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3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.

Zhang X, Zhang L, Tong H, Peng B, Rames MJ, Zhang S, Ren G - Sci Rep (2015)

Bottom Line: 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 Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


Related in: MedlinePlus

Distributions of IgG1 antibody domain distances, directions and orientations. a, By measuring the distance between two corresponding domain centers of each antibody molecule, the histogram of the distances of Fab-Fab and Fab-Fc domains were fitted with sixth degree polynomial curves respectively. b, By measuring the angle of Fab1-Fc-Fab2 domains, the histogram was displayed and fitted with sixth degree polynomial curves. c, By measuring the angles between the directions of two domains, the histograms of the angles of Fab-Fab and Fab-Fc domains were displayed respectively and fitted with a sixth-degree polynomial curve each. d, By measuring the angles between the plane normal directions of each two domains, the histogram of the angles of Fab-Fab and Fab-Fc domains and their corresponding sixth degree polynomial fitting curves are displayed respectively.
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f7: Distributions of IgG1 antibody domain distances, directions and orientations. a, By measuring the distance between two corresponding domain centers of each antibody molecule, the histogram of the distances of Fab-Fab and Fab-Fc domains were fitted with sixth degree polynomial curves respectively. b, By measuring the angle of Fab1-Fc-Fab2 domains, the histogram was displayed and fitted with sixth degree polynomial curves. c, By measuring the angles between the directions of two domains, the histograms of the angles of Fab-Fab and Fab-Fc domains were displayed respectively and fitted with a sixth-degree polynomial curve each. d, By measuring the angles between the plane normal directions of each two domains, the histogram of the angles of Fab-Fab and Fab-Fc domains and their corresponding sixth degree polynomial fitting curves are displayed respectively.

Mentions: Statistical analysis of the antibody conformational flexibility was performed using the four following aspects: i) Histogram of the distances among the domains. The distances between two domains in each molecule were measured based on the mass center of each domain. The results showed that all distances were within a range of 60 to 120 Å. This distance was consistent with that measured by liquid AFM based on the progression of antibody moving on a virus covered flat surface24. However, the distance at peak population was ~82.0 ± 2.5 Å (~17.6% of population) for two Fabs and ~85.0 ± 2.5 Å (~16.1% of population) for Fab to Fc (Fig. 7a), suggesting that the most common antibody conformation had their three domains nearly evenly spaced away from each other in an equilateral triangular shape.


3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography.

Zhang X, Zhang L, Tong H, Peng B, Rames MJ, Zhang S, Ren G - Sci Rep (2015)

Distributions of IgG1 antibody domain distances, directions and orientations. a, By measuring the distance between two corresponding domain centers of each antibody molecule, the histogram of the distances of Fab-Fab and Fab-Fc domains were fitted with sixth degree polynomial curves respectively. b, By measuring the angle of Fab1-Fc-Fab2 domains, the histogram was displayed and fitted with sixth degree polynomial curves. c, By measuring the angles between the directions of two domains, the histograms of the angles of Fab-Fab and Fab-Fc domains were displayed respectively and fitted with a sixth-degree polynomial curve each. d, By measuring the angles between the plane normal directions of each two domains, the histogram of the angles of Fab-Fab and Fab-Fc domains and their corresponding sixth degree polynomial fitting curves are displayed respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4419541&req=5

f7: Distributions of IgG1 antibody domain distances, directions and orientations. a, By measuring the distance between two corresponding domain centers of each antibody molecule, the histogram of the distances of Fab-Fab and Fab-Fc domains were fitted with sixth degree polynomial curves respectively. b, By measuring the angle of Fab1-Fc-Fab2 domains, the histogram was displayed and fitted with sixth degree polynomial curves. c, By measuring the angles between the directions of two domains, the histograms of the angles of Fab-Fab and Fab-Fc domains were displayed respectively and fitted with a sixth-degree polynomial curve each. d, By measuring the angles between the plane normal directions of each two domains, the histogram of the angles of Fab-Fab and Fab-Fc domains and their corresponding sixth degree polynomial fitting curves are displayed respectively.
Mentions: Statistical analysis of the antibody conformational flexibility was performed using the four following aspects: i) Histogram of the distances among the domains. The distances between two domains in each molecule were measured based on the mass center of each domain. The results showed that all distances were within a range of 60 to 120 Å. This distance was consistent with that measured by liquid AFM based on the progression of antibody moving on a virus covered flat surface24. However, the distance at peak population was ~82.0 ± 2.5 Å (~17.6% of population) for two Fabs and ~85.0 ± 2.5 Å (~16.1% of population) for Fab to Fc (Fig. 7a), suggesting that the most common antibody conformation had their three domains nearly evenly spaced away from each other in an equilateral triangular shape.

Bottom Line: 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 Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


Related in: MedlinePlus