Principal Investigators

David Wishart is a Professor in the Departments of Computing Science and Biological Sciences, and in the Faculty of Pharmacy at the University of Alberta. Dr. Wishart is the principal investigator for the APRI and PrioNet grants on prion structure, function and dynamics. His interests lie in NMR spectroscopy and the development of novel methods to characterize protein structure and dynamics. Dr. Wishart is also engaged in research on metabolomics, bioinformatics, drug design and viral protein characterization.

Liang Li is a Professor of Chemistry and a Tier 1 Canada Research Chair in Analytical Chemistry. His research is in the area of analytical mass spectrometry. Since 1987, he has published 133 refereed papers and given 141 invited talks. Dr. Li has won several awards including the McBryde Medal (2001) from the Canadian Society for Chemistry, the Young Explorers Prize (2002) from the Canadian Institute for Advanced Research (CIAR), which was given to Canada's top twenty researchers aged forty or under in science and engineering, and the Rutherford Memorial Medal (2003) from the Royal Society of Canada. He received The F.P. Lossing Award from the Canadian Society for Mass Spectrometry in 2006. Dr. Li is currently an editor of Analytica Chimica Acta, an international journal on analytical chemistry. For this project, he will be responsible for technical and method development and applications of mass spectrometry for structural characterization of prion and prion complexes.

GUOHUI LIN is an Associate Professor of Computing Science at the University of Alberta and a co-investigator for the APRI and PrioNet grants on prion structure. His interests lie in NMR spectral data analysis and combined protein structure prediction and determination. His broader research interests are bioinformatics, computational biology, and medical informatics.

PAUL LU is an Associate Professor of Computing Science at the University of Alberta. His B.Sc. and M.Sc. degrees in Computing Science are from the University of Alberta. His Ph.D. (2000) is from the University of Toronto and is in the area of parallel programming systems. His current research is in the areas of high-performance computing, systems software, and bioinformatics. He is the Principal Investigator of the Trellis Project.

JULIE FORMAN-KAY is a Senior Scientist at the Hospital for Sick Children and a Professor of Biochemistry at the University of Toronto. Her research examines various aspects of protein interactions and dynamics using NMR and other techniques. Protein interaction involving disordered regions of proteins are now recognized as an important mechanism of protein regulation. Her group is characterizing disordered regions of proteins involved in a variety of diseases and their interactions, as well as developing methods to study disordered proteins.

ANDRIY KOVALENKO is Senior Researcher Officer and Group Leader of the Theory and Modeling Group at the National Institute of Nanotechnology (NINT). He is also Adjunct Professor in the Department of Mechanical Engineering at the University of Alberta.. Dr. Kovalenko is a leading international expert in theoretical and computational methods of modeling on multiple space and time scales, including statistical physics and electronic structure theory. His focus is development of theoretical methods able to predict the behavior of nanosystems. He has proposed a new statistical-mechanical theory of molecular solvation which bridges the gap between the electronic structure, atomistic simulations, and the level of system functioning. He has applied it to complex molecular liquids and solutions, electronic and solvation structure and solvation thermodynamics of molecules and solid-liquid interfaces, electrochemistry of solutions sorbed in nanoporous materials, self-assembly of supramolecules in solution, and solvation of biomolecules.

DAVID WESTAWAY is a molecular biologist with a special interest in the use of genetically engineered "transgenic" mice to receate and understand human neurologic disorders. He is a Professor in the Division of Neuorology (Dept of Medicine) and Director of the Alberta Centre for Prions and Protein Folding Diseases at the University of Alberta. His recent work on prion diseases concerns the function of the cellular prion protein and a related protein called shadoo. Dr. Westaway is a CIHR Research Investigator, an AHFMR Scientist and Canada Research Chair in Prion Disease.

BRIAN SYKES is a Professor of Biochemistry at the University of Alberta. Dr. Sykes' research involves the elucidation of the structure, dynamics and function of proteins; including the role of intrinsically unfolded regions in regulating biological interactions. Their major tool is nuclear magnetic resonance spectroscopy, especially the use of multi-nuclear and multi-dimensional NMR techniques combined with the computational techniques of energy minimization and molecular dynamics to determine the structure of proteins in solution. They are studying prion proteins in order to understand the mechanism of the conversion from the cellular to the Scrapie form.

Administration

CONNIE SOBSEY Connie Sobsey is Dr. Wishart's Research Coordinator. Connie completed her BA degree at the University of Alberta with a double-major in Psychology and Sociology. Her previous laboratory experience was in psychopharmacology and electrophysiology labs. She also has extensive experience in administration. Connie has been involved in the Prion Project for two years. She is currently responsible for managing various aspects of metabolomics and prion research projects in Dr. Wishart's lab.

Bioinformatics

BEOMSOO HAN is a postdoctoral fellow in Dr. David Wishart’s group. He is a computational statistician. He is working on the development of an enhanced model for chemical shift prediction from protein secondary structure by using advanced machine learning methods.

Jack Liang is a research assistant in Dr. Wishart's Lab. He has a B.Sc. in Bioinformatics and B.Eng in Mechanics. Jack is developing new algorithms incorporating NOE distance constraints into GAFolder, a protein structure minimization program written in the Wishart Lab. The goal is to improve protein structure evaluation using experimental NOE distances along with the existing analytical measures.

CAM MACDONELL is a PhD student in the Department of Computing Science at the University of Alberta. His interests included file systems, high performance computing and bioinformatics. Currently, I am examining the use of virtual machines to distribute data-parallel workloads across distributed systems. We hope to show that virtual machines impose low overheads in exchange for the ability to specify a complete runtime environment that frees scientists from dealing with heterogeneous clusters in different institutions. We are also integrating distributed file systems into the virtual machines to make remote access to data as simple as possible. We hope this will lead to a better platform for scientists to execute compute-intensive workloads. We are looking at Gromacs and HMMer as applications that may benefit from our approach.

ERKAN UNAL is a MSc student in the Department of Computing Science at the University of Alberta. His research interests are virtual machines and high performance computing. Currently, He is working on packaging scientific applications (primarily bioinformatics applications such as Gromacs and GAFolder) inside virtual machines with thin layer of operating systems also called Virtual Application Appliances (VAAs). The advantages of VAAs include executing applications independent of the OS on the machine, avoiding library conflicts and enabling user specific configuration for individual applications or application groups. He is working on supporting VAAs on distributed systems.

JIANJUN ZHOU is a PhD student in the Department of Computing Science at the University of Alberta. He is currently working in the areas of Databases, Data-mining, and Protein Structure Prediction. Using state-of-the-art data-mining techniques, he is trying to discover new rules for prion structure prediction.

Mass Spectrometry

ANDY LO is a graduate student working for Dr. Liang Li in the Department of Chemistry. He will be using and developing mass spectrometric techniques to gather information about the structure of native prions and their variants. My current focus is to develop protocols to determine the surface exposure of various amino acid residues. In addition to providing simple exposure data (completely exposed vs. completely unexposed), we hope to use isotopic labelling to provide information about degrees of partial exposure. Future work includes utilizing crosslinking reagents to determine low resolution spatial constraints between reactive residues. The surface exposure data will provide a basis for the Bioinformatics group to refine and validate candidate protein stuctures. In addition, crosslinking data can provide distance constraints between various residues to verify proposed structures.

BELA REIZ is a graduate student working for Dr. Liang Li's group. The objective of his research is the development of methods and strategies, based on MS, for the detection and characterization of prions. My research interests while completing my undergrad and master studies were the applications of Optical Emission Spectrometry in the determination of superconducting materials composition and quantitation of Cu, Pb and Zn from environmental samples. I also worked as a research assistant at the Research Institute for Analytical Instrumentation in Cluj-Napoca, Romania. Currently I am working Dr. Li's group. Our group's research is in the area of analytical mass spectrometry (MS). The objectives of my research is the development of methods and strategies, based on MS, for the detection and characterization of prions.

Structural Biology

XueHui Liu is a postdoctoral fellow in Dr. David Wishart’s group. The NMR spectroscopy is his research expertise. He is currently working on the characterization of prion protein conversion by several biophysical methods such as NMR, CD, fluorescence, EM (electronic microscopy), DLS (dynamic light scattering), SAXS (small angle X-ray spectroscopy).

Valentyna Semenchenko is a Technical Officer at the National Institute for Nanotechnology (NINT) working for Dr. David Wishart. By using molecular biology and biochemistry methods Val designs various prion gene constructs and prepares synthetic prion proteins for structural analysis.

GUO-PING ZHOU is a Research Associate in Dr. David Wishart's group. His research interests are in structural and functional studies of protein and protein-ligand interaction by NMR spectroscopy and molecular modeling; as well as in predictions of protein subcellular locations and protein structural classes.

Computational Modeling

MARK BERJANSKII is a post-doctoral fellow in Dr. David Wishart's group. He is working on the development of new methods for predicting of prion flexibility and torsion angles from NMR chemical shifts. He is also involved in solving a variety of molecular modeling problems such as identification of prion essential motions from molecular dynamics simulation, solving prion structure from sparse experimental data, modeling of prion conversion into the infectious form and constructing prion protofibrils.

NIKOLAY BLINOV is a research associate in Dr. Andriy Kovalenko's Theory and Modelling group at HINT. The ultimate goal of his project is to reveal molecular mechanisms behind misfolding and aggregation of prion proteins. Temporal and spatial multiscale modeling of proteins dynamics and interactions, conformational stability of proteins, aggregation of prion proteins, molecular theory of solvation and its application to biophysical and biochemical processes are in the focus of his research.

LYDMYLA DOROSH is a post-doctoral fellow in Dr. Andriy Kovalenko's group. She is working on calculation of the solvation structure, thermodynamics and slow dynamics of aggregation of misfolded prion proteins in solution by using the three-dimensional molecular theory of solvation and molecular dynamics simulations.

MARIA STEPANOVA is Associate Research Officer at the National Institute for Nanotechnology (NINT) and Adjunct Professor in the Department of Electrical and Computer Engineering at the University of Alberta. Research of Dr. Stepanova is part of the program of theory and modeling on multiple space and time scales at NINT, and pursues development of a comprehensive theoretical methodology to characterize and predict the conformational behaviours of proteins based of their essential dynamics. In the prion project, Dr. Stepanova employs the new methodology to build coarse-grained models of conformational behaviours for both native and misfolded prion proteins.

Collaborators

NEIL CASHMAN is a Professor of Neurology at the University of British Columbia and the Director of Prionet Canada.