Web-based visualization of 3D distance restraints integrated with NGL molecular graphics @ BPS17
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Web-based visualizaon of 3D distance restraints integrated with NGL molecular graphics Integrative/Hybrid approaches Funding and acknowledgements NGL library CLMS distances in XI DEER distances in NGL Webapp HIV-1 capsid at three scales 216 hexameric and 12 pentameric subunits, ~2.4M unique atoms Alexander S. Rose and Stephen K. Burley RCSB Protein Data Bank University of California San Diego and Rutgers, The State University of New Jersey NGL library and viewer (hps://github.com/arose/ngl ) AS Rose & PW Hildebrand (2015) NGL Viewer: a web applicaon for molecular visualizaon. Nucl. Acids Res. 43 (W1). doi:10.1093/nar/gkv402 Integrave/Hybrid approaches are increasingly being used to determine three-dimensional (3D) structures of biological macromolecules by combining informaon from X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy with data from diverse complementary experimental and computaonal methods. Two such complementary methods include cross- linking coupled mass spectrometry (CLMS) and double electron-electron resonance (DEER). These techniques can be used to generate distance restraints that need to be visualized in the context of exisng and modeled macromolecular structures. At present, displaying distance restraints as annotaons for structure modeling and validaon is largely limited to specialists. Herein, we ulize the web-based NGL library to provide 3D visualizaon of distance restraints integrated with general molecular graphics. Software availability PDB ID 3J3Q Applicaon 1: Distances derived from chemical cross-linking coupled mass spectrometry (CLMS). Distance restraints between atoms can be depicted with cylinders connecng one atom to the other. Above: CLMS data for human serum albumin mapped onto PDB ID 1AO6 and rendered in 3D using the NGL library. Below: The same CLMS data for human serum albumin shown in an arc diagram.The linked residue pair C476 to K564 is highlighted in both views, the 3D rendering and the 2D diagram. Both views are part of the integrated crosslink idenficaon plaorm XI (hps://github.com/Rappsilber-Laboratory/xi_installaon) Applicaon 2: Distances derived from double electron-electron resonance (DEER) experiments. Distance restraints for the inacve and acve state of bovine rhodopsin shown as probability density distribuons (below) are rendered as volume slices (above) using the NGL library. Note how the density for residue 252 moves outwards in the acve state (orange arrow). Acknowledgements DEER data: M Elge, Altenbach et. al. (doi: 10.1073/pnas.0802515105) XI: M Graham, C Combe, J Rappsilber CLMS data: A Belsom et. al. (doi: 10.1074/mcp.M115.048504) Scalable molecular graphics Library for biophysical/biochemical data WebGL-based, no plug-ins needed Funding RCSB PDB is funded by a grant [DBI- 1338415; PI: SK Burley] from the NSF, the NIH, and the US DoE. ALBU_HUMAN 1 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 585 Rendering of volumetric data as isosurfaces at any density threshold or as volume slices is available in the NGL Webapp (hp://arose.github.io/ngl/). Display of volume slices supports linear and cubic interpolaon as well as filtering by any density threshold.
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Transcript of Web-based visualization of 3D distance restraints integrated with NGL molecular graphics @ BPS17
Web-based visualization of 3D distance restraintsintegrated with NGL molecular graphics
Integrative/Hybrid approaches
Funding and acknowledgements
NGL library
CLMS distances in XI DEER distances in NGL Webapp
HIV-1 capsid at three scales216 hexameric and12 pentameric subunits,~2.4M unique atoms
Alexander S. Rose and Stephen K. BurleyRCSB Protein Data Bank
University of California San Diego and Rutgers, The State University of New Jersey
NGL library and viewer (https://github.com/arose/ngl)AS Rose & PW Hildebrand (2015)NGL Viewer: a web application for molecular visualization.Nucl. Acids Res. 43 (W1). doi:10.1093/nar/gkv402
Integrative/Hybrid approaches are increasingly being used to determinethree-dimensional (3D) structures of biological macromolecules by combininginformation from X-ray crystallography, NMR spectroscopy, and cryo-electronmicroscopy with data from diverse complementary experimental andcomputational methods. Two such complementary methods include cross-linking coupled mass spectrometry (CLMS) and double electron-electronresonance (DEER). These techniques can be used to generate distancerestraints that need to be visualized in the context of existing and modeledmacromolecular structures. At present, displaying distance restraints asannotations for structure modeling and validation is largely limited tospecialists. Herein, we utilize the web-based NGL library to provide 3Dvisualization of distance restraints integrated with general moleculargraphics.
Software availability
PDB ID 3J3Q
Application 1: Distances derived from chemical cross-linking coupledmass spectrometry (CLMS). Distance restraints between atoms can bedepicted with cylinders connecting one atom to the other. Above: CLMSdata for human serum albumin mapped onto PDB ID 1AO6 and renderedin 3D using the NGL library. Below: The same CLMS data for humanserum albumin shown in an arc diagram.The linked residue pair C476 toK564 is highlighted in both views, the 3D rendering and the 2D diagram.Both views are part of the integrated crosslink identification platform XI(https://github.com/Rappsilber-Laboratory/xi_installation)
Application 2: Distances derived from doubleelectron-electron resonance (DEER) experiments.Distance restraints for the inactive and active stateof bovine rhodopsin shown as probability densitydistributions (below) are rendered as volume slices(above) using the NGL library. Note how thedensity for residue 252 moves outwards in theactive state (orange arrow).
Acknowledgements DEER data: M Elgeti, Altenbach et. al.
(doi: 10.1073/pnas.0802515105)
XI: M Graham, C Combe, J Rappsilber CLMS data: A Belsom et. al.
(doi: 10.1074/mcp.M115.048504)
Scalable molecular graphics Library for biophysical/biochemical data WebGL-based, no plug-ins needed
Funding RCSB PDB is funded by a grant [DBI-
1338415; PI: SK Burley] from the NSF,the NIH, and the US DoE.
ALBU_HUMAN1 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 585
Rendering of volumetricdata as isosurfaces at anydensity threshold or asvolume slices is available inthe NGL Webapp(http://arose.github.io/ngl/).Display of volume slicessupports linear and cubicinterpolation as well asfiltering by any densitythreshold.
