title: Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.
abstract: The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.
authors: Early Stage Pharmaceutical Development Department, Genentech Inc., San Francisco, CA, USA.
authors: Ekaterine
authors: E
authors: Kortkhonjia
authors: Relly
authors: R
authors: Brandman
authors: Joe Zhongxiang
authors: JZ
authors: Zhou
authors: Vincent A
authors: VA
authors: Voelz
authors: Ilya
authors: I
authors: Chorny
authors: Bruce
authors: B
authors: Kabakoff
authors: Thomas W
authors: TW
authors: Patapoff
authors: Ken A
authors: KA
authors: Dill
authors: Trevor E
authors: TE
authors: Swartz
mesh_terms: D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000627:therapeutic use; D061067:Antibodies, Monoclonal, Humanized / Q000737:chemistry* / Q000627:therapeutic use; D005454:Fluorescence Polarization; D006801:Humans; D007074:Immunoglobulin G / Q000737:chemistry* / Q000627:therapeutic use; D008390:Markov Chains; D051379:Mice; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D000068878:Trastuzumab
chemical_list: D000911:Antibodies, Monoclonal; D061067:Antibodies, Monoclonal, Humanized; D007074:Immunoglobulin G; D000068878:Trastuzumab
keywords: Monoclonal antibodies; fluorescence anisotropy; molecular dynamics simulations; solution dynamics; therapeutic antibodies
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