Vizbi 2014 Multiscale Visualization of Protein Assemblies
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visualizing molecular data across multiple scales
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Vizbi 2014 Multiscale Visualization of Protein Assemblies
- 1. Multiscale Visualization of Protein Assemblies Andreas Prlić www.rcsb.org @andorsch
- 2. 2014 International Year of Crystallography In June 1912, Max von Laue, Walter Friedrich and Paul Knipping demonstrate and confirm the nature of X-rays as waves by demonstrating their diffraction by crystals of Copper Sulphate and Zincblende Max von Laue source: Wikipedia After returning to Cambridge, Lawrence Bragg set about determining an explanation of the different reflective strengths of diffraction within a crystal of Zincblende. This work lead to the development of Braggs Law, which is a cornerstone of X-ray crystallography
- 3. Although not officially credited with taking part in the work, Rosalind Franklin had taken X-ray diffraction images of DNA and suggested the helical structure prior to the publishing of the work by Watson and Crick. The images she had taken were shown to Watson and Crick without her knowledge or approval, and in fact, Francis Crick later acknowledged that it was her data that was ‘the data we used’ to develop the hypothesis John Kendrew and Max Perutz win the Nobel Prize for Chemistry for their determination of the structures of Myoglobin and Haemoglobin using the technique of Xray crystallography. ! ! ! source: www.rigb.org
- 4. soon: 100k
- 5. The Scale of the Molecular World 5
- 6. 1Å 1nm 10nm 100nm 1μm 10μm Optical resolution limit PDB The Scale of Things 0.1mm chr22 unpacked: 10mm
- 7. We (as a field) are not too bad at visualizing things at one scale
- 9. It is harder to project data across scales
- 10. Biol. Assemb. Disease SNP:rs28940893 causes Metachromatic leukodystrophy (lysosomal storage disorder) ! asym unit ... the exchange of leucine for proline at position 426 increases the susceptibility of arylsulfatase A to lysosomal cysteine proteinases and results in a severe reduction in the half-life of the mutant polypeptides Polten A, Fluharty AL, Fluharty CB, Kappler J, von Figura K, Gieselmann V. N Engl J Med. 1991 Jan 3;324(1):18-22. ! ! Lukatela G, Krauss N, Theis K, Selmer T, Gieselmann V, von Figura K, Saenger W. Biochemistry. 1998 Mar 17;37(11):3654-64. arylsulfatase A -1AUK P-L same structure, but can’t form octamer 1E33
- 11. Thomas Down - www.biodalliance.org
- 12. RCSB PDB - Protein Feature View
- 13. Irving Geis in 1961 Source: HHMI Computer Graphics follows the imagination of Artists …with a delay of many years…
- 14. Jmol - Jsmol up to 4500 page views per day at RCSB PDB Here showing 5-fold symmetry of a protein Bob Hanson www.jmol.org
- 15. http://colorbrewer2.org/ PDB ID 3J69 Peter Rose https://github.com/biojava/rcsb-viewers/
- 16. ~5% of all men are red-green blind http://colorfilter.wickline.org/
- 17. Cyclic radial gradient clockwise around symmetry axis Helical spectral gradient along y-axis Icosahedral gradient along z-axis towards origin Peter Rose https://github.com/rcsb/symmetry
- 18. HIV Capsid currently largest structure ~ 13 million atoms Problem: Scale, Performance, Web
- 19. David Goodsell / RCSB
- 22. diameter: 250nm Mycoplasma mycoides David Goodsell 2011
- 24. OpenWorm
- 25. Acknowledgments Peter Rose Spencer Bliven Wolfgang Bluhm Phil Bourne Cole Christie Chunxiao Bi Ann Kagehiro Jessie Woo Kyle Pang Douglas Myers Turnbull Roshni Bhattacharya ! ! ! ! ! ! David Goodsell ! Stephen Burley, Maria Voigt, Christine Zardecki ! ! RCSB PDB
- 26. rcsb.org!•!info@rcsb.org! The RCSB PDB is managed by two members of the RCSB: The RCSB PDB is a member of: Funding: www.rcsb.org info@rcsb.org Find us at: @buildmodels /RCSBPDB /rcsbpdb /biojava