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Interactive 3D Structural Genomics Articles: Now in PLoS Biology

Next week, the online open-access journal PLoS Biology will release enhanced versions of two new articles in collaboration with the Structural Genomics Consortium (SGC). These articles allow readers to rotate, translate, zoom and examine integrated 3D representations, using a unique platform known as iSee (interactive Structurally enhanced experience), developed in a collaboration between the SGC's co-developers Dr. Brian Marsden and Dr. Wen Hwa Lee, and Prof. Ruben Abagyan and his team from MolSoft L.L.C. This platform, featuring animations that 'fly' the reader through the structural representation to the specific molecular feature being described, has already been successfully employed in a pioneering PLoS ONE collection highlighting a number of protein structures from the SGC. These two new articles will be the first in this enhanced format in PLoS Biology.

Each of the two articles will reveal 3D structures of several medically-relevant proteins, providing critical information for understanding the molecular basis of their physiological functions and roles. In the first article, Dr. Stefan Knapp and colleagues present the structure of CaMKII, an enzyme that plays a central role in cellular signalling by sensing and transmitting calcium signals. CaMKII is activated by undergoing large conformational changes in the presence of calcium and calmodulin. This activated state is then sustained, functioning as a molecular switch to modulate synaptic strength, and is thus implicated in the molecular basis of memory. "We were very excited when we first saw the major structural changes but immediately were concerned that the change should be presented in a more interactive way than in a normal paper. And iSee is the perfect way to accomplish this," said Prof. Stefan Knapp from SGC Oxford, who coordinated the CaMKII study.

In the second study Dr. Sirano Dhe-Paganon from SGC Toronto and colleagues report a thorough, family-wide structure/function analysis of human peptidyl-prolyl isomerases. These proteins are targets of the immunosuppressive drug cyclosporin, which is used to combat organ transplant rejection. The results indicate there are unique structural features in these proteins that may be exploited for improving the efficacy of this class of drugs. "iSee makes it easy to share those comparative details that are too intricate to be represented in static images," said Dhe-Paganon who led the study on peptidyl-prolyl isomerases.

The iSee concept was developed in line with SGC's ethos of promoting open and accessible science. As such, it is one of the main tools for disseminating the SGC's data in a way that can be easily used by anyone. "For 'open science' to be a truly changing endeavour, we have to make it accessible at all levels - and this includes delivering the knowledge in the most intuitive way so even a high school pupil can read, interact and understand what we do," said Prof. Aled Edwards, Chief Executive of the SGC. "We are delighted to collaborate with PLoS Biology, an influential open-access champion, to bring the iSee concept to its readers."

To access the enhanced interactive articles, the reader can download a free web browser plug-in, available for Windows, Mac OS X and Linux. Videos with step-by-step installation instructions and a quick demo are available in the related links section.

Links:
PLoS Biology collection: the two articles mentioned in the text
Video: installing iSee - http://www.thesgc.org/iSee/vide-installing-plos.html
Video: using iSee - http://www.thesgc.org/iSee/video-using-plos.html
The SGC: www.thesgc.org
PLoS ONE SGC collection: http://www.ploscollections.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcol.v02.i04
Molsoft L.L.C.: www.molsoft.com
Press-only preview of the interactive articles: http://www.sgc.ox.ac.uk/PLoSBiology/

Knapp and Colleagues:

Funding: The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research (http://www.cihr.ca), the Canadian Foundation for Innovation (http://www.innovation.ca), Genome Canada (http://www.genomecanada.ca ) through the Ontario Genomics Institute (http://www.ontariogenomics.ca), GlaxoSmithKline (http://www.gsk.com), Karolinska Institutet (http://ki.se), the Knut and Alice Wallenberg Foundation (http://www.wallenberg.com), the Ontario Innovation Trust (http://www.oit.on.ca), the Ontario Ministry for Research and Innovation (http://www.mri.gov.on.ca), Merck & Co. (http://www.merck.com), the Novartis Research Foundation (http://www.novartis.com), the Swedish Agency for Innovation Systems (http://www.vinnova.se), the Swedish Foundation for Strategic Research (http://www.stratresearch.se), and the Wellcome Trust (http://www.wellcome.ac.uk). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests statement: The authors declare that no competing interests exist.

Citation: Rellos P, Pike ACW, Niesen FH, Salah E, Lee WH, et al. (2010) Structure of the CaMKIId/Calmodulin Complex Reveals the Molecular Mechanism of CaMKII
Kinase Activation. PLoS Biol 8(7): e1000426. doi:10.1371/journal.pbio.1000426

PLEASE ADD THE LINK TO THE PUBLISHED ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.1000426

PRESS ONLY PREVIEW OF THE ARTICLE: http://www.plos.org/press/plbi-08-07-Knapp.pdf  

RELATED SYNOPSIS: http://www.plos.org/press/plbi-08-07-KnappSynopsis.pdf 

CONTACT:
Dr. Stefan Knapp
University of Oxford
Structural Genomics Consortium
Oxford, Oxfordshire OX3 7DQ
United Kingdom
+44 1865 617587
Stefan.knapp@sgc.ox.ac.uk

Dhe-Paganon and colleagues:

Funding: The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canadian Foundation for Innovation, Genome Canada through the Ontario Genomics Institute, GlaxoSmithKline, Karolinska Institutet, the Knut and Alice Wallenberg Foundation, the Ontario Innovation Trust, the Ontario Ministry for Research and Innovation, Merck & Co., the Novartis Research Foundation, the Swedish Agency for Innovation Systems, the Swedish Foundation for Strategic Research, and the Wellcome Trust. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests statement: The authors declare that no competing interests exist.

Citation: Davis TL, Walker JR, Campagna-Slater V, Finerty PJ Jr, Paramanathan R, et al. (2010) Structural and Biochemical Characterization of the Human
Cyclophilin Family of Peptidyl-Prolyl Isomerases. PLoS Biol 8(7): e1000439. doi:10.1371/journal.pbio.1000439

PLEASE ADD THE LINK TO THE PUBLISHED ARTICLE IN ONLINE VERSIONS OF YOUR REPORT: http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.1000439

PRESS ONLY PREVIEW OF THE ARTICLE: http://www.plos.org/press/plbi-08-07-Dhe-Paganon.pdf 

CONTACT:
Dr. Sirano Dhe-Paganon
University of Toronto
Structural Genomics Consortium and Department of Physiology
Canada
4169463876
sirano.dhepaganon@utoronto.ca