Faculty of Medicine
Department of Biochemistry & Molecular Biology
HALIFAX, NOVA SCOTIA | CANADA B3H 4R2 | 1 (902) 494-2480

Jan K. Rainey, Ph.D. (Toronto)


Associate Professor
Director, Nuclear Magnetic Resonance Research Resource (NMR-3)
Cross-appointment to Chemistry

Tupper 10-N1,H1,SBB6
(902) 494-4632 - office
(902) 494-4812 - lab
Email
Lab Homepage

Research Areas

Structural & biophysical studies of membrane proteins & the extracellular matrix

Proteins in the cell membrane and extracellular matrix function in highly organized supramolecular assemblies, groupings of many molecules. Both classes of protein are critical for life, but are notoriously difficult to study. Our research goal is to determine not only how these classes of proteins function, but to carry out studies of these proteins in highly physiologically relevant environments. The primary aim is to understand the contribution of each constituent atom to the biological activity of a protein, providing fundamental understanding of biochemical processes, new routes for drug design, and alternative approaches for disease diagnosis and treatment. Current systems under study include a G-protein coupled receptor and its peptidic ligand, the extracellular matrix protein collagen (the most abundant protein in animals), Na+/H+ exchange and intramembrane proteolysis.

Protein preparation
Two major approaches are used in our laboratory to produce proteins. In the organic chemistry based solid-phase peptide synthesis, a polypeptide is built by adding each amino acid in sequence. This provides us the ability to alter or tailor any individual amino acid residue we wish, either to determine effects of substitutions or to allow highly specific stable-isotope for nuclear magnetic resonance (NMR) spectroscopy or fluorescent labelling for biophysical study. Alternatively, molecular biology based cloning and expression is used to produce larger proteins. Beyond production of proteins, this readily allows both uniform and selective stable-isotope labelling . In each case, purification may be performed by high-performance liquid chromatography (HPLC) or other chromatographic methods, as appropriate. Mass spectrometry is typically used to characterize our synthetic or expression products.

NMR spectroscopy & structure calculations
NMR spectroscopy is our primary experimental technique, allowing us to determine protein structure and dynamics at the level of the individual nucleus. We use both solution-state and solid-state NMR to understand protein function in a variety of situations ranging from polypeptides in aqueous buffer to large protein assemblies and proteins embedded in phospholipid bilayers. In the case of solid-state NMR, we are currently working towards new methods that will allow characterization of not only the structure of proteins in membranes or extracellular matrix, but the structure of these proteins relative to their supramolecular environment. Structure calculations are a critical component of biomolecular NMR, and we spend a lot of time ensuring that our calculations are truly providing a structural ensemble accurately representing the experimental data.

Scanning probe microscopy & force spectroscopy
Scanning probe microscopy (SPM), also known as atomic force microscopy (AFM), is the other major technique employed by our laboratory. This type of microscopy uses a very sharp tip to image a surface, making use of the force of interaction between the tip and the surface to produce a topological and/or chemical image of the surface. This technique is capable of probing individual atoms, but for biological samples a more realistic resolution limit is on the order of a nanometer. SPM can also be used for study of the interaction forces between pairs of molecules, providing picoNewton level accuracy. A major focus in our research is the development of methods to allow exactly the same sample to be studied by solid-state NMR and SPM.

Circular dichroism & fluorescence spectroscopy

Circular dichroism (CD) spectroscopy allows rapid determination of protein secondary structure under various conditions. Fluorescence spectroscopy allows us to quickly assess the environment surrounding individual amino acids (i.e. are they exposed to solvent vs. buried in a protein core?) and the free- or bound-state of a protein. These methods provide an important counterpoint to our NMR and SPM experiments, since characterization is often much more rapidly achieved and provide different classes of information.

Funding

Operating: NSERC, CIHR, NSHRF, Dalhousie Cancer Research Program. Infrastructure: CFI, NSERC, Dalhousie Medical Research Foundation.

Keywords:
Protein NMR spectroscopy, Solid-state NMR spectroscopy, scanning probe microscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, solid-phase peptide synthesis, cloning & expression, cell-free expression, HPLC, Langmuir-Blodgettry

Graduate Students


Nigel Chapman Masters Program
Tim Key PhD (Micro & Immuno) Program
Aditya Pandey Masters Program
Jolene Read PhD (Micro & Immuno) Program
Kyungsoo Shin Masters Program
Marie-Laurence Tremblay Masters Program
Lingling Xu PhD (visiting) Program

Postdoctoral Fellows


Muzaddid Sarker Memorial University of Newfoundland

Honours Students


Ryan Holstead Biochemistry/Neuroscience & NSERC USRA Summer Student
Matthew Speckert Biochemistry/Microbiology

Lab Personnel


Jessica Beattie Co-op Student (Citadel High School)
Erica Connors Warr Award Summer Student (2011); NSERC USRA Summer Student (2010)
Ponthea Pouramin Volunteer (2nd year Biochem)
Lesley Seto Technician
Bruce Stewart Lab Manager
Nathan Weatherbee-Martin Co-op student (Acadia University)

Publications

  1. Xu, L., Tremblay, M-L., Rainey, J.K., Meng, Q. and Liu, X-Q., (2012) Nano-structures self-assembled from recombinant miniature AcSp1 of spider wrapping silk. Proceedings of the 6th International Conference on Bioinformatics and Biomedical Engineering. Accepted:
  2. Langelaan, D.N.*, Ngweniform, P.*, Rainey, J.K. (*contributed equally), (2011) Biophysical characterization of G-protein coupled receptor-peptide ligand binding. Biochem Cell Biol 89:98-105 [PubMed]
  3. Xu, L.*, Tremblay, M-L.*, Meng, Q., Liu, X-Q. and Rainey, J.K. (* contributed equally), (2011) 1H, 13C and 15N NMR assignments of the aciniform spidroin (AcSp1) repetitive domain of Argiope trifasciata wrapping silk. Biomol. NMR Assign. In press: [PubMed]
  4. Reddy, T., Li, X., Fliegel, L., Sykes, B.D. and Rainey, J.K., (2010) Correlating structure, dynamics, and function in transmembrane segment VII of the Na+/H+ exchanger isoform 1. Biochim Biophys Acta Biomembranes 1798:94-104 [PubMed]
  5. Langelaan, D.N. and Rainey, J.K., (2010) Membrane catalysis of peptide-receptor binding. Biochem Cell Biol 88:203-210 [PubMed]
  6. Reddy, T. and Rainey, J.K., (2010) Interpretation of biomolecular NMR spin relaxation parameters. Biochem Cell Biol 88:131-142 [PubMed]
  7. Tremblay, M-L., Banks, A.W. and Rainey, J.K., (2010) The predictive accuracy of secondary chemical shifts is more affected by protein secondary structure than solvent environment. J Biomol NMR 46:257-270 [PubMed]
  8. Langelaan, D.N., Wieczorek, M., Blouin, C. and Rainey, J.K., (2010) Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. J. Chem. Inf. Model. 50:2213-2220 [PubMed]
  9. Langelaan, D.N., Bebbington, E.M., Reddy, T. and Rainey, J.K., (2009) Structural insight into G-protein coupled receptor binding by apelin Biochemistry 48:537-548 [PubMed]
  10. Langelaan, D.N. and Rainey, J.K., (2009) Headgroup-dependent membrane catalysis of apelin-receptor interactions is likely. J Phys Chem B 113:10465-10471 [PubMed]
  11. Reddy, T., Ding, J., Li, X., Sykes, B.D., Rainey, J.K. and Fliegel, L., (2008) Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na+/H+ exchanger. J. Biol. Chem. 283:22018-22030 [PubMed]
  12. Slepkov, E.R., Rainey, J.K., Sykes, B.D. and Fliegel, L., (2007) Structural and functional analysis of the Na+/H+ exchanger. Biochem. J. 401:623-631 [PubMed]
  13. Rainey, J.K., DeVries, J.S. and Sykes B.D., (2007) Estimation and measurement of flat or solenoidal coil inductance for radiofrequency NMR coil design J. Magn. Reson. 187:27-37 [PubMed]
  14. Rainey, J.K.*, Ding, J.*, Xu, C., Sykes, B.D. and Fliegel, L. (* contributed equally), (2006) Structural and functional characterization of TM VII of the NHE1 isoform of the Na+/H+ exchanger. J. Biol. Chem. 281:29817-29829 [PubMed]
  15. Rainey, J.K., Fliegel, L. and Sykes, B.D., (2006) Strategies for dealing with conformational sampling in structural calculations of flexible or kinked transmembrane peptides. Biochem. Cell Biol. 84:918-929 [PubMed]
  16. Baryshnikova, O.K., Rainey, J.K. and Sykes, B.D., (2005) Nuclear magnetic resonance studies of CXC chemokine receptor 4 allosteric peptide agonists in solution. J. Pept. Res. 66(s1):12-21 [PubMed]
  17. Rainey, J.K. and Sykes, B.D., (2005) Optimizing oriented planar-supported lipid samples for solid-state protein NMR. Biophys. J. 89:2792-2805 [PubMed]
  18. Rainey, J.K., DeVries, J.S. and Sykes, B.D., (2005) A rotatable flat-coil for static solid-state nuclear magnetic resonance spectroscopy. Rev. Sci. Instrum. 76:086102
  19. Slepkov, E.R., Rainey, J.K., Li, X., Liu, Y., Cheng, F.J., Lindhout, D.A., Sykes, B.D. and Fliegel, L., (2005) Structural and functional characterization of transmembrane segment IV of the NHE1 isoform of the Na+/H+ exchanger. J. Biol. Chem. 280:17863-17872 [PubMed]
  20. Rainey, J.K. and Goh, M.C., (2004) An interactive triple-helical collagen builder. Bioinformatics 20:2458-2459 [PubMed]
  21. Rainey, J.K. and Goh, M.C., (2004) Statistically based reduced representation of amino acid side chains. J. Chem. Inf. Comput. Sci. 44:817-830 [PubMed]
  22. Rainey, J.K., Wen, C.K. and Goh, M.C., (2002) Hierarchical assembly and the onset of banding in fibrous long spacing collagen revealed by atomic force microscopy. Matrix Biol. 21:647-660. [PubMed]
  23. Rainey, J.K. and Goh, M.C., (2002) A statistically derived parameterization for the collagen triple-helix. Protein Sci. 11:2748-2754 [PubMed]
  24. Rainey, J.K. and Goh, M.C., (2002) Parallel atomic force microscopy and NMR spectroscopy to investigate self-assembled protein-nucleotide aggregates. J. Phys. Chem. B 106:5553-5560
  25. Paige, M.F., Rainey, J.K. and Goh, M.C., (2001) A study of fibrous long spacing collagen ultrastructure and assembly by atomic force microscopy. Micron 32:341-353 [PubMed]
Last modified: 2012-05-01