Measurement of the signs of methyl 13C chemical shift differences between interconverting ground and excited protein states by R(1ρ): an application to αB-crystallin

Methyl TROSY spectroscopy: A versatile NMR approach to study challenging biological systems

A major goal in structural biology is to unravel how molecular machines function in detail. To that end, solution-state NMR spectroscopy is ideally suited as it is able to study biological assemblies in a near natural environment. Based on methyl TROSY methods, it is now possible to record high-quality data on complexes that are far over 100 kDa in molecular weight. In this review, we discuss the theoretical background of methyl TROSY spectroscopy, the information that can be extracted from methyl TROSY spectra and approaches that can be used to assign methyl resonances in large complexes. In addition, we touch upon insights that have been obtained for a number of challenging biological systems, including the 20S proteasome, the RNA exosome, molecular chaperones and G-protein-coupled receptors. We anticipate that methyl TROSY methods will be increasingly important in modern structural biology approaches, where information regarding static structures is complemented with insights into conformational changes and dynamic intermolecular interactions.

Proline isomerization in the C-terminal region of HSP27

In mammals, small heat-shock proteins (sHSPs) typically assemble into interconverting, polydisperse oligomers. The dynamic exchange of sHSP oligomers is regulated, at least in part, by molecular interactions between the α-crystallin domain and the C-terminal region (CTR). Here we report solution-state nuclear magnetic resonance (NMR) spectroscopy investigations of the conformation and dynamics of the disordered and flexible CTR of human HSP27, a systemically expressed sHSP. We observed multiple NMR signals for residues in the vicinity of proline 194, and we determined that, while all observed forms are highly disordered, the extra resonances arise from cis-trans peptidyl-prolyl isomerization about the G193-P194 peptide bond. The cis-P194 state is populated to near 15% at physiological temperatures, and, although both cis- and trans-P194 forms of the CTR are flexible and dynamic, both states show a residual but differing tendency to adopt β-strand conformations. In NMR spectra of an isolated CTR peptide, we observed similar evidence for isomerization involving proline 182, found within the IPI/V motif. Collectively, these data indicate a potential role for cis-trans proline isomerization in regulating the oligomerization of sHSPs.

Protein folding by NMR

Protein folding is a highly complex process proceeding through a number of disordered and partially folded nonnative states with various degrees of structural organization. These transiently and sparsely populated species on the protein folding energy landscape play crucial roles in driving folding toward the native conformation, yet some of these nonnative states may also serve as precursors for protein misfolding and aggregation associated with a range of devastating diseases, including neuro-degeneration, diabetes and cancer. Therefore, in vivo protein folding is often reshaped co- and post-translationally through interactions with the ribosome, molecular chaperones and/or other cellular components. Owing to developments in instrumentation and methodology, solution NMR spectroscopy has emerged as the central experimental approach for the detailed characterization of the complex protein folding processes in vitro and in vivo. NMR relaxation dispersion and saturation transfer methods provide the means for a detailed characterization of protein folding kinetics and thermodynamics under native-like conditions, as well as modeling high-resolution structures of weakly populated short-lived conformational states on the protein folding energy landscape. Continuing development of isotope labeling strategies and NMR methods to probe high molecular weight protein assemblies, along with advances of in-cell NMR, have recently allowed protein folding to be studied in the context of ribosome-nascent chain complexes and molecular chaperones, and even inside living cells. Here we review solution NMR approaches to investigate the protein folding energy landscape, and discuss selected applications of NMR methodology to studying protein folding in vitro and in vivo. Together, these examples highlight a vast potential of solution NMR in providing atomistic insights into molecular mechanisms of protein folding and homeostasis in health and disease.

Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists

The majority of proteins depend on a well-defined three-dimensional structure to obtain their functionality. In the cellular environment, the process of protein folding is guided by molecular chaperones to avoid misfolding, aggregation, and the generation of toxic species. To this end, living cells contain complex networks of molecular chaperones, which interact with substrate polypeptides by a multitude of different functionalities: transport them towards a target location, help them fold, unfold misfolded species, resolve aggregates, or deliver them towards a proteolysis machinery. Despite the availability of high-resolution crystal structures of many important chaperones in their substrate-free apo forms, structural information about how substrates are bound by chaperones and how they are protected from misfolding and aggregation is very sparse. This lack of information arises from the highly dynamic nature of chaperone-substrate complexes, which so far has largely hindered their crystallization. This highly dynamic nature makes chaperone-substrate complexes good targets for NMR spectroscopy. Here, we review the results achieved by NMR spectroscopy to understand chaperone function in general and details of chaperone-substrate interactions in particular. We assess the information content and applicability of different NMR techniques for the characterization of chaperones and chaperone-substrate complexes. Finally, we highlight three recent studies, which have provided structural descriptions of chaperone-substrate complexes at atomic resolution.

An exact solution for R2,eff in CPMG experiments in the case of two site chemical exchange

The Carr-Purcell-Meiboom-Gill (CPMG) experiment is widely used to quantitatively analyse the effects of chemical exchange on NMR spectra. In a CPMG experiment, the effective transverse relaxation rate, R2,eff, is typically measured as a function of the pulse frequency, νCPMG. Here, an exact expression for how R2,eff varies with νCPMG is derived for the commonly encountered scenario of two-site chemical exchange of in-phase magnetisation. This result, summarised in Appendix A, generalises a frequently used equation derived by Carver and Richards, published in 1972. The expression enables more rapid analysis of CPMG data by both speeding up calculation of R2,eff over numerical methods by a factor of ca. 130, and yields exact derivatives for use in data analysis. Moreover, the derivation provides insight into the physical principles behind the experiment.

Evaluating the uncertainty in exchange parameters determined from off-resonance R1ρ relaxation dispersion for systems in fast exchange

Spin relaxation in the rotating frame (R1ρ) is a powerful NMR technique for characterizing fast microsecond timescale exchange processes directed toward short-lived excited states in biomolecules. At the limit of fast exchange, only k(ex)=k(1)+k(-1) and Φex=p(G)p(E)(Δω)(2) can be determined from R1ρ data limiting the ability to characterize the structure and energetics of the excited state conformation. Here, we use simulations to examine the uncertainty with which exchange parameters can be determined for two state systems in intermediate-to-fast exchange using off-resonance R1ρ relaxation dispersion. R1ρ data computed by solving the Bloch-McConnell equations reveals small but significant asymmetry with respect to offset (R1ρ (ΔΩ)≠R1ρ (-ΔΩ)), which is a hallmark of slow-to-intermediate exchange, even under conditions of fast exchange for free precession chemical exchange line broadening (k(ex)/Δω>10). A grid search analysis combined with bootstrap and Monte-Carlo based statistical approaches for estimating uncertainty in exchange parameters reveals that both the sign and magnitude of Δω can be determined at a useful level of uncertainty for systems in fast exchange (k(ex)/Δω<10) but that this depends on the uncertainty in the R1ρ data and requires a thorough examination of the multidimensional variation of χ(2) as a function of exchange parameters. Results from simulations are complemented by analysis of experimental R1ρ data measured in three nucleic acid systems with exchange processes occurring on the slow (k(ex)/Δω=0.2; pE=∼0.7%), fast (k(ex)/Δω=∼10-16; p(E)=∼13%) and very fast (k(ex)=39,000 s(-1)) chemical shift timescales.

Chemical exchange in biomacromolecules: past, present, and future

The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.

C-terminal interactions mediate the quaternary dynamics of αB-crystallin

αB-crystallin is a highly dynamic, polydisperse small heat-shock protein that can form oligomers ranging in mass from 200 to 800 kDa. Here we use a multifaceted mass spectrometry approach to assess the role of the C-terminal tail in the self-assembly of αB-crystallin. Titration experiments allow us to monitor the binding of peptides representing the C-terminus to the αB-crystallin core domain, and observe individual affinities to both monomeric and dimeric forms. Notably, we find that binding the second peptide equivalent to the core domain dimer is considerably more difficult than the first, suggesting a role of the C-terminus in regulating assembly. This finding motivates us to examine the effect of point mutations in the C-terminus in the full-length protein, by quantifying the changes in oligomeric distribution and corresponding subunit exchange rates. Our results combine to demonstrate that alterations in the C-terminal tail have a significant impact on the thermodynamics and kinetics of αB-crystallin. Remarkably, we find that there is energy compensation between the inter- and intra-dimer interfaces: when one interaction is weakened, the other is strengthened. This allosteric communication between binding sites on αB-crystallin is likely important for its role in binding target proteins.

An R(1ρ) expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates

An analytical expression is derived for the rotating frame relaxation rate, R(1ρ), of a spin exchanging between two sites with different transverse relaxation times. A number of limiting cases are examined, with the equation reducing to formulae derived previously under the assumption of equivalent relaxation rates at each site. The measurement of a pair off-resonance R(1ρ) values, with the carrier displaced equally on either side of the observed correlation, forms the basis of one of the approaches for obtaining signs of chemical shift differences, Δω, of exchanging nuclei. The results presented here establish that this method is relatively insensitive to differential transverse relaxation rates between the exchaning states, greatly simplifying the calculation of optimal parameters in R(1ρ) based experiments that are used for measurement of signs of Δω.

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.