A Tool to Make 3 D Structural Data

A Tool to Make 3 D Structural Data More Comprehensible Eran Hodis, Jaime Prilusky, Eric Martz, Joel Sussman Proteopedia

Thank you Markus Fisher, Katie Rosa, Barry Honig

It’s hard to believe, but… 3 D structures are often times hard to understand -- even for a structural biologist!

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Levinthal and the Kluge 1965, MIT

Structural biology everywhere • 13 Nobel prizes since 1 st protein structure solved • Covers on Nature, Science, Cell, …

Oct 7, 2008 Growth in PDB 53, 521 structures but…

But, structural biology still suffers from a communication problem • Often communicating 3 D in 2 D • And not that accessible to non-structural biologists that don’t have experience with molecular visualization programs • Structural Biology, needs to make a special effort to develop tools for communication and accessibility, specifically better tools to integrate 3 D structure with functional information

i. See Abagyan, Lee, Raush, Budagyan, Totrov, Sundstrom & Marsden (2006) Disseminating structural genomics data to the public: from a data dump to an animated story TIBS 31 76 -8

Just some of the Great tools! • • • KING (“kinemage” kinetic image) Protein Explorer First. Glance in Jmol PDBSum Kumar & Ziegler

GOAL: to make structural information instantly accessible to a broad scientific audience 3 Key Elements: • Present 3 D information in an intuitive manner • A web browser is all you need • Content can be added by anyone, easily, without need to add on/purchase a program

Proteopedia aids in making structural information more understandable & accessible 3 Key Elements: • Present 3 D information in an intuitive manner • A web browser is all you need • Content can be added by anyone, easily, without need to add on/purchase a program

Lets take a look at another example poly(A) polymerase

PDB entry pages (seeded pages) vs protein or protein class pages (topic pages) Dr. Jaime Prilusky

Adding scenes is easy!

How easy is it to add a scene? (green link) 1 acj

Narrated video tutorial at Main Page www. proteopedia. org

http: //www. proteopedia. org Proteopedia • Built on Open Source tools: – Media. Wiki – Jmol • Content is free under GNU FDL license (same as Wikipedia). Proteopedia just the vehicle for creation & dissemination • Content - can be added by anyone, easily via user friendly authoring tools to link text to 3 D structures.

A wiki for the scientific community • Names of contributors are listed on each page to give credit & add responsibility

A wiki for the scientific community Each User can have a special area that only she/he can edit - useful for: • Tutorials • Lectures • Supplementary information for journal articles

Proteopedia is already in use & evolving with feedback (over 200 registered users)

How are people using it? • As a 3 D encyclopedia • and…

Fig. 2 The structure of a human p 110 alpha/p 85 alpha complex elucidates the effects of oncogenic PI 3 Kalpha mutations. , Huang CH, Mandelker D, Schmidt-Kittler O, Samuels Y, Velculescu VE, Kinzler KW, Vogelstein B, Gabelli SB, Amzel LM, Science. 2007 Dec 14; 318(5857): 1744 -8. 2 rd 0

Assignments for class Prof. Karl Oberholser Messiah College, PA Student: • Ms. Emily Forscher Photosystem II

Supplementary material Crystal structure of the Agrobacterium virulence complex Vir. E 1 -Vir. E 2 reveals a flexible protein that can accommodate different partners Orly Dym, Shira Albeck, Tamar Unger, Jossef Jacobovitch, Anna Branzburg, Yigal Michael, Daphna Frenkiel-Krispin, Sharon Grayer Wolf, and Michael Elbaum PNAS August 12, 2008 vol. 105 no. 32 1117011175

Conformational Changes Proton Channels

What to expect as a Viewing User? • Explore, but don’t expect to find a well-developed page on your favorite protein • Use the PDB entry pages to get Abstract + 3 D structure on the same page

Proteopedia allows you to be creative • Even though the tools are here, and the technical barriers lowered dramatically via Proteopedia’s relative ease of use … • It still takes some thought to make a good page!

Proteopedia linked to from PSI-Nature Knowledge Base

Coming soon • Biological molecule vs asymmetric unit • Color by evolutionary conservation • Save high resolution snapshots of 3 D structures

You’re invited! Proteopedia can help you with 1) Effective & intuitive communication of structural information 2) Creating 3 D figures for publications 3) Engaging structural tutorials & lectures Without you, Proteopedia is just a tool

The Proteopedia Team Dr. Jaime Prilusky Prof. Joel Sussman Eran Hodis Prof. Eric Martz Thanks also to John Moult and Israel Silman

Thank you www. proteopedia. org Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman: Proteopedia - a scientific 'wiki' bridging the rift between 3 D structure and function of biomacromolecules, Genome Biology 2008, 9: R 121