Co-reporter:Rivkah Rogawski, Ann E. McDermott
Archives of Biochemistry and Biophysics 2017 Volume 628(Volume 628) pp:
Publication Date(Web):15 August 2017
DOI:10.1016/j.abb.2017.06.010
•DNP has enabled detection of dilute biological species in complex contexts, such as cell lysates or whole viruses.•Selective DNP sensitization through specifically tagged radicals has been demonstrated in a range of experimental designs.•Although a number of challenges remain, these experiments can enable in cell NMR experiments with heightened sensitivity.Magic angle spinning solid state NMR studies of biological macromolecules [1–3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
Co-reporter:Rivkah RogawskiIvan V. Sergeyev, Yongjun Li, M. Francesca Ottaviani, Virginia CornishAnn E. McDermott
The Journal of Physical Chemistry B 2017 Volume 121(Issue 6) pp:
Publication Date(Web):January 18, 2017
DOI:10.1021/acs.jpcb.6b09021
Dynamic nuclear polarization is an emerging technique for sensitizing solid-state NMR experiments by transferring polarization from electrons to nuclei. Stable biradicals, the polarization source for the cross effect mechanism, are typically codissolved at millimolar concentrations with proteins of interest. Here we describe the high-affinity biradical tag TMP-T, created by covalently linking trimethoprim, a nanomolar affinity ligand of dihydrofolate reductase (DHFR), to the biradical polarizing agent TOTAPOL. With TMP-T bound to DHFR, large enhancements of the protein spectrum are observed, comparable to when TOTAPOL is codissolved with the protein. In contrast to TOTAPOL, the tight binding TMP-T can be added stoichiometrically at radical concentrations orders of magnitude lower than in previously described preparations. Benefits of the reduced radical concentration include reduced spectral bleaching, reduced chemical perturbation of the sample, and the ability to selectively enhance signals for the protein of interest.
Co-reporter:Benjamin J. Wylie;Manasi P. Bhate;
Proceedings of the National Academy of Sciences 2014 111(1) pp:185-190
Publication Date(Web):December 16, 2013
DOI:10.1073/pnas.1319577110
It has been hypothesized that transmembrane allostery is the basis for inactivation of the potassium channel KcsA: opening
the intracellular gate is spontaneously followed by ion expulsion at the extracellular selectivity filter. This suggests a
corollary: following ion expulsion at neutral pH, a spontaneous global conformation change of the transmembrane helices, similar
to the motion involved in opening, is expected. Consequently, both the low potassium state and the low pH state of the system
could provide useful models for the inactivated state. Unique NMR studies of full-length KcsA in hydrated bilayers provide
strong evidence for such a mutual coupling across the bilayer: namely, upon removing ambient potassium ions, changes are seen
in the NMR shifts of carboxylates E118 and E120 in the pH gate in the hinges of the inner transmembrane helix (98–103), and
in the selectivity filter, all of which resemble changes seen upon acid-induced opening and inhibition and suggest that ion
release can trigger channel helix opening.
Co-reporter:Jaclyn Catalano, Kianoush Sadre-Bazzaz, Gabriele A. Amodeo, Liang Tong, and Ann McDermott
Biochemistry 2013 Volume 52(Issue 39) pp:
Publication Date(Web):July 6, 2013
DOI:10.1021/bi4000645
Cytochrome P450 BM-3 is a bacterial enzyme with sequence similarity to mammalian P450s that catalyzes the hydroxylation of fatty acids with high efficiency. Enzyme–substrate binding and dynamics has been an important topic of study for cytochromes P450 because most of the crystal structures of substrate-bound structures show the complex in an inactive state. We have determined a new crystal structure for cytochrome P450 BM-3 in complex with N-palmitoylglycine (NPG), which unexpectedly showed a direct bidentate ion pair between NPG and arginine 47 (R47). We further explored the role of R47, the only charged residue in the binding pocket in cytochrome P450 BM-3, through mutagenesis and crystallographic studies. The mutations of R47 to glutamine (R47Q), glutamic acid (R47E), and lysine (R47K) were designed to investigate the role of its charge in binding and catalysis. The oppositely charged R47E mutation had the greatest effect on activity and binding. The crystal structure of R47E BMP shows that the glutamic acid side chain is blocking the entrance to the binding pocket, accounting for NPG’s low binding affinity and charge repulsion. For R47Q and R47K BM-3, the mutations caused only a slight change in kcat and a large change in Km and Kd, which suggests that R47 mostly is involved in binding and that our crystal structure, 4KPA, represents an initial binding step in the P450 cycle.
Co-reporter:Wenbo Li, Ann McDermott
Journal of Magnetic Resonance 2012 222() pp: 74-80
Publication Date(Web):
DOI:10.1016/j.jmr.2012.05.019
Co-reporter:Caitlin M. Quinn, Ann E. McDermott
Journal of Magnetic Resonance 2012 222() pp: 1-7
Publication Date(Web):
DOI:10.1016/j.jmr.2012.05.014
Co-reporter:Manasi P. Bhate
PNAS 2012 Volume 109 (Issue 38 ) pp:
Publication Date(Web):2012-09-18
DOI:10.1073/pnas.1211900109
The prototypical prokaryotic potassium channel KcsA alters its pore depending on the ambient potassium; at high potassium,
it exists in a conductive form, and at low potassium, it collapses into a nonconductive structure with reduced ion occupancy.
We present solid-state NMR studies of KcsA in which we test the hypothesis that an important channel-inactivation process,
known as C-type inactivation, proceeds via a state similar to this collapsed state. We test this using an inactivation-resistant
mutant E71A, and show that E71A is unable to collapse its pore at both low potassium and low pH, suggesting that the collapsed
state is structurally similar to the inactivated state. We also show that E71A has a disordered selectivity filter. Using
site-specific K+ titrations, we detect a local change at E71 that is coupled to channel collapse at low K+. To gain more insight into this change, we site specifically measure the chemical shift tensors of the side-chain carboxyls
of E71 and its hydrogen bond partner D80, and use the tensors to assign protonation states to E71 and D80 at high K+ and neutral pH. Our measurements show that E71 is protonated at pH 7.5 and must have an unusually perturbed pKa (> 7.5) suggesting that the change at E71 is a structural rearrangement rather than a protonation event. The results offer
new mechanistic insights into why the widely used mutant KcsA–E71A does not inactivate and establish the ambient K+ level as a means to populate the inactivated state of KcsA in a controlled way.
Co-reporter:Ivan V. Sergeyev ; Loren A. Day ; Amir Goldbourt
Journal of the American Chemical Society 2011 Volume 133(Issue 50) pp:20208-20217
Publication Date(Web):August 22, 2011
DOI:10.1021/ja2043062
Solid-state NMR spectra, including dynamic nuclear polarization enhanced 400 MHz spectra acquired at 100 K, as well as non-DNP spectra at a variety of field strengths and at temperatures in the range 213–243 K, have allowed the assignment of the 13C and 15N resonances of the unusual DNA structure in the Pf1 virion. The 13C chemical shifts of C3′ and C5′, considered to be key reporters of deoxyribose conformation, fall near or beyond the edges of their respective ranges in available databases. The 13C and 15N chemical shifts of the DNA bases have above-average values for AC4, AC5, CC5, TC2, and TC5, and below average values for AC8, GC8, and GN2, pointing to an absence of Watson–Crick hydrogen bonding, yet the presence of some type of aromatic ring interaction. Crosspeaks between Tyr40 of the coat protein and several DNA atoms suggest that Tyr40 is involved in this ring interaction. In addition, these crosspeak resonances and several deoxyribose resonances are multiply split, presumably through the effects of ordered but differing interactions between capsid protein subunits and each type of nucleotide in each of the two DNA strands. Overall, these observations characterize and support the DNA model proposed by Liu and Day and refined by Tsuboi et al., which calls for the most highly stretched and twisted naturally occurring DNA yet encountered.
Co-reporter:Kuo-Ying Huang, Ansgar B. Siemer, Ann E. McDermott
Journal of Magnetic Resonance 2011 Volume 208(Issue 1) pp:122-127
Publication Date(Web):January 2011
DOI:10.1016/j.jmr.2010.10.015
We tested the performance of several 13C homonuclear mixing sequences on perdeuterated microcrystalline ubiquitin. All sequences were applied without 1H decoupling and at relatively low MAS frequencies. We found that RFDR gave the highest overall transfer efficiency and that DREAM performs surprisingly well under these conditions being twice as efficient in the aliphatic region of the spectrum than the other mixing sequences tested.Graphical abstractDREAM and RFDR are efficient 13C–13C mixing sequences for perdeuterated proteins.Research highlights► Comparing homonuclear 13C solid-state NMR mixing sequences on perdeuterated proteins. ► All sequences work without 1H decoupling and at relatively low MAS frequencies. ► RFDR gave the highest overall transfer efficiency. ► DREAM gave the most intense cross peaks in the aliphatic region of the spectrum.
Co-reporter:Andras J. Bauer, Simone Gieschler, Kathryn M. Lemberg, Ann E. McDermott, and Brent R. Stockwell
Biochemistry 2011 Volume 50(Issue 17) pp:
Publication Date(Web):March 22, 2011
DOI:10.1021/bi2003247
Voltage-dependent anion channels (VDACs) are critical regulators of outer mitochondrial membrane permeability in eukaryotic cells. VDACs have also been postulated to regulate cell death mechanisms. Erastin, a small molecule quinazolinone that is selectively lethal to tumor cells expressing mutant RAS, has previously been reported as a ligand for hVDAC2. While significant efforts have been made to elucidate the structure and function of hVDAC1, structural and functional characterization of hVDAC2 remains lacking. Here, we present an in vitro system that provides a platform for both functional and structural investigation of hVDAC2 and its small molecule modulator, erastin. Using this system, we found that erastin increases permeability of VDAC2 liposomes to NADH in a manner that requires the amino-terminal region of VDAC2. Furthermore, we confirmed that this VDAC2-lipsome sample is folded using solid-state NMR.
Co-reporter:Ansgar B. Siemer;Kuo-Ying Huang
PNAS 2010 Volume 107 (Issue 41 ) pp:17580-17585
Publication Date(Web):2010-10-12
DOI:10.1073/pnas.1009369107
NMR on frozen solutions is an ideal method to study fundamental questions of macromolecular hydration, because the hydration
shell of many biomolecules does not freeze together with bulk solvent. In the present study, we present previously undescribed
NMR methods to study the interactions of proteins with their hydration shell and the ice lattice in frozen solution. We applied
these methods to compare solvent interaction of an ice-binding type III antifreeze protein (AFP III) and ubiquitin a non-ice-binding
protein in frozen solution. We measured 1H-1H cross-saturation and cross-relaxation to provide evidence for a molecular contact surface between ice and AFP III at moderate
freezing temperatures of -35 °C. This phenomenon is potentially unique for AFPs because ubiquitin shows no such cross relaxation
or cross saturation with ice. On the other hand, we detected liquid hydration water and strong water–AFP III and water–ubiquitin
cross peaks in frozen solution using relaxation filtered 2H and HETCOR spectra with additional 1H-1H mixing. These results are consistent with the idea that ubiquitin is surrounded by a hydration shell, which separates it
from the bulk ice. For AFP III, the water cross peaks indicate that only a portion of its hydration shell (i.e., at the ice-binding
surface) is in contact with the ice lattice. The rest of AFP III’s hydration shell behaves similarly to the hydration shell
of non-ice-interacting proteins such as ubiquitin and does not freeze together with the bulk water.
Co-reporter:Justin L. Lorieau;Loren A. Day
PNAS 2008 Volume 105 (Issue 30 ) pp:10366-10371
Publication Date(Web):2008-07-29
DOI:10.1073/pnas.0800405105
This study has examined the atomic-level dynamics of the protein in the capsid of filamentous phage Pf1. This capsid consists
of ≈7,300 small subunits of only 46 aa in a helical array around a highly extended, circular single-stranded DNA molecule
of 7,349 nt. Measurements were made of site-specific, solid-state NMR order parameters, 〈S〉, the values which are dimensionless quantities between 0 (mobile) and 1 (static) that characterize the amplitudes of molecular
bond angular motions that are faster than microseconds. It was found that the protein subunit backbone is very static, and
of particular interest, it appears to be static at residues glycine 15 and glutamine 16 where it had been previously thought
to be mobile. In contrast to the backbone, several side chains display large-amplitude angular motions. Side chains on the
virion exterior that interact with solvent are highly mobile, but surprisingly, the side chains of residues arginine 44 and
lysine 45 near the DNA deep in the interior of the virion are also highly mobile. The large-amplitude dynamic motion of these
positively charged side chains in their interactions with the DNA were not previously expected. The results reveal a highly
dynamic aspect of a DNA–protein interface within a virus.
Co-reporter:Amir Goldbourt, Loren A. Day, Ann E. McDermott
Journal of Magnetic Resonance 2007 Volume 189(Issue 2) pp:157-165
Publication Date(Web):December 2007
DOI:10.1016/j.jmr.2007.07.011
In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many 13C–13C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner–Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1-13C d-glucose (13C in position 1) as the sole carbon source, as well as 15NH4Cl as the only nitrogen source. The 37 MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D 15N–15N data provided strong verification of many previous assignments of 15N amide and 13C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.
Co-reporter:Sharon Rozovsky
PNAS 2007 Volume 104 (Issue 7 ) pp:2080-2085
Publication Date(Web):2007-02-13
DOI:10.1073/pnas.0608876104
The highly efficient glycolytic enzyme, triosephosphate isomerase, is expected to differentially stabilize the proposed stable
reaction species: ketone, aldehyde, and enediol(ate). The identity and steady-state populations of the chemical entities bound
to triosephosphate isomerase have been probed by using solid- and solution-state NMR. The 13C-enriched ketone substrate, dihydroxyacetone phosphate, was bound to the enzyme and characterized at steady state over a
range of sample conditions. The ketone substrate was observed to be the major species over a temperature range from −60°C
to 15°C. Thus, there is no suggestion that the enzyme preferentially stabilizes the reactive intermediate or the product.
The predominance of dihydroxyacetone phosphate on the enzyme would support a mechanism in which the initial proton abstraction
in the reaction from dihydroxyacetone phosphate to d-glyceraldehyde 3-phosphate is significantly slower than the subsequent chemical steps.
Co-reporter:Justin Lorieau
Magnetic Resonance in Chemistry 2006 Volume 44(Issue 3) pp:334-347
Publication Date(Web):14 FEB 2006
DOI:10.1002/mrc.1773
Order parameters describing conformational exchange processes on the nanosecond to microsecond timescale can be obtained from powder patterns in solid-state NMR (SSNMR) experiments.1–3 Extensions of these experiments to magic-angle spinning (MAS) based high-resolution experiments have been demonstrated,4–6 which show a great promise for site-specific probes of biopolymers. In this study, we present a detailed comparison of two pulse sequences, transverse Manfield–Rhim–Elleman–Vaughn (T-MREV) and Lee–Goldburg cross-polarization (LGCP), using experimental and simulation tools to explore their utility in the study of order parameters. We discuss systematic errors due to passively coupled 13C or 1H nuclei, as well as due to B1 inhomogeneity. Both pulse sequences can provide quantitative measurements of the order parameter, but the LGCP experiment is capable of greater accuracy provided that the B1 field is highly homogeneous. The T-MREV experiment is far better compensated for B1 inhomogeneity, and it also performs better in situations with limited signal. Copyright © 2006 John Wiley & Sons, Ltd.
Co-reporter:Benjamin J. Gross, Joseph M. Tanski, Ann E. McDermott
Journal of Magnetic Resonance 2005 Volume 176(Issue 2) pp:223-233
Publication Date(Web):October 2005
DOI:10.1016/j.jmr.2005.06.008
Single crystal rotational echo double resonance (REDOR) experiments can be used to determine the three-dimensional orientation of heteronuclear bond vectors in an amino acid, as well as the crystal’s orientation relative to the rotor fixed frame (RFF). We also demonstrate that for samples uniaxially aligned along the rotor axis, the polar tilt angle of a bond vector relative to the RFF can be measured by use of an analytical expression that describes the REDOR curve for that system. These bond orientations were verified by X-ray indexing of the single crystal sample, and were shown to be as accurate as ±1°.
Co-reporter:Xiang-jin Song
Magnetic Resonance in Chemistry 2001 Volume 39(Issue S1) pp:S37-S43
Publication Date(Web):5 NOV 2001
DOI:10.1002/mrc.957
Hydrogen-bonded pairs of the 2-methylimidazolium cation and 2-methylimidazole are expected to have matched pKa values, owing to chemical symmetry. These structures serve as models for enzyme active sites. Several crystalline salts of this system were prepared and characterized by crystallography and solid-state NMR. Short N···N distances are observed (∼2.65 Å), and fast (>105 s−1) proton transfer through the N—H···N bridge was suggested by NMR lineshape measurements at temperatures from 200 to 320 K. The equilibrium constants for these transfer processes were found to differ from unity, and to be strongly temperature and counter-ion dependent. For the perchlorate salt, the proton is observed to be mainly attached to one of the bridge nitrogens across this temperature range, for the iodide salt, the proton is substantially delocalized on to both bridging nitrogens across the temperature range. Interestingly, for the chloride and bromide salts, a temperature-dependent equilibrium constant is observed, with equal populations of the two isomers in rapid exchange at room temperature and an effectively trapped proton (or very strong population of one isomer) at 200 K. This temperature-dependent equilibrium constant indicates that the proton transfer is associated with an enthalpy of the order the 20 kJ mol−1. This study underscores the power of NMR spectroscopy to account for protons, and the important influence of remote ionic interactions on proton transfer coordinates. Copyright © 2001 John Wiley & Sons, Ltd.
Co-reporter:Xiang-jin Song;Chad M. Rienstra
Magnetic Resonance in Chemistry 2001 Volume 39(Issue S1) pp:S30-S36
Publication Date(Web):5 NOV 2001
DOI:10.1002/mrc.956
N—H bond lengths in imidazolium–carboxylate pairs were studied as models for enzyme active site motifs. The bond lengths were measured using ‘2D 2ϕ-DipShift,’ a solid-state NMR method wherein the N,H dipolar coupling is determined using heteronuclear dipolar spinning sideband patterns. Like the situation for compressed O—H···O systems, some complexes exhibit very short N···O distances and weaker N,H dipolar coupling. The weaker time-average N,H dipolar coupling for systems with short N···O hydrogen bonds can be most likely associated with an altered potential well for the proton, or a ‘stretched’ covalent bond, although other interpretations involving a double well potential are discussed. The range or variation in average bond lengths seen in this study is much narrower than that previously reported for O—H···O systems (1.01–1.07 Å for N—H vs 1.0–1.3 Å for O—H bonds). Copyright © 2001 John Wiley & Sons, Ltd.
Co-reporter:Krisztina Varga, Lin Tian, Ann E. McDermott
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics (December 2007) Volume 1774(Issue 12) pp:
Publication Date(Web):December 2007
DOI:10.1016/j.bbapap.2007.08.029
The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly 13C, 15N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.
Co-reporter:Manasi P. Bhate, Benjamin J. Wylie, Lin Tian, Ann E. McDermott
Journal of Molecular Biology (13 August 2010) Volume 401(Issue 2) pp:155-166
Publication Date(Web):13 August 2010
DOI:10.1016/j.jmb.2010.06.031
Conformational change in the selectivity filter of KcsA as a function of ambient potassium concentration is studied with solid-state NMR. This highly conserved region of the protein is known to chelate potassium ions selectively. We report solid-state NMR chemical shift fingerprints of two distinct conformations of the selectivity filter; significant changes are observed in the chemical shifts of key residues in the filter as the potassium ion concentration is changed from 50 mM to 1 μM. Potassium ion titration studies reveal that the site-specific Kd for K+ binding at the key pore residue Val76 is on the order of ∼ 7 μM and that a relatively high sample hydration is necessary to observe the low-K+ conformer. Simultaneous detection of both conformers at low ambient potassium concentration suggests that the high-K+ and low-K+ states are in slow exchange on the NMR timescale (kex < 500 s− 1). The slow rate and tight binding for evacuating both inner sites simultaneously differ from prior observations in detergent in solution, but agree well with measurements by electrophysiology and appear to result from our use of a hydrated bilayer environment. These observations strongly support a common assumption that the low-K+ state is not involved in ion transmission, and that during transmission one of the two inner sites is always occupied. On the other hand, these kinetic and thermodynamic characteristics of the evacuation of the inner sites certainly could be compatible with participation in a control mechanism at low ion concentration such as C-type inactivation, a process that is coupled to activation and involves closing of the outer mouth of the channel.