Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion

Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD

Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine ¹H-¹³C/²H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.

Characterizing Fast Conformational Exchange of Aromatic Rings Using Residual Dipolar Couplings: Distinguishing Jumplike Flips from Other Exchange Mechanisms

Aromatic ring flips are a hallmark of protein dynamics. They are experimentally studied by NMR spectroscopy, where recent advances have led to improved characterization across a wide range of time scales. Results on different proteins have been interpreted as continuous diffusive ring rotations or jumplike flips, leading to diverging views of the protein interior as being fluidlike or solidlike, respectively. It is challenging to distinguish between these mechanisms and other types of conformational exchange because chemical-shift-mediated line broadening provides only conclusive evidence for ring flips only if the system can be moved from the slow- to intermediate/fast-exchange regime. Moreover, whenever the chemical shift difference between the two symmetry-related sites is close to zero, it is not generally possible to determine the exchange time scale. Here we resolve these issues by measuring residual dipolar coupling (RDC)-mediated exchange contributions using NMR relaxation dispersion experiments on proteins dissolved in dilute liquid crystalline media. Excellent agreement is found between the experimental difference in RDC between the two symmetry-related sites and the value calculated from high-resolution X-ray structures, demonstrating that dynamics measured for F52 in the B1 domain of protein G reports on distinct, jumplike flips rather than other types of conformational exchange.

1H R1ρ relaxation dispersion experiments in aromatic side chains

Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic ¹H R_1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated ¹H-¹³C spin pairs with vicinal ²H-¹²C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the ³J_HH couplings and limited chemical shift differences among ¹H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, k_flip, agree well with previous results from ¹³C R_1ρ relaxation dispersion experiments, and yield ¹H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic¹H R_1ρ relaxation dispersion experiment in combination with the site-selective ¹H-¹³C/²H-¹²C labeling scheme enable measurement of exchange rates up to k_ex = 2k_flip = 80,000 s^-1, and serve as a useful complement to previously developed ¹³C-based methods.

Broadband measurement of true transverse relaxation rates in systems with coupled protons: application to the study of conformational exchange

Accurate measurement of transverse relaxation rates in coupled spin systems is important in the study of molecular dynamics, but is severely complicated by the signal modulations caused by scalar couplings in spin echo experiments. The most widely used experiments for measuring transverse relaxation in coupled systems, CPMG and PROJECT, can suppress such modulations, but they also both suppress some relaxation contributions, and average relaxation rates between coupled spins. Here we introduce a new experiment which for the first time allows accurate broadband measurement of transverse relaxation rates of coupled protons, and hence the determination of exchange rate constants in slow exchange from relaxation measurements. The problems encountered with existing methods are illustrated, and the use of the new method is demonstrated for the classic case of hindered amide rotation and for the more challenging problem of exchange between helical enantiomers of a gold(i) complex.

Transition-State Compressibility and Activation Volume of Transient Protein Conformational Fluctuations

Proteins are dynamic entities that intermittently depart from their ground-state structures and undergo conformational transitions as a critical part of their functions. Central to understanding such transitions are the structural rearrangements along the connecting pathway, where the transition state plays a special role. Using NMR relaxation at variable temperature and pressure to measure aromatic ring flips inside a protein core, we obtain information on the structure and thermodynamics of the transition state. We show that the isothermal compressibility coefficient of the transition state is similar to that of short-chain hydrocarbon liquids, implying extensive local unfolding of the protein. Our results further indicate that the required local volume expansions of the protein can occur not only with a net positive activation volume of the protein, as expected from previous studies, but also with zero activation volume by compaction of remote void volume, when averaged over the ensemble of states.

Evaluation of the Rotating-Frame Relaxation (T1ρ) Filter and Its Application in Metabolomics as an Alternative to the Transverse Relaxation (T2) Filter

Nuclear magnetic resonance (NMR)-based metabolomic studies commonly involve the use of T2 filter pulse sequences to eliminate or attenuate the broad signals from large molecules and improve spectral resolution. In this paper, we demonstrate that the T1ρ filter-based pulse sequence represents an interesting alternative because it allows the stability and the reproducibility needed for statistical analysis. The integrity of the samples and the stability of the instruments were assessed for different filter durations and amplitudes. We showed that the T1ρ filter pulse sequence did not induce sample overheating for a filter duration of up to 500 ms. The reproducibility was evaluated and compared with the T2 filter in serum and liver samples. The implementation is relatively simple and provides the same statistical and analytical results as those obtained with the standard filters. Regarding tissues analysis, because the duration of the filter is the same as that of the spin-lock, the synchronization of the echo delays with the magic angle spinning (MAS) rate is no longer necessary as for T2 filter-based sequences. The results presented in this article aim at establishing a new protocol to improve metabolomic studies and pave the way for future developments on T1ρ alternative filters, in liquid and HR-MAS NMR experiments.

Modulating Enzyme Function via Dynamic Allostery within Biliverdin Reductase B

The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic "dials" to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.

Site-selective 1H/2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains

Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic ¹³C or ¹H CPMG relaxation dispersion experiments. Aromatic ¹H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by ³J ¹H-¹H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective ¹H/²H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding-unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from ¹³C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective ¹H/²H labeling enables artifact-free aromatic ¹H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.