|Current Funding:||Scientific profiles:||
L.M. Alkhalaf, S.M. Barry, D. Ray, A. Gallo, D. Griffths, J. R. Lewandowski, V. Fulop and G.L. Challis. "Binding of distinct substrate conformations enables hydroxylation of remote sites in thaxtomin D by cytochrome P450 TxtC." J. Am. Chem. Soc. (2018) 141 (1), 216–222. DOI: 10.1021/jacs.8b08864
Cytochromes P450 (CYPs) catalyze various oxidative transformations in drug metabolism, xenobiotic degradation and natural product biosynthesis. Here we report biochemical, structural and theoretical studies of TxtC, an unusual bifunctional CYP in-volved in the biosynthesis of the EPA-approved herbicide thaxtomin A. TxtC was shown to hydroxylate two remote sites with-in the Phe residue of its diketopiperazine substrate thaxtomin D. The reactions follow a preferred order, with hydroxylation of the α-carbon preceding functionalization of the phenyl group. To illuminate the molecular basis for remote site functionaliza-tion, X-ray crystal structures of TxtC in complex with the substrate and monohydroxylated intermediate were determined. Electron density corresponding to a diatomic molecule (probably dioxygen) was sandwiched between the heme iron atom and Thr237 in the TxtC-intermediate structure, providing insight into the mechanism for conversion of the ferrous-dioxygen com-plex into the reactive ferryl intermediate. The substrate and monohydroxylated intermediate adopted similar conformations in the active site, with the π-face of the phenyl group positioned over the heme iron atom. Docking simulations reproduced this observation and identified a second, energetically similar but conformationally-distinct binding mode in which the α-hydrogen of the Phe residue is positioned over the heme prosthetic group. Molecular dynamics simulations confirmed that the α-hydrogen is sufficiently close to the ferryl oxygen atom to be extracted by it and indicated that the two substrate conformations cannot readily interconvert in the active site. These results indicate that TxtC is able to hydroxylate two spatially remote sites by binding distinct conformations of the substrate and monohydroxylated intermediate.
B. Busi, J. R. Yarava, A. Hofstetter, N. Salvi, D. Cala-De Paepe, J. R. Lewandowski, M. Blackledge, and L. Emsley "Protein Dynamics from Multi-Field Variable Temperature NMR Relaxation and MD Simulation" J. Phys. Chem. B (2018) 122 (42), 9697–9702. DOI: 10.1021/acs.jpcb.8b08578
Submitted: 3 Sept 2018, Accepted: 2 Oct 2018, Published online: 2 Oct 2018
Understanding the interplay between protein function and dynamics is currently one of the fundamental challenges of physical biology. Recently a method using variable temperature solid state nuclear magnetic resonance relaxation measurements was proposed for the simultaneous measurement of 12 different activation energies reporting on distinct dynamic modes in the protein GB1. Here, we extend this approach to measure relaxation at multiple magnetic field strengths, allowing us to better constrain the motional models, and to simultaneously evaluate the robustness and physical basis of the method. The data reveal backbone and sidechain motions exhibiting low and high-energy modes with temperature coefficients around 5 kJ·mol-1 and 25 kJ·mol-1. The results are compared to variable temperature molecular dynamics simulation of the crystal lattice, providing further support for the interpretation of the experimental data in terms of molecular motion.
Submitted: 26 July 2018, Published online: 3 Oct 2018
The construction of polyketide natural products by type I modular polyketide synthases (PKSs) requires the coordinated action of several protein subunits to ensure biosynthetic fidelity. This is particularly the case for trans-AT PKSs, which in contrast to most cis-AT PKSs, contain split modules and employ several transacting catalytic domains. This article summarises recent advances in understanding the protein–protein interactions underpinning subunit assembly and intra-subunit communication in such systems and highlights potential avenues and approaches for future research.
C. Öster, G. P. Walkowiak, D. E. Hughes, A. L. Spoering, A. J. Peoples, A. C. Catherwood, J. A. Tod, A. J. Lloyd, T. Herrmann, K. Lewis, C. G. Dowson, Józef R. Lewandowski "Structural studies suggest aggregation as one of the modes of action for teixobactin" Chem. Sci. (2018) 9, 8850-8859. DOI: 10.1039/C8SC03655A
Submitted: 15 Jun 2018 (rev.: 16 Aug 2018), Accepted: 19 Sept 2018, Published online: 20 Sept 2018 | Open Access | Available from WRAP
Associated data: Raw NMR data: http://wrap.warwick.ac.uk/108554/ | BMRB entries: 27478 (solution; teixobactin in DPC micelles), 27479 (solution; teixobactin in aqueous solution) and 27480 (teixobactin in a sedimeneted complex with Gram-negative lipid II in a presence of DPC) | Structure of teixobactin in DPC micelles PDB
Teixobactin is a new promising antibiotic that targets cell wall biosynthesis by binding to lipid II and has no detectable resistance thanks to its unique but yet not fully understood mechanism of operation. To aid in structure-based design of teixobactin analogues with improved pharmacological properties, we present a 3D structure of native teixobactin in membrane mimetics and characterise its binding to lipid II through a combination of solution NMR and fast (90 kHz) magic angle spinning solid state NMR. In NMR titrations, we observe a pattern strongly suggesting interactions between the backbone of the C-terminal “cage” with the pyrophosphate moiety in lipid II. We find that the N-terminal part of teixobactin does not only act as a membrane anchor, as previously thought, but is actively involved in binding. Moreover, teixobactin forms a well-structured and specific complex with lipid II, where the N-terminal part of teixobactin assumes a β conformation that is highly prone to aggregation, which likely contributes to the antibiotic’s high bactericidal efficiency. Overall, our study provides several new clues to teixobactin’s modes of action.
35.H line width dependence on MAS speed in solid state NMR - Comparison of experiment and simulation.
U. Sternberg, R. Witter, I. Kuprov, J.M. Lamley, A. Oss, J.R. Lewandowski and A. Samoson "1H Line Width Dependence on MAS Speed in Solid State NMR - Comparison of Experiment and Simulation" J. Magn. Reson. (2018) 291, 32-39. DOI://10.1016/j.jmr.2018.04.003 (Open Access article)
Submitted: 30 Nov 2017 (rev.: 4 Apr 2018), Accepted: 6 Apr 2018, Published online: 7 Apr 2018 | Open Access | Available from WRAP
Associated data: https://data.mendeley.com/datasets/rrc9pzc4wk/1
Recent developments in magic angle spinning (MAS) technology permit spinning frequencies of ≥100 kHz. The effect of such fast MAS rates upon nuclear magnetic resonance (NMR) proton line widths on the multiple 1H-spin-system of β-Asp-Ala crystal structure had been examined. Powder pattern simulations were performed applying Fokker-Plank approach as implemented in Spinach with periodic boundary conditions, using crystal coordinates and 1H-chemical shift tensors calculated using the bond polarization theory (BPT). The theoretical predictions mirror well the experimental results. Both approaches demonstrate that homogeneous broadening has a linear-quadratic dependency on the inverse of the MAS spinning frequency and that, at the faster end of the spinning frequencies, the residual spectral line broadening becomes dominated by chemical shift distributions and susceptibility effects even for crystalline systems.
M. Jenner, S. Kosol, D. Griffiths, P. Prasongpholchai, L. Manzi, A.S. Barrow, J. E. Moses, N. J. Oldham, J. R. Lewandowski, G. L. Challis "Mechanism of intersubunit ketosynthase–dehydratase interaction in polyketide synthases." Nat. Chem. Biol. (2018) 14(3), 270-275. DOI:10.1038/nchembio.2549
Submitted: 30 Nov 2017 (rev.: 4 Apr 2018), Accepted: 6 Apr 2018, Published online: 7 Apr 2018 | Accepted version freely available from WRAP
Modular polyketide synthases (PKSs) produce numerous structurally complex natural products that have diverse applications in medicine and agriculture. PKSs typically consist of several multienzyme subunits that utilize structurally defined docking domains (DDs) at their N and C termini to ensure correct assembly into functional multiprotein complexes. Here we report a fundamentally different mechanism for subunit assembly in trans-acyltransferase (trans-AT) modular PKSs at the junction between ketosynthase (KS) and dehydratase (DH) domains. This mechanism involves direct interaction of a largely unstructured docking domain (DD) at the C terminus of the KS with the surface of the downstream DH. Acyl transfer assays and mechanism-based crosslinking established that the DD is required for the KS to communicate with the acyl carrier protein appended to the DH. Two distinct regions for binding of the DD to the DH were identified using NMR spectroscopy, carbene footprinting, and mutagenesis, providing a foundation for future elucidation of the molecular basis for interaction specificity.
Associated data: assignment for GbnD4 KS14 DHDD BMRB 27016
33. C. Öster, S. Kosol, C. Hartlmüller, J.M. Lamley, D. Iuga, A. Oss, M.-L. Org, K. Vanatalu, A. Samoson, T. Madl, J.R. Lewandowski "Characterization of protein-protein interfaces in large complexes by solid state NMR solvent paramagnetic relaxation enhancements" J. Am. Chem. Soc. (2017) 139 (35), 12165–12174. DOI: 10.1021/jacs.7b03875 (Open Access Article)
Raw NMR data available from: http://wrap.warwick.ac.uk/91300/1/All_data_sPRE.zip
Solid-state NMR is becoming a viable alternative for obtaining information about structures and dynamics of large biomolecular complexes including ones that are not accessible to other high resolution biophysical techniques. In this context, methods for probing protein-protein interfaces at atomic resolution are highly desirable. Solvent paramagnetic relaxation enhancements (sPREs) proved to be a powerful method for probing protein-protein interfaces in large complexes in solution but have not been employed towards this goal in the solid state. We demonstrate that 1H and 15N relaxation-based sPREs provide a powerful tool for characterizing intermolecular interactions in large assemblies in the solid state. We present approaches for measuring sPREs in practically the entire range of magic angle spinning frequencies used for biomolecular studies and discuss their benefits and limitations. We validate the approach on crystalline GB1 with our experimental results in good agreement with theoretical predictions. Finally, we use sPREs to characterize protein-protein interfaces in the GB1 complex with immunoglobulin (IgG). Our results suggest the potential existence of an additional binding site and provide new insights into GB1:IgG complex structure that amend and revise the current model available from studies with IgG fragments. We demonstrate sPREs as a practical, widely applicable, robust and very sensitive technique for determining intermolecular interaction interfaces in large biomolecular complexes in the solid state.
|32. Good, D., Pham, C., Jagas, J., Lewandowski, J.R and Ladizhansky V. "Solid-state NMR provides evidence for small-amplitude slow domain motions in a multi-spanning transmembrane α-helical protein" J. Am. Chem. Soc. (2017) 139 (27), 9246–9258. DOI: 10.1021/jacs.7b03974 (Open Access Publication)|
|Proteins are dynamic entities and populate ensembles of conformations. Transitions between states within a conformational ensemble occur over a broad spectrum of amplitude and time scales, and are often related to biological function. Whereas solid-state NMR (SSNMR) spectroscopy has recently been used to characterize conformational ensembles of proteins in the microcrystalline states, its applications to membrane proteins remain limited. Here we use SSNMR to study conformational dynamics of a seven-helical transmembrane (TM) protein, Anabaena Sensory Rhodopsin (ASR) reconstituted in lipids. We report on site-specific measurements of the 15N longitudinal R1 and rotating frame R1ρ relaxation rates at two fields of 600 and 800 MHz and at two temperatures of 7 and 30 °C. Quantitative analysis of the R1 and R1ρ values and of their field and temperature dependencies provides evidence of motions on at least two time scales. We modeled these motions as fast local motions and slower collective motions of TM helices and of structured loops, and used the simple model-free and extended model-free analyses to fit the data and estimate the amplitudes, time scales and activation energies. Faster picosecond (tens to hundreds of picoseconds) local motions occur throughout the protein and are dominant in the middle portions of the TM helices. In contrast, the amplitudes of the slower collective motions occurring on the nanosecond (tens to hundreds of nanoseconds) time scales, are smaller in the central parts of helices, but increase toward their cytoplasmic sides as well as in the interhelical loops. ASR interacts with a soluble transducer protein on its cytoplasmic surface, and its binding affinity is modulated by light. The larger amplitude of motions on the cytoplasmic side of the TM helices correlates with the ability of ASR to undergo large conformational changes in the process of binding/unbinding the transducer.
31. Lamley, J.M., Lewandowski, J. R. Relaxation-Based Magic-Angle Spinning NMR Approaches for Studying Protein Dynamics eMagRes (2016) 5(3), 1423–1434. DOI: 10.1002/9780470034590.emrstm1417
Solid-state magic angle spinning (MAS) NMR relaxation measurements provide a powerful tool for characterizing protein dynamics. We provide a general introduction to contemporary relaxation-based MAS NMR approaches by reviewing the basic theoretical concepts, experimental considerations, and example procedures for quantitative analysis. We discuss methods suitable for characterization of motions occurring on time scales in the range from picoseconds to milliseconds. We also sketch out strategies to obtain time scales, amplitudes, and directions of molecular motions.
30. Hoop , C.L., Lin, H.-K., Kar, K., Magyarfalvi, G. Lamley, J.M., Boatz, J.C., Mandal, A., Lewandowski, J.R., Wetzel, R., van der Wel P.C.A. Huntingtin exon 1 fibrils feature an interdigitated β-hairpin–based polyglutamine core PNAS (2016) 113(6) 1546–1551. DOI: 10.1073/pnas.1521933113
Accepted version of the article is freely available from WRAP: http://wrap.warwick.ac.uk/76070/
29. VIP: Lamley, J.M., Öster, C., Stevens, R.A., Lewandowski, J.R. Intermolecular interactions and protein dynamics by SSNMR Angewandte Chemie (2015) 54(51), 15374–15378. DOI: 10.1002/anie.201509168
Open Access Article. Published version also freely available from WRAP: http://wrap.warwick.ac.uk/id/eprint/73941
Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and precipitated >300 kDa GB1-antibody complex. We perform these measurements on samples containing as little as 8 nanomoles of protein. From measurements of site-specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of time scale. Comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast (ps-ns) motions), much greater differences occur for slow motions with >500 ns range motions being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex.
28. Lamley, J.M., Lougher, M.J., Sass, H.J., Rogowski, M., Grzesiek, S., Lewandowski, J.R. Unraveling the complexity of protein backbone dynamics with combined 13C and 15N solid-state NMR relaxation measurements PCCP 17(34), 21997-22008. DOI: 10.1039/C5CP03484A
Open Access Article. Published version also freely available from WRAP: http://wrap.warwick.ac.uk/id/eprint/73677
|Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce 13C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of 13C’ R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz 1H Larmor frequencies and compare them to 13C’ R1, 15N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when 15N data is used alone. We also discuss how internal motions characterized by different time scales contribute to 15N and 13C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.|
27. Lewandowski, J.R., Halse, M.E.; Blackledge, M., Emsley, L. Direct observation of hierarchical protein dynamics Science 348 (6234), 578-581 (2015). http://www.sciencemag.org/content/348/6234/578 Accepted version of the article is freely available from WRAP: http://wrap.warwick.ac.uk/id/eprint/71583
|One of the fundamental challenges of physical biology is to understand the relationship between protein dynamics and function. At physiological temperatures, functional motions arise from the complex interplay of thermal motions of proteins and their environments. Here, we determine the hierarchy in the protein conformational energy landscape that underlies these motions, based on a series of temperature-dependent magic-angle spinning multinuclear nuclear-magnetic-resonance relaxation measurements in a hydrated nanocrystalline protein. The results support strong coupling between protein and solvent dynamics above 160 kelvin, with fast solvent motions, slow protein side-chain motions, and fast protein backbone motions being activated consecutively. Low activation energy, small-amplitude local motions dominate at low temperatures, with larger-amplitude, anisotropic, and functionally relevant motions involving entire peptide units becoming dominant at temperatures above 220 kelvin.|
26. JACS Spotlights article: Lamley, J.M., Iuga, D., Öster, C., Sass, H.J., Rogowski, M., Oss, A., Past, J., Reinhold, A., Grzesiek, S., Samoson, A., Lewandowski, J.R. Solid-State NMR of a Protein in a Precipitated Complex with a Full-Length Antibody J. Am. Chem. Soc. 136, 16800-16806 (2014). http://pubs.acs.org/doi/abs/10.1021/ja5069992
Open Access publication. Published version of the article also freely available from WRAP: http://wrap.warwick.ac.uk/id/eprint/66503
|We demonstrate that the application of 1H-detected experiments at magic-angle spinning frequencies of >50 kHz enables the recording, in a matter of minutes to hours, of solid-state NMR spectra suitable for quantitative analysis of protein complexes present in quantities as small as a few nanomoles (tens of micrograms for the observed component). This approach enables direct structure determination and quantitative dynamics measurements in domains of protein complexes with masses of hundreds of kilodaltons. Protein–protein interaction interfaces can be mapped out by comparison of the chemical shifts of proteins within solid-state complexes with those of the same constituent proteins free in solution. We employed this methodology to characterize a >300 kDa complex of GB1 with full-length human immunoglobulin, where we found that sample preparation by simple precipitation yields spectra of exceptional quality, a feature that is likely to be shared with some other precipitating complexes. Finally, we investigated extensions of our methodology to spinning frequencies of up to 100 kHz.|
25. JACS Spotllights article: Good, D.B., Wang, S., Ward, M.E., Struppe, J.O., Brown, L.S., Lewandowski, J.R., Ladizhansky, V. Conformational dynamics of a seven transmebrane helical protein Anabaena Sensory Rhodopsin probed by solid-state NMR. J. Am. Chem. Soc. 136, 2833–2842 (2014). http://pubs.acs.org/doi/abs/10.1021/ja411633w
Accepted version of the manuscript freely available from WRAP: http://wrap.warwick.ac.uk/62548/
In this study, we report solid-state NMR site-specific measurements of the dipolar order parameters and 15N rotating frame spin–lattice (R1ρ) relaxation rates in a seven transmembrane helical protein Anabaena Sensory Rhodopsin reconstituted in lipids. The magnitudes of the observed order parameters indicate that both the well-defined transmembrane regions and the less structured intramembrane loops undergo restricted submicrosecond time scale motions. In contrast, the R1ρ rates, which were measured under fast magic angle spinning conditions, vary by an order of magnitude between the TM and exposed regions and suggest the presence of intermediate time scale motions. Using a simple model, which assumes a single exponential autocorrelation function, we estimated the time scales of dominant stochastic motions to be on the order of low tens of nanoseconds for most residues within the TM helices and tens to hundreds of nanoseconds for the extracellular B–C and F–G loops. These relatively slow time scales could be attributed to collective anisotropic motions. We used the 3D Gaussian axial fluctuations model to estimate amplitudes, directions, and time scales of overall motions for helices and the extracellular B–C and F–G loops. Within this model, the TM helices A,B,C,D,E,F undergo rigid body motions on a time scale of tens of nanoseconds, while the time scale for the seventh helix G approaches 100 ns. Similar time scales of roughly 100–200 ns are estimated for the B–C and F–G loops.
The manuscript was featured in JACSSelect: Protein Dynamics in Simulation and Experiment
24. Lewandowski, J.R. Advances in Solid-State Relaxation Methodology for Probing Site-Specific Protein Dynamics. Acc. Chem. Res. 46, 2018-27 (2013). DOI
|In this review I discuss recent developments in solid-state NMR relaxation methodology for probing site-specific protein dynamics.|
23. Mollica, L. Baias, M., Lewandowski, J.R., Wylie, B.J., Sperling, L.J., Rienstra, C.M., Emsley, L., Blackledge, M. Atomic-Resolution Structural Dynamics in Crystalline Proteins from NMR and Molecular Simulation. J. Phys. Chem. Lett. 3, 3657–3662 (2012). DOI
|We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to test the accuracy of commonly applied procedures for the interpretation of experimental solid-state relaxation data in terms of dynamic modes and time scales.|
22. Lamley, J.M. & Lewandowski, J.R. Simultaneous acquisition of homonuclear and heteronuclear long-distance contacts with time-shared third spin assisted recoupling. J. Magn. Reson. 218, 30-4 (2012). DOI
|Time-shared Third Spin Assisted Recoupling (TSTSAR) experiment allows for simultaneous acquisition of homonuclear (13C-13C) and heteronuclear (15N-13C) long-distance contacts in biomolecular solids under magic angle spinning. TSTSAR leads to substantial time savings and increases the information content of 2D correlation spectra.|
21. Giffard, M., Hediger, S., Lewandowski, J.R., Bardet, M., Simorre, J-P., Griffin, R.G., De Paëpe, G. Compensated second-order recoupling: application to third spin assisted recoupling. Phys. Chem. Chem. Phys. 14, 7246-55 (2012). DOI
|The modified pulse sequences of PAR and PAIN-CP involving phase inversions: Phase-Shifted Proton Assisted Recoupling (AH-PS-PAR) and Phase-Shifted Proton-Assisted Insensitive Nuclei Cross Polarization (ABH-PS-PAIN-CP) are characterized by improved polarization transfer as well as substantial broadening of the matching conditions. PS-TSAR greatly improves on the standard TSAR based methods by alleviating their sensitivity to precise RF settings and thus rendering them more robust.|
20. Lewandowski, J.R., Sass, H.J., Grzesiek, S., Blackledge, M. & Emsley, L. Site-specific measurement of slow motions in proteins. J. Am. Chem. Soc. 133, 16762-5 (2011).
|We demonstrate that site-specific 15N rotating-frame relaxation rates at high magic-angle-spinning frequencies provide a quantitative measure of slow protein motions in the solid state. This methodology is applicable to both perdeuterated and fully protonated protein samples.|
19. Lewandowski, J.R., van der Wel, P.C.A., Rigney, M., Grigorieff, N., Griffin, R.G. Structural Complexity of a Composite Amyloid Fibril. J. Am. Chem. Soc. 133, 14686-14698 (2011). DOI: 10.1021/ja206815h
18. De Paëpe, G., Lewandowski, J.R., Loquet, A., Eddy, M., Megy, S., Böckmann, A., Griffin, R.G. Heteronuclear proton assisted recoupling. J. Chem. Phys. 134, 095101 (2011). DOI: http://dx.doi.org/10.1063/1.3541251
17. Lewandowski, J.R., Dumez, J-N., Akbey, Ü., Lange, S., Emsley, L., Oschkinat, H. Enhanced Resolution and Coherence Lifetimes in the Solid-State NMR Spectroscopy of Perdeuterated Proteins under Ultrafast Magic-Angle Spinning. J. Phys. Chem. Lett. 2, 2205-2211 (2011). DOI: http://dx.doi.org/10.1021/jz200844n
16. Bertini I., Emsley L., Felli I.C., Laage S., Lesage A., Lewandowski J.R., Marchetti A., Pierattelli R., Pintacuda G. High-resolution and sensitivity through-bond correlations in ultra-fast magic angle spinning (MAS) solid-state NMR. Chem. Sci. 2011;2(2):345.
15. Bertini, I., Bhaumik, A., De Paëpe, G.,Griffin, R.G., Lelli, M.,Lewandowski, J.R.,Luchinat, C. High-resolution solid-state NMR structure of a 17.6 kDa protein. J. Am. Chem. Soc. 132, 1032-40 (2010).
14. Barbet-Massin E., Ricagno S., Lewandowski, J.R., Giorgetti, S., Bellotti, V., Bolognesi, M., Emsley, L., Pintacuda, G. Fibrillar vs crystalline full-length beta-2-microglobulin studied by high-resolution solid-state NMR spectroscopy. J. Am. Chem. Soc. 132, 5556-7 (2010).
13. van der Wel, P.C.A., Lewandowski, J.R., Griffin, R.G. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR. Biochemistry 49, 9457-69 (2010).
12. Lewandowski, J.R. et al. Measurement of site-specific 13C spin-lattice relaxation in a crystalline protein. J. Am. Chem. Soc. 132, 8252-4 (2010).
11. Lewandowski, J.R., Sein, J., Blackledge, M. & Emsley, L. Anisotropic collective motion contributes to nuclear spin relaxation in crystalline proteins. J. Am. Chem. Soc. 132, 1246-8 (2010).
10. Lewandowski, J.R. De Paëpe, G., Eddy, M.T., Struppe, J., Maas, W., Griffin, R.G. Proton assisted recoupling at high spinning frequencies. J. Phys. Chem. B 113, 9062-9 (2009). DOI: http://dx.doi.org/10.1021/jp810280t
|We demonstrate the successful application of 13C−13C proton assisted recoupling (PAR) on [U−13C,15N] N-f-MLF-OH and [U−13C,15N] protein GB1 at high magic angle spinning (MAS) frequencies (ωr/2π = 65 kHz). Specifically, by combining PAR mixing with low power heteronuclear decoupling (ω1H/2π ∼ 16 kHz) and high spinning frequencies, we obtain high resolution 2D spectra displaying long-range 13C−13C contacts from which distance estimates can be extracted. These experiments therefore demonstrate the possibility of performing high resolution structural studies in the limit of high spinning frequency and low power 1H decoupling, a regime which optimizes the resolution of protein samples and preserves their integrity.|
9. Lewandowski, J.R., De Paëpe, G., Eddy, M.T. & Griffin, R.G. 15N-15N proton assisted recoupling in magic angle spinning NMR. J. Am. Chem. Soc. 131, 5769-76 (2009). DOI: http://dx.doi.org/10.1021/ja806578y
|We describe a new magic angle spinning (MAS) NMR experiment for obtaining 15N−15N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of α-helical stretches and interstrand connectivity in antiparallel β-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, 15N−15N proton assisted recoupling (PAR), relies on a second-order mechanism, third spin assisted recoupling (TSAR), used previously in the context of 15N−13C and 13C−13C polarization transfer schemes. In comparison to 15N−15N proton-driven spin diffusion experiments, the PAR technique accelerates polarization transfer between 15N’s by a factor of ∼102−103 and is furthermore applicable over the entire range of currently available MAS frequencies (10−70 kHz).|
8. De Paëpe, G., Lewandowski, J.R., Loquet, A., Böckmann, A. & Griffin, R.G. Proton assisted recoupling and protein structure determination. J. Chem. Phys. 129, 245101 (2008). DOI: http://dx.doi.org/10.1063/1.3036928
7. De Paëpe, G., Lewandowski, J.R. & Griffin, R.G. Spin dynamics in the modulation frame: application to homonuclear recoupling in magic angle spinning solid-state NMR. J. Chem. Phys. 128, 124503 (2008).
|We introduce a family of solid-state NMR pulse sequences that generalizes the concept of second
averaging in the modulation frame and therefore provides a new approach to perform magic angle
spinning dipolar recoupling experiments. Here, we focus on two particular recoupling
mechanisms—cosine modulated rotary resonance CMpRR and cosine modulated recoupling with
isotropic chemical shift reintroduction COMICS. The first technique, CMpRR, is based on a
cosine modulation of the rf phase and yields broadband double-quantum DQ 13C recoupling using
70 kHz ω1,C/2π rf field for the spinning frequency ωr/2π=10–30 kHz and 1H Larmor frequency ω0,H /2π up to 900 MHz. Importantly, for p ≤ 5, CMpRR recouples efficiently in the absence of 1H decoupling. Extension to lower p values 3.5 ≤p ≤5 and higher spinning frequencies is possible
using low power 1H irradiation 0.25ωr/2π. This phenomenon is explained through higher order
cross terms including a homonuclear third spin assisted recoupling mechanism among protons.
CMpRR mitigates the heating effects of simultaneous high power 13C recoupling and 1H decoupling. The second technique, COMICS, involves low power 13C irradiation that induces
simultaneous recoupling of the 13C DQ dipolar and isotropic chemical shift terms. In contrast to
CMpRR, where the DQ bandwidth 30 kHz at ω0,H/2π=750 MHz covers the entire 13C spectral
width, COMICS recoupling, through the reintroduction of the isotropic chemical shift, is selective
with respect to the carrier frequency, having a typical bandwidth of 100 Hz. This approach is
intended as a general frequency selective method circumventing dipolar truncation supplementary
to R2 experiments. These new γ-encoded sequences with attenuated rf requirements extend the
applicability of homonuclear recoupling techniques to new regimes—high spinning and Larmor
frequencies—and therefore should be of major interest for high resolution biomolecular studies.
6. Lewandowski, J.R., De Paëpe, G. & Griffin, R.G. Proton assisted insensitive nuclei cross polarization. J. Am. Chem. Soc. 129, 728-9 (2007).
5. van der Wel, P.C.A., Lewandowski, J.R. & Griffin, R.G. Solid-state NMR study of amyloid nanocrystals and fibrils formed by the peptide GNNQQNY from yeast prion protein Sup35p. J. Am. Chem. Soc. 129, 5117-30 (2007).
4. Ramachandran, R., Lewandowski, J.R., van der Wel, P.C.A. & Griffin, R.G. Multipole-multimode Floquet theory of rotational resonance width experiments: 13C-13C distance measurements in uniformly labeled solids. J. Chem. Phys. 124, 214107 (2006).
3. van der Wel, P.C.A., Hu, K.-N., Lewandowski, J.R. & Griffin, R.G. Dynamic nuclear polarization of amyloidogenic peptide nanocrystals: GNNQQNY, a core segment of the yeast prion protein Sup35p. J. Am. Chem. Soc. 128, 10840-6 (2006).
2. De Paëpe, G., Lewandowski, J.R., Bayro, M.J. & Griffin, R.G. Broadband homonuclear correlation spectroscopy at high magnetic fields and MAS frequencies. J. Am. Chem. Soc. 128, 1776-7 (2006).
1. Pecul, M., Lewandowski, J.R. & Sadlej, J. Benchmark calculations of the shielding constants in the water dimer. Chem. Phys. Lett. 333, 139-145 (2001).