A constant-time (13)C- (1)H HSQC with uniform excitation over the complete (13)C chemical shift range

Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II

Eukaryotic gene regulation and pre-mRNA transcription depend on the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. Due to its highly repetitive, intrinsically disordered sequence, the CTD enables clustering and phase separation of Pol II. The molecular interactions that drive CTD phase separation and Pol II clustering are unclear. Here, we show that multivalent interactions involving tyrosine impart temperature- and concentration-dependent self-coacervation of the CTD. NMR spectroscopy, molecular ensemble calculations and all-atom molecular dynamics simulations demonstrate the presence of diverse tyrosine-engaging interactions, including tyrosine-proline contacts, in condensed states of human CTD and other low-complexity proteins. We further show that the network of multivalent interactions involving tyrosine is responsible for the co-recruitment of the human Mediator complex and CTD during phase separation. Our work advances the understanding of the driving forces of CTD phase separation and thus provides the basis to better understand CTD-mediated Pol II clustering in eukaryotic gene transcription.

Multipurpose Broadband NMR Inversion Sequences

Solution-state 2D correlation experiments increase signal-to-noise, provide improved resolution, and inform about molecular connectivity. NMR experiments are compromised when the nuclei have broad chemical shift ranges that exceed the bandwidth of the experiment. Spectra acquired under these conditions are unphasable and artifact-prone, and peaks may disappear from the spectrum altogether. Existing remedies provide usable spectra only in specific experimental contexts. Here, we introduce a general broadband strategy that leads to a library of high performing NMR experiments. We achieve arbitrary and independent evolution of NMR interactions by only changing delays in our pulse block, letting the block replace inversion elements in any NMR experiment. The experiments improve the experimental bandwidth for both nuclei by an order of magnitude over conventional sequences, covering chemical shift ranges of most molecules, even at ultrahigh field. This library enables robust spectroscopy of molecules such as perfluorinated oils (¹⁹F{¹³C}) and fluorophosphorous compounds in battery electrolytes (¹⁹F{³¹P}).

Simultaneous measurement of 1HC/N-R2's for rapid acquisition of backbone and sidechain paramagnetic relaxation enhancements (PREs) in proteins

Paramagnetic relaxation enhancements (PREs) are routinely used to provide long-range distance restraints for the determination of protein structures, to resolve protein dynamics, ligand-protein binding sites, and lowly populated species, using Nuclear Magnetic Resonance Spectroscopy (NMR). Here, we propose a simultaneous ¹H-¹⁵ N, ¹H-¹³C SESAME based pulse scheme for the rapid acquisition of ¹H^C/N-R₂ relaxation rates for the determination of backbone and sidechain PREs of proteins. The ¹H^N-R₂ rates from the traditional and our approach on Ubiquitin (UBQ) are well correlated (R² = 0.99), revealing their potential to be used quantitatively. Comparison of the S57C UBQ calculated and experimental PREs provided backbone and side chain Q factors of 0.23 and 0.24, respectively, well-fitted to the UBQ NMR structure, showing that our approach can be used to acquire accurate PRE rates from the functionally important sites of proteins but in at least half the time as traditional methods.

Chirp excitation

The paper describes the design of broadband chirp excitation pulses. We first develop a three stage model for understanding chirp excitation in NMR. We then show how a chirp π pulse can be used to refocus the phase of the chirp excitation pulse. The resulting magnetization still has some phase dispersion in it. We show how a combination of two chirp π pulses instead of one can be used to eliminate this dispersion, leaving behind a small residual phase dispersion. The excitation pulse sequence presented here allows exciting arbitrary large bandwidths without increasing the peak rf-amplitude. Experimental excitation profiles for the residual HDO signal in a sample of 99.5% D₂O are displayed as a function of resonance offset. Although methods presented in this paper have appeared elsewhere, we present complete analytical treatment that elucidates the working of these methods.

Ultra broadband NMR spectroscopy using multiple rotating frame technique

The paper describes the design of broadband excitation and inversion pulses by method of multiple rotating frame technique. The ideal situation for perfect excitation and inversion is to have no chemical shift offset and thereby everything on resonance. However, when chemical shifts span a wide range, this condition is not realized. We achieve this condition using a multiply modulated rf-field, whose effect can be understood by progressing into multiple frames. As we progress through the frames, the ratio of chemical shift dispersion to strength of static rf-field decreases, resulting in a final frame, where there is negligible chemical shift as compared to the effective rf-field and we get good excitation and inversion. Increasing the number of frames, increases excitation bandwidth and the ratio of bandwidth to rms excitation amplitude. We show, in principle, it is possible to excite arbitrary large bandwidth for a given rms rf-amplitude by increasing the number of frames. The time of excitation increases linearly with the bandwidth when we keep the rms rf-amplitude constant. Experimental demonstration of proposed method is presented on (1)H excitation over a bandwidth of 52 kHz with a rms amplitude of 10 kHz. Increasing the frames increases excitation bandwidth for same rms amplitude of 10 kHz. Experimental spectra obtained from 100%(13)C labeled arginine shows uniform excitation over the entire carbon spectra, obtained with a 8-frame pulse sequence.

Robust INEPT and refocused INEPT transfer with compensation of a wide range of couplings, offsets, and B1-field inhomogeneities (COB3)

Following the two-step optimization procedure previously introduced with the COB-INEPT (Ehni and Luy, 2012), a corresponding inphase-to-antiphase transfer element with close to optimal transfer efficiencies over a coupling range comprising approximately J-6J has been derived. The hard pulse sequence length is only 5.5 ms for coupling constants within 125-750 Hz. Robustness with respect to an offset range of 37.5 kHz on carbon (corresponding to 250 ppm on a 600 MHz spectrometer) and 10 kHz on protons (16.6 ppm at 600 MHz) is achieved with corresponding BUBI and BURBOP broadband pulses. As the sequence achieves a three times higher upper limit of J-compensation compared to the COB-INEPT, we name the transfer element COB3-INEPT. Next to the description of optimization and pulse sequence details, the performance of the resulting element is demonstrated on a test sample and partially aligned sample with actual total couplings in the range of 134 Hz⩽(1)TCH⩽391 Hz. The sequence can also be used for inphase-to-antiphase transfer starting from carbon, where the upper limit of J-compensation is 6J for CH-groups, 3J for CH2-groups, and slightly less than 2J for CH3. Theoretical transfers and experimental verification for the different multiplicities in an refocused INEPT are given.

Chemical shift assignments of domain 4 from the phosphohexomutase from Pseudomonas aeruginosa suggest that freeing perturbs its coevolved domain interface

A domain needed for the catalytic efficiency of an enzyme model of simple processivity and domain-domain interactions has been characterized by NMR. This domain 4 from phosphomannomutase/phosphoglucomutase (PMM/PGM) closes upon glucose phosphate and mannose phosphate ligands in the active site, and can modestly reconstitute activity of enzyme truncated to domains 1-3. This enzyme supports biosynthesis of the saccharide-derived virulence factors (rhamnolipids, lipopolysaccharides, and alginate) of the opportunistic bacterial pathogen Pseudomonas aeruginosa. (1)H, (13)C, and (15)N NMR chemical shift assignments of domain 4 of PMM/PGM suggest preservation and independence of its structure when separated from domains 1-3. The face of domain 4 that packs with domain 3 is perturbed in NMR spectra without disrupting this fold. The perturbed residues overlap both the most highly coevolved positions in the interface and residues lining a cavity at the domain interface.

The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing NMR spectroscopy

We present highly robust, optimal control-based shaped pulses designed to replace all 90° and 180° hard pulses in a given pulse sequence for improved performance. Special attention was devoted to ensuring that the pulses can be simply substituted in a one-to-one fashion for the original hard pulses without any additional modification of the existing sequence. The set of four pulses for each nucleus therefore consists of 90° and 180° point-to-point (PP) and universal rotation (UR) pulses of identical duration. These 1ms pulses provide uniform performance over resonance offsets of 20kHz ((1)H) and 35kHz ((13)C) and tolerate reasonably large radio frequency (RF) inhomogeneity/miscalibration of ±15% ((1)H) and ±10% ((13)C), making them especially suitable for NMR of small-to-medium-sized molecules (for which relaxation effects during the pulse are negligible) at an accessible and widely utilized spectrometer field strength of 600MHz. The experimental performance of conventional hard-pulse sequences is shown to be greatly improved by incorporating the new pulses, each set referred to as the Fantastic Four (Fanta4).

A systematic approach for optimizing the robustness of pulse sequence elements with respect to couplings, offsets, and B1-field inhomogeneities (COB)

Robust experiments that cover a wide range of chemical shift offsets and J-couplings are highly desirable for a multitude of applications in small molecule NMR spectroscopy. Many attempts to improve individual aspects of the robustness of pulse sequence elements based on rational and numerical design have been reported, but a general optimization strategy to cover all necessary aspects for a fully robust sequence is still lacking. In this article, a viable optimization strategy is introduced that covers a defined range of couplings, offsets, and B(1)-field inhomogeneities (COB) in a time-optimal way. Individual components of the optimization strategy can be optimized in any adequate way. As an example for the COB approach, we present the (1)H -(13)C-COB-INEPT with transfer of approximately 99% over the full carbon and proton bandwidth and (1)J(CH) -couplings in the range of 120-250 Hz, which have been optimized using efficient algorithms derived from optimal control theory. The theoretical performance is demonstrated in a number of corresponding COB-HSQC experiments.

Performance evaluation of quantitative adiabatic (13)C NMR pulse sequences for site-specific isotopic measurements

(2)H/(1)H and (13)C/(12)C site-specific isotope ratios determined by NMR spectroscopy may be used to discriminate pharmaceutically active ingredients based on the synthetic process used in production. Extending the Site-specific Natural Isotope Fractionation NMR (SNIF-NMR) method to (13)C is highly beneficial for complex organic molecules when measurements of (2)H/(1)H ratios lead to poorly defined molecular fingerprints. The current NMR methodology to determine (13)C/(12)C site-specific isotope ratios suffers from poor sensitivity and long experimental times. In this work, several NMR pulse sequences based on polarization transfer were evaluated and optimized to measure precise quantitative (13)C NMR spectra within a short time. Adiabatic 180 degrees (1)H and (13)C pulses were incorporated into distortionless enhancement by polarization transfer (DEPT) and refocused insensitive nuclei enhanced by polarization transfer (INEPT) to minimize the influence of 180 degrees pulse imperfections and of off-resonance effects on the precision of the measured (13)C peak areas. The adiabatic DEPT sequence was applied to draw up a precise site-specific (13)C isotope profile of ibuprofen. A modified heteronuclear cross-polarization (HCP) experiment featuring (1)H and (13)C spin-locks with adiabatic 180 degrees pulses is also introduced. This sequence enables efficient magnetization transfer across a wide (13)C frequency range although not enough for an application in quantitative (13)C isotopic analysis.

Quantitative two-dimensional HSQC experiment for high magnetic field NMR spectrometers

The finite RF power available on carbon channel in proton-carbon correlation experiments leads to non-uniform cross peak intensity response across carbon chemical shift range. Several classes of broadband pulses are available that alleviate this problem. Adiabatic pulses provide an excellent magnetization inversion over a large bandwidth, and very recently, novel phase-modulated pulses have been proposed that perform 90 degrees and 180 degrees magnetization rotations with good offset tolerance. Here, we present a study how these broadband pulses (adiabatic and phase-modulated) can improve quantitative application of the heteronuclear single quantum coherence (HSQC) experiment on high magnetic field strength NMR spectrometers. Theoretical and experimental examinations of the quantitative, offset-compensated, CPMG-adjusted HSQC (Q-OCCAHSQC) experiment are presented. The proposed experiment offers a formidable improvement to the offset performance; (13)C offset-dependent standard deviation of the peak intensity was below 6% in range of+/-20 kHz. This covers the carbon chemical shift range of 150 ppm, which contains the protonated carbons excluding the aldehydes, for 22.3 T NMR magnets. A demonstration of the quantitative analysis of a fasting blood plasma sample obtained from a healthy volunteer is given.

The CLIP/CLAP-HSQC: pure absorptive spectra for the measurement of one-bond couplings

Heteronuclear residual dipolar one-bond couplings of organic molecules at natural abundance are most easily measured using t2 coupled HSQC spectra. However, inevitably mismatched transfer delays result in phase distortions due to residual dispersive antiphase coherences in such experiments. In this article, slightly modified t2 coupled HSQC experiments with clean inphase (CLIP) multiplets are introduced which also reduce the intensities of undesired long-range cross peaks. With the corresponding antiphase (CLAP) experiment, situations where alpha and beta components overlap can be resolved for all multiplicities in an IPAP manner. A comparison of the experiments using hard pulses and shaped broadband excitation and inversion pulses on the heteronucleus is given and potential spectral artefacts are discussed in detail.

Frequency-swept HSQC sequences for high-throughput NMR analysis

This article describes new versions of the DEPT phase-edited heteronuclear single quantum correlation (HSQC) pulse sequence with sensitivity enhancement. The sequences incorporate frequency-swept carbon and proton pulses. The new experiments are inherently robust, well-suited for a high-throughput setting in which sample-to-sample variations may be ignored. The observed signal has the obvious benefit of sensitivity enhancement resulting from the preservation of two magnetization transfer pathways. The two pathways are maintained even in the version of the sequence in which all pulses are frequency-swept. There is an additional signal gain of roughly 10% that derives from the use of both proton and carbon frequency-swept pulses. Furthermore, the sequences use J compensation to provide optimal signal over a range of heteronuclear coupling constants. We demonstrate that the new sequences offer good sensitivity and perform well even when the NMR probe is deliberately mistuned.

Sensitivity improvement for correlations involving arginine side-chain Nepsilon/Hepsilon resonances in multi-dimensional NMR experiments using broadband 15N 180 degrees pulses

Due to practical limitations in available 15N rf field strength, imperfections in 15N 180 degrees pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amide groups, cross-peaks arising from the Arg guanidino 15Nepsilon (approximately 85 ppm) are highly attenuated by the presence of multiple INEPT transfer steps. To improve the sensitivity for correlations involving Arg Nepsilon-Hepsilon groups, we have incorporated 15N broadband 180 degrees pulses into 3D 15N-separated NOE-HSQC and HNCACB experiments. Two 15N-WURST pulses incorporated at the INEPT transfer steps of the 3D 15N-separated NOE-HSQC pulse sequence resulted in a approximately 1.5-fold increase in sensitivity for the Arg Nepsilon-Hepsilon signals at 800 MHz. For the 3D HNCACB experiment, five 15N Abramovich-Vega pulses were incorporated for broadband inversion and refocusing, and the sensitivity of Arg1Hepsilon-15Nepsilon-13Cgamma/13Cdelta correlation peaks was enhanced by a factor of approximately 1.7 at 500 MHz. These experiments eliminate the necessity for additional experiments to assign Arg 1Hepsilon and 15Nepsilon resonances. In addition, the increased sensitivity afforded for the detection of NOE cross-peaks involving correlations with the 15Nepsilon/1Hepsilon of Arg in 3D 15N-separated NOE experiments should prove to be very useful for structural analysis of interactions involving Arg side-chains.

Optimal control design of constant amplitude phase-modulated pulses: application to calibration-free broadband excitation

An optimal control algorithm for generating purely phase-modulated pulses is derived. The methodology is applied to obtain broadband excitation with unprecedented tolerance to RF inhomogeneity. Design criteria were transformation of Iz-->Ix over resonance offsets of +/-25 kHz for constant RF amplitude anywhere in the range 10-20 kHz, with a pulse length of 1 ms. Simulations transform Iz to greater than 0.99 Ix over the targetted ranges of resonance offset and RF variability. Phase deviations in the final magnetization are less than 2-3 degrees over almost the entire range, with sporadic deviations of 6-9 degrees at a few offsets for the lowest RF (10 kHz) in the optimized range. Experimental performance of the new pulse is in excellent agreement with the simulations, and the robustness of the excitation pulse and a derived refocusing pulse are demonstrated by insertion into conventional HSQC and HMBC-type experiments.

Extended flip-back schemes for sensitivity enhancement in multidimensional HSQC-type out-and-back experiments

In many NMR experiments, only polarisation of a limited sub-set of all protons is converted into observable coherence. As recently shown by the "longitudinal" TROSY implementation (Pervushin et al. (2002) J. Am. Chem. Soc., 124, 12898-12902) and SOFAST-HMQC (Schanda and Brutscher (2005) J. Am. Chem. Soc., 127, 8014-8015), recovery of unused polarisation can be used indirectly and unspecifically to cool the proton lattice and, thus, accelerate re-equilibration for the selected proton subset. Here we illustrate transfer of this principle to HSQC-based multi-dimensional out-and-back experiments that exploit only polarisation of 15N-bound protons. The presented modifications to the pulse sequences can be implemented broadly and easily, extending standard flip-back of water polarisation to a much larger pool of protons that may comprise all non-15N-bound protons. The underlying orthogonal separation of H(N) polarisation (selected by the main transfer path) from unused H(u) polarisation (flipped-back on the recovery path) is thereby achieved through positive or negative selection by J-coupling, or using band-selective pulses. In practice, H(u) polarisation recovery degrades mostly through cumulative pulse imperfections and transverse relaxation; we present, however, strategies to substantially minimise such losses particularly during interim proton decoupling. Depending on the protein's relaxation properties and the extended flip-back scheme employed, we recovered up to 60% H(u) equilibrium polarisation. The concomitant cooling of the proton lattice afforded substantial gains of more than 40%, relative to the water-only flip-back version, in the fast pulsing regime with re-equilibration delays tau much shorter than optimal (tau(opt) = 1.25 x T1(H(N))). These would be typically employed if resolution requirements dominate the total measurement time. Contrarily, if sensitivity is limiting and optimal interscan delays tau(opt) can be set (optimal pulsing regime), the best of the presented flip-back schemes may still afford up to ca. 10% absolute sensitivity enhancement.

Tailoring the optimal control cost function to a desired output: application to minimizing phase errors in short broadband excitation pulses

The de facto standard cost function has been used heretofore to characterize the performance of pulses designed using optimal control theory. The freedom to choose new, creative quality factors designed for specific purposes is demonstrated. While the methodology has more general applicability, its utility is illustrated by comparison to a consistently chosen example--broadband excitation. The resulting pulses are limited to the same maximum RF amplitude used previously and tolerate the same variation in RF homogeneity deemed relevant for standard high-resolution NMR probes. Design criteria are unchanged: transformation of I(z)--> I(x) over resonance offsets of +/-20 kHz and RF variability of +/-5%, with a peak RF amplitude equal to 17.5 kHz. However, the new cost effectively trades a small increase in residual z magnetization for improved phase in the transverse plane. Compared to previous broadband excitation by optimized pulses (BEBOP), significantly shorter pulses are achievable, with only marginally reduced performance. Simulations transform I(z) to greater than 0.98 I(x), with phase deviations of the final magnetization less than 2 degrees, over the targeted ranges of resonance offset and RF variability. Experimental performance is in excellent agreement with the simulations.

Reducing the duration of broadband excitation pulses using optimal control with limited RF amplitude

Combining optimal control theory with a new RF limiting step produces pulses with significantly reduced duration and improved performance for a given maximum RF amplitude compared to previous broadband excitation by optimized pulses (BEBOP). The resulting pulses tolerate variations in RF homogeneity relevant for standard high-resolution NMR probes. Design criteria were transformation of Iz-->Ix over resonance offsets of +/-20kHz and RF variability of +/-5%, with a pulse length of 500 micros and peak RF amplitude equal to 17.5 kHz. Simulations transform Iz to greater than 0.995 Ix, with phase deviations of the final magnetization less than 2 degrees, over ranges of resonance offset and RF variability that exceed the design targets. Experimental performance of the pulse is in excellent agreement with the simulations. Performance tradeoffs for yet shorter pulses or pulses with decreased digitization are also investigated.

Adiabatic Single Scan Two-Dimensional NMR Spectrocopy

New excitation schemes, based on the use adiabatic pulses, for single scan two-dimensional NMR experiments (Frydman et al., Proc. Nat. Acad. Sci. 2002, 99, 15 858-15 862) are introduced. The advantages are discussed. Applications in homo- and heteronuclear experiments are presented.

Application of optimal control theory to the design of broadband excitation pulses for high-resolution NMR

Optimal control theory is considered as a methodology for pulse sequence design in NMR. It provides the flexibility for systematically imposing desirable constraints on spin system evolution and therefore has a wealth of applications. We have chosen an elementary example to illustrate the capabilities of the optimal control formalism: broadband, constant phase excitation which tolerates miscalibration of RF power and variations in RF homogeneity relevant for standard high-resolution probes. The chosen design criteria were transformation of I(z)-->I(x) over resonance offsets of +/- 20 kHz and RF variability of +/-5%, with a pulse length of 2 ms. Simulations of the resulting pulse transform I(z)-->0.995I(x) over the target ranges in resonance offset and RF variability. Acceptably uniform excitation is obtained over a much larger range of RF variability (approximately 45%) than the strict design limits. The pulse performs well in simulations that include homonuclear and heteronuclear J-couplings. Experimental spectra obtained from 100% 13C-labeled lysine show only minimal coupling effects, in excellent agreement with the simulations. By increasing pulse power and reducing pulse length, we demonstrate experimental excitation of 1H over +/-32 kHz, with phase variations in the spectra <8 degrees and peak amplitudes >93% of maximum. Further improvements in broadband excitation by optimized pulses (BEBOP) may be possible by applying more sophisticated implementations of the optimal control formalism.

A novel method for the determination of stereochemistry in six-membered chairlike rings using residual dipolar couplings

A novel method for the determination of the relative stereochemistry of six-membered chairlike ring molecules by residual dipolar couplings is presented. C-H residual dipolar couplings were used to investigate the relative stereochemistry of 4,6-O-ethylidene-d-glucopyranose. For this and similar systems it is not necessary to acquire redundant dipolar couplings and to calculate the orientation order tensor. The presented methodology is a paradigmatic leap for the determination of the relative stereochemistry or remote stereochemistry in this kind of fused ring system. Residual dipolar coupling data were collected by 1D and 2D direct-measurement heteronuclear multiple quantum coherence (HMQC) spectroscopy. It was demonstrated that direct measurement of HMQC was quick and accurate for small molecules at natural abundance.

Adjustable, broadband, selective excitation with uniform phase

An advance in the problem of achieving broadband, selective, and uniform-phase excitation in NMR spectroscopy of liquids is outlined. Broadband means that, neglecting relaxation, any frequency bandwidth may be excited even when the available radiofrequency (RF) field strength is strictly limited. Selective means that sharp transition edges can be created between pure-phase excitation and no excitation at all. Uniform phase means that, neglecting spin-spin coupling, all resonance lines have nearly the same phase. Conventional uniform-phase excitation pulses (e.g., E-BURP), mostly based on amplitude modulation of the RF field, are not broadband: they have an achievable bandwidth that is strictly limited by the peak power available. Other compensated pulses based on adiabatic half-passage, like BIR-4, are not selective. By contrast, inversion pulses based on adiabatic fast passage can be broadband (and selective) in the sense above. The advance outlined is a way to reformulate these frequency modulated (FM) pulses for excitation, rather than just inversion.

Fast broadband inversion by adiabatic pulses

Despite the advantages of compensation for resonance offset and B1 inhomogeneity, adiabatic pulses are not yet in general use in high-resolution NMR, often because of the conception that these pulses require longer time or increased power to perform. We show that adiabatic pulses with tangential frequency sweeps and other frequency-modulation functions can be optimized to accomplish 13C and 1H broadband inversion using pulse lengths of 192 and 64 micro(s), respectively, at B1 strengths available with modern high-resolution probes.

13C-NOESY-HSQC with Split Carbon Evolution for Increased Resolution with Uniformly Labeled Proteins

Two new pulse sequences are presented for the recording of 2D 13C-HSQC and 3D 13C-NOESY-HSQC experiments, containing two consecutive carbon evolution periods. The two periods are separated by a z-filter which creates a clean CxHz-quantum state for evolution in the second period. Each period is incremented (in a non-constant-time fashion) only to the extent that the defocusing of carbon inphase magnetization through J-coupling with neighboring carbons remains insignificant. Therefore, 13C homonuclear J-couplings are rendered ineffective, reducing the loss of signal and peak splitting commonly associated with long 13C evolution times. The two periods are incremented according to a special acquisition protocol employing a 13C-13C gradient echo to yield a data set analogous to one obtained by evolution over the added duration of both periods. The spectra recorded with the new technique on uniformly 13C-labeled proteins at twice the evolution time of the standard 13C-HSQC experiment display a nearly twofold enhancement of resolution in the carbon domain, while maintaining a good sensitivity even in the case of large proteins. Applied to the IIAMan protein of E. coli (31 kDa), the 13C-HSQC experiment recorded with a carbon evolution time of 2 x 8 ms showed a 36% decrease in linewidths compared to the standard 13C-HSQC experiment, and the S/N ratio of representative cross-peaks was reduced to 40%. This reduction reflects mostly the typical loss of intensity observed when recording with an increased resolution. The 13C-NOESY-HSQC experiment derived from the 13C-HSQC experiment yielded additional NOE restraints between resonances which previously had been unresolved. Copyright 1998 Academic Press.

Iron regulatory element and internal loop/bulge structure for ferritin mRNA studied by cobalt(III) hexammine binding, molecular modeling, and NMR spectroscopy

The ferritin IRE, a highly conserved (96-99% in vertebrates) mRNA translation regulatory element in animal mRNA, was studied by molecular modeling (using MC-SYM and DOCKING) and by NMR spectroscopy. Cobalt(III) hexammine was used to model hydrated Mg2+. IRE isoforms in other mRNAs regulate mRNA translation or stability; all IREs bind IRPs (iron regulatory proteins). A G.C base pair, conserved in ferritin IREs, spans an internal loop/bulge in the middle of an A-helix and, combined with a dynamic G.U base pair, formed a pocket suitable for Co(III) hexammine binding. On the basis of the effects of Co(III) hexammine on the 1H NMR spectrum and results of automatic docking into the IRE model, the IRE bound Co(III) hexammine at the pocket in the major groove; Mg2+ may bind to the IRE at the same site on the basis of an analogy to Co(III) hexammine and on the Mg2+ inhibition of Cu-(phen)2 cleavage at the site. Distortion of the IRE helix by the internal loop/bulge near a conserved unpaired C required for IRP binding and adjacent to an IRP cross-linking site suggests a role for the pocket in ferritin IRE/IRP interactions.

RNA recognition by a bent alpha-helix regulates transcriptional antitermination in phage lambda

A novel RNA recognition motif is characterized in an arginine-rich peptide. The motif, derived from lambda transcriptional antitermination protein N, regulates an RNA-directed genetic switch. Its characterization by multidimensional nuclear magnetic resonance (NMR) demonstrates specific RNA-dependent folding of N- and C-terminal recognition helices separated by a central bend. The biological importance of the bent alpha-helix is demonstrated by mutagenesis: binding is blocked by substitutions in the N peptide or its target (the boxB RNA hairpin) associated in vivo with loss of transcriptional antitermination activity. Although arginine side chains are essential, the peptide is also anchored to boxB by specific nonpolar contacts. An alanine in the N-terminal helix docks in the major groove of the RNA stem whereas a tryptophan in the C-terminal helix stacks against a purine in the RNA loop. At these positions all 19 possible amino acid substitutions have been constructed by peptide synthesis; each impairs binding to boxB. The pattern of allowed and disallowed substitutions is in accord with the results of random-cassette mutagenesis in vivo. The helix-bend-helix motif rationalizes genetic analysis of N-dependent transcriptional antitermination and extends the structural repertoire of arginine-rich domains observed among mammalian immunodeficiency viruses.

NMR structure determination of tick anticoagulant peptide (TAP)

Tick anticoagulant peptide (TAP) is a potent and selective 60-amino acid inhibitor of the serine protease Factor Xa (fXa), the penultimate enzyme in the blood coagulation cascade. The structural features of TAP responsible for its remarkable specificity for fXa are unknown, but the binding to its target appears to be unique. The elucidation of the TAP structure may facilitate our understanding of this new mode of serine protease inhibition and could provide a basis for the design of novel fXa inhibitors. Analyses of homo- and heteronuclear two-dimensional NMR spectra (total correlation spectroscopy, nuclear Overhauser effect spectroscopy [NOESY], constant time heteronuclear single quantum correlation spectroscopy [CT-HSQC], and HSQC-NOESY; 600 MHz; 1.5 mM TAP; pH 2.5) of unlabeled, 13C-labeled, and 15N-labeled TAP provided nearly complete 1H sequence-specific resonance assignments. Secondary structural elements were identified by characteristic NOE patterns and D2O amide proton-exchange experiments. A three-dimensional structure of TAP was generated from 412 NOESY-derived distance and 47 dihedral angle constraints. The structural elements of TAP are similar in some respects to those of the Kunitz serine protease inhibitor family, with which TAP shares weak sequence homology. This structure, coupled with previous kinetic and biochemical information, confirms previous suggestions that TAP has a unique mode of binding to fXa.