PENCE Proteocols The Official Newsletter of the Protein Engineering Network of Centres of Excellence

The PENCE AGM & CPI 2003 Conference Wrap-up In This Issue

The 2003 PENCE Annual General Meeting and the third annual AGM & CPI 2003 Wrap Up...... 1 meeting of the Canadian Proteomics Initiative (CPI 2003) were held The 2003 PENCE AGM...... 1 st th May 21 to May 27 2003 at Vancouver’s Forest Sciences Centre, AGM & CPI 2004...... 1 located on the University of British Columbia’s Main Campus. AGM Poster Prize Recipients...2 CPI 2003...... 3 The success of this years PENCE AGM as well as CPI 2003 CPI Poster Prize Winners...... 3 was evident from the large participant turnout (approximately 100 A Focus on New PENCE PIs: and 300 attendees respectively). A wonderful selection of seminars, David Vocadlo...... 4 posters, and tutorials helped to make this years conference an Congratulations to...... 4 overwhelming success. Congratulations to the PENCE office staff HUPO/IUBMB...... 4 for coordinating such excellent back-to-back conferences! 2002-2003 Annual Report...... 4 NSERC Discovery Grants...... 4 Recent Publications...... 5 PENCE Welcomes The 2003 PENCE AGM Orly Weinberg...... 5 Financial & Statistical Info....5 The 2003 PENCE AGM began Wednesday May 21st with a INPEC 2003 Meeting...... 5 reception at the Gage Towers to give PIs and their students a chance Contributors...... 5 to mix and mingle.

On Thursday, May 22nd, the morning sessions of 2004 PENCE AGM & CPI 2004 the 2003 AGM began with an introduction of the first PENCE Supported Chair in Protein With the 2003 AGM and CPI Sciences Research, Justin meetings successfully behind us, it is MacDonald from the University time to start planning for 2004! The of Calgary. Following this 2004 PENCE AGM and CPI 2004 will introduction, PENCE PIs Sean be held in Montreal over the weekend Cutler, Guohui Lin, David of May 14th. Perrin, and David Rose spoke about the recently funded New Additional information will be Ideas Projects 1 through 4 A busy registration day, as the available shortly. In the meantime, respectively. After coffee, 2003 PENCE AGM gets please contact Ryan Leskiw by e-mail Andrew Emili and Nabil Seidah underway. ([email protected]) if you would provided the AGM participants like information on attending the 2004 with progress overviews on PENCE AGM and CPI 2004. We hope their PENCE funded projects. to see you there!

To bring the participants up-to-date on the newly funded PENCE SARS Initiative, Rachel Roper, from the University of Victoria, provided an overview of coronaviruses and the SARS Bioinformatics Suite at www.sarsresearch.ca. Lindsay Eltis discussed his project studying the 3CL protease of Urbani Coronavirus and Jim Rini talked about approaches to production of Spike protein.

After lunch and poster viewing, PENCE PIs Harry Schachter, Jim Rini, and Liang Li updated the AGM participants on their PENCE funded projects. Lawyer Roger Kuypers provided an overview of intellectual property issues for the PENCE PIs. The afternoon sessions were followed by a lively discussion on the future of PENCE, Conference attendees listening led by Steve Withers. The evening ended with a lovely BC salmon intently to Dr. Howard dinner at the Sage Bistro on the UBC Campus. Schachman’s talk entitled “Science Under Seige” at the On the morning of Friday, May 23rd, the 2003 PENCE AGM CPI 2003 Banquet. concluded with informal Project Group Meetings, and a tribute to the late Dr. Ian Clark-Lewis.

Issue: 2003 June / July PENCE NETWORK NEWSLETTER 1 PENCE Proteocols The Official Newsletter of the Protein Engineering Network of Centres of Excellence

2003 PENCE AGM Poster Prize Recipients

The 2003 PENCE AGM Poster Competition consisted of many outstanding posters, and as such, the competition for the poster prizes was tight. Among the contenders, Daniel Gauthier, Chris Tarling, and Rachel Roper came out on top, as first, second, and third-prize winners respectively. Congratulations to all of the winners! ****************************************************************************** First Prize – Daniel Gauthier

Daniel Gauthier won First Prize at the 2003 PENCE AGM for his poster entitled Development of a non-discriminatory investigative approach for membrane proteins. Daniel is currently working in Dr. Claude Lazure’s lab at IRCM in the research unit on structure and metabolism of neuropeptides. They have been working on this novel method in order to bypass some of the current limitations in the study of membrane proteins using proteomics. Overall, they hope to get a clearer picture of the surface and a reliable means to identify those proteins involved in communication, transport, and interaction. In particular, Daniel would like to apply this technique to the study of spermatozoa-egg interaction in order to identify factors involved in fertilization, as this is the specific goal of his project.

Daniel grew up in Varennes, a small town near Montreal. He completed his B.Sc. in biochemistry at McGill, and is now registered with the Division of Experimental Medicine, in McGill’s Faculty of Medicine. Daniel is also currently a member of the student committee at IRCM. In between all of his hard work Daniel enjoys playing tennis, riding his bike, and having a beer or two with colleagues and friends.

Second Prize - Chris Tarling Chris’ poster entitled Identification of the Catalytic Machinery of a Family 29 Alpha-L-Fucosidase from Thermotoga Maritima Via Trapping of a Glycosyl- Enzyme Intermediate earned second prize in this year’s competition. This poster details how fucose-containing glycoconjugates are key antigenic determinants in many biological processes. A change in expression levels of the enzymes responsible for tailoring these glycoconjugates has been associated with many pathological conditions and it is therefore surprising that little information is known regarding the mechanism of action of these important catabolic enzymes.

The catalytic nucleophile of this enzyme was identified to be Asp224 using a mechanism-based

covalent inactivator. This result was confirmed by the 5000 fold lower activity (kcat/KM) of the site-directed mutant Asp224Ala, and the subsequent rescue of activity upon addition of exogenous nucleophiles. This research presents the first identification of the catalytic nucleophile of an Alpha-L-Fucosidase, a key step in the understanding of these important enzymes.

Chris received his undergraduate degree from Bristol in 1994 and his PhD from Cambridge in 2000. Following the completion of his PhD, Chris started as a post-doc in Steve Withers lab at UBC, and in May 2003 Chris became a Research Associate in Dr. Withers group. In his spare time, Chris enjoys outdoor activities such as skiing, mountaineering, and climbing through the beautiful BC terrain.

Third Prize - Rachel Roper

The poster entitled The SARS Bioinformatics Suite details the SARS Bioinformatics website www.sarsresearch.ca, supported by PENCE and SAVI (BC SARS Accelerated Vaccine Initiative). This is a collaborative effort from the labs of Dr. Rachel Roper (Adjunct Assistant ) and Dr. Chris Upton (Associate Professor) at the University of Victoria.

There are two computer programmers, Angelika Ehlers and Ryan Brodie, working on developing the bioinformatics software and website. Cristalle Watson, a Biochemistry & Microbiology co-op student is researching SARS and Coronavirus literature on processing of the polyprotein, doing protein analyses, and drawing diagrams of the virus genome and predicted membrane proteins in the virus particle. Vasily Tcherepanov is annotating new SARS genomes and analyzing the spike glycoprotein.

Both Chris and Rachel have worked in poxvirus bioinformatics www.poxvirus.org and, together with lab members, have redesigned the software to analyze coronavirus genomes. This site is available for all SARS researchers.

Issue: 2003 June / July PENCE NETWORK NEWSLETTER 2 PENCE Proteocols The Official Newsletter of the Protein Engineering Network of Centres of Excellence

CPI 2003 CPI 2003 Poster Prize Winners

The CPI 2003 program provided a great forum for the Federico Zahariev won first dissemination of cutting-edge research in proteomics and protein prize at the CPI 2003 conference for . his poster entitled “Theoretical Studies of the Catalytic Mechanisms of the After a lively and informative welcoming address by Martha Periplasmic Nitrate Reductase.” Piper, CPI 2003 was underway. Ruedi Aebersold brought the Federico is a post-doctoral in the attendees up-to-date on recent advances in quantitative proteomics lab of Prof. Yan Alex Wang in the technologies, while John Aitchison described the application of Department of Chemistry at the systems biology to the study of University of British Columbia. peroxisome biogenesis and function. Katie Meehan won third Fiona Brinkman spoke prize for her poster entitled about the use of bioinformatics “Quantitation and Identification of analyses to reveal patterns in the Androgen-Regulated Proteins in evolution of microbial virulence. Prostate Cancer Cells Using Isotope- Mitsu Ikura described structural Coded Affinity Tags and Mass studies of protein-protein and protein- Spectrometry.” Katie is a post-doctoral ligand complexes while Natalie fellow in Dr. Marianne Sadar’s Strynadka discussed challenges and laboratory in the Department of approaches in the crystallographic Cancer Endocrinology at the BC analysis of membrane proteins. Cancer Research Centre in Vancouver. Organellar proteomics were described by John Bergeron, while Jolyne Drummelsmith won provided an update on CPI 2003 banquet second prize for her poster entitled his research of interaction domains in speaker Dr. Howard “Proteomic Analyses of Drug cellular regulation. John Moult Schachman from UC Resistance in the Protozoan Parasite described a structure based model of Berkeley. Leishmania.” Jolyne is currently a the impact of SNPs on protein structure postdoctoral fellow in the lab of Dr. and function. Chris Dobson provided Marc Ouellette at the Infectious an analysis of how proteins can Diseases Research Centre of Laval misfold in vivo and showed that this phenomenon is linked with a University. wide range of diseases.

Mike Moran described hybrid mass spectrometry technologies that enable measurements of disease and drug-induced changes in cellular states in terms of protein expression levels, organellar protein composition, protein-protein interactions, and phospho-protein profiles.

In addition, three BC Focus talks were given: Marianne Sadar described proteomic approaches that are being used for prostate cancer research. Juergen Kast discussed issues in protein sequencing by mass spectrometry and Bob Olafson provided an overview of proteomics in BC, describing the University of Victoria/ Genome BC Proteomics Centre.

The field of proteomics is exploding, and has become an Some of the PENCE HQ exciting and innovative area of scientific research. This was personnel enjoying the pre-CPI particularly evidenced by the very spirited and lively roundtable banquet festivities at the Brock session on the ‘State of Proteomics in Canada’ chaired by Steve House Restaurant (left to right: Withers and Roger Foxall. The roundtable session was very well- Dianne Wilchak, Erynn attended, and the energy and interest of the participants was Shannon, and Rachel apparent. Yakimchuk) Finally, at the CPI banquet, Howard Schachman gave a witty and insightful account of how government leaders in the United States have initiated policies likely to have a major impact on the conduct of scientific research, in his talk entitled “Science Under Seige”.

Issue: 2003 June / July PENCE NETWORK NEWSLETTER 3 PENCE Proteocols The Official Newsletter of the Protein Engineering Network of Centres of Excellence

2002-2003 Annual Report A Focus on New PENCE PIs: David Vocadlo

It’s that time again! Dr. David Vocadlo joins PENCE as the recipient of the second Preparations have begun on the 2002- PENCE Supported Chair in Protein Sciences Research. David is 2003 PENCE Annual Report. currently located at the University of California at Berkeley, but will be joining the Network as a Faculty Member at Simon Fraser We are looking for your University in Vancouver in 2004. David was born in Brantford, Ontario success stories in both your current and lived in a number of places while growing up. Once David and past PENCE Projects. For example, completed his B.Sc. in combined honours, studying chemistry and if any of the results from your past biochemistry, he worked as a research assistant in the Biotechnology PENCE research have been adopted Laboratory at UBC with Drs. Warren and Kilburn. The experience by industry, send us a short that David gained in these 2 labs prompted him to continue his paragraph, detailing the research, and research and thus he joined the laboratory of Dr. Withers at UBC. your success story may be featured While working in Dr. Withers lab, David’s thesis focused on the catalytic in this year’s Annual Report. mechanism of retaining b-glycosidases. In order for this year’s Following his time in Dr. Withers lab, he pursued his continuing publication to surpass the success interests in carbohydrate chemistry by obtaining a postdoctoral of last year’s Annual Report, we position with Dr. Carolyn Bertozzi at the University of California at need to include some great pictures. Berkeley. While studying in Dr. Bertozzi’s lab, David’s main goal We are looking for pictures of your was to develop a novel chemical approach to identifying intracellular personnel, as well as your most proteins that are post-translationally glycosylated. David is interested impressive protein images. The in how cellular metabolism alters the state of protein post-translational selected images will appear between modifications and how, in turn, these modifications affect protein the covers of the 2002-2003 PENCE function. Annual Report and one lucky person…who will be rewarded…will For exercise beyond the page turning involved in reading have their image grace the cover! piles of scientific articles, David enjoys rock climbing, kayaking, and backcountry skiing. For alternative mental exercise he reads Please e-mail your images extensively, plays chess, and dreams about painting (which he never and success stories to Erynn Shannon has time to do). at [email protected] Congratulations to… NSERC Discovery Grants The University of Alberta recently purchased a computer that will be the fastest computer at any Canadian University. PENCE’s On Monday, June 2, 2003, own Dr. Jonathan Schaeffer, was the the Natural Sciences and Engineering driving force behind the acquisition of Research Council of Canada (NSERC) the nations third fastest computer. The announced its new round of grants. $3 Million price tag is a small price to In total, the NSERC funding will pay to assist the U of A in becoming a introduce 2,752 research grants world leader in nanotechnology and worth $325 million over five years cellular studies. The computer, about into 67 Canadian post-secondary 4,000 times quicker than the average institutions across the country. home or business PC, is capable of doing a year’s worth of scientific 156 researchers at the calculations in a day. For more University of Alberta alone were information, please click HERE to view awarded a total of $18.7 million in the Edmonton Journal article, or click funding over the next five years to HERE to view the U of A article. aid in supporting a variety of research. HUPO 2nd Annual & IUBMB XIX Joint World Congress PENCE would like to A combination of SARS, heightened tensions regarding congratulate all of the PIs who security, and a general reluctance to travel, have dealt a devastating received funding from NSERC’s new blow to major scientific meetings recently in Toronto. In this round of grants. light, the decision to combine the previously cancelled International Union of Biochemistry & Molecular Biology (IUBMB) Congress For more information please (the principal international conference for Biochemistry and Molecular visit, http://www.nserc.ca/news/ Biology) with the Human Proteome Organization (HUPO) 2003/p030602.htm World Congress in Montreal (October 8-11) comes as a welcome solution. For more information, please visit the IUBMB website at http://www.iubmb.unibe.ch/ or the HUPO website at http://www.hupo2003.com/.

Issue: 2003 June / July PENCE NETWORK NEWSLETTER 4 PENCE Proteocols The Official Newsletter of the Protein Engineering Network of Centres of Excellence

Recent Publications INPEC 2003 Meeting

Dr. Nabil Seidah and his collegues recently published an The International Network of article online in the May 5, 2003 edition of Genetics. Protein Engineering Centers (INPEC) was created in 1991 to promote the The article shows that their enzyme NARC-1 (gene called field of protein engineering. The PCSK9) is directly responsible for a human disease known as founding organizations were GBF dominant familial hypercholesterolemia. This is very exciting as it is (Germany), BERI (Japan) and BRI the first ever dominant human disease associated with mutations in (Canada). INPEC membership a proprotein convertase. expanded rapidly, and at the present time national organizations & To view the entire article, please click the following link. laboratories from 20 countries http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v34/ participate in the Network of which n2/full/ng1161.html Canada is represented by PENCE and BRI.

Running from July 25, 2003 – PENCE Welcomes Orly Weinberg July 28, 2003, this annual meeting provides the opportunity to present to PENCE would like to welcome Orly Weinberg to the Regional INPEC members the accomplishments Centre team. Orly will be assisting with the office operations of the of Canadian researchers in the Montreal node, and is available to help local researchers with any broadly viewed field of protein pertinent questions. In addition to troubleshooting, she will be engineering as well as to receive the planning meetings and seminars, and instituting a student-training latest news from other member program. organizations. The 2003 meeting will feature many well-known speakers Her background includes research in molecular biology labs, from around the world, including medical writing, and consulting for industry about federal R&D grant PENCE’s own Steve Withers, Tony applications. Welcome aboard Orly! Warren, and Mirek Cygler.

For more information on the INPEC Financial & Statistical Information 2003 meeting, please visit http:// www.inpec.ca PENCE would like to thank all of the PIs who submitted their financial and statistical information in a timely manner. This allowed PENCE to meet the June 30th NCE reporting deadline.

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Contributors

Erynn Shannon Newsletter Editor [email protected]

Ryan Leskiw PENCE Logistics & Communications Manager [email protected]

Steve Withers PENCE Scientific Director [email protected]

Sue Abrams Regional Reporter (Sask) [email protected]

Lawrence McIntosh Regional Reporter (BC) [email protected]

David Rose Regional Reporter (Ont) [email protected]

Nabil Seidah Regional Reporter (Que) [email protected]

David Wishart Regional Reporter (Alta) [email protected]

What do you think of the Newsletter? Write your comments to Erynn Shannon or your Regional Reporter

Issue: 2003 June / July PENCE NETWORK NEWSLETTER 5