Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody  J. Paul Brandt, Thomas W. Patapoff, Sergio R. Aragon  Biophysical Journal  Volume 99, Issue 3, Pages 905-913 (August 2010) DOI: 10.1016/j.bpj.2010.05.003 Copyright © 2010 Biophysical Society Terms and Conditions

Figure 1 DLS extrapolations for the determination of trastuzumab's translational diffusion coefficient at 20°C (squares) and 27°C (circles); each measurement is in triplicate. Biophysical Journal 2010 99, 905-913DOI: (10.1016/j.bpj.2010.05.003) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 2 (A) Trastuzumab (T0,t=0). (B) Trastuzumab at t=7.4 ns of simulation T0. (C) RMSD, during initial trajectory, of the trastuzumab model as a whole (circles), Fab1 (diamond), Fab2 (square), and Fc (triangle). (D) MM-GBSA analysis of the trastuzumab model during initial trajectory. (E) MM-GBSA analysis of the trastuzumab Fab-only simulation; molecular graphics produced with UCSF Chimera (33). Biophysical Journal 2010 99, 905-913DOI: (10.1016/j.bpj.2010.05.003) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 3 Plots of the eigenvalues of the rotational diffusion tensor, Dr, of structures from simulation T5; Fig. S1 has corresponding plots for all simulation trajectories T1–T8. Biophysical Journal 2010 99, 905-913DOI: (10.1016/j.bpj.2010.05.003) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 4 Plots of hydrodynamic analysis results; values are adjusted for each transport property using the average slope obtained from full hydrodynamic analysis of the trajectories' last structure. Note: The density of the data points displayed is 20% of each trajectory's data included in the numerical data presented in Table 2. Biophysical Journal 2010 99, 905-913DOI: (10.1016/j.bpj.2010.05.003) Copyright © 2010 Biophysical Society Terms and Conditions