University of Toronto
people & news	publications

William Reynolds (Chemistry)

Peter Macdonald (Chemistry, Mississauga)

Scott Prosser (group page) (Chemistry, Mississauga)

Andre Simpson (Chemistry, Scarborough)

Myrna Simpson (Environmental Science, Scarborough)

Lewis Kay (Biochemistry)

Cheryl Arrowsmith (Ontario Cancer Institute)

Mitsu Ikura (Medical Biophysics UofT, Ontario Cancer Institute)

Julie Forman-Kay (SickKids)

Simon Sharpe (SickKids)

Genevieve Seabrook (NMR Facility, Ontario Cancer Institute)

Tim Burrow (CSICOMP, Chemistry)

CSICOMP (Chemistry)

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Dear Colleagues,

A reminder that online registration is now open for the MOOT XXIV NMR Symposium which will be taking place October 22nd-23rd (2011) in Toronto, Ontario, hosted at the Hospital for Sick Children and the University of Toronto. Details are available on the conference website, http://www.mootnmr.org

The abstract submission deadline for this year's MOOT is 23 September, and abstracts for both oral and poster presentations can be submitted online during the registration process.

Agilent Technologies will be holding a day long symposium and mixer the day before this year's MOOT (Oct. 21). More information regarding the agenda and location for this symposium will be posted soon at http://www.spinsights.net/

We have arranged conference pricing for accomodation downtown at the Delta Chelsea hotel near the Hospital for Sick Children, as well as discounted airfares through Porter Airlines (serving Toronto Island airport). Please see the "Travel" section of http://www.mootnmr.org for more details!

OF NOTE: Porter airlines is currently having a 50% off all fares sale, on all bookings made by September 7. Use promotion code WOW50. See the Porter website for details!

If you have any questions or comments, please send a message to (mootnmr "at" gmail.com), or contact Simon Sharpe (ssharpe "at" sickkids.ca).

We look forward to seeing you in October!

Sharpe lab - Molecular Structure and Function Programme, Hospital for Sick Children / Dept. of Biochemistry, U. Toronto

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Stable Isotopes for Structural Biomolecular NMR (July 22/11)

Cambridge Isotope Laboratories (CIL) made available a series of application notes on the use of stable isotopes in Biomolecular NMR. These application notes were written by some of the world's leading researches in the field, including several Canadian scientists.

Lewis Kay (University of Toronto) "Alanine Probes of Supra-Molecular Structure and Dynamics", page 9.

Leonid S. Brown and Vladimir Ladizhansky (University of Guelph) "Pichia pastoris as a Eukaryotic Protein Isotope-Labeling System", pages 14-15.

Ying Fan, Lichi Shi, Vladimir Ladizhansky and Leonid S. Brown (University of Guelph) "Uniform Isotope Labeling of Eukaryotic Proteins in Methylotrophic Yeast for High-Resolution NMR Studies - Extension to Membrane Proteins", Application Note 26, pages 71-74.

Recent research by Gang Wu's group (Queen's University) is cited as an example of advanced 17O NMR spectroscopy in large protein-ligand complexes in solution and in the solid state, "17O NMR reagents", page 34.

These application notes are available for download as a PDF file (5.1MB) "Stable Isotopes for Structural Biomolecular NMR Catalog" at:
http://www.isotope.com/cil/literature/research_literature/index.cfm

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ICSG 2011: International Conference on Structural Genomics (April 6/11)

ICSG 2011 Program Now Available

Dear Colleague,

We hope that you are planning to join us in Toronto, Canada for the International Conference on Structural Genomics 2011 which will be held on May 10-14, 2011. We have an excellent scientific program prepared which includes both oral and poster presentations (scientific program). Participants will also enjoy the fabulous view of the city of Toronto during the banquet to be held at the revolving 360 Restaurant at the top of the CN tower. An optional post-conference tour to Niagara Falls will also be available. We invite you to register on line by April 15, 2011 at 11:59 pm EST. A limited number of late poster abstracts will be accepted until April 12, 2011 at 11:59 pm EST

In addition to the main ICSG meeting, there will be a whole day of concurrent satellite workshops (May 10, 2011) that are free for ICSG 2011 registrants, including: Small Molecule Screening Workshop - This hands-on workshop will allow participants to screen a protein of their choice for binding of selected compounds, using thermal shift assays.

iSee: Interactive 3D Documents for the Dissemination of Structural Biology - This hands-on workshop will familiarize participants with the iSEE 3D graphical software which allows interactive viewing of 3 dimensional molecular structures and is currently used by journals such as Nature Structural & Molecular Biology and PLoS Biology and PLoS ONE Eukaryotic

Gene Expression Systems Workshop - This workshop will provide participants with a detailed understanding of the state-of-the-art for production of eukaryotic proteins destined for biochemical, biophysical, and structural analyses..

Workshop on NMR Methods for Structural Biology - This workshop will survey technologies for structure/function investigations of proteins, developed in (or in collaboration with) structural genomics projects, that are ready for widespread use by the wider biological community.

Phenix Crystallography Software Workshop - This workshop will introduce the PHENIX software for macromolecular structure determination and the core algorithms that it uses. It will provide hands-on tutorials for crystallographers of all levels.

The workshop registration deadline is Monday April 11, 2011 at 11:59 pm EST

Please visit http://www.icsg2011.org for ICSG 2011 meeting and workshop registration details and to submit your poster abstract.

We hope to see you there!

Best regards,

Cheryl Arrowsmith - ICSG 2011 Organizer

Ted Baker, Stephen Burley, Dino Moras, Joel Sussman, Shigeyuki Yokoyama,
Tom Terwilliger - ISGO Executive Committe

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A.J. Simpson, D.J. McNally, M.J. Simpson "NMR Spectroscopy in Environmental Research: From Molecular Interactions to Global Processes," Progress in Nuclear Magnetic Resonance Spectroscopy (2010) in press. (Invited Review) http://dx.doi.org/10.1016/j.pnmrs.2010.09.001

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L.E. Kay, "Structure and Dynamics of Proteins – Big and Small", Encyclopedia of Magnetic Resonance (2010). http://dx.doi.org/10.1002/9780470034590.emrhp1027

W.F. Reynolds, "Heteronuclear Multiple Bond Correlation (HMBC) Spectra", Encyclopedia of Magnetic Resonance (2010). http://dx.doi.org/10.1002/9780470034590.emrstm1176

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D.M. Korzhnev, T.L. Religa, W.Banachewicz, A.R. Fersht, L.E. Kay, "A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution", Science 329 (2010) 1312-1316. http://dx.doi.org/10.1126/science.1191723

Abstract: "Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift–based method for structure elucidation, to determine an atomic-resolution structure of an "invisible" folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states."

This research article by Lewis Kay (University of Toronto) and colleagues is also accompanied by the Science Perspective

H.M. Al-Hashimi, "Exciting Structures", Science 329 (2010) 1295-1296. http://dx.doi.org/10.1126/science.1195571

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Postdoctoral position, University of Toronto Mississauga (August 14/10)

A postdoctoral position is available for a Canadian Institutes of Health Research funded project in the laboratory of Professor Voula Kanelis at the University of Toronto Mississauga (UTM). The successful candidate will investigate the nucleotide binding domains (NBDs) of the sulfonyl urea receptors (SURs) using biophysical approaches, including NMR spectroscopy. SUR proteins are ABC transporters that form the regulatory subunits of ATP-sensitive potassium (KATP) channels. We are studying the effects of disease-causing mutations in the SUR NBDs on their stability, structure, and interactions with other regions in the SURs and in KATP channels. A Ph.D. in biochemistry or a related discipline is required. Candidates should have experience with protein expression and purification and protein NMR spectroscopy.

Located 30 km west of downtown Toronto, The University of Toronto Mississauga (www.utm.utoronto.ca) is a campus of the University of Toronto (www.utoronto.ca), the largest research University in Canada. UTM provides all of the advantages of research at the University of Toronto, while additionally providing a smaller, friendly campus environment in a beautiful natural setting by the Credit river.

Our newly renovated and well-equipped laboratory contains all the equipment necessary for protein biochemistry and fluorescence spectroscopy. Other equipment (CD spectrophotometer, isothermal titration calorimeter, differential scanning calorimeter) is available in the Center for Applied Bioscience and Biotechnology at the University of Toronto Mississauga. NMR experiments will be performed primarily on a Varian 600 MHz spectrometer equipped with a cryoprobe at UTM. We also have access to high-field spectrometers located at the University of Toronto NMR facility.

Interested applicants should submit their CV, contact information for three references, and a description of previous research experience to Voula Kanelis (voula.kanelis "at" utoronto.ca).

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NMR Scientist at the Environmental NMR Centre, University of Toronto Scarborough (August 10/10)

The Environmental NMR Centre and the Department of Physical and Environmental Sciences at the University of Toronto Scarborough are seeking a Senior NMR Research Associate to oversee the daily operation, training, and management of the Environmental NMR Centre. The position has a very large research and development component and the candidate is expected to work closely in and with the facilities Directors to maintain the centre at the cutting-edge of Environmental NMR globally and be central to pioneering new developments in NMR in general.

The Environmental NMR Centre currently houses two unique, Bruker BioSpin NMR systems. The first is a fully hyphenated 2D-HPLC-SPE-NMR-MS, and is novel both in Canada and Environmental Research in general. The second system has capabilities to perform in situ multiphase NMR analyses of heterogeneous samples that contain solid, gel and solution phase samples, the hardware is globally unique and being co-developed directly with Bruker BioSpin. The Centre focuses on the development and application of NMR techniques to study a range of environmental problems. The current topics of research include: environmental metabolomics, LC-SPE-NMR-MS applications to complex environmental mixtures, in vivo NMR spectroscopy imaging, hyperpolarization, DNP, development of multiphase NMR methods (solids, HR-MAS, solutions NMR as a single technique). In addition, the Centre focuses on the development and application of novel NMR approaches to complex systems (including soils, ocean sediments, atmospheric deposits (particles, rain, snow, glacial ice), cells, tissues, small organisms and other environmental matrices) to better understand structure and environmental reactivity.

After an initial probationary period, this will be a continuing full-time appointment.

The NMR scientist will report to the Chair of the Department and work closely with the Director and Associate Director of the Environmental NMR Centre. The research associate will be responsible for instrument maintenance, training of graduate students/postdoctoral fellows/visiting scientists assist in writing grant applications to upgrade the centre and co-publication of research with the facility's principal investigators and collaborators. The candidate will also be expected to lead research projects publishing both as a primary and secondary author. The successful candidate will take an active role in all aspects of the research of the NMR Centre and will strive to ensure that he/she becomes recognized as a leader in the field of Environmental NMR spectroscopy.

The candidate will also be involved in undergraduate thesis supervision in the Department's chemistry program and will be encouraged to apply to instruct one course in the undergraduate chemistry program on a yearly basis. The candidate will also oversee the operation/maintenance of a teaching/research Departmental NMR system (Bruker BioSpin 500MHz Avance) and ensure that faculty and students can acquire high quality data required for the teaching and research programs. These duties will include the set up of new experiments, training of students/faculty, maintenance and calibration. Candidates should note that the departmental NMR system is fully automated (BACS) with a single automatic tuning and matching probe (ATM) and that the department has only a small number of users, once running smoothly should require minimal intervention on a daily basis.

Applicants must have a Ph.D. in Chemistry or related discipline with a very strong background in NMR spectroscopy and a drive/passion for the development of NMR spectroscopy. In exceptional circumstances, an established leader in the field with a MSc degree but more than 10 years of experience may be considered. In addition, experience with metabolomics, chromatography, mass spectrometry and working with complex biological and/or environmental systems are a strong assets. Experience with pulse programming, custom processing of NMR data (MATLAB, ACD, etc.) and programming/webpage design is also beneficial. Experience with Bruker instruments is very important and the ideal candidate will have experience in (or enthusiastic to learn) all areas of NMR including solutions, HR-MAS, solids and imaging.

Salary will be commensurate with the candidate's qualifications and experience.

Applicants should send a cover letter, curriculum vitae, a statement of research, a statement of teaching and three letters of reference to:

Rose Jones (Assistant to the Chair)
NMR Scientist Search Committee
Department of Physical & Environmental Sciences
University of Toronto Scarborough
1265 Military Trial
Toronto, Ontario M1C 1A4

Email submissions should be sent to: rjones "at" utsc.utoronto.ca

Unfortunately, applications that are not accompanied by at least three references cannot be considered.

We will start reviewing applications beginning September 13, 2010, although the search will remain open until the position is filled.

The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.

the Department of Physical and Environmental Sciences, UTSC
http://www.utsc.utoronto.ca/~physsci/

Andre Simpson's Environmental research group
http://www.utsc.utoronto.ca/~asimpson/

Myrna Simpson's Research Group in Environmental Chemistry
http://www.utsc.utoronto.ca/~msimpson/

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New NMR book (June 3/10)

Multidimensional NMR Methods for the Solution State edited by Gareth A. Morris and James W. Emsley Hardcover: 580 pages Publisher: Wiley; June 2010 Language: English ISBN: 978-0470770757 http://www.amazon.com/dp/0470770759 http://www.amazon.ca/dp/0470770759

Wiley: "Multidimensional NMR methods have transformed the way in which solution state NMR is used to elucidate the structures of chemical and biochemical systems. The first book covering new developments in nearly a decade, this much-needed resource explains recent experimental methods for the rapid measurement of multidimensional solution-state NMR spectra. With articles written by key developers of the techniques, the coverage deals with both the theoretical tools and the latest practical applications, giving an unmatched guide to students, researchers, technicians, and anyone else working with NMR techniques today"

Canadian contributions

A.D. Bain "COSY: Quantitative Analysis," Chapter 13, Multidimensional NMR Methods for the Solution State (EMR Books), Eds. G.A. Morris and J.W. Emsley, Wiley (2010) pp. 167-176. http://dx.doi.org/10.1002/9780470034590.emrstm0095

T.T. Nakashima and R.E.D. McClung "Heteronuclear Shift Correlation Spectroscopy," Chapter 22, Multidimensional NMR Methods for the Solution State (EMR Books), Eds. G.A. Morris and J.W. Emsley, Wiley (2010) pp. 289-304. http://dx.doi.org/10.1002/9780470034590.emrstm0209

R. Muhandiram and L.E. Kay "3D HMQC-NOESY, NOESY-HMQC, and NOESY-HSQC," Chapter 25, Multidimensional NMR Methods for the Solution State (EMR Books), Eds. G.A. Morris and J.W. Emsley, Wiley (2010) pp. 335-350. http://dx.doi.org/10.1002/9780470034590.emrstm0563

The complete Table of Contents is available on Stan's NMR blog.

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Tim Burrow (University of Toronto) wrote a utility application for the iPhone/iPod touch that calculates attenuation values:

http://itunes.apple.com/ca/app/attenuator/id367216554

Attenuator is a utility for anyone working with radio frequency sources and needs to know power and voltage after attenuation.

You can specify an input voltage (Vpp or Vrms) and dB of attenuation to get the output voltage, power and attenuation. The impedance can be specified, typically 50 Ohm for most systems.

This free application is available in English, French, Chinese and Japanese and is sponsored by Open Technologies.

For more information visit: http://www.attenuator.ca/

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Recognition: Andre Simpson (Dec 14/09)

Andre Simpson (University of Toronto Scarborough) is the recipient of the 2010 CSC Fred Beamish Award. This award is presented to individuals who demonstrate innovation in research in the field of Analytical Chemistry, in particular, where research is anticipated to have significant potential for practical applications.

Web: Andre Simpson's Group at the University of Toronto Scarborough

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Hospital for Sick Children, Toronto (Nov 24/09)

Postdoctoral position in biological solid-state NMR

Postdoctoral positions in biomolecular solid state NMR are available at The Hospital for Sick Children. These positions will focus on structure determination and dynamic characterization of protein and peptide assemblies by solid state NMR, with an emphasis on systems relevant to human health and disease. Ongoing projects include structural studies of oligomeric states of mammalian prion proteins, membrane interactions of amyloid peptides, and structure determination of integral membrane complexes that play a key role in HIV-1 infection. These projects are highly multidisciplinary in nature, and will provide candidates with the opportunity to learn a broad range of biophysical techniques, in addition to NMR, and to collaborate with a number of other research groups.

http://www.sickkids.ca/Research/Sharpe-lab/index.html

Our lab is located within the Molecular Structure and Function Program at the Hospital for Sick Children and the Department of Biochemistry at the University of Toronto, providing a diverse and stimulating research environment. We are fully equipped for cloning, mutagenesis, protein expression and purification, with access to peptide synthesis, computational biology facilities and full-time use of a 500 MHz spectrometer for solids MAS and static experiments. In addition, access to the National 900 MHz NMR facility in Ottawa is also available for most projects.

Highly motivated candidates are sought, who must possess a PhD with a strong track record of scientific productivity, and who should have extensive experience in either biological NMR (solution or solid state) or protein biophysics and structure determination. The start date for this position is negotiable, but is available immediately.

Qualified candidates should send a complete CV to ssharpe "at" sickkids.ca and arrange for 3 letters of reference to be sent to:

Simon Sharpe
Scientist, Molecular Structure and Function Program
The Hospital for Sick Children
Assistant Professor, Dept. of Biochemistry
University of Toronto

555 University Ave,
Toronto, Ontario
Canada M5G 1X8
Email: ssharpe "at" sickkids.ca

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Recognition: Lewis Kay (October 1/09)

The University of Alberta honours Lewis Kay with the Distinguished Alumnus Award (more ).

From the citation: "One of the world's leading biochemists, Kay is recognized for his cutting-edge research in biomolecular nuclear magnetic resonance spectroscopy. The University of Toronto professor and researcher has been instrumental in developing new three- and four-dimensional nuclear magnetic resonance methods for obtaining pictures of complex biomolecules. This revolutionary work has led to important discoveries, helping researchers understand the underlying biological characteristics of diseases. This understanding has increased the probability of finding ways to cure or prevent diseases such as cancer."

Don't miss the video profile of Distinguished Alumnus Lewis Kay (5 min, 23.1 MB .mov)

Web: Lewis Kay's Group at the University of Toronto

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Canada's first 950 MHz NMR spectrometer ! (June 18/09)

The Canada Foundation for Innovation (CFI) has announced today major investment in Canadian Research Infrastructure. More than $665 million was awarded to 133 projects at 41 Canadian research institutions through the CFI’s Leading Edge Fund and New Initiatives Fund. Among infrastructure projects receiving Government's support is the Canada's first 950 MHz NMR spectrometer at the University of Toronto (Lewis Kay, Biochemistry) to enable studies of the structure and dynamics of complex biological molecules, as well as the technological development of biological NMR.

Project title: "High Field NMR Studies of Protein Molecules in Health and Disease" (CFI contribution $4,595,843)

This very significant hardware acquisition will ensure Canada's leading role in biological NMR research.

Congratulations are due to Lewis Kay and his team at the UofT !

A complete list of awarded projects (CFI web-site)  

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Review in Biophysical Journal (March 16/09)

Lewis Kay and colleagues from the University of Toronto have published an article in Biophysical Journal reviewing recently developed NMR relaxation dispersion technique and its applications to protein folding research.

P. Neudecker, P. Lundström, L.E. Kay, "Relaxation Dispersion NMR Spectroscopy as a Tool for Detailed Studies of Protein Folding," Biophysical Journal 96 (2009) 2045-2054. (review)
http://dx.doi.org/10.1016/j.bpj.2008.12.3907

This review and all previous issues of Biophysical Journal are available free of charge until April 5, 2009. The free access is provided by Cell Press, who is taking over publishing Biophysical Journal starting in 2009.

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NMR paper in Science Signaling (March 7/09)

A research team from the Ontario Cancer Institute and the University of Toronto has developed a real-time, nuclear magnetic resonance (NMR)–based assay to monitor the intrinsic GTPase activity of the small guanosine triphosphatase (GTPase) Rheb. This method can now be used to gain further understanding of the mechanisms of action of other GTPases and their GAP partners.

C.B. Marshall, J. Ho, C. Buerger, M.J. Plevin, Guang-Yao Li, Z. Li, M. Ikura, and V. Stambolic, "Characterization of the Intrinsic and TSC2-GAP–Regulated GTPase Activity of Rheb by Real-Time NMR," Science Signaling 2 (#55) (2009) ra3. http://dx.doi.org/10.1126/scisignal.2000029

Abstract: http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2/55/ra3

Editor's summary:
http://stke.sciencemag.org/cgi/content/summary/sigtrans;2/55/ra3

Science Signaling is a weekly AAAS journal as well as an online resource and information management tool that enables experts and novices in cell signaling to find, organize, and utilize information relevant to processes of cellular regulation. As of September 2008, Science Signaling is adding original research articles to the weekly journal. Science Signaling publishes research that represents a major advance in cell signaling, including key research papers in the rapidly expanding areas of signaling networks, systems biology, synthetic biology, computation and modeling of regulatory pathways, and drug discovery.

More about Science Signaling:
http://stke.sciencemag.org/about/

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Climate warming and soils: NMR paper in Nature Geoscience (November 25, 2008)

A research team from the University of Toronto Scarborough led by Myrna Simpson reports an accelerated rate of decomposition of some soil organics and accumulation of others due to soil warming.

X. Feng, A.J. Simpson, K.P. Wilson, D.D. Williams and M.J. Simpson, "Increased cuticular carbon sequestration and lignin oxidation in response to soil warming," Nature Geoscience (2008) online. http://dx.doi.org/10.1038/ngeo361

This paper has generated considerable media attention including a feature interview "Soil Alert" with Myrna on Daily Planet (aired on Nov 27, 2008).

http://www.sciencedaily.com/

https://webapps-new.utsc.utoronto.ca/

http://www.spectroscopynow.com/

http://www.discoverychannel.ca/

web : Myrna Simpson's Group (external link)

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Nanochemistry: A Chemical Approach to Nanomaterials

Authors Geoffrey A. Ozin, Andre C. Arsenault and Ludovico Cademartiri
Hardcover: 770 pages
Publisher: Royal Society of Chemistry; 2nd Revised edition (January 2009)
Language: English
ISBN-10: 184755895X
ISBN-13: 978-1847558954


RSC: “… The global success of the 1st edition of "Nanochemistry", and exceptionally rapid change in the field, has necessitated the publication of a 2nd edition after only three years. This truly major update highlights the latest breakthroughs using over 80 new case histories, more problem sets, and more teaching principles. Written for teachers and students, the book catapults the reader to the forefront of the field. Using simple language, and focusing on the concepts, it covers all chemistry techniques commonly used to synthesize nanomaterials. In this book, case histories enable readers to 'connect the dots' and understand the possibilities ahead whilst problem sets encourage students to think creatively and laterally about what they have learnt. The extensive bibliography will satisfy those hungry for more detail.”

http://www.amazon.com/gp/product/184755895X/

web: Geoffrey Ozin (University of Toronto)