMSF, root mean squared fluctuation; SDFs, spatial distribution functions; TF Thomsen-Friedenreich.
From the root mean squared fluctuation (RMSF) values of the alpha carbons per residue, we can see that the fluctuation of PLA2 residues from 1300 ps to 5000 ps is very low (except for the residues in the terminal loop, 119 133), indicating that there are no significant changes in the conformation of the residues.
The MD simulations agree with the time-resolved fluorescence anisotropy results because the root mean squared fluctuation (RMSF) values of the main-chain atoms of the nonmyristylated protein are much greater than the myristylated protein in both apo and ternary states.
In addition to the coarse-grained approach, we also use all-atom replica exchange molecular dynamics (MD) trajectories to estimate the root-mean squared fluctuation (rmsf) of the atoms around their original positions for computing dfi (See Data S1 and Figure S1).
