Takuya F. Segawa

Exact Distances and Internal Dynamics of Perdeuterated Ubiquitin from NOE Buildups

It is proposed to convert nuclear Overhauser effects (NOEs) into relatively precise distances for detailed structural studies of proteins. To this purpose, it is demonstrated that the measurement of NOE buildups between amide protons in perdeuterated human ubiquitin using a designed (15)N-resolved HMQC-NOESY experiment enables the determination of (1)H(N)-(1)H(N) distances up to 5 A with high accuracy and precision. These NOE-derived distances have an experimental random error of approximately 0.07 A, which is smaller than the pairwise rmsd (root-mean-square deviation) of 0.24 A obtained with corresponding distances extracted from either an NMR or an X-ray structure (pdb codes: 1D3Z and 1UBQ), and also smaller than the pairwise rmsd between distances from X-ray and NMR structures (0.15 A). Because the NOE contains both structural and dynamical information, a comparison between the 3D structures and NOE-derived distances may also give insights into through-space dynamics. It appears that the extraction of motional information from NOEs by comparison to the X-ray structure or the NMR structure is challenging because the motion may be masked by the quality of the structures. Nonetheless, a detailed analysis thereof suggests motions between beta-strands and large complex motions in the alpha-helix of ubiquitin. The NOE-derived motions are, however, of smaller amplitude and possibly of a different character than those present in a 20 ns molecular dynamic simulation of ubiquitin in water using the GROMOS force field. Furthermore, a recently published set of structures representing the conformational distribution over time scales up to milliseconds (pdb: 2K39) does not satisfy the NOEs better than the single X-ray structure. Hence, the measurement of possibly thousands of exact NOEs throughout the protein may serve as an excellent probe toward a correct representation of both structure and dynamics of proteins.

Exchange Rate Constants of Invisible Protons in Proteins Determined by NMR Spectroscopy

Although labile protons that are exchanging rapidly with those of the solvent cannot be observed directly, their exchange rate constants can be determined by indirect detection of scalar‐coupled neighboring nuclei. We have used heteronuclear NMR spectroscopy to measure the exchange rate constants of labile protons in the side chains of lysine and arginine residues in ubiquitin enriched in carbon‐13 and nitrogen‐15 at neutral pH. Exchange rate constants as fast as 40×103 s−1 were thus measured. These results demonstrate that NMR spectroscopy is a powerful tool for the characterization of lysine NH3+ and arginine NH groups in proteins at physiologically relevant pH values.

Apparent Transverse Relaxation Rates in Systems with Scalar-Coupled Protons

The modulation of spin echoes by homonuclear scalar couplings render the determination of transverse relaxation rates of individual spins difficult, in particular for molecules that are isotopically enriched in (13)C or (15)N, and for all molecules with scalar-coupled protons. To avoid echo modulations, most studies using refocusing pulses have so far been restricted to isolated (1)H, (13)C, or (15)N spins. We report measurements of apparent (1)H transverse relaxation rates of backbone and side-chain protons in Cyclosporin A (CsA) determined by quenching the echo modulations that arise from homonuclear scalar couplings between protons.

Polychromatic Decoupling of a Manifold of Homonuclear Scalar Interactions in Solution‐State NMR

Window-acquired tetrachromatic irradiation allows one to decouple simultaneously four amide protons in cyclosporine A (wavy arrows; see figure) leading to simplified multiplets of the alpha protons. By inserting a manifold of polychromatic pulses in each dwell time, several subsystems can be decoupled simultaneously.

Transverse Relaxation of Scalar-Coupled Protons

In a preliminary communication (B. Baishya, T. F. Segawa, G. Bodenhausen, J. Am. Chem. Soc. 2009, 131, 17538-17539), we recently demonstrated that it is possible to obtain clean echo decays of protons in biomolecules despite the presence of homonuclear scalar couplings. These unmodulated decays allow one to determine apparent transverse relaxation rates R(2) (app) of individual protons. Herein, we report the observation of R(2) (app) for three methyl protons, four amide H(N) protons, and all 11 backbone H(α) protons in cyclosporin A. If the proton resonances overlap, their R(2) (app) rates can be measured by transferring their magnetization to neighboring (13)C nuclei, which are less prone to overlap. The R(2) (app) rates of protons attached to (13)C are faster than those attached to (12)C because of (13)C-(1)H dipolar interactions. The differences of these rates allow the determination of local correlation functions. Backbone H(N) and H(α) protons that have fast decay rates R(2) (app) also feature fast longitudinal relaxation rates R(1) and intense NOESY cross peaks that are typical of crowded environments. Variations of R(2) (app) rates of backbone H(α) protons in similar amino acids reflect differences in local environments.

Determination of transverse relaxation rates in systems with scalar-coupled spins: The role of antiphase coherences

Homogeneous line-widths that arise from transverse relaxation tend to be masked by B0 field inhomogeneity and by multiplets due to homonuclear J-couplings. Besides well-known spin-locking sequences that lead to signals that decay with a rate R1ρ without any modulations, alternative experiments allow one to determine the transverse relaxation rates R2 in systems with scalar-coupled spins. We evaluate three recent strategies by experiment and simulation: (i) moderate-amplitude SITCOM-CPMG sequences (Dittmer and Bodenhausen, 2006), (ii) multiple-quantum filtered (MQF) sequences (Barrère et al., 2011) and (iii) PROJECT sequences (Aguilar et al., 2012). Experiments where the J-evolution is suppressed by spin-locking measure the pure relaxation rate R2(Ix) of an in-phase component. Experiments based on J-refocusing yield a mixture of in-phase rates R2(Ix) and antiphase rates R2(2IySz), where the latter are usually faster than the former. Moderate-amplitude SITCOM-CPMG and PROJECT methods can be applied to systems with many coupled spins, but applications of MQF sequences are limited to two-spin systems since modulations in larger systems can only partly be suppressed.

Apparent transverse relaxation rates in systems with coupled carbon-13 spins

In systems with homonuclear scalar couplings, the envelopes of spin echoes obtained with simple refocusing pulses or trains of such pulses are normally modulated so that it is difficult to extract transverse relaxation rates. It has been shown recently that echo modulations can be quenched by cumulative pulse errors that arise after applying a large number of refocusing pulses with moderate rf amplitudes. The resulting unmodulated decays allow one to extract apparent transverse relaxation rates. Early work on systems comprising only two nitrogen-15 nuclei or two carbon-13 spins has recently been extended to systems with coupled protons. This work focuses on systems with three coupled carbon-13 spins, which in turn are coupled to several neighbouring protons. Unmodulated echo trains can be obtained by optimizing the pulse interval, the carrier frequency and the rf amplitude of the refocusing pulses.

Quenching homonuclear couplings in magnetic resonance by trains of non-refocusing pulses.

Trains of 2π or 4π pulses fail to refocus offsets but can suppress the effects of bilinear interactions such as homonuclear scalar couplings.

Control of Cross Relaxation of Multiple-Quantum Coherences Induced by Fast Chemical Exchange under Heteronuclear Double-Resonance Irradiation

A fully analytical description of the control of the cross-correlated cross relaxation of multiple-quantum coherences in the presence of local dynamics under heteronuclear double-resonance radio-frequency (RF) irradiation is presented. The contribution of chemical exchange to relaxation can be partly or fully quenched by RF fields. We assume a correlated two-site chemical exchange model with arbitrary populations, and show that in the limit of fast exchange the dependence of the effective multiple-quantum cross-relaxation rate on the applied RF amplitude can be described by a compact analytical expression. Numerical simulations and preliminary experiments support our theoretical results. The relaxation dispersion as a function of RF amplitude can provide accurate information on the kinetics of correlated processes.