3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.
Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1-3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.
1] The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA [2] Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
Xing
X
Zhang
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Lei
L
Zhang
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Huimin
H
Tong
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Bo
B
Peng
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Matthew J
MJ
Rames
Department of Applied Physics, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China.
Shengli
S
Zhang
The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Gang
G
Ren
D003461:Crystallography / Q000379:methods*; D055032:Electron Microscope Tomography / Q000379:methods*; D004583:Electrons; D006801:Humans; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D007074:Immunoglobulin G / Q000648:ultrastructure*; D011487:Protein Conformation
D007074:Immunoglobulin G