Publications

Refereed journal articles (trainees listed in bold)

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80. Jahan, S., Doyle, C., Ghimire, A., Combita, D., Rainey, J.K., Wagner, B.D., and Ahmed, M. (2024) Elucidating the role of optical activity of polymers in protein-polymer interactions. Polymers. 16: 65.

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79. Kumar, P., Kermanshahi-Pour, A., Brar, S.K., Xu, C.C., He, Q.S., Evans, S., and Rainey, J.K. (2023) Enzymatic digestibility of lignocellulosic wood biomass: Effect of enzyme treatment in supercritical carbon dioxide and biomass pretreatment. Heliyon. 9: e21811.

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78. Rajan, V., Prykhozhij, S.V., Pandey, A., Cohen, A.M., Rainey, J.K., and Berman, J.N. (2023) KIT D816V is dimerization-independent and activates downstream pathways frequently perturbed in mastocytosis. British Journal of Haematology. 202: 960-970.

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77. Kumar, P., Kermanshahi-Pour, A., Brar, S.K., He, Q.S., and Rainey, J.K. (2023) Influence of elevated pressure and pressurized fluids on microenvironment and activity of enzymes. Biotechnology Advances. 68: 108219.

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76. Simmons, J.R., Gasmi-Seabrook, G., and Rainey, J.K. (2023) Structural features, intrinsic disorder, and modularity of a pyriform spidroin 1 core repetitive domain. Biochemistry and Cell Biology. 101: 271-283.

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75. Song, Q., Liu, X-Q., and Rainey, J.K. (2023)  1H, 15N and 13C backbone resonance assignments of the acidic domain of the human MDM2 protein. Biomolecular NMR Assignments. 17: 9-16.

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74. Visser, Z.B.+, Verma, S.K.+, Rainey, J.K., and Frampton, J.P. (+ contributed equally; 2022) Loading and release of quercetin from contact-drawn polyvinyl alcohol fiber scaffolds. ACS Pharmacology & Translational Science. 5: 1305-1317.

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73. Baker, L.A., Xu, L., Badichi Akher, F., Robertson, M.K., Pugsley-DeBruyn, L., Ma, C.X., Liu, X-Q., Frampton, J.P., and Rainey, J.K. (2022) Nerve growth factor-binding engineered silk films promote neuronal attachment and neurite outgrowth. Advanced Functional Materials. 32: 2205178.

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72. Song, Q., Liu, X-Q., and Rainey, J.K. The MDMX acidic domain competes with the p53 transactivation domain for MDM2 N-terminal domain binding. Biochimica et Biophysica Acta - Molecular Cell Research. 1869: 119319.

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71. Verma, S.K., Yaghoobi, H., Slaine, P., Baldwin, S.K., Rainey, J.K., Kreplak, L., and Frampton, J.P. (2022) Multi-pin contact drawing enables production of anisotropic collagen fiber substrates for alignment of fibroblasts and monocytes. Colloids and Surfaces B: Biointerfaces. 215: 112525.

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70. Song, Q., Liu, X-Q., and Rainey, J.K. (2022)  1H, 15N and 13C backbone resonance assignments of the acidic domain of the human MDMX protein. Biomolecular NMR Assignments. 16: 171-178.

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69. Dagamajalu, S., Rex, D.A.B., Suchitha, G.P., Rai, A.B., Rainey, J.K., and Prasad, T.S.K. (2022) The network map of Elabela signaling pathway in physiological and pathological conditions. Journal of Cell Communication and Signaling. 16: 145-154.

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 68. Dagamajalu, S., Rex, D.A.B., Devi Philem, P., Rainey, J.K., and Prasad, T.S.K. (2022) A network map of apelin-mediated signaling. Journal of Cell Communication and Signaling. 16: 137-143.

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67. Nazeer, N., Simmons, J.R., Rainey, J.K., Rodriguez-Lecompte, J.C., and Ahmed, M. (2021) Antibacterial activities of physiologically stable, self-assembled peptide nanoparticles. Journal of Materials Chemistry B. 9: 9041-9054.

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66. Phạm, T.T.T. and Rainey, J.K. (2021) On-cell nuclear magnetic resonance spectroscopy to probe cell surface interactions. Biochemistry and Cell Biology. 99: 683-692.

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65. Tam, N.W., Chung, D., Baldwin, S.J., Simmons, J.R., Xu, L., Rainey, J.K., Dellaire, G., and Frampton, J.P. (2020) Material properties of disulfide-crosslinked hyaluronic acid hydrogels influence prostate cancer cell growth and metabolism. Journal of Materials Chemistry B. 8: 9718-9733.

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64. Simmons, J.R., Xu, L., and Rainey, J.K. (2019) Recombinant pyriform silk fiber mechanics are modulated by wet-spinning conditions. ACS Biomaterials Science & Engineering. 5: 4985-4993.

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63. Getz, L.J., Runte, C.S., Rainey, J.K., and Thomas, N.A. (2019) Tyrosine phosphorylation as a widespread regulatory mechanism in prokaryotes. Journal of Bacteriology. 201: e00205-19.

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62. Pandey, A., LeBlanc, D.M., Parmar, H.B., Phạm, T.T.T., Sarker, M., Xu, L., Duncan, R., Liu, X-Q., and Rainey, J.K. (2019) Structure, amphipathy, and topology of the membrane-proximal helix 8 influence apelin receptor plasma membrane localization. Biochimica et Biophysica Acta - Biomembranes. 1861: 183036.

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61. Simmons, J.R., Murza, A., Lumsden, M.D., Kenward, K., Marsault, É., and Rainey, J.K. (2019)  Simultaneous ligand and receptor tracking through NMR spectroscopy enabled by distinct 19F labels. International Journal of Molecular Sciences. 20: 3658.

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 (Invited peer reviewed submission for Special Issue on "Structure and Function of Membrane Proteins")

60. Sarker, M., Speckert, M., and Rainey, J.K. (2019) Bicelle composition-dependent modulation of phospholipid dynamics by apelin peptides. Biochemistry and Cell Biology. 97: 325-332. 

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 59. Xu, L.+, Weatherbee-Martin, N.+, Liu, X-Q. and Rainey, J.K. (+contributed equally; 2019) Recombinant silk fiber properties correlate to prefibrillar self-assembly. Small. 15: 1805294.

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58. Shin, K., Landsman, M. Pelletier S., Alamri, B., Anini, Y. and Rainey, J.K. (2019) Proapelin is processed extracellularly in a cell-line dependent manner with clear modulation by proprotein convertases. Amino Acids. 51: 395-405.

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 57. Morash, B.+, Sarker, M.+, and Rainey, J.K. (+contributed equally; 2018) Concentration-dependent changes to diffusion and chemical shift of internal standard molecules in aqueous and micellar solutions. Journal of Biomolecular NMR. 71: 79-89.

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 56. Kenward, C., Shin, K. and Rainey, J.K. (2018) Mixed fluorotryptophan substitutions at the same residue expand the versatility of 19F protein NMR spectroscopy. Chemistry - A European Journal. 24: 3391-3396.

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55. Shin, K., Kenward, C. and Rainey, J.K. (2018) Apelinergic system structure and function. Comprehensive Physiology. 8: 407-450.

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 (Peer-reviewed invited Overview Article.) 54. Shin, K.,  Sarker, M., Huang, S.K. and Rainey, J.K. (2017) Apelin conformational and binding equilibria upon micelle interaction primarily depend on membrane-mimetic headgroup. Scientific Reports. 7: 15433.

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 53. Xu, L., Lefèvre, T., Orrell, K.E., Meng, Q., Auger, M., Liu, X-Q. and Rainey, J.K. (2017) Structural and mechanical roles for the C-terminal non-repetitive domain become apparent in recombinant spider aciniform silk. Biomacromolecules. 18: 3678-3686.

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52. Das, D., Shin, K.,  Rainey, J.K. and Fliegel L. (2017) Transmembrane segment XI of the Na+/H+ antiporter of S. pombe is a critical part of the ion translocation pore.  Scientific Reports. 7: 12793.

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 51. Shin, K., Chapman, N.A., Sarker, M., Kenward, C., Huang, S.K., Weatherbee-Martin, N., Pandey, A., Dupré, D.J. and Rainey, J.K. (2017) Bioactivity of the putative apelin proprotein expands the repertoire of apelin receptor ligands. Biochimica et Biophysica Acta - General Subjects. 1861: 1901-1912.

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50. Langelaan, D.N., Pandey, A., Sarker, M. and Rainey, J.K. (2017) Preserved transmembrane segment topology, structure, and dynamics in disparate micellar environments. The Journal of Physical Chemistry Letters. 8: 2381-2386.

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49. Patterson, R.E., Weatherbee-Martin, N. and Rainey, J.K. (2017) Pyrene-apelin conjugation modulates fluorophore- and peptide-micelle interactions. The Journal of Physical Chemistry B. 121: 4768-4777.

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48. Huang, S.K.+, Shin, K.+, Sarker, M. and Rainey, J.K. (+contributed equally; 2017)  Apela exhibits isoform- and headgroup-dependent modulation of micelle binding, peptide conformation and dynamics. Biochimica et Biophysica Acta - Biomembranes. 1859: 767-778. Permanent

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47. Zhong, X.Z., Zou, Y., Sun, X., Dong, G., Cao, Q., Pandey, A., Rainey, J.K., Zhu, X. and Dong, X-P. (2017) Inhibition of TRPML1 by lysosomal adenosine involved in severe combined immunodeficiency diseases. Journal of Biological Chemistry. 292: 3445-3455.

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 46. Young, B.M., Nguyen, E., Chedraw, M.A.J., Rainey, J.K. and Dupré, D.J. (2017) Differential contribution of transmembrane domains IV, V, VI, and VII to human angiotensin II type 1 receptor homomer formation. Journal of Biological Chemistry. 292: 3341-3350.

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 45. Pandey, A., Shin, K., Patterson, R.E., Liu, X-Q. and Rainey, J.K. (2016) Current strategies for protein production and purification enabling membrane protein structural biology. Biochemistry and Cell Biology. 94: 507-527.

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 44. Tremblay, M-L., Xu, L., Sarker, M., Liu, X-Q. and Rainey, J.K. (2016) Characterizing aciniform silk repetitive domain backbone dynamics and hydrodynamic modularity. International Journal of Molecular Sciences. 17: 1305.

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 (Invited peer reviewed submission for Special Issue on "Silk-Based Materials: From Production to Characterization") TOC figure
43. Weatherbee-Martin, N., Xu, L., Hupe, A., Kreplak, L., Fudge, D.S., Liu, X-Q. and Rainey, J.K. (2016) Identification of wet-spinning and post-spin stretching methods amenable to recombinant spider aciniform silk. Biomacromolecules. 17: 2737-2746.

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42. Sarker, M.+, Orrell, K.E.+, Xu, L., Tremblay, M-L., Bak, J.J., Liu, X-Q. and Rainey, J.K. (+contributed equally; 2016) Tracking transitions in spider wrapping silk conformation and dynamics by 19F nuclear magnetic resonance spectroscopy. Biochemistry. 55: 3048-3059.

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41. Eftaiha, A.F., Tremblay, M-L., Rainey, J.K. and Paige, M.F. (2015) The effect of perfluorooctadecanoic acid on a model phosphatidylcholine-peptide pulmonary lung surfactant mixture. Journal of Fluorine Chemistry. 177: 55-61.

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40. Tremblay, M-L.+, Xu, L.+, Lef�vre, T., Sarker, M., Orrell, K.E., Leclerc, J., Meng, Q., Pezolet, M., Auger, M., Liu, X-Q. and Rainey, J.K. (+ contributed equally; 2015) Spider wrapping silk fiber architecture arising from its modular soluble protein precursor. Scientific Reports. 5: 11502.

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 39. Read, J.+, Clancy, E.K.+, Sarker, M., de Antueno, R., Langelaan, D.N., Parmar, H.B., Shin, K., Rainey, J.K. and Duncan, R. (+contributed equally; 2015) Reovirus FAST proteins drive pore formation and syncytiogenesis using a novel helix-loop-helix fusion-inducing lipid packing sensor. PLoS Pathogens. 11: e1004962.

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38. Clattenburg, L., Wigerius, M., Qi, J., Rainey, J.K., Rourke, J.L., Muruganandan, S., Sinal, C.J. and Fawcett, J.P. (2015) NOS1AP functionally associates with YAP to regulate Hippo signaling. Molecular and Cellular Biology. 35: 2265-2277.

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37. Sarker, M., Fraser, R.E., Lumsden, M.D., Anderson, D.J. and Rainey, J.K. (2015) Characterization of variant soft nanoparticle structure and morphology in solution by NMR spectroscopy. The Journal of Physical Chemistry C. 119: 7461-7471.

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36. Key, T., Sarker, M., de Antueno, R., Rainey, J.K. and Duncan, R. (2015) The p10 FAST protein fusion peptide functions as a cystine noose to induce cholesterol-dependent liposome fusion without liposome tubulation. Biochmica et Biophysica Acta - Biomembranes. 1848: 408-416.

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35.Chapman, N.A., Dupr�, D.J. and Rainey, J.K. (2014) The apelin receptor: Physiology, pathology, cell signalling, and ligand modulation of a peptide-activated class A GPCR. Biochemistry and Cell Biology. 92: 431-440.

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34. Pandey, A., Sarker, M., Liu, X-Q. and Rainey, J.K. (2014) Small expression tags enhance bacterial expression of the first three transmembrane segments of the apelin receptor. Biochemistry and Cell Biology. 92: 269-278.

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33. Xu, L., Tremblay, M-L., Orrell, K.E., Leclerc, J., Meng, Q., Liu, X-Q. and Rainey, J.K. (2013) Nanoparticle self-assembly by a highly stable recombinant spider wrapping silk protein subunit. FEBS Letters. 587: 3273-3280.

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32. Shin, K., Pandey, A., Liu, X-Q., Anini, Y. and Rainey, J.K. (2013) Preferential apelin-13 production by the proprotein convertase PCSK3 is implicated in obesity. FEBS Open Biology. 3: 328-333.

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(open access)

31. Kehoe, S., Tremblay, M-L., Coughlan, A., Towler, M.R., Rainey, J.K., Abraham, R.J. and Boyd, D. (2013) Preliminary Investigation of the Dissolution Behavior, Cytocompatibility, Effects of Fibrinogen Conformation and Platelet Activation for Radiopaque Embolic Particles. Journal of Functional Biomaterials. 4: 89-113.

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(open access)

30. Langelaan, D.N., Reddy, T., Banks, A.W., Dellaire, G., Dupr�, D.J. and Rainey, J.K. (2013) Structural features of the apelin receptor N-terminal tail and first transmembrane segment implicated in ligand binding and receptor trafficking. Biochimica et Biophysica Acta - Biomembranes. 1828: 1471-1483.

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(freely available) PDB entry (2LOU) BMRB entry (18225)

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29. Ramu, T., Prasad, M., Connors, E., Mishra, A., Thomassin, J., Leblanc, J., Rainey, J.K. and Thomas, N. (2013) A novel C-terminal region within the multicargo type III secretion chaperone CesT contributes to effector secretion. Journal of Bacteriology. 195: 740-756. Pubmed link

28. Xu, L., Rainey, J.K., Meng, Q. and Liu, X-Q. (2012) Recombinant minimalist spider wrapping silk proteins capable of native-like fiber formation. PLOS ONE. 7: e50227.

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 27. Xu, L.+, Tremblay, M-L.+, Meng, Q., Liu, X-Q. and Rainey, J.K. (+contributed equally; 2012) 1H, 13C and 15N NMR assignments of the aciniform spidroin (AcSp1) repetitive domain of Argiope trifasciata wrapping silk. Biomolecular NMR Assignments. 6: 147-151. Pubmed link.

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 26. Reddy, T. and Rainey, J.K. (2012) The multifaceted substrate capture scheme of a rhomboid protease. The Journal of Physical Chemistry B. 116: 8942-8954.

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25. Langelaan, D.N.+, Ngweniform, P.+ and Rainey, J.K. (+contributed equally; 2011) Biophysical characterization of G-protein coupled receptor-peptide ligand binding. Biochemistry and Cell Biology. 89: 98-105.

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 24. 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. Journal of Chemical Information and Modeling. 50: 2213-2220.

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23. 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. Journal of Biomolecular NMR. 46: 257-270.

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 Link to CS-CHEMeleon web interface

22. Langelaan, D.N. and Rainey, J.K. (2010) Membrane catalysis of peptide-receptor binding. Biochemistry and Cell Biology. 88: 203-210. Link to article

21. Reddy, T. and Rainey, J.K. (2010) Interpretation of biomolecular NMR spin relaxation parameters. Biochemistry and Cell Biology. 88: 131-142. Link to article Link to relaxation calculation web interface.

20. 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. Biochimica et Biophysica Acta - Biomembranes. 1798: 94-104. Pubmed link;

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 (Invited peer reviewed submission.) 

19. Langelaan, D.N. and Rainey, J.K. (2009) Headgroup-dependent membrane catalysis of apelin-receptor interactions is likely. The Journal of Physical Chemistry B. 113: 10465-10471.  Abstract/Download (open access availability); PDB file & chemical shifts for apelin-17 bound to SDS micelles: BMRB entry 20082;  chemical shifts for apelin-17 in presence of DPC micelles: BMRB entry 16275 TOC fig
18. 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. Abstract/Download; Download link for non-subscribers; BMRB entries with chemical shifts & PDB files: Apelin-17 at 35�C (20029). Apelin-17 at 5�C - major conformer (20030). Apelin-17 at 5�C - minor conformer (20031)

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17. Reddy, T.+, Ding, J.+, Li, X., Sykes, B.D., Rainey, J.K.and Fliegel, L. (+contributed equally; 2008) Structural and functional characterization of transmembrane segment IX of the NHE1 isoform of the Na+/H+ exchanger. Journal of Biological Chemistry. 283: 22018-22030. Abstract/Download;

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(840 kB); PDB entry (2KC3) BMRB entry (15747).

Covering work by Dr. Rainey prior to arrival at Dalhousie:

16. 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. Journal of Magnetic Resonance. 187: 27-37. Abstract/Download;

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(544 kB); Supplementary Data; Excel spreadsheet for coil calculation

15. Slepkov, E.R., Rainey, J.K., Sykes, B.D. and Fliegel, L. (2007) Structural and functional analysis of the Na+/H+ exchanger. Biochemical Journal. 401: 623-633. Abstract/download;

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(620 kB)

14. 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. Biochemistry and Cell Biology. 84: 918-929. Abstract/download;

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(932 kB)

13.  Ding, J.+, Rainey, J.K.+, Xu, C., Sykes, B.D. and Fliegel, L. (+contributed equally; 2006) Structural and functional characterization of transmembrane segment VII of the Na+/H+ exchanger isoform 1. Journal of Biological Chemistry. 281: 29817-29829. Abstract/download;

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(740 kB); Supplemental data PDB entry (2HTG) BMRB entry (7245)

12. 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. Journal of Peptide Research. 66 (s1): 12-21. Abstract/download (free)

11. Rainey, J.K. and Sykes, B.D. (2005) Optimizing oriented planar supported lipid samples for solid-state protein NMR. Biophysical Journal, 89: 2792-2805. Abstract/download;

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(344 kB); Supplementary information
10. Rainey, J.K., DeVries, J.S., and Sykes, B.D. (2005) A rotatable flat-coil for static solid-state nuclear magnetic resonance spectroscopy. Review of Scientific Instruments, 76: 086102. Abstract/download;

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(252 kB)
9. 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. Journal of Biological Chemistry. 280: 17863-17872. Abstract/download;

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(560 kB); PDB entry (1Y4E) BMRB entry (6446)
8. Rainey, J.K. and Goh, M.C. (2004) An interactive triple-helical collagen builder. Bioinformatics. 20: 2458-2459. Paper download (no subscription required) Supplementary Information and Tcl/Tk Script

7. Rainey, J.K. and Goh, M.C. (2004) Statistically based reduced representation of amino acid side-chains. Journal of Chemical Information and Computer Sciences. 44: 817-830.

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(521 kB); Supporting information

6. 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 Biology. 21: 647-661.

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(2.4 MB)

5. Rainey, J.K. and Goh, M.C. (2002) A statistically derived parameterization for the collagen triple-helix. Protein Science. 11: 2748-2754.

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(136 kB - includes Correction published in 13: 2276) and Supplementary material

4. Rainey, J.K. and Goh, M.C. (2002) Parallel atomic force microscopy and NMR spectroscopy to investigate self-assembled protein-nucleotide aggregates. The Journal of Physical Chemistry B. 106: 5553-5560.

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(280 kB)

3. 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: 341-53.

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(1.8 MB)

2. Mayo, P., Poirier, M., Rainey, J., and Tam, W. (1999) Effect of a remote substituent on regioselectivity in oxymercuration of unsymmetrically substituted norborenes. Tetrahedron Letters. 40: 7727-30.

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(200 kB)

1. Paige, M.F., Rainey, J.K., and Goh, M.C. (1998) Fibrous long spacing collagen ultrastructure elucidated by atomic force microscopy. Biophysical Journal. 74: 3211-16.

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(248 kB)

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