Research Synopsis: Magic angle spinning solid-state NMR of proteins and membranes.
The Nieuwkoop lab focuses on using magic-angle-spinning solid-state NMR (ssNMR) to address challenging areas of structural biology. We focus on methods development, especially through very fast spinning, to access samples that would otherwise be hard to investigate. In particular, the lab focuses on 1H-detection, which is becoming more and more powerful as the spinning possible available increase. We seek to investigate the structure and dynamics of lipids and the membranes they form, in order to better understand their function. In addition, we study membrane proteins, whose activity depends upon interactions with lipid bilayers, for which ssNMR is a great tool for atomic resolution investigations.
Lipids and Membranes
Lipid bilayers are a key component of a cell. In addition to providing a barrier, they control the activity of a vast array of proteins and are used to transmit molecules and signals within and outside of the cell. The atomic details of how these signals and interactions take place can be investigated via ssNMR. We seek to understand how subtle differences in lipid head-groups and dynamics have dramatic effects on the properties fo the bilayer and the specific interactions with proteins.
Membrane proteins make up a large and understudied portion of the human genome. Because of the challenges of studying them in their native lipid environment, much of what we know about their structure and function comes from samples in detergent or bilayer mimetics. However, we know that the exact composition of the membrane can have large effects on the activity of membrane proteins. Therefore, we are developing methods to investigate membrane proteins in native or near-native environments. This includes assignment and structure determination, as well as site-specific protein lipid interactions.
1H Detection methods
We seek to apply the power of 1H-detected ssNMR to growing numbers of areas in ssNMR. Due to the fact 1H’s gyromagnetic ratio is 4 times that of 13C, experiments detecting 1H are more sensitive and therefore faster. While 1H detection is increasing well developed in terms of chemical shift assignments, there is still a wide array of areas where it has not yet been deployed. We are developing new pulse sequences to determine intermolecular distances both within a protein and intermolecularly, as well as study dynamics at many timescales.
- Retel, J. S., Nieuwkoop, A. J., Hiller, M., Higman, V. A., Barbet-Massin, E., Stanek, J., Andreas, L. B., Franks, W. T., VanRossum, B., Vinothkumar, K. R., Handel, L., Giuseppe-Palma, G., Bardiaux, B., Pintacuda, G., Emsley, L., Kühlbrandt, W., Oschkinat, H. “Structure of Outer Membrane Protein G in Lipid Bilayers” Nat. Comm. 2017 8(1), 2073. (http://doi.org/10.1038/s41467-017-02228-2)
- Tuttle, M. D., Comellas, G., Nieuwkoop, A. J., Covell, D. J., Berthold, D. A., Kloepper, K. D., Courtney, J. M., Kim, J. K., Barclay, A. M., Kendall, A., Wan, W., Stubbs, G., Schwieters, C. D., Lee, V. M. Y., George, J. M. and Rienstra, C. M. "Solid-state NMR structure of a pathogenic fibril of full-length human alpha-synuclein" Nat. Struct. Mol. Biol. 2016 23(5), 409-15. (http://doi.org/10.1038/nsmb.3194)
- Nieuwkoop, A. J., Franks, W. T., Rehbein, K., Diehl, A., Akbey, U., Engelke, F., Emsley, L., Pintacuda, G. and Oschkinat, H. "Sensitivity and resolution of proton detected spectra of a deuterated protein at 40 and 60 kHz magic-angle-spinning" J. Biomol. NMR. 2015 61(2), 161-71. (http://doi.org/10.1007/s10858-015-9904-0)
- Barbet-Massin, E., Pell, A. J., Retel, J. S., Andreas, L. B., Jaudzems, K., Franks, W. T., Nieuwkoop, A. J., Hiller, M., Higman, V., Guerry, P., Bertarello, A., Knight, M. J., Felletti, M., Le Marchand, T., Kotelovica, S., Akopjana, I., Tars, K., Stoppini, M., Bellotti, V., Bolognesi, M., Ricagno, S., Chou, J. J., Griffin, R. G., Oschkinat, H., Lesage, A., Emsley, L., Herrmann, T. and Pintacuda, G. "Rapid proton-detected NMR assignment for proteins with fast magic angle spinning" J. Am. Chem. Soc. 2014 136(35), 12489-97. (http://doi.org/10.1021/ja507382j)
- Anderson, T. M., Clay, M. C., Cioffi, A. G., Diaz, K. A., Hisao, G. S., Tuttle, M. D., Nieuwkoop, A. J., Comellas, G., Maryum, N., Wang, S., Uno, B. E., Wildeman, E. L., Gonen, T., Rienstra, C. M. and Burke, M. D. "Amphotericin forms an extramembranous and fungicidal sterol sponge" Nat. Chem. Biol. 2014 10(5), 400-6. (http://doi.org/10.1038/nchembio.1496)
- Akbey, U., Nieuwkoop, A. J., Wegner, S., Voreck, A., Kunert, B., Bandara, P., Engelke, F., Nielsen, N. C. and Oschkinat, H. "Quadruple-resonance magic-angle spinning NMR spectroscopy of deuterated solid proteins" Angew Chem Int Ed Engl. 2014 53(9), 2438-42. (http://doi.org/10.1002/anie.201308927)
- Zhou, D. H., Nieuwkoop, A. J., Berthold, D. A., Comellas, G., Sperling, L. J., Tang, M., Shah, G. J., Brea, E. J., Lemkau, L. R. and Rienstra, C. M. "Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy" J. Biomol. NMR. 2012 54(3), 291-305. (http://doi.org/10.1007/s10858-012-9672-z)
- Wylie, B. J., Sperling, L. J., Nieuwkoop, A. J., Franks, W. T., Oldfield, E. and Rienstra, C. M. "Ultrahigh resolution protein structures using NMR chemical shift tensors" Proc. Natl. Acad. Sci. U. S. A. 2011 108(41), 16974-9. (http://doi.org/10.1073/pnas.1103728108)
- Tang, M., Sperling, L. J., Berthold, D. A., Schwieters, C. D., Nesbitt, A. E., Nieuwkoop, A. J., Gennis, R. B. and Rienstra, C. M. "High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data" J. Biomol. NMR. 2011 51(3), 227-33. (http://doi.org/10.1007/s10858-011-9565-6)
- Comellas, G., Lopez, J. J., Nieuwkoop, A. J., Lemkau, L. R. and Rienstra, C. M. "Straightforward, effective calibration of SPINAL-64 decoupling results in the enhancement of sensitivity and resolution of biomolecular solid-state NMR" J Magn Reson. 2011 209(2), 131-5. (http://doi.org/10.1016/j.jmr.2010.12.011)
- Comellas, G., Lemkau, L. R., Nieuwkoop, A. J., Kloepper, K. D., Ladror, D. T., Ebisu, R., Woods, W. S., Lipton, A. S., George, J. M. and Rienstra, C. M. "Structured regions of alpha-synuclein fibrils include the early-onset Parkinson's disease mutation sites" J. Mol. Biol. 2011 411(4), 881-95. (http://doi.org/10.1016/j.jmb.2011.06.026)
- Boettcher, J. M., Davis-Harrison, R. L., Clay, M. C., Nieuwkoop, A. J., Ohkubo, Y. Z., Tajkhorshid, E., Morrissey, J. H. and Rienstra, C. M. "Atomic view of calcium-induced clustering of phosphatidylserine in mixed lipid bilayers" Biochemistry. 2011 50(12), 2264-73. (http://doi.org/10.1021/bi1013694)
- Sperling, L. J., Nieuwkoop, A. J., Lipton, A. S., Berthold, D. A. and Rienstra, C. M. "High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field" J. Biomol. NMR. 2010 46(2), 149-55. (http://doi.org/10.1007/s10858-009-9389-9)
- Nieuwkoop, A. J. and Rienstra, C. M. "Supramolecular protein structure determination by site-specific long-range intermolecular solid state NMR spectroscopy" J. Am. Chem. Soc. 2010 132(22), 7570-1. (http://doi.org/10.1021/ja100992y)
- Nielsen, A. B., Straaso, L. A., Nieuwkoop, A. J., Rienstra, C. M., Bjerring, M. and Nielsen, N. C. "Broadband Heteronuclear Solid-State NMR Experiments by Exponentially Modulated Dipolar Recoupling without Decoupling" J. Phys. Chem. Lett. 2010 1(13), 1952-6. (http://doi.org/10.1021/jz100564j)
- Kijac, A., Shih, A. Y., Nieuwkoop, A. J., Schulten, K., Sligar, S. G. and Rienstra, C. M. "Lipid-protein correlations in nanoscale phospholipid bilayers determined by solid-state nuclear magnetic resonance" Biochemistry. 2010 49(43), 9190-8. (http://doi.org/10.1021/bi1013722)
- Nieuwkoop, A. J., Wylie, B. J., Franks, W. T., Shah, G. J. and Rienstra, C. M. "Atomic resolution protein structure determination by three-dimensional transferred echo double resonance solid-state nuclear magnetic resonance spectroscopy" J. Chem. Phys. 2009 131(9), 095101. (http://doi.org/10.1063/1.3211103)
- Franks, W. T., Wylie, B. J., Schmidt, H. L., Nieuwkoop, A. J., Mayrhofer, R. M., Shah, G. J., Graesser, D. T. and Rienstra, C. M. "Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR" Proc. Natl. Acad. Sci. U. S. A. 2008 105(12), 4621-6. (http://doi.org/10.1073/pnas.0712393105)
- Zhou, D. H., Shea, J. J., Nieuwkoop, A. J., Franks, W. T., Wylie, B. J., Mullen, C., Sandoz, D. and Rienstra, C. M. "Solid-state protein-structure determination with proton-detected triple-resonance 3D magic-angle-spinning NMR spectroscopy" Angew Chem Int Ed Engl. 2007 46(44), 8380-3. (http://doi.org/10.1002/anie.200702905)
- Graesser, D. T., Wylie, B. J., Nieuwkoop, A. J., Franks, W. T. and Rienstra, C. M. "Long-range 19F-15N distance measurements in highly-13C, 15N-enriched solid proteins with 19F-dephased REDOR shift (FRESH) spectroscopy" Magn. Reson. Chem. 2007 45 Suppl 1(S129-34. (http://doi.org/10.1002/mrc.2126)