Paper Citing NAMD - Abstract
Clark, Nicholas J.; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R.; Kerwin, Bruce; Kanapuram, Sekhar R.; Treuheit, Michael J.; McAuley, Arnold; Curtis, Joseph E.
Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14029-14038, NOV 14 2013
Monoclonal antibodies (mAbs) contain hinge-like regions that enable structural flexibility of globular domains that have a direct effect on biological function. A subclass of mAbs, IgG2, have several interchain disulfide bonds in the hinge region that could potentially limit structural flexibility of the globular domains and affect the overall configuration space available to the mAb. We have characterized human IgG2 mAb in solution via small-angle neutron scattering (SANS) and interpreted the scattering data using atomistic models. Molecular Monte Carlo combined with molecular dynamics simulations of a model mAb indicate that a wide range of structural configurations are plausible, spanning radius of gyration values from similar to 39 to similar to 55 angstrom. Structural ensembles and representative single structure solutions were derived by comparison of theoretical SANS profiles of mAb models to experimental SANS data. Additionally, molecular mechanical and solvation free-energy calculations were carried out on the ensemble of best-fitting mAb structures. The results of this study indicate that low-resolution techniques like small-angle scattering combined with atomistic molecular simulations with free-energy analysis may be helpful to determine the types of intramolecular interactions that influence function and could lead to deleterious changes to mAb structure. This methodology will be useful to analyze small-angle scattering data of many macromolecular systems.
