Magic‐Angle‐Pulse Driven Separation of Degenerate 1 H Transitions in Methyl Groups of Proteins: Application to Studies of Methyl Axis Dynamics

Precision measurements of relaxation rates of degenerate 1H transitions in methyl groups of small proteins

An NMR experiment is designed for accurate and robust measurement of transverse relaxation rates of degenerate 1H transitions in selectively 13CH3-labeled, deuterated small proteins. The measurement is based on the use of acute (<90°) angle 1H radio-frequency pulses and relies on selection of the slow- and fast-relaxing components of methyl magnetization following the relaxation period in separate experiments. The R2 decay series recorded with selection of the fast-relaxing components serves as a useful complement to the R2 series acquired with selection of the slow-relaxing part, and permits the extension of the range of relative contributions of the fast- and slow-relaxing parts to apparent signal decay. The approach is experimentally verified on 13CH3 methyl groups of the ILV-{13CH3}-labeled protein ubiquitin at 10 °C and 25 °C. The obtained methyl 1H relaxation rates are in remarkably good agreement with the values obtained from well-established NMR techniques.

Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy

Molecular chaperones are the guardians of the proteome inside the cell. Chaperones recognize and bind unfolded or misfolded substrates, thereby preventing further aggregation; promoting correct protein folding; and, in some instances, even disaggregating already formed aggregates. Chaperones perform their function by means of an array of weak protein-protein interactions that take place over a wide range of timescales and are therefore invisible to structural techniques dependent upon the availability of highly homogeneous samples. Nuclear magnetic resonance (NMR) spectroscopy, however, is ideally suited to study dynamic, rapidly interconverting conformational states and protein-protein interactions in solution, even if these involve a high-molecular-weight component. In this review, we give a brief overview of the principles used by chaperones to bind their client proteins and describe NMR methods that have emerged as valuable tools to probe chaperone-substrate and chaperone-chaperone interactions. We then focus on a few systems for which the application of these methods has greatly increased our understanding of the mechanisms underlying chaperone functions. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Observation of Sub-Microsecond Protein Methyl-Side Chain Dynamics by Nanoparticle-Assisted NMR Spin Relaxation

Amino-acid side-chain properties in proteins are key determinants of protein function. NMR spin relaxation of side chains is an important source of information about local protein dynamics and flexibility. However, traditional solution NMR relaxation methods are most sensitive to sub-nanosecond dynamics lacking information on slower ns-μs time-scale motions. Nanoparticle-assisted NMR spin relaxation (NASR) of methyl-side chains is introduced here as a window into these ns-μs dynamics. NASR utilizes the transient and nonspecific interactions between folded proteins and slowly tumbling spherical nanoparticles (NPs), whereby the increase of the relaxation rates reflects motions on time scales from ps all the way to the overall tumbling correlation time of the NPs ranging from hundreds of ns to μs. The observed motional amplitude of each methyl group can then be expressed by a model-free NASR S² order parameter. The method is demonstrated for ²H-relaxation of CH₂D methyl moieties and cross-correlated relaxation of CH₃ groups for proteins Im7 and ubiquitin in the presence of anionic silica-nanoparticles. Both types of relaxation experiments, dominated by either quadrupolar or dipolar interactions, yield highly consistent results. Im7 shows additional dynamics on the intermediate time scales taking place in a functionally important loop, whereas ubiquitin visits the majority of its conformational substates on the sub-ns time scale. These experimental observations are in good agreement with 4-10 μs all-atom molecular dynamics trajectories. NASR probes side-chain dynamics on a much wider range of motional time scales than previously possible, thereby providing new insights into the interplay between protein structure, dynamics, and molecular interactions that govern protein function.

The measurement of relaxation rates of degenerate 1H transitions in methyl groups of proteins using acute angle radiofrequency pulses

A simple NMR experiment for the measurement of transverse relaxation rates of degenerate ¹H spins in ¹³CH₃ methyl groups of deuterated proteins, is described. The experiment relies on the use of acute-angle ¹H radio-frequency pulses, whereby a series of methyl ¹H R₂ decays is acquired with different values of the ¹H pulse flip-angle, which modulates the relative contributions of the slow- and fast-relaxing components of ¹H magnetization during the relaxation delay. These are subsequently analyzed simultaneously to extract the transverse relaxation rates of both components (R_S and R_F), along with the rate of cross-relaxation between these components, δ. The dipolar ¹H-¹H cross-correlated relaxation rate η = (R_F - R_S)/2 and the cross-relaxation rate δ, extracted from such acute-angle-pulse R₂ decay series are compared with those derived from well-established methodology that uses relaxation-violated methyl ¹H coherence transfer (so-called 'forbidden' experiments). Good agreement is achieved for the rates η derived from the two techniques, while slightly more accurate values of δ are obtained from analysis of acute-angle-pulse R₂ series. Recording of acute-angle-pulse R₂ series represents an attractive alternative to existing methodologies for quantifying methyl ¹H relaxation and dynamics of the methyl three-fold symmetry axis in selectively [¹³CH₃]-methyl-labeled, deuterated proteins - particularly so for very high-molecular-weight proteins, where the measurements of R_F rates or the build-up of methyl ¹H magnetization in relaxation-violated coherence transfer experiments, are problematic due to low sensitivity.

Methodological advancements for characterising protein side chains by NMR spectroscopy

The surface of proteins is covered by side chains of polar amino acids that are imperative for modulating protein functionality through the formation of noncovalent intermolecular interactions. However, despite their tremendous importance, the unique structures of protein side chains require tailored approaches for investigation by nuclear magnetic resonance spectroscopy and so have traditionally been understudied compared with the protein backbone. Here, we review substantial recent methodological advancements within nuclear magnetic resonance spectroscopy to address this issue. Specifically, we consider advancements that provide new insight into methyl-bearing side chains, show the potential of using non-natural amino acids and reveal the actions of charged side chains. Combined, the new methods promise unprecedented characterisations of side chains that will further elucidate protein function.

Optimal design of adaptively sampled NMR experiments for measurement of methyl group dynamics with application to a ribosome-nascent chain complex

NMR measurements of cross-correlated nuclear spin relaxation provide powerful probes of polypeptide dynamics and rotational diffusion, free from contributions due to chemical exchange or interactions with external spins. Here, we report on the development of a sensitivity-optimized pulse sequence for the analysis of the differential relaxation of transitions within isolated ¹³CH₃ spin systems, in order to characterise rotational diffusion and side chain order through the product S²τ_c. We describe the application of optimal design theory to implement a real-time 'on-the-fly' adaptive sampling scheme that maximizes the accuracy of the measured parameters. The increase in sensitivity obtained using this approach enables quantitative measurements of rotational diffusion within folded states of translationally-arrested ribosome-nascent chain complexes of the FLN5 filamin domain, and can be used to place strong limits on interactions between the domain and the ribosome surface.

Probing Side-Chain Dynamics in Proteins by NMR Relaxation of Isolated 13C Magnetization Modes in 13CH3 Methyl Groups

The dynamics of methyl-bearing side chains in proteins were probed by ¹³C relaxation measurements of a number of ¹³C magnetization modes in selectively ¹³CH₃-labeled methyl groups of proteins. We first show how ¹³C magnetization modes in a ¹³CH₃ spin-system can be isolated using acute-angle ¹H radio-frequency pulses. The parameters of methyl-axis dynamics, a measure of methyl-axis ordering (S_axis²) and the correlation time of fast local methyl-axis motions (τ_f), derived from ¹³C relaxation in ¹³CH₃ groups are compared with their counterparts obtained from ¹³C relaxation in ¹³CHD₂ methyl isotopomers. We show that in high-molecular-weight proteins, excellent correlations are obtained between the [¹³CHD₂]-derived S_axis² values and those extracted from relaxation of the ¹³C magnetization of the I = 1/2 manifold in ¹³CH₃ methyls. In smaller proteins, a certain degree of anticorrelation is observed between the S_axis² and τ_f values obtained from ¹³C relaxation of the I = 1/2 manifold magnetization in ¹³CH₃ methyls. These parameters can be partially decorrelated by inclusion in the analysis of relaxation data of the I = 3/2 manifold ¹³C magnetization.

Optimized selection of slow-relaxing 13C transitions in methyl groups of proteins: application to relaxation dispersion

Optimized selection of the slow-relaxing components of single-quantum ¹³C magnetization in ¹³CH₃ methyl groups of proteins using acute (< 90°) angle ¹H radio-frequency pulses, is described. The optimal selection scheme is more relaxation-tolerant and provides sensitivity gains in comparison to the experiment where the undesired (fast-relaxing) components of ¹³C magnetization are simply 'filtered-out' and only 90° ¹H pulses are employed for magnetization transfer to and from ¹³C nuclei. When applied to methyl ¹³C single-quantum Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments for studies of chemical exchange, the selection of the slow-relaxing ¹³C transitions results in a significant decrease in intrinsic (exchange-free) transverse spin relaxation rates of all exchanging species. For exchanging systems involving high-molecular-weight species, the lower transverse relaxation rates translate into an increase in the information content of the resulting relaxation dispersion profiles.

An S/T motif controls reversible oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of a β sheet backbone

Chaperone oligomerization is often a key aspect of their function. Irrespective of whether chaperone oligomers act as reservoirs for active monomers or exhibit a chaperoning function themselves, understanding the mechanism of oligomerization will further our understanding of how chaperones maintain the proteome. Here, we focus on the class-II Hsp40, human DNAJB6b, a highly efficient inhibitor of protein self-assembly in vivo and in vitro that forms functional oligomers. Using single-quantum methyl-based relaxation dispersion NMR methods we identify critical residues for DNAJB6b oligomerization in its C-terminal domain (CTD). Detailed solution NMR studies on the structure of the CTD showed that a serine/threonine-rich stretch causes a backbone twist in the N-terminal β strand, stabilizing the monomeric form. Quantitative analysis of an array of NMR relaxation-based experiments (including Carr-Purcell-Meiboom-Gill relaxation dispersion, off-resonance R _1ρ profiles, lifetime line broadening, and exchange-induced shifts) on the CTD of both wild type and a point mutant (T142A) within the S/T region of the first β strand delineates the kinetics of the interconversion between the major twisted-monomeric conformation and a more regular β strand configuration in an excited-state dimer, as well as exchange of both monomer and dimer species with high-molecular-weight oligomers. These data provide insights into the molecular origins of DNAJB6b oligomerization. Further, the results reported here have implications for the design of β sheet proteins with tunable self-assembling properties and pave the way to an atomic-level understanding of amyloid inhibition.