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

Abstract

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.

Authors:
 [1];  [2];  [2];  [2];  [2];  [3];  [2]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Xi'an Jiaotong Univ., Xi'an, Shaanxi (China)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Xi'an Jiaotong Univ., Xi'an, Shaanxi (China)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Fusion Energy Sciences (FES) (SC-24); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1187107
Alternate Identifier(s):
OSTI ID: 1407354
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 5; Journal Issue: 5; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; electron microscopy; single-molecule biophysics

Citation Formats

Zhang, Xing, Zhang, Lei, Tong, Huimin, Peng, Bo, Rames, Matthew J., Zhang, Shengli, and Ren, Gang. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography. United States: N. p., 2015. Web. doi:10.1038/srep09803.
Zhang, Xing, Zhang, Lei, Tong, Huimin, Peng, Bo, Rames, Matthew J., Zhang, Shengli, & Ren, Gang. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography. United States. doi:10.1038/srep09803.
Zhang, Xing, Zhang, Lei, Tong, Huimin, Peng, Bo, Rames, Matthew J., Zhang, Shengli, and Ren, Gang. Tue . "3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography". United States. doi:10.1038/srep09803. https://www.osti.gov/servlets/purl/1187107.
@article{osti_1187107,
title = {3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography},
author = {Zhang, Xing and Zhang, Lei and Tong, Huimin and Peng, Bo and Rames, Matthew J. and Zhang, Shengli and Ren, Gang},
abstractNote = {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.},
doi = {10.1038/srep09803},
journal = {Scientific Reports},
number = 5,
volume = 5,
place = {United States},
year = {2015},
month = {5}
}

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