Proteopedia Outreach 2013-2014
Joel L. Sussman & Jaime Prilusky
Weizmann Institute of Science
Introduction
Proteopedia is a Wiki-web based encyclopedia (any platform, any browser) with a
descriptive text, a '3D' structure that the user can rotate and change at will, and green 'hot'
words between the text that interact with the 3D structure when clicked. With
Proteopedia, the sequence of events is: click on the green words while reading the text
description; then, observe the structure coming alive, rotating and changing its form to
demonstrate what the text suggests. A whole new and rich experience of discovery for
students and for teachers, see e.g. the page on Hemoglobin (Fig. 1).
Fig. 1. Hemoglobin page in Proteopedia (http://proteopedia.org/w/Hemoglobin), showing the
green 'hot' words that link the text to the 3D images on the web page.
Proteopedia was created in 2007 at the Weizmann Institute of Science, Israel, by Joel
Sussman, Eran Hodis, and Jaime Prilusky, with brainstorming and suggestions from
Israel Silman, John Moult, and Eric Martz (Hodis et al, 2008). Since its inception, the
number of users who are creating pages has grown steadily (~2700 from 54 countries),
with now over 107,000 different pages that have been added to Proteopedia.
It’s not surprising that education is one of the fields where Proteopedia’s scenes have
more impact. Teaching how data in a PDB file from a NMR experiment differs from that
of an X-ray experiment might be possible, but it’s easier if the student is able to compare,
play, and manipulate representations of the 3D model of NMR and X-ray structures. Fig
2 shows successive snapshots of a rotating representation of the PDB entry 2gmd, from
an antimicrobial protein solved by NMR. The balanced use of solid and semi-transparent
colors enhances the browsing of NMR structures.
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Fig. 2. View of PDB entry 2gmd (http://proteopedia.org/w/2gmd) (Japelj et al, 2007) Proteopedia.
Outreach to high school & Undergraduates
A series of workshop and have been held at the Davidson Institute and the Science
Teaching Center at the Weizmann Institute of Science. These include one for High
School Student in April 2014 conducted by Dr. Yael Schwartz of the Science
Teaching Center (Fig. 3) and another by Dr. Angel Herraez (from Dept. of Systems
Biology, University of Alcalá, Spain) for the members of the of the Science Teaching
Center.
Fig. 3. High-School students from throughout Israel learning to use Proteopedia at the workshop
held in the Davidson Center on 6-Apr-2014.
High-school students have also come on a regular basis to the Weizmann Institute on
for special tutorials on Proteopedia and working with physical models of proteins, e.g. 7th
Graders from the Gifted Teen Center in Emek Hefer in May 2014 (Fig. 4) (see also
(Appendix – I) of warm letter of thanks from the students parents).
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(a)
(b)
(c)
th
Fig. 4. 7 Graders from Gifted Teen Center in Emek Hefer visiting the Weizmann Institute of
Science (23-May-2014) (a) Joel Sussman with two students and their teacher, Irit Levi examining
physical models of 3D protein structures; (b) Students learning Proteopedia; (c) Shai Biran (PhD
student at the Weizmann Institute) giving a short lecture in the 3D Molecular Visualization
Theatre at the Weizmann Institute to the 7th Grade Students and their teacher.
Several of the Proteopedia pages have been translated into Hebrew and Arabic:
 List of Hebrew pages: http://proteopedia.org/wiki/index.php/Entry_list_(Hebrew)
 Pages in Arabic:
o http://www.proteopedia.org/w/1eve (Arabic)
o http://proteopedia.org/w/Beta_Secretase (Arabic)
o http://www.proteopedia.org/w/Lysozyme (Arabic)
o http://www.proteopedia.org/w/Myoglobin (Arabic)
In 2013, Jaime Prilusky and Joel Sussman were guest editors to a special issue of the
Israel Journal of Chemistry in which they also published an article on “JSmol and the
Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to
Proteopedia” (Hanson et al, 2013). Proteopedia as well as ConSurf (from Nir Ben-Tal’s
lab) were featured on the cover of that issue of the Journal (Fig. 5).
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Fig. 5. The cover of The Israel Journal of Chemistry (Vol 53, Issue 3-4) shows on the left a
ConSurf analysis of the influenza neuraminidase protein. The 3D tetramer colored by conservation
grades is shown in (A) with maroon indicating the most conserved amino acids, and close-up
views (B, C) are shown of one of the conserved regions with the anti-flu drug, oseltamivir
(tamiflu) bound (Celniker et al, 2013); On the right is a page from Proteopedia as viewed on an
iPad, via the JSmol viewer, showing a complex of HIV-Protease and Saquinavir (Invirase), the
first protease inhibitor approved by the FDA for the treatment of HIV (Hanson et al, 2013).
During the Fall Semester 2014-15, Jaime Prilusky and Joel Sussman will be giving a
one-semester course at the Hebrew University of JerusalemFaculty of Agriculture
(Rehovot Branch) to undergraduates and MSc student entitled: “Proteopedia – in silico
lab course”. The syllabus of the course, in Hebrew, is attached (Appendix – II)
Jaime Prilusky & Joel Sussman also gave a 2-day workshop on Proteopedia at the
Biennial Conference on Chemical Education at the Grad Valley State University,
Allendale, MI on (http://bcce-submissions.com/showSympPap.php?id=773) in August,
2014.
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References:
Celniker G, Nimrod G, Ashkenazy H, Glaser F, Martz E, Mayrose I, Pupko T, Ben-Tal N
(2013) ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein
Function. Israel J Chem 53: 199-206
Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL (2013) JSmol and the NextGeneration Web-Based Representation of 3D Molecular Structure as Applied to
Proteopedia. Israel J Chem 53: 207-216
Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL (2008) Proteopedia – a
scientific ‘wiki’ bridging the rift between 3D structure and function of
biomacromolecules. Genome Biol 9: R121
Japelj B, Zorko M, Majerle A, Pristovšek P, Sanchez-Gomez S, de Tejada GM, Moriyon
I, Blondelle SE, Brandenburg K, Andrä J, Lohner K, Jerala R (2007) The Acyl Group as
the Central Element of the Structural Organization of Antimicrobial Lipopeptide. J Am
Chem Soc 129: 1022-1023
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Appendix I –Parents’ letter of 7th Graders from the Gifted Teen Center in Emek Hefer
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Appendix II –Syllabus for Proteopedia – in silico lab course at the Faculty of
Agriculture of the Hebrew University in Jerusalem (Rehovot Branch)
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