Nuclear Magnetic Resonance Time Scale Research Articles

Ion Dynamics in Nanocrystalline Li2S‐LiI – on the Influence of Local Disorder on Short‐Range Hopping and Long‐Range Ion Transport

The enormous interest in developing powerful Li‐based batteries leads to a boost in materials research. Though Li–sulfur batteries offer very high energy densities, the nature of Li‐ion dynamics in the final discharge product has not been fully understood yet. While nanocrystalline shows enhanced ion dynamics compared to its coarse‐grained counterpart, the interaction of with another binary such as LiI seems to be rather unexplored. Herein, an equimolar mixture of and LiI is treated in a high‐energy ball mill, and both the overall and local structural changes are studied by X‐ray powder diffraction and nuclear magnetic resonance (NMR), respectively . Besides the formation of amorphous regions, evidences are found for the generation of anion‐mixed sites that give rise to facile Li exchange on the 2D exchange NMR timescale. Compared to a coarse‐grained reference sample, the overall (bulk) ionic conductivity of nanocrystalline ‐LiI increases by two orders of magnitude. Besides the anion‐mixing effect, this increase benefits from nanosize effects that include the formation of defect‐rich interfacial regions. NMR relaxation measurements fully support this result and reveal heterogeneous dynamics with lower activation energies for both the localized hopping processes and long‐range ion transport in nm‐sized ‐LiI.

Charge transport in protic ionic liquids: Effect of protonation state in 1-methylimidazolium – acetate/trifluoroacetate mixtures

Despite the potential to overcome slow charge transport in ionic liquids by decoupling charge transport from mass transport in protic ionic liquids (PILs), the average proton distribution and the contribution of proton conduction to the overall charge transport in PILs has not been fully established. To elucidate the predominant underlying molecular species in the PILs and the molecular dynamics of the PILs, we study the dipolar response and conductivity using dielectric relaxation (DR) spectroscopy and the nucleis chemical environment and molecular mobility using nuclear magnetic resonance (NMR) spectroscopy of prototypical PILs based on 1–methylimidazolium as Brønsted base. To elucidate the effect of the acidity of the Brønsted acid we gradually vary the composition of the PILs from 1–methylimidazoliumacetate [MimH][AcO] to 1–methylimidazoliumtrifluoroacetate [MimH][TFA]. Both, 15N-NMR chemical shifts and the sample conductivities suggest that in neat [MimH][AcO] electro-neutral molecular species dominate, consistent with earlier findings. The dipolar response of these molecular species as detected via the DR spectra is stronger than what one would expect based on the molecular dipole moments estimated from density functional theory calculations, which points to the formation of an extended hydrogen-bonded network. Upon addition of [MimH][TFA], this dipolar response is reduced as the degree of protonation of 1–methylimidazolium gradually increases, which is apparent from the conductance and 15N chemical shifts. Interestingly, diffusion ordered NMR spectroscopy indicates protons to become more mobile than the constituting acid and base molecules, consistent with Grotthuss-like proton transport. To vary the immediate environment of the PILs, we study solutions of the PIL mixtures in aprotic dimethylformamide (DMF) and protic methanol (MeOH) as two limiting cases. We find that [MimH][AcO] exclusively forms electroneutral species in DMF, as evident from the negligible conductivity, while with increasing TFA content the fraction of charged molecular species increases. Although these ionic species give rise to a finite conductivity, demonstrating the presence of mobile ions, a large fraction of these ions is bound in [MimH][TFA] ion-pairs, as detected in the DR spectra. Yet, temperature dependent 1H-NMR linewidths of the acidic proton signals suggest proton exchange to occur on the NMR timescale, presumably between [MimH]+ and [Mim]. Conversely, in MeOH we find no evidence for the presence of ion-pairs, while the high conductivity of these solutions shows that MeOH can efficiently solvate ions and may participate in proton transfer. Together, our results highlight the sensitivity of protonation equilibria to the immediate environment and of proton dynamics to these protonation equilibria. Our results show that tuning these equilibria using PIL mixtures can provide routes to tailor the contribution of proton transport to charge transport in PILs.

Porosity of Molecularly Imprinted Polymers Investigated by 129Xe NMR Spectroscopy.

Molecularly imprinted polymers (MIPs) display intriguing recognition properties and can be used as sensor recognition elements or in separation. In this work, we investigated the formation of hierarchical porosity of compositionally varied MIPs using 129Xe Nuclear Magnetic Resonance (NMR) and 1H Time Domain Nuclear Magnetic Resonance (TD-NMR). Variable temperature 129Xe NMR established the morphological variation with respect to the degree of cross-linking, supported by 1H TD-NMR determination of polymer chain mobility. Together, the results indicate that a high degree of cross-linking stabilizes the porous structure: highly cross-linked samples display a significant amount of accessible mesopores that instead collapse in less structured polymers. No significant differences can be detected due to the presence of templated pores in molecularly imprinted polymers: in the dry state, these specific shapes are too small to accommodate xenon atoms, which, instead, probe higher levels in the porous structure, allowing their study in detail. Additional resonances at a high chemical shift are detected in the 129Xe NMR spectra. Even though their chemical shifts are compatible with xenon dissolved in bulk polymers, variable temperature experiments rule out this possibility. The combination of 129Xe and TD-NMR data allows attribution of these resonances to softer superficial regions probed by xenon in the NMR time scale. This can contribute to the understanding of the surface dynamics of polymers.

Surprising Rigidity of Functionally Important Water Molecules Buried in the Lipid Headgroup Region.

Understanding water dynamics and structure is an important topic in biological systems. It is generally held in the literature that the interfacial water of hydrated phospholipids is highly mobile, in fast exchange with the bulk water ranging from the nano- to femtosecond timescale. Although nuclear magnetic resonance (NMR) is a powerful tool for structural and dynamic studies, direct probing of interfacial water in hydrated phospholipids is formidably challenging due to the extreme population difference between bulk and interfacial water. We developed a novel 17O solid-state NMR technique in combination with an ultra-high-field magnet (35.2 T) to directly probe the functionally important interfacial water. By selectively suppressing the dominant bulk water signal, we observed two distinct water species in the headgroup region of hydrated dimyristoylphosphatidylcholine (DMPC) lipid bilayers for the first time. One water species denoted as "confined water" is chemically and dynamically different from the bulk water (∼0.17 ppm downfield and a slightly shorter spin-lattice relaxation time). Another water species denoted as "bound water" has severely restricted motion and a distinct chemical shift (∼12 ppm upfield). Additionally, the bulk water is not as "free" as pure water, resulting from the fast exchange with the water molecules that weakly and transiently interact with the lipid choline groups. These new discoveries clearly indicate the existence of the interfacial water molecules that are relatively stable over the NMR timescale (on the order of milliseconds), providing an opportunity to characterize water dynamics on the millisecond or slower timescale in biomacromolecules.

Molecular enantiodiscrimination by NMR spectroscopy in chiral oriented systems: Concept, tools, and applications.

The study of enantiodiscriminations in relation to various facets of enantiomorphism (chirality/prochirality) and/or molecular symmetry is an exciting area of modern organic chemistry and an ongoing challenge for nuclear magnetic resonance (NMR) spectroscopists who have developed many useful analytical approaches to solve stereochemical problems. Among them, the anisotropic NMR using chiral aligning solvents has provided a set of new and original tools by making accessible all intramolecular, order-dependent NMR interactions (anisotropic interactions), such as residual chemical shift anisotropy (RCSA), residual dipolar coupling (RDC), and residual quadrupolar coupling (RQC) for spin I>1/2, while preserving high spectral resolution. The force of NMR in enantiopure, oriented solvents lies on its ability to orient differently in average on the NMR timescale enantiomers of chiral molecules and enantiotopic elements of prochiral ones, leading distinct NMR spectra or signals to be detected. In this compendium mainly written for all chemists playing with (pro)chirality, we overview various key aspects of NMR in weakly aligning chiral solvents as the lyotropic liquid crystals (LLCs), in particular those developed in France to study (pro)chiral compounds in relation with chemists needs: study of enantiopurity of mixture, stereochemistry, natural isotopic fractionation, as well as molecular conformation and configuration. Key representative examples covering the diversity of enantiomorphism concept, and the main and most recent applications illustrating the analytical potential of this NMR in polypeptide-based chiral liquid crystals (CLCs) are examined. The latest analytical strategy developed to determine in-solution conformational distribution of flexibles solutes using NMR in polypeptide-based aligned solvents is also proposed.

Serine protease dynamics revealed by NMR analysis of the thrombin-thrombomodulin complex

Serine proteases catalyze a multi-step covalent catalytic mechanism of peptide bond cleavage. It has long been assumed that serine proteases including thrombin carry-out catalysis without significant conformational rearrangement of their stable two-β-barrel structure. We present nuclear magnetic resonance (NMR) and hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments on the thrombin-thrombomodulin (TM) complex. Thrombin promotes procoagulative fibrinogen cleavage when fibrinogen engages both the anion binding exosite 1 (ABE1) and the active site. It is thought that TM promotes cleavage of protein C by engaging ABE1 in a similar manner as fibrinogen. Thus, the thrombin-TM complex may represent the catalytically active, ABE1-engaged thrombin. Compared to apo- and active site inhibited-thrombin, we show that thrombin-TM has reduced μs-ms dynamics in the substrate binding (S1) pocket consistent with its known acceleration of protein C binding. Thrombin-TM has increased μs-ms dynamics in a β-strand connecting the TM binding site to the catalytic aspartate. Finally, thrombin-TM had doublet peaks indicative of dynamics that are slow on the NMR timescale in residues along the interface between the two β-barrels. Such dynamics may be responsible for facilitating the N-terminal product release and water molecule entry that are required for hydrolysis of the acyl-enzyme intermediate.

Determining chemical exchange rate constants in nanoemulsions using nuclear magnetic resonance.

In this work, the second-order kinetics of molecules exchanging between chemically distinct microenvironments, such as those found in nanoemulsions, is studied using nuclear magnetic resonance (NMR). A unique aspect of NMR exchange studies in nanoemulsions is that the difference in molecular resonance frequencies between the two phases, which determines whether the exchange is fast, intermediate, or slow on the NMR timescale, can depend upon the emulsion droplet composition, which is also determined by the kinetic exchange constants themselves. Within the fast-exchange regime, changes in resonance frequencies and line widths with dilution were used to extract the exchange rate constants from the NMR spectra in a manner analogous to determining the kinetic parameters in NMR ligand binding experiments. As a demonstration, the kinetic exchange parameters of isoflurane release from an emulsification of isoflurane and perflurotributylamine (FC43) were determined using NMR dilution and diffusion studies.

Conformational Complexity and Dynamics in a Muscarinic Receptor Revealed by NMR Spectroscopy.

The M2 muscarinic acetylcholine receptor (M2R) is a prototypical GPCR that plays important roles in regulating heart rate and CNS functions. Crystal structures provide snapshots of the M2R in inactive and active states, but the allosteric link between the ligand binding pocket and cytoplasmic surface remains poorly understood. Here we used solution NMR to examine the structure and dynamics of the M2R labeled with 13CH3-ε-methionine upon binding to various orthosteric and allosteric ligands having a range of efficacy for both G protein activation and arrestin recruitment. We observed ligand-specific changes in the NMR spectra of 13CH3-ε-methionine probes in the M2R extracellular domain, transmembrane core, and cytoplasmic surface, allowing us to correlate ligand structure with changes in receptor structure and dynamics. We show that the M2R has a complex energy landscape in which ligands with different efficacy profiles stabilize distinct receptor conformations.

Development of a Molecular Probe Targeting Mitochondrial Fission Protein Fis1

Excessive mitochondrial fragmentation – caused by decreased mitochondrial fusion or increased fission – leads to mitochondrial dysfunction and has been implicated in ischemia‐reperfusion injury and diabetic cardiomyopathy. Genetic or pharmacological inhibition of fission is protective against hyperglycemic‐induced loss of mitochondrial connectivity and reactive oxygen species production. Dynamin‐related protein 1 (Drp1) is a cytosolic GTPase mechanoenzyme or “cutter” known to cause scission of the mitochondria, but what determines a site of scission is unknown. Drp1 is recruited to mitochondria by one of four mitochondrial anchored recruiters; one of which is the tetratricopeptide repeat protein, fission protein 1 (Fis1). Cell lines lacking individual, all, or a combination of Drp1 recruiter proteins demonstrate each recruiter supports Drp1 recruitment in unique pathways. Of the four Drp1 recruiters, Fis1 is the only recruiter conserved in all species with mitochondria, but the involvement of Fis1 in mammalian mitochondrial fission has been disputed. Recent data suggests mammalian Fis1 is specialized for stress‐induced fission but the molecular basis remains unknown. We aimed to develop a molecular probe targeting Fis1 to be used in testing the hypothesis that Fis1 recruits and subsequently activates Drp1 in stress‐induced mammalian mitochondrial fission. If successful, a molecular probe targeting Fis1 could be used to determine the ability of Fis1 to modulate Drp1 activity under a variety of cellular stresses. We are using two approaches to develop molecular probe(s): 1) fragment‐based screening by nuclear magnetic resonance (NMR) and 2) peptide design using molecular docking, molecular dynamics simulations, and NMR validation experiments. Fis1 was screened against ~ 2000 fragments using 1H‐15N SOFAST‐HMQC and 1H‐15N NUS‐HSQC NMR experiments. Fragments that bound Fis1 (hits) were identified using a novel scoring metric, Difference Intensity Analysis (DIA), which quantitates spectral changes in 2D difference spectra and functions regardless of NMR time scale. To determine binding modalities of Fis1‐peptide interactions, we used molecular docking followed by molecular dynamics simulations to dock and sample the conformational space of previously identified Fis1 interacting peptides. To obtain binding affinities and putative binding sites, NMR titration experiments of 15N‐Fis1 with individual fragment hits and synthesized peptides were performed. Our results to date on developing molecular probe(s) against Fis1 will be presented.Support or Funding InformationThis project was supported by the Clinical & Translational Science Institute (CTSI) through the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant Number UL1TR001436. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. Project also supported by NIH grants NIH R01‐GM067180, and NIH R01‐HL128240.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Apelin conformational and binding equilibria upon micelle interaction primarily depend on membrane-mimetic headgroup

Apelin is one of two peptide hormones that activate the apelin receptor (AR or APJ) to regulate the cardiovascular system, central nervous system, and adipoinsular axis. Here, we apply circular dichroism (CD) spectropolarimetry and nuclear magnetic resonance (NMR) spectroscopy to characterize the potential membrane binding by the two longest bioactive apelin isoforms, apelin-55 and -36, using membrane-mimetic dodecylphosphocholine (DPC), sodium dodecyl sulfate (SDS), and 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] (LPPG) micelles. Pulsed field gradient diffusion NMR experiments demonstrated preferential interaction of both apelin-55 and -36 with anionic SDS and LPPG micelles over zwitterionic DPC micelles. Chemical shift perturbations and changes in ps-ns scale dynamics of apelin-55 in all micelles were similarly localized along the polypeptide backbone, demonstrating clear dependence upon detergent headgroup, while comparison of chemical shifts between apelin-55 and apelin-36 showed negligible differences indicative of highly similar modes of micelle interaction. Notably, the observed behaviour was consistent with an ensemble averaged pair of free and bound states in fast exchange on the NMR timescale proportional to the fraction of micelle-bound protein, implying a similar conformational equilibrium regardless of headgroup and tailgroup. Membrane catalysis of apelin-AR binding would thus give rise to analogous behaviour in the essential C-terminal region common to all apelin isoforms.

NMR spectroscopic conformational analysis of 4-methylene-cyclohexyl pivalate-The effect of sp2 hybridization.

The conformational equilibrium of the axial/equatorial conformers of 4-methylene-cyclohexyl pivalate is studied by dynamic NMR spectroscopy in a methylene chloride/freon mixture. At 153K, the ring interconversion gets slow on the nuclear magnetic resonance timescale, the conformational equilibrium (-ΔG°) can be examined, and the barrier to ring interconversion (ΔG# ) can be determined. The structural influence of sp2 hybridization on both ΔG° and ΔG# of the cyclohexyl moiety can be quantified.

Solid-Solid Phase Transitions and tert-Butyl and Methyl Group Rotation in an Organic Solid: X-ray Diffractometry, Differential Scanning Calorimetry, and Solid-State 1H Nuclear Spin Relaxation.

Using solid-state 1H nuclear magnetic resonance (NMR) spin-lattice relaxation experiments, we have investigated the effects of several solid-solid phase transitions on tert-butyl and methyl group rotation in solid 1,3,5-tri-tert-butylbenzene. The goal is to relate the dynamics of the tert-butyl groups and their constituent methyl groups to properties of the solid determined using single-crystal X-ray diffraction and differential scanning calorimetry (DSC). On cooling, the DSC experiments see a first-order, solid-solid phase transition at either 268 or 155 K (but not both) depending on thermal history. The 155 K transition (on cooling) is identified by single-crystal X-ray diffraction to be one from a monoclinic phase (above 155 K), where the tert-butyl groups are disordered (that is, with a rotational 6-fold intermolecular potential dominating), to a triclinic phase (below 155 K), where the tert-butyl groups are ordered (that is, with a rotational 3-fold intermolecular potential dominating). This transition shows very different DSC scans when both a 4.7 mg polycrystalline sample and a 19 mg powder sample are used. The 1H spin-lattice relaxation experiments with a much larger 0.7 g sample are very complicated and, depending on thermal history, can show hysteresis effects over many hours and over very large temperature ranges. In the high-temperature monoclinic phase, the tert-butyl groups rotate with NMR activation energies (closely related to rotational barriers) in the 17-23 kJ mol-1 range, and the constituent methyl groups rotate with NMR activation energies in the 7-12 kJ mol-1 range. In the low-temperature triclinic phase, the rotations of the tert-butyl groups and their methyl groups in the aromatic plane are quenched (on the NMR time scale). The two out-of-plane methyl groups in the tert-butyl groups are rotating with activation energies in the 5-11 kJ mol-1 range.

Tris(2-mercaptoimidazolyl)hydroborato Cadmium Thiolate Complexes, [TmBut]CdSAr: Thiolate Exchange at Cadmium in a Sulfur-Rich Coordination Environment.

A series of cadmium thiolate compounds that feature a sulfur-rich coordination environment, namely [TmBut]CdSAr, have been synthesized by the reactions of [TmBut]CdMe with ArSH (Ar = C6H4-4-F, C6H4-4-But, C6H4-4-OMe, and C6H4-3-OMe). In addition, the pyridine-2-thiolate and pyridine-2-selenolate derivatives, [TmBut]CdSPy and [TmBut]CdSePy have been obtained via the respective reactions of [TmBut]CdMe with pyridine-2-thione and pyridine-2-selone. The molecular structures of [TmBut]CdSAr and [TmBut]CdEPy (E = S or Se) have been determined by X-ray diffraction and demonstrate that, in each case, the [CdS4] motif is distorted tetrahedral and approaches a trigonal monopyramidal geometry in which the thiolate ligand adopts an equatorial position; [TmBut]CdSPy and [TmBut]CdSePy, however, exhibit an additional long-range interaction with the pyridyl nitrogen atoms. The ability of the thiolate ligands to participate in exchange was probed by 1H and 19F nuclear magnetic resonance (NMR) spectroscopic studies of the reactions of [TmBut]CdSC6H4-4-F with ArSH (Ar = C6H4-4-But or C6H4-4-OMe), which demonstrate that (i) exchange is facile and (ii) coordination of thiolate to cadmium is most favored for the p-fluorophenyl derivative. Furthermore, a two-dimensional EXSY experiment involving [TmBut]CdSC6H4-4-F and 4-fluorothiophenol demonstrates that degenerate thiolate ligand exchange is also facile on the NMR time scale.

(1)H and (19)F spin-lattice relaxation and CH3 or CF3 reorientation in molecular solids containing both H and F atoms.

The dynamics of methyl (CH3) and fluoromethyl (CF3) groups in organic molecular (van der Waals) solids can be exploited to survey their local environments. We report solid state (1)H and (19)F spin-lattice relaxationexperiments in polycrystalline 3-trifluoromethoxycinnamic acid, along with an X-ray diffraction determination of the molecular and crystal structure, to investigate the intramolecular and intermolecular interactions that determine the properties that characterize the CF3 reorientation. The molecule is of no particular interest; it simply provides a motionless backbone (on the nuclear magnetic resonance(NMR) time scale) to investigate CF3 reorientation occurring on the NMR time scale. The effects of (19)F-(19)F and (19)F-(1)H spin-spin dipolar interactions on the complicated nonexponential NMRrelaxation provide independent inputs into determining a model for CF3 reorientation. As such, these experiments provide much more information than when only one spin species (usually (1)H) is present. In Sec. IV, which can be read immediately after the Introduction without reading the rest of the paper, we compare the barrier to CH3 and CF3 reorientation in seven organic solids and separate this barrier into intramolecular and intermolecular components.

Solid-State Nuclear Magnetic Resonance on the Static and Dynamic Domains of Huntingtin Exon-1 Fibrils.

Amyloid-like fibrils formed by huntingtin exon-1 (htt_ex1) are a hallmark of Huntington's disease (HD). The structure of these fibrils is unknown, and determining their structure is an important step toward understanding the misfolding processes that cause HD. In HD, a polyglutamine (polyQ) domain in htt_ex1 is expanded to a degree that it gains the ability to form aggregates comprising the core of the resulting fibrils. Despite the simplicity of this polyQ sequence, the structure of htt_ex1 fibrils has been difficult to determine. This study provides a detailed structural investigation of fibrils formed by htt_ex1 using solid-state nuclear magnetic resonance (NMR) spectroscopy. We show that the polyQ domain of htt_ex1 forms the static amyloid core similar to polyQ model peptides. The Gln residues of this domain exist in two distinct conformations that are found in separate domains or monomers but are relatively close in space. The rest of htt_ex1 is relatively dynamic on an NMR time scale, especially the proline-rich C-terminus, which we found to be in a polyproline II helical and random coil conformation. We observed a similar dynamic C-terminus in a soluble form of htt_ex1, indicating that the conformation of this part of htt_ex1 is not changed upon its aggregation into an amyloid fibril. From these data, we propose a bottlebrush model for the fibrils formed by htt_ex1. In this model, the polyQ domains form the center and the proline-rich domains the bristles of the bottlebrush.

How Fast is Your Camera? Timescales for Molecular Motion and their Role in Restraining Molecular Dynamics

How Fast is Your Camera? Timescales for Molecular Motion and their Role in Restraining Molecular Dynamics

Spin fluctuations and frustrated magnetism in multiferroicFeVO4

We report $^{51}$V nuclear magnetic resonance (NMR) studies on single crystals of the multiferroic material FeVO$_4$. The high-temperature Knight shift shows Curie-Weiss behavior, $^{51}K = a/(T + \theta)$, with a large Weiss constant $\theta \approx$ 116 K. However, the $^{51}$V spectrum shows no ordering near these temperatures, splitting instead into two peaks below 65 K, which suggests only short-ranged magnetic order on the NMR time scale. Two magnetic transitions are identified from peaks in the spin-lattice relaxation rate, $1/^{51}T_1$, at temperatures $T_{N1} \approx$ 19 K and $T_{N2} \approx$ 13 K, which are lower than the estimates obtained from polycrystalline samples. In the low-temperature incommensurate spiral state, the maximum ordered moment is estimated as 1.95${\mu}_B$/Fe, or 1/3 of the local moment. Strong low-energy spin fluctuations are also indicated by the unconventional power-law temperature dependence $1/^{51}T_1 \propto T^2$. The large Weiss constant, short-range magnetic correlations far above $T_{N1}$, small ordered moment, significant low-energy spin fluctuations, and incommensurate ordered phases all provide explicit evidence for strong magnetic frustration in FeVO$_4$.

Recognition of O6-benzyl-2'-deoxyguanosine by a perimidinone-derived synthetic nucleoside: a DNA interstrand stacking interaction.

The 2′-deoxynucleoside containing the synthetic base 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-perimidin-2(3H)-one] (dPer) recognizes in DNA the O6-benzyl-2′-deoxyguanosine nucleoside (O6-Bn-dG), formed by exposure to N-benzylmethylnitrosamine. Herein, we show how dPer distinguishes between O6-Bn-dG and dG in DNA. The structure of the modified Dickerson–Drew dodecamer (DDD) in which guanine at position G4 has been replaced by O6-Bn-dG and cytosine C9 has been replaced with dPer to form the modified O6-Bn-dG:dPer (DDD-XY) duplex [5′-d(C1G2C3X4A5A6T7T8Y9G10C11G12)-3′]2 (X = O6-Bn-dG, Y = dPer) reveals that dPer intercalates into the duplex and adopts the syn conformation about the glycosyl bond. This provides a binding pocket that allows the benzyl group of O6-Bn-dG to intercalate between Per and thymine of the 3′-neighbor A:T base pair. Nuclear magnetic resonance data suggest that a similar intercalative recognition mechanism applies in this sequence in solution. However, in solution, the benzyl ring of O6-Bn-dG undergoes rotation on the nuclear magnetic resonance time scale. In contrast, the structure of the modified DDD in which cytosine at position C9 is replaced with dPer to form the dG:dPer (DDD-GY) [5′-d(C1G2C3G4A5A6T7T8Y9G10C11G12)-3′]2 duplex (Y = dPer) reveals that dPer adopts the anti conformation about the glycosyl bond and forms a less stable wobble pairing interaction with guanine.

Solution Nuclear Magnetic Resonance Structure of the GATase Subunit and Structural Basis of the Interaction between GATase and ATPPase Subunits in a two-subunit-type GMPS from Methanocaldococcus jannaschii

The solution structure of the monomeric glutamine amidotransferase (GATase) subunit of the Methanocaldococcus janaschii (Mj) guanosine monophosphate synthetase (GMPS) has been determined using high-resolution nuclear magnetic resonance methods. Gel filtration chromatography and ¹⁵N backbone relaxation studies have shown that the Mj GATase subunit is present in solution as a 21 kDa (188-residue) monomer. The ensemble of 20 lowest-energy structures showed root-mean-square deviations of 0.35 ± 0.06 Å for backbone atoms and 0.8 ± 0.06 Å for all heavy atoms. Furthermore, 99.4% of the backbone dihedral angles are present in the allowed region of the Ramachandran map, indicating the stereochemical quality of the structure. The core of the tertiary structure of the GATase is composed of a seven-stranded mixed β-sheet that is fenced by five α-helices. The Mj GATase is similar in structure to the Pyrococcus horikoshi (Ph) GATase subunit. Nuclear magnetic resonance (NMR) chemical shift perturbations and changes in line width were monitored to identify residues on GATase that were responsible for interaction with magnesium and the ATPPase subunit, respectively. These interaction studies showed that a common surface exists for the metal ion binding as well as for the protein-protein interaction. The dissociation constant for the GATase-Mg(2+) interaction has been found to be ∼1 mM, which implies that interaction is very weak and falls in the fast chemical exchange regime. The GATase-ATPPase interaction, on the other hand, falls in the intermediate chemical exchange regime on the NMR time scale. The implication of this interaction in terms of the regulation of the GATase activity of holo GMPS is discussed.

The Denatured State Ensemble Contains Significant Local and Long-Range Structure under Native Conditions: Analysis of the N-Terminal Domain of Ribosomal Protein L9

The denatured state ensemble (DSE) represents the starting state for protein folding and the reference state for protein stability studies. Residual structure in the DSE influences the kinetics of protein folding, the propensity to aggregate, and protein stability. The DSE that is most relevant for folding is the ensemble populated under native conditions, but the stability of proteins and the cooperativity of their folding normally prevent direct characterization of this ensemble. Indirect experiments have been used to infer residual structure in the DSE under nondenaturing conditions, but direct characterization is rare. The N-terminal domain of ribosomal protein L9 (NTL9) is a small mixed α-β domain that folds cooperatively on the millisecond time scale. A destabilized double mutant of NTL9, V3A/I4A-NTL9, populates the DSE in the absence of denaturant and is in slow exchange with the native state on the nuclear magnetic resonance time scale. The DSE populated in buffer was compared to the urea-induced DSE. Analysis of (1)H and (13)C chemical shifts reveals residual secondary structure in the DSE in buffer, which is stabilized by both local and long-range interactions. (15)N R2 relaxation rates deviate from random coil models, suggesting hydrophobic clustering in the DSE. Paramagnetic relaxation enhancement experiments show that there are transient long-range contacts in the DSE in buffer. In contrast, the urea-induced DSE has significantly less residual secondary structure and markedly fewer long-range contacts; however, the urea-induced DSE deviates from a random coil.