Solution-state NMR Research Articles

NMR Chemical Shift and Methylation of 4-Nitroimidazole: Experiment and Theory

Nitroimidazoles and derivatives are a class of active pharmaceutical ingredients (APIs) first introduced sixty years ago. As anti-infection agents, the structure–activity relationships of nitroimidazole compounds have been particularly difficult to study due to their low reduction potentials and unique electronic structures. In this study, we combine dynamic nuclear polarization (DNP)-enhanced solid-state (100K), solid-state (298K), and 1H-13C heteronuclear single quantum coherence (HSQC) solution-state NMR techniques (303K) with density functional theory (DFT) to study the 1H, 13C, and 15N chemical shifts of 4-nitroimidazole (4-NI) and 1-methyl-4-nitroimidazole (CH3-4NI). The 4-NI chemical shifts were observed at 119.4, 136.4, and 144.7ppm for 13C, and at 181.5, 237.4, and 363.0ppm for 15N. The measurements revealed that methylation (deprotonation) of the amino nitrogen N(1) of 4-NI had less effect (Δδ=−4.8ppm) on the N(1) chemical shift but was compensated by shielding of the N(3) (Δδ=11.6ppm) in CH3-4NI. The calculated chemical shifts using DFT for 4-NI and CH3-4NI agreed well with the experimental values (within 2%) for the imidazole carbons. However, larger discrepancies (up to 13%) were observed between the calculated and measured 15N NMR chemical shifts for the imidazole nitrogen atoms of both molecules, which indicate that effects such as imidazole ring resonant structures and molecular dynamics may also contribute to the nitrogen chemical environment.

Cholesterol-containing lipid nanodiscs promote an α-synuclein binding mode that accelerates oligomerization.

Dysregulation of the biosynthesis of cholesterol and other lipids has been implicated in many neurological diseases, including Parkinson's disease. Misfolding of α-synuclein (α-Syn), the main actor in Parkinson's disease, is associated with changes in a lipid environment. However, the exact molecular mechanisms underlying cholesterol effect on α-Syn binding to lipids as well as α-Syn oligomerization and fibrillation remain elusive, as does the relative importance of cholesterol compared to other factors. We probed the interactions and fibrillation behaviour of α-Syn using styrene-maleic acid nanodiscs, containing zwitterionic and anionic lipid model systems with and without cholesterol. Surface plasmon resonance and thioflavin T fluorescence assays were employed to monitor α-Syn binding, as well as fibrillation in the absence and presence of membrane models. 1 H-15 N-correlated NMR was used to monitor the fold of α-Syn in response to nanodisc binding, determining individual residue apparent affinities for the nanodisc-contained bilayers. The addition of cholesterol inhibited α-Syn interaction with lipid bilayers and, however, significantly promoted α-Syn fibrillation, with a more than a 20-fold reduction of lag times before fibrillation onset. When α-Syn bilayer interactions were analysed at an individual residue level by solution-state NMR, we observed two different effects of cholesterol. In nanodiscs made of DOPC, the addition of cholesterol modulated the NAC part of α-Syn, leading to stronger interaction of this region with the lipid bilayer. In contrast, in the nanodiscs comprising DOPC, DOPE and DOPG, the NAC part was mostly unaffected by the presence of cholesterol, while the binding of the N and the C termini was both inhibited.

Conformations in Solution and in Solid-State Polymorphs: Correlating Experimental and Calculated Nuclear Magnetic Resonance Chemical Shifts for Tolfenamic Acid

A new approach for quantitively assessing putative crystal structures with applications in crystal structure prediction (CSP) is introduced that is based upon experimental solution- and magic-angle spinning (MAS) solid-state NMR data and density functional theory (DFT) calculation. For the specific case of tolfenamic acid (TFA), we consider experimental solution-state NMR for a range of solvents, experimental MAS NMR of polymorphs I and II, and DFT calculations for four polymorphs. The change in NMR chemical shift observed in passing from the solution state to the solid state (ΔδExperimental) is calculated as the difference between 1H and 13C experimental solid-state chemical shifts for each polymorphic form (δSolidexpt) and the corresponding solution-state NMR chemical shifts (δSolutionexpt). Separately, we use the gauge-included projector augmented wave (GIPAW) method to calculate the NMR chemical shifts for each form (δSolidcalc) and for TFA in solution (δSolutioncalc) using the dynamic 3D solution conformational ensemble determined from NMR spectroscopy. The calculated change in passing from the solution state to the solid state (ΔδCalculated) is then calculated as the difference of δSolidcalc and δSolutioncalc. Regression analysis for ΔδCalculated against ΔδExperimental followed by a t-test for statistical significance provides a robust quantitative assessment. We show that this assessment clearly identifies the correct polymorph, i.e., when comparing ΔδExperimental based on the experimental MAS NMR chemical shifts of form I or II with ΔδCalculated based on calculated chemical shifts for polymorphs I, II, III, and IV. Complementarity to the established approach of comparing δSolidexpt to δSolidcalc is explored. We further show that our approach is applicable if there are no solid-state crystal structure data. Specifically, δSolidcalc in ΔδCalculated is replaced by the chemical shift for an isolated molecule with a specific conformation. Sampling conformations at specific 15° angle values and comparing them against experimental 13C chemical shift data for forms I and II identifies matching narrow ranges of conformations, successfully predicting the conformation of tolfenamic acid in each form. This methodology can therefore be used in crystal structure prediction to both reduce the initial conformational search space and also quantitatively assess subsequent putative structures to reliably and unambiguously identify the correct structure.

An Internuclear J-Coupling of 3He Induced by Molecular Confinement.

The solution-state 13C NMR spectrum of the endofullerene 3He@C60 displays a doublet structure due to a J-coupling of magnitude 77.5 ± 0.2 mHz at 340 K between the 3He nucleus and a 13C nucleus of the enclosing carbon surface. The J-coupling increases in magnitude with increasing temperature. Quantum chemistry calculations successfully predict the approximate magnitude of the coupling. This observation shows that the mutual proximity of molecular or atomic species is sufficient to induce a finite scalar nuclear spin-spin coupling, providing that translational motion is restricted by confinement. The phenomenon may have applications to the study of surface interactions and to mechanically bound species.

Clarification of the Dissolution Mechanism of an Indomethacin/Saccharin/Polyvinylpyrrolidone Ternary Solid Dispersion by NMR Spectroscopy

Here, an indomethacin (IMC)/saccharin (SAC)/polyvinylpyrrolidone (PVP) ternary solid dispersion (SD) prepared by spray-drying was characterized to clarify its dissolution mechanism. Solid-state NMR spectroscopy revealed that IMC and SAC in the ternary SD interacted via hydrogen bonding in a similar manner as that in the IMC/SAC co-crystal. Initial IMC dissolution from the ternary SD was slower than that from the binary SD, although IMC supersaturation was maintained for a relatively longer time in the ternary SD. Solid- and solution-state NMR measurements for dispersed particles in the dissolution test revealed that the particle for IMC/PVP binary SD was composed of amorphous IMC dispersed in PVP matrix and α-form IMC. In contrast, the particles for the ternary SPD was composed of amorphous IMC dispersed in PVP matrix and IMC/SAC co-crystals. Scanning electron microscopy indicated that in the binary SD, amorphous IMC microfiber-gel was generated on the surface of particles after the dissolution test, preventing amorphous IMC from contacting with water. In contrast, in the ternary SD, IMC/SAC co-crystals were generated on the surface of particles, and intermediate spaces were formed on the surface, which allowed water intrusion into the particles and continuous dissolution of IMC.

2D Assignment and quantitative analysis of cellulose and oxidized celluloses using solution-state NMR spectroscopy

The limited access to fast and facile general analytical methods for cellulosic and/or biocomposite materials currently stands as one of the main barriers for the progress of these disciplines. To that end, a diverse set of narrow analytical techniques are typically employed that often are time-consuming, costly, and/or not necessarily available on a daily basis for practitioners. Herein, we rigorously demonstrate a general quantitative NMR spectroscopic method for structural determination of crystalline cellulose samples. Our method relies on the use of a readily accessible ionic liquid electrolyte, tetrabutylphosphonium acetate ([P4444][OAc]):DMSO-d6, for the direct dissolution of biopolymeric samples. We utilize a series of model compounds and apply now classical (nitroxyl-radical and periodate) oxidation reactions to cellulose samples, to allow for accurate resonance assignment, using 2D NMR. Quantitative heteronuclear single quantum correlation (HSQC) was applied in the analysis of key samples to assess its applicability as a high-resolution technique for following cellulose surface modification. Quantitation using HSQC was possible, but only after applying T2 correction to integral values. The comprehensive signal assignment of the diverse set of cellulosic species in this study constitutes a blueprint for the direct quantitative structural elucidation of crystalline lignocellulosic, in general, readily available solution-state NMR spectroscopy.Graphic abstract

Maturation of the functional mouse CRES amyloid from globular form

The epididymal lumen contains a complex cystatin-rich nonpathological amyloid matrix with putative roles in sperm maturation and sperm protection. Given our growing understanding for the biological function of this and other functional amyloids, the problem still remains: how functional amyloids assemble including their initial transition to early oligomeric forms. To examine this, we developed a protocol for the purification of nondenatured mouse CRES, a component of the epididymal amyloid matrix, allowing us to examine its assembly to amyloid under conditions that may mimic those in vivo. Herein we use X-ray crystallography, solution-state NMR, and solid-state NMR to follow at the atomic level the assembly of the CRES amyloidogenic precursor as it progressed from monomeric folded protein to an advanced amyloid. We show the CRES monomer has a typical cystatin fold that assembles into highly branched amyloid matrices, comparable to those in vivo, by forming β-sheet assemblies that our data suggest occur via two distinct mechanisms: a unique conformational switch of a highly flexible disulfide-anchored loop to a rigid β-strand and by traditional cystatin domain swapping. Our results provide key insight into our understanding of functional amyloid assembly by revealing the earliest structural transitions from monomer to oligomer and by showing that some functional amyloid structures may be built by multiple and distinctive assembly mechanisms.

Elucidating the Molecular Interactions of Encapsulated Doxorubicin within a Nonionic, Thermoresponsive Polyester Coacervate.

Thermoresponsive polymers that display a lower critical solution temperature (LCST) are attractive drug delivery systems (DDSs) due to their potential to encapsulate and release therapeutics in a sustained manner as a function of temperature input. To attain the full potential of such DDSs, methods that illustrate the details of drug-polymer interactions are necessary. Here, we synthesized a nonionic, coacervate-forming, thermoresponsive polyester to encapsulate doxorubicin (Dox) and used solution state NMR spectroscopy and fluorescence microscopy techniques to probe the interactions between the polymer and Dox at the molecular level. The incomplete dehydration provides a matrix for encapsulation of sensitive therapeutics and preserving their activity, while the low hysteresis property of the polyester provides rapid transition from soluble to coacervate phase. Saturation transfer difference (STD) NMR revealed the Dox-polymer interactions within the coacervates. 1H-1H nuclear Overhauser effect spectroscopy (NOESY) cross-peak differences of Dox confirmed the Dox-polymer interactions. Diffusion-ordered spectroscopy (DOSY) revealed the slower diffusion rate of Dox in the presence of polyester coacervates. These studies illustrate how the state of the polyester (below and above LCST) affects the polyester-Dox interactions and offers details of the specific functional groups involved in these interactions. Our results provide a framework for future investigations aimed at characterizing fundamental interactions in polymer-based DDSs.

1H, 13C and 15N NMR assignments of solubility tag protein Msyb of Escherichia coli.

Biochemical and structural characterizations of a protein are the prerequisite for the further understanding of its biological role and potential applications. The expression of recombinant protein is almost unavoidable to produce the amount of the protein required for these studies, especially at the industrial level. Escherichia coli is the single most used system for recombinant protein expression and the first choice for a trial expression. Besides the inherited defects of its prokaryotic origin, the E. coli system has problems like low protein solubility and formation of inclusion bodies. To improve the solubility while assisting correct folding of the target protein, fusing a tag protein prior to its N-terminus is one of the common approaches. GST, MBP, Trx and SUMO proteins are among the most used tags by providing different advantages during recombinant protein expression. Msyb, a small and acidic protein native to E. coli, is another example that could improve the solubility of the target protein. While the biophysical and biochemical properties of these common tag proteins have been studied to a great extent, Msyb protein remains largely uncharacterized. Here, using solution-state NMR, our near-complete resonance assignment of Msyb provides a basis for future structure determination which would help to expand its usage as a common tag protein.

Optimized High-Yield Purification of Obesity-Associated Melanocortin 4 Receptor.

Obesity has emerged as a global public health challenge associated with increased risk of hyperlipidemia and hypertension. It contributes to high sympathetic activity and increased catecholamine levels. The hypothalamic melanocortin system is known to regulate the energy homeostasis. The role of melanocortin 4 receptor (MC4R) has been demonstrated pharmacologically and in animal studies, which showed that severe obesity in MC4R knockout mice was caused by increased food intake and decreased energy consumption. Over 70 multiple different mis- -sense and nonsense mutations in hMC4R have been found at a high frequency of 2-8% in severe early onset or hereditary obesity. The single amino acid variation (D90N) located in the second transmembrane domain (TM2) of MC4R results in accelerated growth and childhood onset obesity. Interestingly, the functional characterization of D90N hMC4R mutant TM2 (m-hMC4R-TM2) revealed normal cell surface expression and binding with agonist similar to the hMC4R wild-type TM2 (wt-hMC4R-TM2) but loss of signal transduction mediated via Gs/adenylyl cyclase activation. It is essential to delineate the three-dimensional structure of MC4Rs in order to elucidate their functional aspects. In this study, we demonstrate the optimized expression and isolation of wt/m-hMC4R-TM2 proteins under different chemical cleavage reaction times and purification procedures via SDS precipitation. The solid-state NMR spectroscopy was carried out to study the structure of wt/m-hMC4R- TM2 protein in the anisotropic phospholipid bicelles. The KSI-wt/m-hMC4R-TM2 fusion proteins developed in cell culture with LB medium. In order to isolate the expressed fusion protein from the cell, ultrasonication, Ni-NTA affinity chromatography, dialysis, and lyophilization techniques were used. Then, to obtain a protein with higher purity and higher yield, the CNBr chemical cleavage time was subdivided into 30 minutes, 1 h, 2 h, 3 h, and 4 h. Purification process was performed using FPLC, and 100 mM KCl and dialysis were used to remove the SDS. CD spectrometer, MALDI-TOF, solution-state NMR, and solid-state NMR were used to confirmed purity and structure of the wt/m-hMC4R-TM2. The precipitation method was used to remove the SDS bound to proteins as KCl-SDS. We optimized the 2 h cleavage reaction times for both wt-hMC4R-TM2 and m-hMC4R-TM2 depending on the purity based on mass spectra and 1H-15N HSQC spectra and the yield after final purification. The 1D 1H-15N CP (Cross polarization) solid-state NMR spectra suggest that the wt/m-hMC4R- TM2 undergo rotational diffusion around a perpendicular axis along the bilayer normal. We expressed wt/m-hMC4R-TM2 in E.coli and optimized the isolation and purification process, especially CNBr chemical cleavage time. The efficiency of KCl-SDS precipitation was confirmed via MALDI-TOF MS and the pure proteins obtained using this method were characterized by CD spectroscopy and solution-state NMR. The results of 1H-15N HSQC spectra in solution- state NMR also show the probability for structural studies. The 1D 1H-15N CP solid-state NMR spectra indicate that most of the residues in both the wt/m-hMC4R-TM2 peptides are integrated into the membrane.

Probing contacts of inhibitor locked in transition states in the catalytic triad of DENV2 type serine protease and its mutants by 1H, 19F and 15\u2009N NMR spectroscopy

BackgroundDetailed structural knowledge of enzyme-inhibitor complexes trapped in intermediate state is the key for a fundamental understanding of reaction mechanisms taking place in enzymes and is indispensable as a structure-guided drug design tool. Solution state NMR uniquely allows the study of active sites of enzymes in equilibrium between different tautomeric forms. In this study 1H, 19F and 15 N NMR spectroscopy has been used to probe the interaction contacts of inhibitors locked in transition states of the catalytic triad of a serine protease. It was demonstrated on the serotype II Dengue virus NS2B:NS3pro serine protease and its mutants, H51N and S135A, in complex with high-affinity ligands containing trifluoromethyl ketone (tfk) and boronic groups in the C-terminal of tetra-peptides.ResultsMonitoring 19F resonances, shows that only one of the two isomers of the tfk tetra-peptide binds with NS2B:NS3pro and that access to the bulk of the active site is limited. Moreover, there were no bound water found in proximity of the active site for any of the ligands manifesting in a favorable condition for formation of low barrier hydrogen bonds (LBHB) in the catalytic triad. Based on this data we were able to identify a locked conformation of the protein active site. The data also indicates that the different parts of the binding site most likely act independently of each other.ConclusionsOur reported findings increases the knowledge of the detailed function of the catalytic triad in serine proteases and could facilitate the development of rational structure based inhibitors that can selectively target the NS3 protease of Dengue type II (DENV2) virus. In addition the results shows the usefulness of probing active sites using 19F NMR spectroscopy.

Hyperpolarized Magnetic Resonance of Exchangeable Protons Using Parahydrogen and Aminosilane

Efficient, room temperature hyperpolarization of exchangeable solvent protons combining parahydrogen (p-H2), aminopropyldiethoxymethylsilane (APDMS), and IrCl(COD)(IMes) to generate an active aminosilane–iridium complex broadens the capabilities of signal amplification by reversible exchange (SABRE)-type hyperpolarization of protons. A primary pool of hyperpolarized exchangeable protons transfers its hyperpolarization to cosolutes with labile protons, partly overcoming the catalytic specificity of SABRE-type spin-transfer catalysis. The silane functionality of APDMS appears to be crucial to its improvement. Its role is unprecedented in p-H2-based hyperpolarization of nuclear spins and promises to broaden its applicability of ultrasensitive solution-state NMR spectroscopy for the detection and elucidation of molecular behavior, at concentrations undetectable by conventional NMR spectroscopy.

Mechanistic insights into the thermal deposition of highly thermal-stable jet fuel

Highly thermal-stable jet fuel plays an important role in the advanced supersonic aircrafts, but its oxidation to the insoluble deposits is a serious problem when serving as a coolant. However, there are few reports as to the deep insights of insoluble deposits formation. Here we apply the PetroOxy device to investigate the thermal oxidation and deposition behaviors of highly thermal-stable jet fuel, using decalin as the model jet fuel, in order to explore the formation mechanism of insoluble deposits. All oxidation products (gas, liquid and solid) of fuel at different oxidation stages were separated and carefully characterized. The initial oxidation of fuel produces hydroperoxides, which then decompose rapidly to produce gas products (H2, CO or CO2) as well as large amounts of polar species (soluble oxidized products, e.g., alcohols, ketones, and molecular growth products). Meanwhile, these polar monomer species condense to produce soluble macromolecular oxidatively reactive species (SMORS) and insoluble deposits. The SMORS amount increases during the overall oxidation process, but the amount of insoluble deposits increases only in the presence of oxygen. The characterizations of liquid chromatography/electrospray ionization mass spectrometry and solution-state 2D heteronuclear single quantum coherence NMR confirm that the concentration of highly polar macromolecular species in insoluble deposits is much higher than that in SMORS, which causes the precipitation of the insoluble deposits from the bulk fuel. We further propose the detailed formation process and chemical structures of the insoluble deposits during the autoxidation of highly thermal-stable jet fuel, which would be helpful for a better understanding of the deposition mechanism of jet fuel and the improvement of its thermal stability.

Backbone assignments and conformational dynamics in the S. typhimurium tryptophan synthase α-subunit from solution-state NMR.

Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are predicted. Titration with the 3-indole-D-glycerol 3'-phosphate analog, N-(4'-trifluoromethoxybenzenesulfonyl)-2-aminoethyl phosphate (F9), leads to chemical shift perturbations indicative of conformational changes from which an estimate of the dissociation constant is obtained. Comparisons of the backbone chemical-shifts, RCI-S2 values, and site-specific relaxation times with and without F9 reveal allosteric changes including modulation in secondary structures and loop rigidity induced upon ligand binding. A comparison is made to the X-ray crystal structure of the α-subunit in the full TS αββα bi-enzyme complex and to two new X-ray crystal structures of the isolated TS α-subunit reported in this work.

NMR insights into the pre-amyloid ensemble and secretion targeting of the curli subunit CsgA

The biofilms of Enterobacteriaceae are fortified by assembly of curli amyloid fibres on the cell surface. Curli not only provides structural reinforcement, but also facilitates surface adhesion. To prevent toxic intracellular accumulation of amyloid precipitate, secretion of the major curli subunit, CsgA, is tightly regulated. In this work, we have employed solution state NMR spectroscopy to characterise the structural ensemble of the pre-fibrillar state of CsgA within the bacterial periplasm, and upon recruitment to the curli pore, CsgG, and the secretion chaperone, CsgE. We show that the N-terminal targeting sequence (N) of CsgA binds specifically to CsgG and that its subsequent sequestration induces a marked transition in the conformational ensemble, which is coupled to a preference for CsgE binding. These observations lead us to suggest a sequential model for binding and structural rearrangement of CsgA at the periplasmic face of the secretion machinery.

Silver(I) and gold(I) complexes with sulfasalazine: Spectroscopic characterization, theoretical studies and antiproliferative activities over Gram-positive and Gram-negative bacterial strains

The emergence of bacterial strains resistant to antibiotics, such as the sulfonamides (sulfa drugs), is currently a case of concern. The synthesis of metal complexes using well-known antibacterial agents and bioactive metals has proven to be an excellent strategy in the development of new and more active metallodrugs. Herein, we report the synthesis, structural characterization and antibacterial analysis of new gold(I) and silver(I) complexes with the sulfa drug sulfasalazine (ssz). Elemental, thermal and high-resolution mass spectrometric measurements indicated a 1:1:1 Au/ssz/Ph3P molar composition for the gold(I) complex (Ph3P - triphenylphosphine), while for the silver(I) complex the molar composition was 1:1 Ag/ssz. Solution state NMR and infrared spectroscopic data suggest that ssz coordinates to silver(I) and gold(I) by the oxygen atoms of the deprotonated carboxylic group. The coordination mode of the carboxylate was supported by density functional theory (DFT) calculations, which reinforces a monodentate coordination for the gold(I) complex and a bridged bidentate mode for the silver(I) one, with the molecular formulas [(Ph3P)Au(ssz)] and [Ag(ssz)]2, respectively. Antibacterial activity assays indicated the sensitivity of Gram-positive (Staphylococcus aureus and Bacillus cereus) and Gram-negative (Escherichia coli and Pseudomonas aeruginosa) bacterial strains to [Ag(ssz)]2 and [(Ph3P)Au(ssz)] complexes, while the free ligand was not able to inhibit the growth of any tested bacteria. The non-interaction of the complexes with deoxyribonucleic acid (DNA) was also demonstrated, which suggests that this biomolecule is not a preferential target for the compounds.

Understanding and solving abnormal peak splitting in 3D HCCH-TOCSY and HCC(CO)NH-TOCSY.

The 3D HCCH-TOCSY and HCC(CO)NH-TOCSY experiments provide through bond connectivity and are used for side-chain chemical shift assignment by solution-state NMR. Careful design and implementation of the pulse sequence are key to the successful application of the technique particularly when trying to extract the maximum information out of challenging biomolecules. Here we investigate the source of and propose solutions for abnormal peak splitting ranging from 152 to 80Hz and below that were found in three popular TOCSY-based experiment types: H(F1)-C(F2)-DIPSI-H(F3), C(F1)-DIPSI-C(F2)-H(F3), and C(F1)-DIPSI-N(F2)-HN(F3). Peak splitting occurs in the indirect C(F1) or C(F2) dimension before DIPSI and analyses indicate that the artifacts are resulted mainly from the DIPSI transforming a double spin order [Formula: see text] from 13C-13C scalar 1JCC coupling during t1 into observable megnetization. The splitting is recapitulated by numerical simulation and approaches are proposed to remove it. Adding a pure delay of 3.7ms immediately before DIPSI is a simple and effective strategy to achieve 3D HCCH-TOCSY and HCC(CO)NH-TOCSY spectra free of splitting with full crosspeak intensity.

When Small becomes Too Big: Expanding the Use of In-Cell Solid-State NMR Spectroscopy.

Solution-state NMR spectroscopy has become a powerful tool to study soluble proteins in cells, provided that they tumble sufficiently fast. In addition, cryo-electron tomography (cryo-ET) has recently displayed a tremendous potential to probe structures of large proteins and assemblies in their native cellular environments. However, challenges remain to obtain atomic-level information in native cell settings for proteins that are small, disordered, or are strongly engaged in intermolecular interactions. In this Minireview, we discuss recent progress in using sensitivity enhanced solid-state NMR spectroscopy methods in the context of cellular structural biology.

Mutation of Conserved Mre11 Residues Alter Protein Dynamics to Separate Nuclease Functions

Naked and protein-blocked DNA ends occur naturally during immune cell development, meiosis, and at telomeres as well as from aborted topoisomerase reactions, collapsed replication forks, and other stressors. Damaged DNA ends are dangerous in cells and if left unrepaired can lead to genomic rearrangement, loss of genetic information, and eventually cancer. Mre11 is part of the Mre11–Rad50–Nbs1 complex that recognizes DNA double-strand breaks and has exonuclease and endonuclease activities that help to initiate the repair processes to resolve these broken DNA ends. In fact, these activities are crucial for proper DNA damage repair pathway choice. Here, using Pyrococcus furiosus Mre11, we question how two Mre11 separation-of-function mutants, one previously described but the second first described here, maintain endonuclease activity in the absence of exonuclease activity. To start, we performed solution-state NMR experiments to assign the side-chain methyl groups of the 64-kDa Mre11 nuclease and capping domains, which allowed us to describe the structural differences between Mre11 bound to exo- and endonuclease substrates. Then, through biochemical and biophysical characterization, including NMR structural and dynamics studies, we compared the two mutants and determined that both affect the dynamic features and double-stranded DNA binding properties of Mre11, but in different ways. In total, our results illuminate the structural and dynamic landscape of Mre11 nuclease function.

Characterization of multimeric daptomycin bound to lipid nanodiscs formed by calcium-tolerant styrene-maleic acid copolymer

Daptomycin is a lipopeptide antibiotic that is important in the treatment of infections with Gram-positive bacteria. In the presence of calcium, daptomycin binds to phosphatidylglycerol in the bacterial cytoplasmic membrane and then forms oligomers that mediate its bactericidal effect. The structure of these bactericidal oligomers has not been elucidated. We here explore the feasibility of structural studies on the oligomer by solution-state NMR. To this end, we use nanodiscs that contain DMPC and DMPG, stabilized with a styrene-maleic acid copolymer that has been modified to minimize calcium chelation. We show that these nanodiscs bind daptomycin and induce the formation of stable oligomers under physiologically relevant conditions. The findings suggest that this membrane model is suitable for structural and functional characterization of oligomeric daptomycin, and possibly of other calcium-dependent lipopeptide antibiotics. We show that these nanodiscs bind daptomycin and induce the formation of stable oligomers, under conditions that are suitable for biomolecular NMR. The findings suggest that this membrane model is suitable for structural elucidation of oligomeric daptomycin, and possibly of other calcium-dependent lipopeptide antibiotics.