Chi1 torsion angle dynamics in proteins from dipolar couplings

Optimization of TROSY- and anti-TROSY-based 15N CPMG relaxation dispersion experiments through phase cycling

CPMG relaxation dispersion studies of biomolecular dynamics on the μs-ms timescale can provide detailed kinetic, thermodynamic, and structural insights into function. Frequently, the 15N spin serves as the probe of choice, as uniform incorporation of the 15N isotope is facile and cost-effective, and the interpretation of the resulting data is often relatively straightforward. In conventional CPMG relaxation dispersion experiments the application of CPMG pulses with constant radiofrequency (RF) phase can lead to artifactual dispersion profiles that result from off-resonance effects, RF field inhomogeneity, and pulse miscalibration. The development of CPMG experiments with the [0013]-phase cycle has significantly reduced the impact of pulse imperfections over a greater bandwidth of frequency offsets in comparison to constant phase experiments. Application of 15N-TROSY-based CPMG schemes to studies of the dynamics of large molecules is necessary for high sensitivity, yet the correct incorporation of the [0013]-phase cycle is non-trivial. Here we present TROSY- and anti-TROSY-based 15N CPMG experiments with the [0013]-phase cycling scheme and demonstrate, through comprehensive numerical simulations and experimental validation, enhanced resistance to pulse imperfections relative to traditional schemes utilizing constant phase CPMG pulses. Notably, exchange parameters derived from the new experiments are in good agreement with those obtained using other, more established, 15N-based CPMG approaches.

Sometimes pulses just have to be perfect - An example based on the measurement of amide proton transverse relaxation rates in proteins

The measurement of spin relaxation rates provides a unique avenue for quantifying dynamic processes in biomolecules. In order to simplify analysis of the measurements so that a few key intuitive parameters can be extracted, it is often the case that experiments are designed to eliminate interference effects between different classes of spin relaxation. One example emerges in the measurement of amide proton (¹H^N) transverse relaxation rates in ¹⁵N labeled proteins, where ¹⁵N inversion pulses are applied during a relaxation element to eliminate cross-correlated spin relaxation between ¹H^N-¹⁵N dipole-¹H^N CSA interactions. We show that unless these pulses are essentially perfect, significant oscillations in magnetization decay profiles can be obtained, due to the excitation of multiple-quantum coherences, leading potentially to errors in measured R₂ rates. With the recent development of experiments for quantifying electrostatic potentials via amide proton relaxation rates, the need for highly accurate measurement schemes becomes critical. Straightforward modifications to existing pulse sequences are suggested to achieve this goal.

Less is more: A simple methyl-TROSY based pulse scheme offers improved sensitivity in applications to high molecular weight complexes

The HMQC pulse sequence and variants thereof have been exploited in studies of high molecular weight protein complexes, taking advantage of the fact that fast and slow relaxing magnetization components are sequestered along two distinct magnetization transfer pathways. Despite the simplicity of the HMQC scheme an even shorter version can be designed, based on elimination of the terminal refocusing period, as a further means of increasing signal. Here we present such an experiment, and show that significant sensitivity gains, in some cases by factors of two or more, are realized in studies of proteins varying in molecular masses from 100 kDa to 1 MDa.

Proton TOCSY NMR relaxation rates quantitate protein side chain mobility in the Pin1 WW domain

Protein side chain dynamics play a vital role in many biological processes, but differentiating mobile from rigid side chains remains a technical challenge in structural biology. Solution NMR spectroscopy is ideally suited for this but suffers from limited signal-to-noise, signal overlap, and a need for fractional ¹³C or ²H labeling. Here we introduce a simple strategy measuring initial ¹H relaxation rates during a ¹H TOCSY sequence like DIPSI-2, which can be appended to the beginning of any multi-dimensional NMR sequence that begins on ¹H. The TOCSY RF field compels all ¹H atoms to behave similarly under the influence of strong coupling and rotating frame cross-relaxation, so that differences in relaxation rates are due primarily to side chain mobility. We apply the scheme to a thermostable mutant Pin1 WW domain and demonstrate that the observed ¹H relaxation rates correlate well with two independent NMR measures of side-chain dynamics, cross-correlated ¹³C relaxation rates in ¹³C^βH₂ methylene groups and maximum observable ³J couplings sensitive to the χ₁ side chain dihedral angle (³J_Hα,Hβ, ³J_N,Hβ, and ³J_CO,Hβ). The most restricted side chains belong to Trp26 and Asn40, which are closely packed to constitute the folding center of the WW domain. None of the other conserved aromatic residues is as immobile as the first tryptophan side chain of the WW domain. The proposed ¹H relaxation methodology should make it relatively easy to measure side chain dynamics on uniformly ¹⁵N- or ¹³C-labeled proteins, so long as chemical shift assignments are obtainable.

Advances in NMR Spectroscopy of Weakly Aligned Biomolecular Systems

The measurement and application of residual dipolar couplings (RDCs) in solution NMR studies of biological macromolecules has become well established over the past quarter of a century. Numerous methods for generating the requisite anisotropic orientational molecular distribution have been demonstrated, each with its specific strengths and weaknesses. In parallel, an enormous number of pulse schemes have been introduced to measure the many different types of RDCs, ranging from the most widely measured backbone amide ¹⁵N-¹H RDCs, to ¹H-¹H RDCs and couplings between low-γ nuclei. Applications of RDCs range from structure validation and refinement to the determination of relative domain orientations, the measurement of backbone and domain motions, and de novo structure determination. Nevertheless, it appears that the power of the RDC methodology remains underutilized. This review aims to highlight the practical aspects of sample preparation and RDC measurement while describing some of the most straightforward applications that take advantage of the exceptionally precise information contained in such data. Some emphasis will be placed on more recent developments that enable the accurate measurement of RDCs in larger systems, which is key to the ongoing shift in focus of biological NMR spectroscopy from structure determination toward gaining improved understanding of how molecular flexibility drives protein function.

Determining methyl sidechain conformations in a CS-ROSETTA model using methyl 1H-13C residual dipolar couplings

Modelling of protein structures based on backbone chemical shifts, using programs such as CS-ROSETTA, is becoming increasingly popular, especially for systems where few restraints are available or where homologous structures are already known. While the reliability of CS-ROSETTA calculations can be improved by incorporation of some additional backbone NMR data such as those afforded by residual dipolar couplings or minimal NOE data sets involving backbone amide protons, the sidechain conformations are largely modelled by statistical energy terms. Here, we present a simple method based on methyl residual dipolar couplings that can be used to determine the rotameric state of the threefold symmetry axis of methyl groups that occupy a single rotamer, determine rotameric distributions, and identify regions of high flexibility. The method is demonstrated for methyl side chains of a deletion variant of the human chaperone DNAJB6b.

Revisiting 1HN CPMG relaxation dispersion experiments: a simple modification can eliminate large artifacts

Carr-Purcell-Meiboom-Gill relaxation dispersion experiments are commonly used to probe biomolecular dynamics on the millisecond timescale. The simplest experiment involves using backbone ¹⁵N spins as probes of motion and pulse sequences are now available for providing accurate dispersion profiles in this case. In contrast, ¹H-based experiments recorded on fully protonated samples are less common because of difficulties associated with homonuclear scalar couplings that can result in transfer of magnetization between coupled spins, leading to significant artifacts. Herein we examine a version of the ¹H^N CPMG experiment that has been used in our laboratory where a pair of CPMG pulse trains comprising non-selective, high power ¹H refocusing pulses sandwich an amide selective pulse that serves to refocus scalar-coupled evolution by the end of the train. The origin of the artifacts in our original scheme is explained and a new, significantly improved sequence is presented. The utility of the new experiment is demonstrated by obtaining flat ¹H^N dispersion profiles in a protonated protein system that is not expected to undergo millisecond timescale dynamics, and subsequently by measuring profiles on a cavity mutant of T4 lysozyme that exchanges between a pair of distinct states, establishing that high quality data can be generated even for fully protonated samples.

Exploring methods to expedite the recording of CEST datasets using selective pulse excitation

Chemical Exchange Saturation Transfer (CEST) has emerged as a powerful tool for studies of biomolecular conformational exchange involving the interconversion between a major, visible conformer and one or more minor, invisible states. Applications typically entail recording a large number of 2D datasets, each of which differs in the position of a weak radio frequency field, so as to generate a CEST profile for each nucleus from which the chemical shifts of spins in the invisible state(s) are obtained. Here we compare a number of band-selective CEST schemes for speeding up the process using either DANTE or cosine-modulated excitation approaches. We show that while both are essentially identical for applications such as ¹⁵N CEST, in cases where the probed spins are dipolar or scalar coupled to other like spins there can be advantages for the cosine-excitation scheme.

An enhanced sensitivity methyl 1H triple-quantum pulse scheme for measuring diffusion constants of macromolecules

We present a pulse scheme that exploits methyl ¹H triple-quantum (TQ) coherences for the measurement of diffusion rates of slowly diffusing molecules in solution. It is based on the well-known stimulated echo experiment, with encoding and decoding of TQ coherences. The size of quantifiable diffusion coefficients is thus lowered by an order of magnitude with respect to single-quantum (SQ) approaches. Notably, the sensitivity of the scheme is high, approximately ¾ that of the corresponding single quantum experiment, neglecting relaxation losses, and on the order of a factor of 4 more sensitive than a previously published sequence for AX₃ spin systems (Zheng et al. in JMR 198:271-274, 2009) for molecules that are only ¹³C labeled at the methyl carbon position. Diffusion coefficients measured from TQ- and SQ-based experiments recorded on a range of protein samples are in excellent agreement. We present an application of this technique to the study of phase-separated proteins where protein concentrations in the condensed phase can exceed 400 mg/mL, diffusion coefficients can be as low as ~10^-9 cm²s^-1 and traditional SQ experiments fail.

Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings

Accurate quantitative measurement of structural dispersion in proteins remains a prime challenge to both X-ray crystallography and NMR spectroscopy. Here we use a model-free approach based on measurement of many residual dipolar couplings (RDCs) in differentially orienting aqueous liquid crystalline solutions to obtain the side chain χ₁ distribution sampled by each residue in solution. Applied to the small well-ordered model protein GB3, our approach reveals that the RDC data are compatible with a single narrow distribution of side chain χ₁ angles for only about 40% of the residues. For more than half of the residues, populations greater than 10% for a second rotamer are observed, and four residues require sampling of three rotameric states to fit the RDC data. In virtually all cases, sampled χ₁ values are found to center closely around ideal g^–, g⁺ and t rotameric angles, even though no rotamer restraint is used when deriving the sampled angles. The root-mean-square difference between experimental ³J_HαHβ couplings and those predicted by the Haasnoot-parametrized, motion-adjusted Karplus equation reduces from 2.05 to 0.75 Hz when using the new rotamer analysis instead of the 1.1-Å X-ray structure as input for the dihedral angles. A comparison between observed and predicted ³J_HαHβ values suggests that the root-mean-square amplitude of χ₁ angle fluctuations within a given rotamer well is ca. 20°. The quantitatively defined side chain rotamer equilibria obtained from our study set new benchmarks for evaluating improved molecular dynamics force fields, and also will enable further development of quantitative relations between side chain chemical shift and structure.

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (ϕ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ(1) rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

Measurement of proton chemical shifts in invisible states of slowly exchanging protein systems by chemical exchange saturation transfer

Chemical exchange saturation transfer (CEST) NMR spectroscopy has emerged as a powerful technique for studies of transiently formed, sparsely populated (excited) conformational states of protein molecules in slow exchange with a dominant structure. The most popular form of the experiment, and the version originally developed, uses a weak (1)H radio frequency field to perturb longitudinal magnetization of one state with the effect transferred to magnetization in the second conformation via chemical exchange. A significant limitation of the method for protein applications emerges from (1)H magnetization transfer via dipolar relaxation (NOE effect) that can severely complicate analysis of the resulting CEST profile. This is particularly an issue since the (1)H chemical shifts of the excited state, critical for structural studies of these elusive conformers, become difficult to extract. Here we present a method for measurement of these shifts via CEST experiments in which the NOE effect is not an issue. The methodology is illustrated through applications to a pair of exchanging systems where the results are cross-validated.

A 2D ¹³C-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding

A 2D (13)C Chemical Exchange Saturation Transfer (CEST) experiment is presented for studying slowly exchanging protein systems using methyl groups as probes. The utility of the method is first established through studies of protein L, a small protein, for which chemical exchange on the millisecond time-scale is not observed. Subsequently the approach is applied to a folding exchange reaction of a G48M mutant Fyn SH3 domain, for which only cross-peaks derived from the folded ('ground') state are present in spectra. Fits of (15)N and methyl (13)C CEST profiles of the Fyn SH3 domain establish that the exchange reaction involves an interchange between folded and unfolded conformers, although elevated methyl (13)C transverse relaxation rates for some of the residues of the unfolded ('invisible, excited') state indicate that it likely exchanges with a third conformation as well. In addition to the kinetics of the exchange reaction, methyl carbon chemical shifts of the excited state are also obtained from analysis of the (13)C CEST data.

An optimized relaxation-based coherence transfer NMR experiment for the measurement of side-chain order in methyl-protonated, highly deuterated proteins

Relaxation violated coherence transfer NMR spectroscopy has emerged as a powerful experimental tool for the quantitative measurement of amplitudes of motion of methyl containing side-chains. Typically, the experiments, performed on proteins that are highly deuterated and methyl-protonated, monitor the build-up of methyl (1)H double-quantum magnetization. Because all three protons in a methyl group are degenerate, such coherences can only result from differential relaxation of transverse magnetization components, which in turn reflect the extent and time-scale of motion of the methyl probe [Tugarinov, V., Sprangers, R.; Kay, L.E. J. Am. Chem. Soc. 2007, 129, 1743-1750]. We show here that a 50% gain in the sensitivity of the experiment can be achieved through selection of (1)H triple-quantum coherence, thereby significantly increasing the utility of the approach. A theoretical treatment rationalizes the sensitivity gain that is subsequently verified through experiment. The utility of the methodology is demonstrated on a number of proteins, including the 360 kDa α(7)α(7) "half-proteasome".

Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein

Histone modifications and DNA methylation represent two layers of heritable epigenetic information that regulate eukaryotic chromatin structure and gene activity. UHRF1 is a unique factor that bridges these two layers; it is required for maintenance DNA methylation at hemimethylated CpG sites, which are specifically recognized through its SRA domain and also interacts with histone H3 trimethylated on lysine 9 (H3K9me3) in an unspecified manner. Here we show that UHRF1 contains a tandem Tudor domain (TTD) that recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). Solution NMR and crystallographic data reveal the TTD simultaneously recognizes H3K9me3 through a conserved aromatic cage in the first Tudor subdomain and unmodified H3K4 within a groove between the tandem subdomains. The subdomains undergo a conformational adjustment upon peptide binding, distinct from previously reported mechanisms for dual histone mark recognition. Mutant UHRF1 protein deficient for H3K4me0/K9me3 binding shows altered localization to heterochromatic chromocenters and fails to reduce expression of a target gene, p16(INK4A), when overexpressed. Our results demonstrate a novel recognition mechanism for the combinatorial readout of histone modification states associated with gene silencing and add to the growing evidence for coordination of, and cross-talk between, the modification states of H3K4 and H3K9 in regulation of gene expression.

Accessing ns-micros side chain dynamics in ubiquitin with methyl RDCs

This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time tau (c). In fact, the average amplitude of motion expressed in terms of order parameters S (2) associated with the supra-tau (c) window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains.

Accurate measurement of methyl 13C chemical shifts by solid-state NMR for the determination of protein side chain conformation: the influenza a M2 transmembrane peptide as an example

The use of side chain methyl (13)C chemical shifts for the determination of the rotameric conformation of Val and Leu residues in proteins by solid-state NMR spectroscopy is described. Examination of the solution NMR stereospecifically assigned methyl groups shows significant correlation between the difference in the two methyl carbons' chemical shifts and the side chain conformation. It is found that alpha-helical and beta-sheet backbones cause different side chain methyl chemical shift trends. In alpha-helical Leu's, a relatively large absolute methyl (13)C shift difference of 2.89 ppm is found for the most populated mt rotamer (chi(1) = -60 degrees, chi(2) = 180 degrees), while a much smaller value of 0.73 ppm is found for the next populated tp rotamer (chi(1) = 180 degrees, chi(2) = 60 degrees). For alpha-helical Val residues, the dominant t rotamer (chi(1) = 180 degrees) has more downfield Cgamma2 chemical shifts than Cgamma1 by 1.71 ppm, while the next populated m rotamer (chi(1) = -60 degrees) shows the opposite trend of more downfield Cgamma1 chemical shift by 1.23 ppm. These significantly different methyl (13)C chemical shifts exist despite the likelihood of partial rotameric averaging at ambient temperature. We show that these conformation-dependent methyl (13)C chemical shifts can be utilized for side chain structure determination once the methyl (13)C resonances are accurately measured by double-quantum (DQ) filtered 2D correlation experiments, most notably the dipolar DQ to single-quantum (SQ) correlation technique. The advantage of the DQ-SQ correlation experiment over simple 2D SQ-SQ correlation experiments is demonstrated on the transmembrane peptide of the influenza A M2 proton channel. The methyl chemical shifts led to predictions of the side chain rotameric states for several Val and Leu residues in this tetrameric helical bundle. The predicted Val rotamers were further verified by dipolar correlation experiments that directly measure the chi(1) torsion angles. It was found that the chemical-shift-predicted side chain conformations are fully consistent with the direct torsion angle results; moreover, the methyl (13)C chemical shifts are sensitive to approximately 5 degrees changes in the chi(1) torsion angle due to drug binding.

Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p

SH3 domains, which are among the most frequently occurring protein interaction modules in nature, bind to peptide targets ranging in length from 7 to more than 25 residues. Although the bulk of studies on the peptide binding properties of SH3 domains have focused on interactions with relatively short peptides (less than 10 residues), a number of domains have been recently shown to require much longer sequences for optimal binding affinity. To gain greater insight into the binding mechanism and biological importance of interactions between an SH3 domain and extended peptide sequences, we have investigated interactions of the yeast Abp1p SH3 domain (AbpSH3) with several physiologically relevant 17-residue target peptide sequences. To obtain a molecular model for AbpSH3 interactions, we solved the structure of the AbpSH3 bound to a target peptide from the yeast actin patch kinase, Ark1p. Peptide target complexes from binding partners Scp1p and Sjl2p were also characterized, revealing that the AbpSH3 uses a common extended interface for interaction with these peptides, despite K(d) values for these peptides ranging from 0.3 to 6 mum. Mutagenesis studies demonstrated that residues across the whole 17-residue binding site are important both for maximal in vitro binding affinity and for in vivo function. Sequence conservation analysis revealed that both the AbpSH3 and its extended target sequences are highly conserved across diverse fungal species as well as higher eukaryotes. Our data imply that the AbpSH3 must bind extended target sites to function efficiently inside the cell.

Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions

Despite the high density within a typical protein fold, the ensemble of sterically permissible side-chain repackings is vast. Here, we examine the extent of this variability that survives energetic biases due to van der Waals interactions, hydrogen bonding, salt bridges, and solvation. Monte Carlo simulations of an atomistic model exhibit thermal fluctuations among a diverse set of side-chain arrangements, even with the peptide backbone fixed in its crystallographic conformation. We have quantified the torsional entropy of this native-state ensemble, relative to that of a noninteracting reference system, for 12 small proteins. The reduction in entropy per rotatable bond due to each kind of interaction is remarkably consistent across this set of molecules. To assess the biophysical importance of these fluctuations, we have estimated side-chain entropy contributions to the binding affinity of several peptide ligands with calmodulin. Calculations for our fixed-backbone model correlate very well with experimentally determined binding entropies over a range spanning more than 80 kJ/(mol x 308 K).

An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of 2H spin relaxation

Protein dynamics is intimately related to biological function. Core dynamics is usually studied with 2H spin relaxation of the 13CDH2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering is axially symmetric. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995-11006.), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15-45 degrees C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries and dynamically by tenfold slower rates of local motion. On average, potential rhombicity decreases, mode-coupling increases, and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 +/- 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 degrees C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences.

Methyl rotation barriers in proteins from 2H relaxation data. Implications for protein structure

Side-chain 2H and backbone 15N relaxation data have been collected at multiple temperatures in the samples of the SH3 domain from alpha-spectrin. Combined analyses of the data allowed for determination of the temperature-dependent correlation times tauf characterizing fast methyl motion. Molecular dynamics simulations confirmed that tauf are dominated by methyl rotation; the corresponding activation energies approximate methyl rotation barriers. For 33 methyl groups in the alpha-spectrin SH3 domain the average barrier height was thus determined to be 2.8 +/- 0.9 kcal/mol. This value is deemed representative of the "fluid" hydrophobic protein core where some barriers are increased and others are lowered because of the contacts with surrounding atoms, but there is no local order that could produce systematically higher (lower) barriers. For comparison, the MD simulation predicts the average barrier of 3.1 kcal/mol (calculated via the potential of mean force) or 3.4-3.5 kcal/mol (rigid barriers after appropriate averaging over multiple MD snapshots). The latter result prompted us to investigate rigid methyl rotation barriers in a series of NMR structures from the Protein Databank. In most cases the barriers proved to be higher than expected, 4-6 kcal/mol. To a certain degree, this is caused by tight packing of the side chains in the NMR structures and stems from the structure calculation procedure where the coordinates are first annealed toward the temperature of 0 K and then subjected to energy minimization. In several cases the barriers >10 kcal/mol are indicative of van der Waals violations. The notable exceptions are (i) the structures solved using the GROMOS force field where tight methyl packing is avoided (3.0-3.6 kcal/mol) and (ii) the structure solved by means of the dynamic ensemble refinement method (Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Nature 2005, 433, 128) (3.5 kcal/mol). These results demonstrate that methyl rotation barriers, derived from the experiments that are traditionally associated with studies of protein dynamics, can be also used in the context of structural work. This is particularly interesting in view of the recent efforts to incorporate dynamics data in the process of protein structure elucidation.

Probing Side-Chain Dynamics in the Proteasome by Relaxation Violated Coherence Transfer NMR Spectroscopy

A pair of experiments is presented for measuring intra-methyl 1H-1H dipolar cross-correlated spin relaxation rates in highly deuterated, methyl protonated proteins with significantly improved sensitivity relative to previously developed experiments that measure dynamics via 1H spin relaxation. In applications to proteins with correlation times in the macromolecular limit, these cross-correlation rates are related directly to order parameters, characterizing the amplitude of motion of methyl-containing side-chains. The experimental approach is validated by comparing extracted order parameters with those obtained via 2H and 13C spin relaxation methods for both protein L (7.5 kDa) and malate synthase G (82 kDa), with excellent correlations obtained. The methodology is applied to study Ile, Leu, and Val side-chain dynamics in a 360 kDa "half-proteasome" complex. In particular, order parameters obtained from the WT complex and from a second complex where the proteasome gating residues are deleted establish that the relative levels of dynamics in each of the two molecules are very similar. It thus becomes clear that there is no communication between gating residues and other regions of the molecule involving pico- to nanosecond time-scale dynamics of these methyl-containing side-chains.

Methyl Dynamics in Proteins from NMR Slowly Relaxing Local Structure Spin Relaxation Analysis: A New Perspective

NMR spin relaxation of (2)H nuclei in (13)CH(2)D groups is a powerful method for studying side-chain motion in proteins. The analysis is typically carried out with the original model-free (MF) approach adapted to methyl dynamics. The latter is described in terms of axial local motions around, and of, the methyl averaging axis, mutually decoupled and independent of the global motion of the protein. Methyl motion is characterized primarily by the axial squared order parameter, S(axis)2, associated with fluctuations of the methyl averaging axis. This view is shown to be oversimplified by applying to typical experimental data the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (Adv. Chem. Phys. 1993, 83, 89) which can be considered the generalization of the MF approach. Neglecting mode coupling and the asymmetry of the local ordering and treating approximately features of local geometry imply inaccurate values of S(axis)2, hence of the residual configurational entropy derived from it. S(axis)2, interpreted as amplitude of motion, was found to range from near disorder to almost complete order. Contrary to this picture, we find with the SRLS approach a moderate distribution in the magnitude of asymmetric local ordering and significant variation in its symmetry. The latter important property can be associated implicitly with the contribution of side-chain rotamer jumps. This is consistent with experimental residual dipolar coupling studies and theoretical work based on molecular dynamics simulations and molecular mechanics considerations. Configurational entropy is obtained in the SRLS approach directly from experimentally determined asymmetric potentials. Inconsistency between order parameters from 2H relaxation and from eta(HC-HH) cross-correlation and increase in order parameters with increasing temperature were observed with the MF approach. These discrepancies are reconciled, and physically tenable temperature dependence is obtained with the SRLS approach.

Accurate prediction of protein torsion angles using chemical shifts and sequence homology

Torsion angle restraints are frequently used in the determination and refinement of protein structures by NMR. These restraints may be obtained by J coupling, cross-correlation measurements, nuclear Overhauser effects (NOEs) or secondary chemical shifts. Currently most backbone (phi/psi) torsion angles are determined using a combination of J(HNHalpha) couplings and chemical shift measurements while most side-chain (chi1) angles and cis/trans peptide bond angles (omega) are determined via NOEs. The dependency on multiple experimental (and computational) methods to obtain different torsion angle restraints is both time-consuming and error prone. The situation could be greatly improved if the determination of all torsion angles (phi, psi, chi and omega) could be made via a single type of measurement (i.e. chemical shifts). Here we describe a program, called SHIFTOR, that is able to accurately predict a large number of protein torsion angles (phi, psi, omega, chi1) using only 1H, 13C and 15N chemical shift assignments as input. Overall, the program is 100x faster and its predictions are approximately 20% better than existing methods. The program is also capable of predicting chi1 angles with 81% accuracy and omega angles with 100% accuracy. SHIFTOR exploits many of the recent developments and observations regarding chemical shift dependencies as well as using information in the Protein Databank to improve the quality of its shift-derived torsion angle predictions. SHIFTOR is available as a freely accessible web server at http://wishart.biology.ualberta.ca/shiftor.

Structural Comparison of the Unstable drkN SH3 Domain and a Stable Mutant†,‡

The N-terminal SH3 domain of the Drosophila adapter protein Drk (drkN SH3 domain) is marginally stable (DeltaG(U) = 1 kcal/mol) and exists in equilibrium between folded and highly populated unfolded states. The single substitution T22G, however, completely stabilizes the protein (DeltaG(U) = 4.0 kcal/mol). To probe the causes of instability of the wild-type (WT) protein and the dramatic stabilization of the mutant, we determined and compared nuclear magnetic resonance structures of the folded WT and mutant drkN SH3 domains. Residual dipolar coupling (RDC) and carbonyl chemical-shift anisotropy (C'-CSA) restraints measured for the WT and T22G domains were used for calculating the structures. The structures for the WT and mutant are highly similar. Thr22 of the WT and Gly22 of the mutant are at the i + 2 position of the diverging, type-II beta-turn. Interestingly, not only Gly22 but also Thr22 successfully adopt an alpha(L) conformation, required at this position of the turn, despite the fact that positive phi values are energetically unfavorable and normally disallowed for threonine residues. Forcing the Thr22 residue into this unnatural conformation increases the free energy of the folded state of the WT domain relative to its T22G mutant. Evidence for residual helix formation in the diverging turn region has been previously reported for the unfolded state of the WT drkN SH3 domain, and this, in addition to other residual structure, has been proposed to play a role in decreasing the free energy of the unfolded state of the protein. Together these data provide evidence that both increasing the free energy of the folded state and decreasing the free energy of the unfolded state of the protein contribute to instability of the WT drkN SH3 domain.

Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cgamma-Hgamma/Cbeta-Hbeta residual dipolar couplings: application to the 34-kDa enzyme IIA(chitobiose)

An isotope labeling scheme is described in which specific protonation of methine and methyl protons of leucine and valine is obtained on a 15N/13C labeled background with uniform deuteration of all other non-exchangeable protons. The presence of a protonated methine group has little effect on the favorable relaxation properties of the methyl protons of Leu and Val. This labeling scheme permits the rotameric state of leucine side-chains to be readily determined by simple inspection of the pattern of Hgamma(i)-H(N)(i) and Hgamma(i)-H(N)(i+1) NOEs in a 3D 15N-separated NOE spectrum free of complications arising from spectral overlap and spin-diffusion. In addition, one-bond residual dipolar couplings for the methine 13C-1H bond vectors of Leu and Val can be accurately determined from an intensity J-modulated constant-time HCCH-COSY experiment and used to accurately orient the side-chains of Leu and Val. Incorporation of these data into structure refinement improves the accuracy with which the conformations of Leu and Val side-chains can be established. This is important to ensure optimal packing both within the protein core and at intermolecular interfaces. The impact of the method on protein structure determination is illustrated by application to enzyme IIA(Chitobiose), a 34 kDa homotrimeric phosphotransferase protein.

Estimating the accuracy of protein structures using residual dipolar couplings

It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H-15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable R values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable R values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR

The dynamic aspect of proteins is fundamental to understanding protein stability and function. One of the goals of NMR studies of side-chain dynamics in proteins is to relate spin relaxation rates to discrete conformational states and the timescales of interconversion between those states. Reported here is a physical analysis of side-chain dynamics that occur on a timescale commensurate with monitoring by 2H spin relaxation within methyl groups. Motivated by observations made from tens-of-nanoseconds long MD simulations on the small protein eglin c in explicit solvent, we propose a simple molecular mechanics-based model for the motions of side-chain methyl groups. By using a Boltzmann distribution within rotamers, and by considering the transitions between different rotamer states, the model semi-quantitatively correlates the population of rotamer states with 'model-free' order parameters typically fitted from NMR relaxation experiments. Two easy-to-use, analytical expressions are given for converting S2 (axis') values (order parameter for C-CH3 bond) into side-chain rotamer populations. These predict that S2 (axis') values below 0.8 result from population of more than one rotameric state. The relations are shown to predict rotameric sampling with reasonable accuracy on the ps-ns timescale for eglin c and are validated for longer timescales on ubiquitin, for which side-chain residual dipolar coupling (RDC) data have been collected.

Measurement of eight scalar and dipolar couplings for methine-methylene pairs in proteins and nucleic acids

A new 3D, spin-state-selective coherence transfer NMR experiment is described that yields accurate measurements for eight scalar or dipolar couplings within a spin system composed of a methylene adjacent to a methine group. Implementations of the experiment have been optimized for proteins and for nucleic acids. The experiments are demonstrated for Cbeta-Calpha moieties of the third IgG-binding domain from Streptococcal Protein G (GB3) and for C5'-C4' groups in a 24-nt RNA oligomer. Chemical shifts of Calpha, Cbeta and Hbeta (respectively C4', C5' and H5') are dispersed in the three orthogonal dimensions, and the absence of heteronuclear decoupling leads to distinct and well-resolved E.COSY multiplet patterns. In an isotropic sample, the E.COSY displacements correspond to 1J(CalphaHalpha), 2J(CalphaHbeta2)+2J(CalphaHbeta3), 2J(CbetaHalpha), 1J(CbetaHbeta2)+1J(CbetaHbeta3), 1J(CbetaHbeta2)-2J(Hbeta2Hbeta3), 1J(CbetaHbeta3)-2J(Hbeta2Hbeta3), 3J(HalphaHbeta2) and 3J(HalphaHbeta3) for proteins, and 1J(C4'H4'), 2J(C4'H5')+2J(C4'H5"), 2J(C5'H4'), 1J(C5'H5')+1J(C5'H5"), 1J(C5'H5')-2J(H5'H5"), 1J(C5'H5")-2J(H5'H5"), 3J(H4'H5') and 3J(H4'H5") in nucleic acids. The experiment, based on relaxation-optimized spectroscopy, yields best results when applied to residues where the methine-methylene group corresponds to a reasonably isolated spin system, as applies for C, F, Y, W, D, N and H residues in proteins, or the C5'-C4' groups in nucleic acids. Splittings can be measured under either isotropic or weakly aligned conditions, yielding valuable structural information both through the 3J couplings and the one-, two- and three-bond dipolar interactions. Dipolar couplings for 10 out of 13 sidechains in GB3 are found to be in excellent agreement with its X-ray structure, whereas one residue adopts a different backbone geometry, and two residues are subject to extensive chi1 rotamer averaging. The abundance of dipolar couplings can also yield stereospecific assignments of the non-equivalent methylene protons. For the RNA oligomer, dipolar data yielded stereospecific assignments for six out of the eight C5'H2 groups in the loop region of the oligomer, in all cases confirmed by 1J(C5'H5')>1J(C5'H5"), and H5' resonating downfield of H5".

Application of residual dipolar couplings in organic compounds

Residual dipolar couplings (RDCs) induced by anisotropic media are a powerful tool for the structure determination of biomolecules through NMR spectroscopy. Recent advances have proven it to be a valuable tool for determination of the stereochemistry of organic molecules. By simple inspection or order matrix calculations, RDCs provide unambiguous information about the relative configurations or complete stereochemistry of organic compounds.

Efficient and precise measurement of H(alpha)-C(alpha), C(alpha)-C', C(alpha)-C(beta) and H(N)-N residual dipolar couplings from 2D H(N)-N correlation spectra

A suite of experiments are presented for the measurement of H(alpha)-C(alpha), C(alpha)-C', C(alpha)-C(beta) and H(N)-N couplings from uniformly 15N, 13C labeled proteins. Couplings are obtained from a series of intensity modulated two-dimensional H(N)-N spectra equivalent to the common 1H-15N-HSQC spectra, alleviating many overlap and assignment issues associated with other techniques. To illustrate the efficiency of this method, H(alpha)-C(alpha), C(alpha)-C', and H(N)-N isotropic scalar couplings were determined for ubiquitin from data collected in less than 4.5 h, C(alpha)-C(beta) data collection required 10 h. The resulting couplings were measured with an average error of +/-0.06, +/-0.05, +/-0.04 and +/-0.10 Hz, respectively. This study also shows H(alpha)-C(alpha) and C(alpha)-C(beta) couplings, valuable because they provide orientation of bond vectors outside the peptide plane, can be measured in a uniform and precise way. Superior accuracy and precision to existing 3D measurements for C(alpha)-C' couplings and increased precision compared to IPAP measurements for H(N)-N couplings are demonstrated. Minor modifications allow for acquisition of modulated H(N)-C' 2D spectra, which can yield additional well resolved peaks and significantly increase the number of measured RDCs for proteins with crowded 1H-15N resonances.

Measurement of one-bond heteronuclear dipolar coupling contributions for amine and diastereotopic methylene protons

One-bond heteronuclear and two-bond homonuclear residual dipolar couplings measured at methylene or amine sites can be utilized as long-range constraints in structure determination of molecules as well as to facilitate characterization of local conformation by stereospecific assignment of diastereotopic protons. We present two J-modulated HMQC type experiments to measure the one-bond heteronuclear dipolar coupling contributions of geminal protons individually. In addition two-bond homonuclear residual dipolar couplings between the diastereotopic protons are also obtained.

Measurements of side-chain 13C-13C residual dipolar couplings in uniformly deuterated proteins

13C-only spectroscopy was used to measure multiple residual (13)C-(13)C dipolar couplings (RDCs) in uniformly deuterated and (13)C-labeled proteins. We demonstrate that (13)C-start and (13)C-observe spectra can be routinely used to measure an extensive set of the side-chain residual (13)C-(13)C dipolar couplings upon partial alignment of human ubiquitin in the presence of bacteriophages Pf1. We establish that, among different broadband polarization transfer schemes, the FLOPSY family can be used to exchange magnetization between a J coupled network of spins while largely decoupling dipolar interactions between these spins. An excellent correlation between measured RDCs and the 3D structure of the protein was observed, indicating a potential use of the (13)C-(13)C RDCs in the structure determination of perdeuterated proteins.

Sensitivity-enhanced IPAP experiments for measuring one-bond 13C'-13Calpha and 13Calpha-1Halpha residual dipolar couplings in proteins

Sensitivity-enhanced 2D IPAP experiments using the accordion principle for measuring one-bond 13C'-13Calpha and 1Halpha-13Calpha dipolar couplings in proteins are presented. The resolution of the resulting spectra is identical to that of the decoupled HSQC spectra and the sensitivity of the corresponding 1D acquisitions are only slightly lower than those obtained with 3D HNCO and 3D HN(COCA)HA pulse sequences due to an additional delay 2Delta. For cases of limited resolution in the 2D 15N-1HN HSQC spectrum the current pulse sequences can easily be modified into 3D versions by introducing a poorly digitized third dimension, if so desired. The experiments described here are a valuable addition to the suites available for determination of residual dipolar couplings in biological systems.

Insights into the mobility of methyl-bearing side chains in proteins from (3)J(CC) and (3)J(CN) couplings

Side-chain dynamics in proteins can be characterized by the NMR measurement of (13)C and (2)H relaxation rates. Evaluation of the corresponding spectral densities limits the slowest motions that can be studied quantitatively to the time scale on which the overall molecular tumbling takes place. A different measure for the degree of side-chain order about the C(alpha)-C(beta) bond (chi(1) angle) can be derived from (3)J(C)(')(-)(C)(gamma) and (3)J(N)(-)(C)(gamma) couplings. These couplings can be measured at high accuracy, in particular for Thr, Ile, and Val residues. In conjunction with the known backbone structures of ubiquitin and the third IgG-binding domain of protein G, and an extensive set of (13)C-(1)H side-chain dipolar coupling measurements in oriented media, these (3)J couplings were used to parametrize empirical Karplus relationships for (3)J(C)(')(-)(C)(gamma) and (3)J(N)(-)(C)(gamma). These Karplus curves agree well with results from DFT calculations, including an unusual phase shift, which causes the maximum (3)J(CC) and (3)J(CN) couplings to occur for dihedral angles slightly smaller than 180 degrees, particularly noticeable in Thr residues. The new Karplus curves permit determination of rotamer populations for the chi(1) torsion angles. Similar rotamer populations can be derived from side-chain dipolar couplings. Conversion of these rotamer populations into generalized order parameters, S(J)(2) and S(D)(2), provides a view of side-chain dynamics that is complementary to that obtained from (13)C and (2)H relaxation. On average, results agree well with literature values for (2)H-relaxation-derived S(rel)(2) values in ubiquitin and HIV protease, but also identify a fraction of residues for which S(J,D)(2) < S(rel)(2). This indicates that some of the rotameric averaging occurs on a time scale too slow to be observable in traditional relaxation measurements.

The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings

Recently developed 2H spin relaxation experiments are applied to study the dynamics of methyl-containing side-chains in the B1 domain of protein L and in a pair of point mutants of the domain, F22L and A20V. X-ray and NMR studies of the three variants of protein L studied here establish that their structures are very similar, despite the fact that the F22L mutant is 3.2kcal/mol less stable. Measurements of methyl 2H spin relaxation rates, which probe dynamics on a picosecond-nanosecond time scale, and three-bond 3J(Cgamma-CO), 3J(Cgamma-N) and 3J(Calpha-Cdelta) scalar coupling constants, which are sensitive to motion spanning a wide range of time-scales, reveal changes in the magnitude of side-chain dynamics in response to mutation. Observed differences in the time-scale of motions between the variants have been related to changes in energetic barriers. Of interest, several of the residues with different motional properties across the variants are far from the site of mutation, suggesting the presence of long-range interactions within the protein that can be probed through studies of dynamics.

High-resolution X-ray and NMR structures of the SMN Tudor domain: conformational variation in the binding site for symmetrically dimethylated arginine residues

The SMN protein, which is linked to spinal muscular atrophy (SMA), plays an important role in the assembly of the spliceosomal small nuclear ribonucleoprotein complexes. This function requires binding of SMN to the arginine-glycine (RG) rich C-terminal tails of the Sm proteins, which contain symmetrically dimethylated arginine residues (sDMA) in vivo. Using NMR titrations, we show that the SMN Tudor domain recognizes these sDMAs in the methylated RG repeats. Upon complex formation a cluster of conserved aromatic residues in the SMN Tudor domain interacts with the sDMA methyl groups. We present two high resolution structures of the uncomplexed SMN Tudor domain, a 1.8A crystal structure and an NMR structure that has been refined against a large number of backbone and side-chain residual dipolar couplings. The backbone conformation of both structures is very similar, however, differences are observed for the cluster of conserved aromatic side-chains in the sDMA binding pocket. In order to validate these variations we introduce a novel application of residual dipolar couplings for aromatic rings. We show that structural information can be derived from aromatic ring residual dipolar couplings, even in the presence of internal motions such as ring flipping. These residual dipolar couplings and ring current shifts independently confirm that the SMN Tudor domain adopts two different conformations in the sDMA binding pocket. The observed structural variations may play a role for the recognition of sDMAs.

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.

Side chain orientation from methyl 1H-1H residual dipolar couplings measured in highly deuterated proteins

High-level deuteration is a prerequisite for the study of high molecular weight systems using liquid-state NMR. Here, we present new experiments for the measurement of proton-proton dipolar couplings in CH(2)D methyl groups of (13)C labeled, highly deuterated (70-80%) proteins. (1)H-(1)H residual dipolar couplings (RDCs) have been measured in two alignment media for 57 out of 70 possible methyl containing residues in the 167-residue flavodoxin-like domain of the E. coli sulfite reductase. These data yield information on the orientation of the methyl symmetry axis with respect to the molecular alignment frame. The alignment tensor characteristics were obtained very accurately from a set of backbone RDCs measured on the same protein sample. To demonstrate that accurate structural information is obtained from these data, the measured methyl RDCs for Valine residues are analyzed in terms of chi(1) torsion angles and stereospecific assignment of the prochiral methyl groups. On the basis of the previously determined backbone solution structure of this protein, the methyl RDC data proved sufficient to determine the chi(1) torsion angles in seven out of nine valines, assuming a single-rotamer model. Methyl RDCs are complementary to other NMR data, for example, methyl-methyl NOE, to determine side chain conformation in high molecular weight systems.