3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

Zhang, Xing; Zhang, Lei; Tong, Huimin; Peng, Bo; Rames, Matthew J.; Zhang, Shengli; Ren, Gang

doi:10.1038/srep09803

3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

Journal Article · Tue May 05 00:00:00 EDT 2015 · Scientific Reports

DOI:https://doi.org/10.1038/srep09803· OSTI ID:1187107

Zhang, Xing ^[1]; Zhang, Lei ^[2]; Tong, Huimin ^[2]; Peng, Bo ^[2]; Rames, Matthew J. ^[2]; Zhang, Shengli ^[3]; Ren, Gang ^[2]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xi'an Jiaotong Univ., Xi'an, Shaanxi (China)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Xi'an Jiaotong Univ., Xi'an, Shaanxi (China)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE Office of Science (SC), Fusion Energy Sciences (FES) (SC-24)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1187107

Alternate ID(s):: OSTI ID: 1407354

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 5 Vol. 5; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Journal Article · Wed Apr 18 20:00:00 EDT 2018 · Antibodies · OSTI ID:1629230

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3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

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