Suppression of diagonal peaks in three-dimensional protein NMR TROSY-type HCCH correlation experiments

A novel method for suppression of (13)C-(13)C diagonal peaks without sensitivity loss in three-dimensional HCCH TROSY-type NMR correlation experiments involving aromatic side chains in proteins (Pervushin et al., J. Am. Chem. Soc. 120, 6394-6400 (1998)) is presented. The key element is a spin-state-selective filter in the (13)C-(13)C mixing sequence with the dual effect of selecting the TROSY resonance in the preceding evolution period and interchanging TROSY and anti-TROSY resonances. The cross peaks are invariant to this filter but diagonal peak coherence gets concentrated on the anti-TROSY transition so that it can be eliminated by a (13)C --> (1)H TROSY transfer element. The new method is demonstrated using a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz.     

Optimization of three-dimensional TROSY-type HCCH NMR correlation of aromatic (1)H-(13)C groups in proteins.

Improved methods for three-dimensional TROSY-Type HCCH correlation involving protons of negligible CSA are presented. The TROSY approach differs from the conventional approach of heteronuclear decoupling in evolution and detection periods by not mixing fast and slowly relaxing coherences and usually suppressing the former. Pervushin et al. (J. Am. Chem. Soc. 120, 6394-6400 (1998)) have proposed a 3D TROSY-type HCCH experiment where the TROSY approach is applied only in one of the (13)C dimensions. A new pulse sequence applying the TROSY approach in both indirect dimensions is advantageous when the TROSY effect of the carbons is large or when a relatively high resolution is required. For lower resolutions or moderate TROSY effects we show that it is possible to combine the best of both worlds, namely to suppress heteronuclear couplings without mixing fast and slowly relaxing coherences while at the same time superimpose the two components and thus have both contribute to the detected signal. That is possible using the novel technique of Spin-State-Selective Time-Proportional Phase Incrementation (S(3) TPPI). The new 3D S(3) TPPI TROSY HCCH method is demonstrated on a (13)C,(15)N-labeled protein sample, RAP 18-112 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein), at 750 MHz and average sensitivity enhancements of 10% are obtained for the cross peaks in comparison to methods based on conventional decoupling on one of the carbons or on TROSY on both carbons.     

Optimization of Three-Dimensional TROSY-Type HCCH NMR Correlation of Aromatic H–C Groups in Proteins

Improved methods for three-dimensional TROSY-Type HCCH correlation involving protons of negligible CSA are presented. The TROSY approach differs from the conventional approach of heteronuclear decoupling in evolution and detection periods by not mixing fast and slowly relaxing coherences and usually suppressing the former. Pervushin et al. (J. Am. Chem. Soc. 120, 6394–6400 (1998)) have proposed a 3D TROSY-type HCCH experiment where the TROSY approach is applied only in one of the ¹³C dimensions. A new pulse sequence applying the TROSY approach in both indirect dimensions is advantageous when the TROSY effect of the carbons is large or when a relatively high resolution is required. For lower resolutions or moderate TROSY effects we show that it is possible to combine the best of both worlds, namely to suppress heteronuclear couplings without mixing fast and slowly relaxing coherences while at the same time superimpose the two components and thus have both contribute to the detected signal. That is possible using the novel technique of Spin-State-Selective Time-Proportional Phase Incrementation (S³ TPPI). The new 3D S³ TPPI TROSY HCCH method is demonstrated on a ¹³C,¹⁵N-labeled protein sample, RAP 18–112 (N-terminal domain of α₂-macroglobulin receptor associated protein), at 750 MHz and average sensitivity enhancements of 10% are obtained for the cross peaks in comparison to methods based on conventional decoupling on one of the carbons or on TROSY on both carbons.     

Quantum entanglement formation by repeated spin blockade measurements in a spin field-effect transistor structure embedded with quantum dots

We propose a method of operating a quantum state machine made of stacked quantum dots buried in adjacent to the channel of a spin field-effect transistor (FET) [S. Datta, B. Das, Appl. Phys. Lett. 56 (1990) 665; K. Yoh, et al., Proceedings of the 23rd International Conference on Physics of Semiconductors (ICPS) 2004; H. Ohno, K. Yoh et al., Jpn. J. Appl. Phys. 42 (2003) L87; K. Yoh, J. Konda, S. Shiina, N. Nishiguchi, Jpn. J. Appl. Phys. 36 (1997) 4134]. In this method, a spin blockade measurement extracts the quantum state of a nearest quantum dot through Coulomb blockade [K. Yoh, J. Konda, S. Shiina, N. Nishiguchi, Jpn. J. Appl. Phys. 36 (1997) 4134; K. Yoh, H. Kazama, Physica E 7 (2000) 440] of the adjacent channel conductance. Repeated quantum Zeno-like (QZ) measurements [H. Nakazato, et al., Phys. Rev. Lett. 90 (2003) 060401] of the spin blockade is shown to purify the quantum dot states within several repetitions. The growth constraints of the stacked InAs quantum dots are shown to provide an exchange interaction energy in the range of 0.01–1 meV [S. Itoh, et al., Jpn. J. Appl. Phys. 38 (1999) L917; A. Tackeuchi, et al., Jpn. J. Appl. Phys. 42 (2003) 4278]. We have verified that one can reach the fidelity of 90% by repeating the measurement twice, and that of 99.9% by repeating only eleven QZ measurements. Entangled states with two and three vertically stacked dots are achieved with the sampling frequency of the order of 100 MHz.     

Sensitive detection and separation of fluorescent derivatives using capillary electrophoresis with laser-induced fluorescence detection with 532 nm Nd:YAG laser

Capillary electrophoresis with laser-induced fluorescence detection (CELIF) is a powerful tool for separation and sensitive determination of fluorescent species. Biologically active compounds, such as amino acids, peptides and proteins may exhibit native fluorescence, which is however often low and/or an expensive laser is required for excitation in UV. Therefore, labelling of the analytes with a fluorescent dye is usually necessary.In this work, a home-built CELIF instrument with diode pumped frequency-doubled continuous wave Nd:YAG excitation laser with feedback power regulation (532 nm) was constructed. The suitability of this type of laser for LIF detection in a separation method was found excellent. A limit of detection (LOD) (S/N=3) of 2×10⁻¹³ mol/l was achieved with rhodamine B, which is comparable to those obtained using similar instruments with Ar⁺ laser [Y.F. Cheng, N.J. Dovichi, Science 242 (1988) 562, E.S. Yeung et al., J. Chromatogr. 608 (1992) 73]. LOD of a protein derivatized according to modified procedures [M.J. Little et al., Anal. Chim. Acta 339 (1997) 279, A. Chersi et al., Biochim. Biophys. Acta 1336 (1997) 83] was determined. Detection of the derivatives was found to be limited by insufficient reaction recovery at low analyte concentration, chemical noise, separation efficiency and quality of the derivatizing reagent rather than by the detector performance. As a consequence, a huge gap between the detection ability of CELIF instruments and LOD determined in real samples is revealed.     

Determination of internucleotide (h)J(HN) couplings by the modified 2D J(NN)-correlated [(15)N, (1)H] TROSY

Recent developments in the direct observation of J couplings across hydrogen bonds in proteins and nucleic acids provide additional information for structure and function studies of these molecules by NMR spectroscopy. A J(NN)-correlated [(15)N, (1)H] TROSY experiment proposed by Pervushin et al. (Proc. Natl. Acad. Sci. USA 95, 14147-14151, 1998) can be applied to measure (h)J(HN) in smaller nucleic acids in an E.COSY manner. However, it cannot be effectively applied to large nucleic acids, such as tRNA(Trp), since one of the peaks corresponding to a fast relaxing component will be too weak to be observed in the spectra of large molecules. In this Communication, we proposed a modified J(NN)-correlated [(15)N, (1)H] TROSY experiment which enables direct measurement of (h)J(HN) in large nucleic acids.     

Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes

A couple of recent applications of intermolecular NOE (INOE) experiments as applied to biomolecular systems involve the (i) saturation transfer difference NMR (STD-NMR) method and (ii) the intermolecular cross-saturation NMR (ICS-NMR) experiment. STD-NMR is a promising tool for rapid screening of a large library of compounds to identify bioactive ligands binding to a target protein. Additionally, it is also useful in mapping the binding epitopes presented by a bioactive ligand to its target protein. In this latter application, the STD-NMR technique is essentially similar to the ICS-NMR experiment, which is used to map protein-protein or protein-nucleic acid contact surfaces in complexes. In this work, we present a complete relaxation and conformational exchange matrix (CORCEMA) theory (H. N. B. Moseley et al., J. Magn. Reson. B 108, 243-261 (1995)) applicable for these two closely related experiments. As in our previous work, we show that when exchange is fast on the relaxation rate scale, a simplified CORCEMA theory can be formulated using a generalized average relaxation rate matrix. Its range of validity is established by comparing its predictions with those of the exact CORCEMA theory which is valid for all exchange rates. Using some ideal model systems we have analyzed the factors that influence the ligand proton intensity changes when the resonances from some protons on the receptor protein are saturated. The results show that the intensity changes in the ligand signals in an intermolecular NOE experiment are very much dependent upon: (1) the saturation time, (2) the location of the saturated receptor protons with respect to the ligand protons, (3) the conformation of the ligand-receptor interface, (4) the rotational correlation times for the molecular species, (5) the kinetics of the reversibly forming complex, and (6) the ligand/receptor ratio. As an example of a typical application of the STD-NMR experiment we have also simulated the STD effects for a hypothetical trisaccharide bound to a protein. The CORCEMA theory for INOE and the associated algorithm are useful in a quantitative interpretation of the intensity changes in the ligand in both the STD-NMR and ICS-NMR, provided the identity of the receptor protons experiencing direct RF saturation is known. The formalism presented here is likely to be useful in the design of bioactive ligands to a specific target protein and in the quantitative mapping of binding epitopes and interfaces between molecules in complexes.     

A modified diffusion equation for room-acoustic predication

This letter presents a modified diffusion model using an Eyring absorption coefficient to predict the reverberation time and sound pressure distributions in enclosures. While the original diffusion model [Ollendorff, Acustica 21, 236-245 (1969); J. Picaut et al., Acustica 83, 614-621 (1997); Valeau et al., J. Acoust. Soc. Am. 119, 1504-1513 (2006)] usually has good performance for low absorption, the modified diffusion model yields more satisfactory results for both low and high absorption. Comparisons among the modified model, the original model, a geometrical-acoustics model, and several well-established theories in terms of reverberation times and sound pressure level distributions, indicate significantly improved prediction accuracy by the modification.     

X-filtering for a range of coupling constants: application to the detection of intermolecular NOEs

A new method for heteronuclear X-filtering is presented, which relies on repetitive applications of 90 degrees (1H)-tau(1/41J(HC))-180 degrees (1H,13C)-tau(1/41J(HC))-90 degrees (1H,13C)-PFG building blocks employing gradient-mediated suppression of magnetization built up for directly heteronuclear coupled protons. Thereby, a range of heteronuclear coupling constants can be suppressed by varying the delays of scalar coupling evolution both within and between individual transients. To achieve efficient destruction of 13C-coupled protons in macromolecular systems, the scalar coupling evolution delays were optimized using simulated annealing by including transverse relaxation effects. With a combination of regular hard pulses, delays and pulsed field gradients only, this method yields sufficient X-filtering to allow the observation of intermolecular nuclear overhauser effects in a molecular complex consisting of a 13C, 15N double-labeled, and an unlabeled protein. This is achieved by exciting magnetization of 12C- and 14N-bound protons and detecting 13C-bound 1H magnetization in a 3D 13C-filtered, 13C-edited NOESY-HSQC experiment. The method is tested on the 18 kDa homodimeric bacterial antidote ParD.     

Anomalous Vibrational Dependence of the Rotational and Hyperfine Parameters in the B(4)Pi-X(4)Sigma(-) Transition of NbO

The laser excitation spectrum of jet-cooled NbO in the region 16 000-18 000 cm(-1) has been recorded at high resolution, giving rotational and hyperfine constants for the levels v=0-3 of the B(4)Pi state and v=1 of the X(4)Sigma(-) state; zero gaps have also been measured at low resolution for some weaker bands involving higher vibrational levels. Taken together with the laser data for the B-X (0,0) band from Adam et al. (J. Chem. Phys. 94, 6240-6262 (1994)) and the Fourier transform emission data for the doublet manifold from Launila et al. (J. Mol. Spectrosc. 186, 131-143 (1997)), the new data give a very complete picture of the vibrational energy level pattern in this region. Strong irregularities in the vibrational dependences of the B(4)Pi rotational and hyperfine constants can be interpreted in terms of spin-orbit interaction between the B(4)Pi state and the f(2)Pi, e(2)Phi, and d(2)Delta states. The interaction is strong enough that all three doublet states can be seen in absorption from the X(4)Sigma(-) ground state, adding to the complexity of the spectrum. The hitherto unknown sigmadeltasigma* (4)Delta state is estimated to lie near 17 500 cm(-1), from the change of sign in the spin-rotation parameter gamma of the B(4)Pi state between v=2 and 3. Copyright 2001 Academic Press.     

Target strength of an oily deep-water fish, orange roughy (Hoplostethus atlanticus). II. Modeling

Orange roughy consist of approximately 18% lipids by weight, mostly as wax esters, and the lipids must be taken into account when modeling target strength. A deformed cylinder model incorporating the effect of temperature and pressure on sound speed through wax ester was used to scale experimental measurements of target strength to the temperatures and pressures where orange roughy live (approximately 6 degrees C, depths approximately 800-1300 m). The effect of decreasing temperature and increasing pressure is to increase the sound speed in orange roughy lipids. Modeling shows that the net effect of this is to reduce tilt-averaged target strength, 'TS', by approximately 2 dB. Adjusting experimental results to compensate for temperature and pressure effects gives a predicted 'TS' for a 35-cm orange roughy of -48.3 dB. Adjusting in situ estimates of orange roughy 'TS' for avoidance behavior [McClatchie et al., J. Acoust. Soc. Am. 106, 131-142 (1999)] suggests the correct 'TS' is approximately -47.5 dB, rather than -50 dB as previously reported [Kloser et al., ICES J. Mar. Sci. 54, 60-71 (1997)]. We conclude that experimental and in situ estimates now converge at a 'TS' of approximately -48 dB for a 35-cm fish.     

Through-Bond Correlation of Sugar and Base Protons in Unlabeled Nucleic Acids

This work presents two methods for through-bond correlation between sugar and base protons in view of model-independent assignment in unlabeled or slightly enriched nucleic acids. Each method uses a combination of multiple-bond and one-bond heteronuclear J-couplings to the aromatic carbon C6 for pyrimidines ((3)J(H1',C6) and (1)J(H6,C6)) or C8 for purines ((3)J(H1',C8) and (1)J(H8,C8)). The techniques are demonstrated in the duplex [d(CGCGAATTCGCG)](2) and the dimeric G-quadruplex [d(GGGTTCAGG)](2) at natural abundance.     

Sensitivity enhancement of HCACO by using an HMQC magnetization transfer scheme

Previous theoretical calculations have demonstrated that the multiquantum relaxation rate of (1)H(alpha)-(13)C(alpha)(R(MQ)) is, on average, 1.3 +/- 0.4 or 1.7 +/- 0.6 times slower than the single-quantum relaxation rate of (13)C(alpha)(R(C)) for a sample with or without, respectively, amide protons. By taking advantage of this fact and by using the PEP sensitivity enhancement scheme, an HMQC version of the HCACO experiment has been developed. We demonstrate that this new experiment is 23 and 55% more sensitive than the original HSQC version of the HCACO experiment, at constant times of 7 and 27 ms, respectively, for a sample of the BC domain of the ciliary neurotrophic factor receptor protein dissolved in D(2)O at 20 degrees C.     

Cochlear power flux as an indicator of mechanical activity

The question of whether one can conclude just from basilar membrane (BM) vibration data that the cochlea is an active mechanical system is addressed. To this end, a method is developed which computes the power flux through a channel cross section of a short-wave cochlear model from a given BM vibration pattern. The power flux is an important indicator of mechanical activity because a rise in this function corresponds to creation of mechanical energy. The power flux method is applied to BM velocity patterns as measured by Johnstone and Yates [J. Acoust. Soc. Am. 55, 584-587 (1974)] and by Sellick et al. [Hear. Res. 10, 101-108 (1983)] in the guinea pig and by Robles et al. [Peripheral Auditory Mechanisms, edited by J.B. Allen, J.L. Hall, A.E. Hubbard, S.T. Neely, and A. Tubis (Springer, New York, 1986a), pp. 121-128, and J. Acoust. Soc. Am. 80, 1364-1374 (1986b)] in the chinchilla. Before the calculations are performed, the BM data are interpolated and smoothed in order to avoid numerical errors as a result of too few and noisy data points. The choice of the smoothing method influences the computed power flux function considerably. Nevertheless, the calculations appear to make a clear distinction between the "old" data, showing broad BM tuning (Johnstone and Yates, 1974), and the "new" data, in which the response is much more peaked (Sellick et al., 1983; Robles et al., 1986a, b). The former do not give rise to a significant increase of the power flux; the latter do, although less convincingly for the Sellick et al. (1983) data than for the Robles et al. (1986a,b) data. It is thus concluded that the recently obtained, sharply tuned BM responses reflect the presence of mechanical activity in the cochlea.     

Acoustic properties of naturally produced clear speech at normal speaking rates

Sentences spoken "clearly" are significantly more intelligible than those spoken "conversationally" for hearing-impaired listeners in a variety of backgrounds [Picheny et al., J. Speech Hear. Res. 28, 96-103 (1985); Uchanski et al., ibid. 39, 494-509 (1996); Payton et al., J. Acoust. Soc. Am. 95, 1581-1592 (1994)]. While producing clear speech, however, talkers often reduce their speaking rate significantly [Picheny et al., J. Speech Hear. Res. 29, 434-446 (1986); Uchanski et al., ibid. 39, 494-509 (1996)]. Yet speaking slowly is not solely responsible for the intelligibility benefit of clear speech (over conversational speech), since a recent study [Krause and Braida, J. Acoust. Soc. Am. 112, 2165-2172 (2002)] showed that talkers can produce clear speech at normal rates with training. This finding suggests that clear speech has inherent acoustic properties, independent of rate, that contribute to improved intelligibility. Identifying these acoustic properties could lead to improved signal processing schemes for hearing aids. To gain insight into these acoustical properties, conversational and clear speech produced at normal speaking rates were analyzed at three levels of detail (global, phonological, and phonetic). Although results suggest that talkers may have employed different strategies to achieve clear speech at normal rates, two global-level properties were identified that appear likely to be linked to the improvements in intelligibility provided by clear/normal speech: increased energy in the 1000-3000-Hz range of long-term spectra and increased modulation depth of low frequency modulations of the intensity envelope. Other phonological and phonetic differences associated with clear/normal speech include changes in (1) frequency of stop burst releases, (2) VOT of word-initial voiceless stop consonants, and (3) short-term vowel spectra.     

Determination of J coupling constants between spin-1/2 and quadrupolar nuclei in inorganic solids from spin echo and refocused INEPT experiments: a case study on AlPO₄ berlinite

A systematic study utilizing rotor-synchronized homonuclear ((31)P, (27)Al) and heteronuclear ({(31)P}(27)Al and {(27)Al}(31)P) spin echo, and {(27)Al}(31)P refocused INEPT experiments (employing soft pulses for selective excitation of the central transition for the quadrupolar (27)Al (I=5/2)) have been performed on AlPO(4) berlinite at 30 kHz MAS to better understand the J modulation behavior involving half-integer quadrupolar nuclei in solid materials with framework structure. Analyses of the J modulation on either the (27)Al or (31)P coherence in both the {(31)P}(27)Al and {(27)Al}(31)P spin echo experiments, and both periods of the refocused INEPT experiment yield consistent results for the (2)J(AlP) (Al-O-P) coupling constant (ca. 25 Hz). It is noted that the coupling of each (27)Al to four (31)P spins during the first ((27)Al) evolution period of the refocused INEPT, and the populations of (31)P coupled to different numbers (0-4) of (27)Al in the ± 1/2 Zeeman states during (31)P coherence evolution, which have been neglected in previous studies, must be taken into account for proper treatment. Analysis of J modulation on the spin ((27)Al) coupled to spin-1/2 nuclei in general gives more accurate results. Weak long-range homonuclear (4)J(PP) (P-O-Al-O-P) coupling was also observed from the (31)P spin echo and INADEQUATE experiments.     

Effects of subfemtosecond quantum correlations in neutron scattering on water

Several recent experiments have shown that protons, and to some extent also deuterons, show anomalous cross sections when the neutrons have energies in the range 10-100 eV (this results in a Compton scattering process where an essential part of the energy is transferred to one of the scattering particles). Here, an experiment on partially deuterated water, carried out by Chatzidimitriou-Dreismann et al., is analyzed in terms of a theory, which assumes that during the short duration (<10(-15) s) of this scattering process, protons are exchange correlated and cannot be considered as independent scattering objects. The quantum decoherence time for protons in liquid water is estimated from a simple model for the interaction of the water protons with hydrogen bonds.     

Angular Distributions for

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Improved measurement of (3)J(H(alpha)(i),N(i+1)) coupling constants in H(2)O dissolved proteins.

A modification to the recently proposed alpha/beta-HN(CO)CA-J TROSY pulse sequence (P. Permi et al., J. Magn. Reson. 146, 255-259 (2000)) makes it possible to determine (3)J(H(alpha)(i), N(i+1)) coupling constants from a single E.COSY-type cross-peak pattern rather than from two (1)H(alpha) spin-state-edited subspectra. Advantages are increased (15)N resolution, critical to extracting accurate (1)H(alpha)-(15)N coupling constants, and minimized differential relaxation due to nested (13)C(alpha) and (15)N evolution periods. Application of the improved pulse sequence to Desulfovibrio vulgaris flavodoxin results in (3)J(H(alpha)(i), N(i+1)) values being systematically larger than those obtained with the original scheme. Parametrization of the coupling dependence on the protein backbone torsion angle psi yields the Karplus relation (3)J(H(alpha)(i), N(i+1))=-1.00 cos(2)(psi-120 degrees )+0.65 cos(psi-120 degrees )-0.15 Hz, with a residual root-mean-square difference of 0.13 Hz between measured and back-calculated coupling constants. The curve compares with data derived from ubiquitin (A. C. Wang and A. Bax, J. Am. Chem. Soc. 117, 1810-1813 (1995)), although spanning a slightly larger range of J values in flavodoxin. The orientation of the Ala39/Ser40 peptide link, forming a type-II beta-turn in flavodoxin, is twisted against X-ray-derived torsions by approximately 10 degrees in the NMR structure as evident from the analysis of straight phi- and psi-related (3)J coupling constants. The remaining deviation of some experimental values from the prediction is likely to be due to strong hydrogen bonding, substituent effects, or the additional dependence on the adjacent torsions straight phi.     

3D HCCH(3)-TOCSY for resonance assignment of methyl-containing side chains in (13)C-labeled proteins

Two 3D experiments, (H)CCH(3)-TOCSY and H(C)CH(3)-TOCSY, are proposed for resonance assignment of methyl-containing amino acid side chains. After the initial proton-carbon INEPT step, during which either carbon or proton chemical shift labeling is achieved (t(1)), the magnetization is spread along the amino acid side chains by a carbon spin lock. The chemical shifts of methyl carbons are labeled (t(2)) during the following constant time interval. Finally the magnetization is transferred, in a reversed INEPT step, to methyl protons for detection (t(3)). The proposed experiments are characterized by high digital resolution in the methyl carbon dimension (t(2max) = 28.6 ms), optimum sensitivity due to the use of proton decoupling during the long constant time interval, and an optional removal of CH(2), or CH(2) and CH, resonances from the F(2)F(3) planes. The building blocks used in these experiments can be implemented in a range of heteronuclear experiments focusing on methyl resonances in proteins. The techniques are illustrated using a (15)N, (13)C-labeled E93D mutant of Schizosacharomyces pombe phosphoglycerate mutase (23.7 kDa).