The conformation of an inhibitor bound to the gastric proton pump

How to investigate interactions between membrane proteins and ligands by solid-state NMR

Solid-state NMR is an established method for biophysical studies of membrane proteins within the lipid bilayers and an emerging technique for structural biology in general. In particular magic angle sample spinning has been found to be very useful for the investigation of large membrane proteins and their interaction with small molecules within the lipid bilayer. Using a number of examples, we illustrate and discuss in this chapter, which information can be gained and which experimental parameters need to be considered when planning such experiments. We focus especially on the interaction of diffusive ligands with membrane proteins.

NMR in natural products: understanding conformation, configuration and receptor interactions

Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of natural products in complex with macromolecular receptors.

The conformation of acetylcholine at its target site in the membrane-embedded nicotinic acetylcholine receptor

The conformation of the neurotransmitter acetylcholine bound to the fully functional nicotinic acetylcholine receptor embedded in its native membrane environment has been characterized by using frequency-selective recoupling solid-state NMR. Six dipolar couplings among five resolved (13)C-labeled atoms of acetylcholine were measured. Bound acetylcholine adopts a bent conformation characterized with a quaternary ammonium-to-carbonyl distance of 5.1 A. In this conformation, and with its orientation constrained to that previously determined by us, the acetylcholine could be docked satisfactorily in the agonist pocket of the agonist-bound, but not the agonist-free, crystal structure of a soluble acetylcholine-binding protein from Lymnaea stagnali. The quaternary ammonium group of the acetylcholine was determined to be within 3.9 A of five aromatic residues and its acetyl group close to residues C187/188 of the principle and residue L112 of the complementary subunit. The observed >C O chemical shift is consistent with H bonding to the nicotinic acetylcholine receptor residues gammaY116 and deltaT119 that are homologous to L112 in the soluble acetylcholine-binding protein.

Solid-state NMR spectroscopy as a tool for drug design: from membrane-embedded targets to amyloid fibrils

Structure-based design has gained credibility as a valuable component of the modern drug discovery process. The technique of SSNMR (solid-state NMR) promises to be a useful counterpart to the conventional experimental techniques of X-ray crystallography and solution-state NMR for providing structural features of drug targets that can guide medicinal chemistry towards drug candidates. This article highlights some recent SSNMR approaches from our group for identifying active compounds, such as enzyme inhibitors, receptor antagonists and peptide agents, that prevent the aggregation of amyloid proteins involved in neurodegenerative diseases. It is anticipated that the use of SSNMR in drug discovery will become more widespread in the wake of advances in hardware and methodological developments.

Ligand Docking in the Gastric H+/K+-ATPase: Homology Modeling of Reversible Inhibitor Binding Sites

Using the recent high-resolution X-ray structures determined for the Ca2+-ATPase, we have generated two homology models of the gastric H+/K+-ATPase reflecting the E1 and E2 conformations adopted by P-type ATPases in their catalytic cycle. In regimes where the in situ solid-state NMR-determined structure for 1,2,3-trimethyl-8-(pentafluorophenylmethoxy)imidazo[1,2-a]pyridinium iodide (TMPFPIP), a reversible inhibitor of the gastric H+/K+-ATPase, was retained in its predefined conformation and was allowed full torsional flexibility in docking, the ligands localized to discrete binding volumes in the E1 model and to a single central binding space, together with secondary peripheral locations, in the E2 conformation. The results of these binding studies are in good agreement with current site-directed mutagenesis data and support the suggestion that the binding site is proximal to the loop between TM5 and TM6 and TM8, the transmembrane (TM) region considered important for cation translocation. Furthermore, the results of the simulation with the flexible ligand complement the solid-state NMR structural constraints of this inhibitor when bound in situ to the protein.

Solid-state NMR in drug design and discovery for membrane-embedded targets

Observing drugs and ligands at their site of action in membrane proteins is now possible through the use of a development in biomolecular NMR spectroscopy known as solid-state NMR. Even large, functionally active complexes are being examined using this method, with structural details being resolved at super-high subnanometre resolution. This is supplemented by detailed dynamic and electronic information about the surrounding ligand environment, and gives surprising new insights into the way in which ligands bind, which can aid drug design.

Substrate Affinities for Membrane Transport Proteins Determined by 13C Cross-Polarization Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy

We have devised methods in which cross-polarization magic-angle spinning (CP-MAS) solid-state NMR is exploited to measure rigorous parameters for binding of (13)C-labeled substrates to membrane transport proteins. The methods were applied to two proteins from Escherichia coli: a nucleoside transporter, NupC, and a glucuronide transporter, GusB. A substantial signal for the binding of methyl [1-(13)C]-beta-d-glucuronide to GusB overexpressed in native membranes was achieved with a sample that contained as little as 20 nmol of GusB protein. The data were fitted to yield a K(D) value of 4.17 mM for the labeled ligand and 0.42 mM for an unlabeled ligand, p-nitrophenyl beta-d-glucuronide, which displaced the labeled compound. CP-MAS was also used to measure binding of [1'-(13)C]uridine to overexpressed NupC. The spectrum of NupC-enriched membranes containing [1'-(13)C]uridine exhibited a large peak from substrate bound to undefined sites other than the transport site, which obscured the signal from substrate bound to NupC. In a novel application of a cross-polarization/polarization-inversion (CPPI) NMR experiment, the signal from undefined binding was eliminated by use of appropriate inversion pulse lengths. By use of CPPI in a titration experiment, a K(D) value of 2.6 mM was determined for uridine bound to NupC. These approaches are broadly applicable to quantifying binding of substrates, inhibitors, drugs, and antibiotics to numerous membrane proteins.

2H[19F] REDOR for distance measurements in biological solids using a double resonance spectrometer

A new approach for distance measurements in biological solids employing 2H[19F] rotational echo double resonance was developed and validated on 2H,19F-D-alanine and an imidazopyridine based inhibitor of the gastric H+/K+-ATPase. The 2H-19F double resonance experiments presented here were performed without 1H decoupling using a double resonance NMR spectrometer. In this way, it was possible to benefit from the relatively longer distance range of fluorine without the need of specialized fluorine equipment. A distance of 2.5 +/- 0.3 A was measured in the alanine derivative, indicating a gauche conformation of the two labels. In the case of the imidazopyridine compound a lower distance limit of 5.2 A was determined and is in agreement with an extended conformation of the inhibitor. Several REDOR variants were compared, and their advantages and limitations discussed. Composite fluorine dephasing pulses were found to enhance the frequency bandwidth significantly, and to reduce the dependence of the performance of the experiment on the exact choice of the transmitter frequency.

The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR

An interhelical distance has been precisely measured by REDOR solid-state NMR spectroscopy in the transmembrane tetrameric bundle of M2-TMP, from the M2 proton channel of the influenza A viral coat. The high-resolution structure of the helical backbone has been determined using orientational restraints from uniformly aligned peptide preparations in hydrated dimyristoylphosphatidylcholine bilayers. Here, the distance between (15)N(pi) labeled His37 and (13)C(gamma) labeled Trp41 is determined to be less than 3.9 A. Such a short distance, in combination with the known tilt and rotational orientation of the individual helices, permits not only a determination of which specific side chain pairings give rise to the interaction, but also the side chain torsion angles and restraints for the tetrameric bundle can also be characterized. The resulting proton channel structure is validated in a variety of ways. Both histidine and tryptophan side chains are oriented in toward the pore where they can play a significant functional role. The channel appears to be closed by the proximity of the four indoles consistent with electrophysiology and mutagenesis studies of the intact protein at pH 7.0 and above. The pore maintains its integrity to the N terminal side of the membrane, and at the same time, a cavity is generated that appears adequate for binding amantadine. Finally, the observation of a 2 kHz coupling in the PISEMA spectrum of (15)N(pi)His37 validates the orientation of the His37 side chain based on the observed REDOR distance.

A model of reversible inhibitors in the gastric H+/K+-ATPase binding site determined by rotational echo double resonance NMR

Several close analogues of the noncovalent H(+)/K(+)-ATPase inhibitor SCH28080 (2-methyl-3-cyanomethyl-8-(phenylmethoxy)imidazo[1,2-a]pyridine) have been screened for activity and examined in the pharmacological site of action by solid-state NMR spectroscopy. TMPIP, the 1,2,3-trimethyl analogue of SCH28080, and variants of TMPIP containing fluorine in the phenylmethoxy ring exhibited IC(50) values for porcine H(+)/K(+)-ATPase inhibition falling in the sub-10 microm range. Deuterium NMR spectra of a (2)H-labeled inhibitor titrated into H(+)/K(+)-ATPase membranes revealed that 80-100% of inhibitor was bound to the protein, and K(+)-competition (2)H NMR experiments confirmed that the inhibitor lay within the active site. The active binding conformation of the pentafluorophenylmethoxy analogue of TMPIP was determined from (13)C-(19)F dipolar coupling measurements using the cross-polarization magic angle spinning NMR method, REDOR. It was found that the inhibitor adopts an energetically favorable extended conformation falling between fully planar and partially bowed extremes. These findings allowed a model to be proposed for the binding of this inhibitor to H(+)/K(+)-ATPase based on the results of independent site-directed mutagenesis studies. In the model, the partially bowed inhibitor interacts with Phe(126) close to the N-terminal membrane spanning helix M1 and residues in the extracellular loop bridging membrane helices M5 and M6 and is flanked by residues in M4.

Biomolecular solid state NMR: advances in structural methodology and applications to peptide and protein fibrils

Solid state nuclear magnetic resonance (NMR) methods can provide atomic-level structural constraints on peptides and proteins in forms that are not amenable to characterization by other high-resolution structural techniques, owing to insolubility, high molecular weight, noncrystallinity, or other characteristics. Important examples include peptide and protein fibrils and membrane-bound peptides and proteins. Recent advances in solid state NMR methodology aimed at structural problems in biological systems are reviewed. The power of these methods is illustrated by experimental results on amyloid fibrils and other protein fibrils.

Structural insights into the binding of cardiac glycosides to the digitalis receptor revealed by solid-state NMR

Several biologically active derivatives of the cardiotonic steroid ouabain have been made containing NMR isotopes ((13)C, (2)H, and (19)F) in the rhamnose sugar and steroid moieties, and examined at the digitalis receptor site of renal Na(+)/K(+)-ATPase by a combination of solid-state NMR methods. Deuterium NMR spectra of (2)H-labeled inhibitors revealed that the sugar group was only loosely associated with the binding site, whereas the steroid group was more constrained, probably because of hydrogen bonding to residues around the K(+)-channel region. Crosspolarization magic-angle spinning NMR showed that chemical shifts of inhibitors (13)C-labeled in the sugar group moved downfield by 0.5 ppm after binding to the digitalis site, suggesting that the sugar was close to aromatic side groups. A (19)F, (13)C- rotational-echo double-resonance NMR strategy was used to determine the structure of an inhibitor in the digitalis receptor site, and it showed that the ouabain derivatives adopt a conformation in which the sugar extends out of the plane of the steroid ring system. The combined structural and dynamic information favors a model for inhibition in which the ouabain analogues lie across the surface of the Na(+)/K(+)-ATPase alpha-subunit with the sugar group facing away from the surface of the membrane but free to move into contact with one or more aromatic residues.

Coherence transfer signals in the rotational resonance NMR of a spinning single crystal

A recent analysis of rotational resonance lineshapes (M. Helmle et al., J. Magn. Reson. 140, 379-403, 1999) predicted the existence of coherence transfer signals, which are generated by mechanically induced coherence transfer during the detection process. These signals correspond to the generation of observable coherences at spin sites that have no magnetization at the beginning of the observation interval but which acquire coherence while the detection is underway. The coherence transfer signals disappear for powder samples in conventional magic-angle-spinning solid-state NMR experiments. In this Communication, we report the successful detection of coherence transfer signals in rotor-synchronized experiments performed on a single crystal of [1,2-(13)C(2)]glycine. Copyright 2000 Academic Press.

A solid-state NMR study of the phospholamban transmembrane domain: local structure and interactions with Ca(2+)-ATPase

The structure and dynamics of a double (13)C-labelled 24-residue synthetic peptide ([(13)C(2)]CAPLB(29-52)), corresponding to the membrane-spanning sequence of phospholamban (PLB), were examined using (13)C cross-polarisation magic-angle spinning (CP-MAS) NMR spectroscopy. CP-MAS spectra of [(13)C(2)]CAPLB(29-52) reconstituted into unsaturated lipid membranes indicated that the peptide was mobile at temperatures down to -50 degrees C. The NMR spectra showed that peptide motion became constrained in the presence of the SERCA1 isoform of Ca(2+)-ATPase, and chemical cross-linking experiments indicated that [(13)C(2)]CAPLB(29-52) and Ca(2+)-ATPase came into close contact with one another. These results together suggested that the peptide and the 110-kDa calcium pump were interacting in the membrane. Rotational resonance CP-MAS (13)C-(13)C distance measurements on [(13)C(2)]CAPLB(29-52) reconstituted into lipid bilayers confirmed that the sequence spanning Phe-32 and Ala-36 was alpha-helical, and that this structure was not disrupted by interaction with Ca(2+)-ATPase. These results support the finding that the transmembrane domain of PLB is partially responsible for regulation of Ca(2+) transport through interactions with cardiac muscle Ca(2+)-ATPase in the lipid bilayer, and also demonstrate the feasibility of performing structural measurements on PLB peptides when bound to their physiological target.

31P-CP-MAS NMR studies on TPP+ bound to the ion-coupled multidrug transport protein EmrE

The binding of tetraphenylphosphonium (TPP+) to EmrE, a membrane-bound, 110 residue Escherichia coli multidrug transport protein, has been observed by 31P cross-polarisation-magic-angle spinning nuclear magnetic resonance spectroscopy (CP-MAS NMR). EmrE has been reconstituted into dimyristoyl phosphatidylcholine bilayers. CP-MAS could selectively distinguish binding of TPP+ to EmrE in the fluid membrane. A population of bound ligand appears shifted 4 ppm to lower frequency compared to free ligand in solution, which suggests a rather direct and specific type of interaction of the ligand with the protein. This is also supported by the observed restricted motion of the bound ligand. The observation of another weakly bound substrate population arises from ligand binding to negatively charged residues in the protein loop regions.

Applications of NMR in drug discovery

In the half-century since its discovery, nuclear magnetic resonance (NMR) has become the single most powerful form of spectroscopy in both chemistry and structural biology. The dramatic technical advances over the past 10-15 years, which continue apace, have markedly increased the range of applications for NMR in the study of protein-ligand interactions. These form the basis for its most exciting uses in the drug discovery process, which range from the simple identification of whether a compound (or a component of a mixture) binds to a given protein, through to the determination of the full three-dimensional structure of the complex, with all the information this yields for structure-based drug design.

Analysis of dipolar-coupling-mediated coherence transfer in a homonuclear two spin-12 solid-state system

Homonuclear dipolar-mediated coherence transfer (DCT), a through-space transfer of magnetization between like spins, can yield otherwise difficult-to-obtain structural information for macromolecules by measuring the internuclear distances between two sites of interest. The behavior of a spin-12 system under DCT is analyzed in detail by computing the time development of the density matrix using the product operator formalism. The effect of coherence transfer (CT) via the homonuclear isotropic scalar coupling on DCT is examined. Analytical and computational results that yield useful information on the frequencies, first-maxima, and first-zero of CT for a uniaxially oriented or a single-crystal solid-state system are presented. The results predict that the evolution of the spin angular momentum operators under the homonuclear dipolar coupling Hamiltonian leads to "cylindrical mixing" unlike "isotropic mixing" due to the strong scalar coupling Hamiltonian. These results will find relevance in both the design of RF pulse sequences for the structural studies of uniaxially oriented biological solids and the interpretation of solution NMR results from proteins embedded in partially oriented bicelles. Copyright 1999 Academic Press.

Anomalous rotational resonance spectra in magic-angle spinning NMR

Magic-angle spinning NMR spectra of samples containing dilute spin-1/2 pairs display broadenings or splittings when a rotational resonance condition is satisfied, meaning that a small integer multiple of the spinning frequency matches the difference in the two isotropic shift frequencies. We show experimental rotational resonance NMR spectra of a 13C2-labeled retinal which are in qualitative disagreement with existing theory. We propose an explanation of these anomalous rotational spectra involving residual heteronuclear couplings between the 13C nuclei and the neighboring 1H nuclei. These couplings strongly influence the rotational resonance 13C spectrum, despite the presence of a strong radiofrequency decoupling field at the 1H Larmor frequency. We model the residual heteronuclear couplings by differential transverse relaxation of the 13C single-quantum coherences. We present a superoperator theory of the phenomenon and describe a numerical algorithm for rapid Liouville space simulations in periodic systems. Good agreement with experimental results is obtained by using a biexponential transverse relaxation model for each spin site.

NMR of drugs and ligands bound to membrane receptors

NMR methods are now able to give detailed structural, dynamic and electronic information about drugs and ligands while constrained at their site of action in membrane-embedded receptors, information which is essential for mechanistic descriptions of their action and design of new ligands. Using solid state NMR methods, a peptic ulcer drug analogue has been described at atomic resolution (to +/- 0.3 A between two atoms) at its site of action in the gastric H+/K+-ATPase, and the aromaticity of the agonist binding site of the nicotinic acetylcholine receptor has been demonstrated, with both targets in functionally competent membranes under conditions similar to those used in screening assays. G-protein-coupled receptor ligands and prosthetic groups are also being resolved using NMR methods.

NMR structural studies of membrane proteins

The three-dimensional structures of membrane proteins are essential for understanding their functions, interactions and architectures. Their requirement for lipids has hampered structure determination by conventional approaches. With optimized samples, it is possible to apply solution NMR methods to small membrane proteins in micelles; however, lipid bilayers are the definitive environment for membrane proteins and this requires solid-state NMR methods. Newly developed solid-state NMR experiments enable completely resolved spectra to be obtained from uniformly isotopically labeled membrane proteins in phospholipid lipid bilayers. The resulting operational constraints can be used for the determination of the structures of membrane proteins.

Probing the agonist binding pocket in the nicotinic acetylcholine receptor: a high-resolution solid-state NMR approach

Acetylcholine, the agonist for the nicotinic acetylcholine receptor, has been observed directly when bound specifically to its binding site in the fully functional receptor-enriched membranes from Torpedo nobiliana. High-resolution solid-state, magic angle spinning 13C NMR methods have been used to observe selectively N+(13CH3)3 acetylcholine bound in as few as 20 nmol of receptor binding sites, against a background of natural abundance membrane resonances and excess acetylcholine in free solution. The specificity of the binding has been demonstrated to be pharmacologically significant through the use of the competitive inhibitor alpha bungarotoxin which selectively displaces and prevents binding of acetylcholine to the membrane-bound receptor. The chemical shift assigned to N+(13CH3)3 acetylcholine in solution and crystalline solid is 53.9 +/- 0.04 ppm, and it changes by 1.6 ppm (p < 0.05) for agonist when bound specifically in the receptor binding site. Through the use of computer simulations of chemical shifts carried out on acetylcholine bound to the acetylcholinesterase, we propose that the cause for this change is the presence of aromatic side chains lining the receptor binding site. It is suggested that the binding of acetylcholine to the nicotinic acetylcholine receptor is mediated primarily through the interaction of the quaternary ammonium group of the acetylcholine with the pi bonded systems in the aromatic side chains. Longitudinal relaxation time measurements show that the residency time for the acetylcholine observed in DDCP experiments is long (> 200 ms) with respect to the longitudinal relaxation time of other assignable resonances within the spectrum from the lipid and protein and confirms that the acetylcholine is protein-associated, and not free in solution or nonspecifically bound.

Magic angle-oriented sample spinning (MAOSS): A new approach toward biomembrane studies

The application of magic angle sample spinning (MAS) NMR to uniformly aligned biomembrane samples is demonstrated as a new general approach toward structural studies of membrane proteins, peptides, and lipids. The spectral linewidth from a multilamellar lipid dispersion is dominated, in the case of protons, by the dipolar coupling. For low-gamma or dilute spins, however, the chemical shift anisotropy dominates the spectral linewidth, which is reduced by the two-dimensional order in a uniformly aligned lipid membrane. The remaining line broadening, which is due to orientational defects ("mosaic spread") can be easily removed at low spinning speeds. This orientational order in the sample also allows the anisotropic intermolecular motions of membrane components (such as rotational diffusion, tauc = 10(-10) s) for averaging dipolar interactions to be utilized, e.g., by placing the membrane normal parallel to the rotor axis. The dramatic resolution improvement for protons which are achieved in a lipid sample at only 220 Hz spinning speed in a 9.4 T field is slightly better than any data published to date using ultra-high fields (up to 17.6 T) and high-speed spinning (14 kHz). Additionally, the analysis of spinning sidebands provides valuable orientational information. We present the first 1H, 31P, and 13C MAS spectra of uniformly aligned dimyristoylphosphatidylcholine (DMPC) bilayers. Also, 1H resolution enhancement for the aromatic region of the M13 coat protein reconstituted into DMPC bilayers is presented. This new method combines the high resolution usually achieved by MAS with the advantages of orientational constraints obtained by working with macroscopically oriented samples. We describe the general potential and possible perspectives of this technique.