Conformational Exchange Processes in Biological Systems: Detection by Solid-State NMR

International audienceWe review recent advances in methodologies to study microseconds-to-milliseconds exchange processes in biological molecules using magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy. The particularities of MAS ssNMR, as compared to solution-state NMR, are elucidated using numerical simulations and experimental data. These simulations reveal the potential of MAS NMR to provide detailed insight into short-lived conformations of biological molecules. Recent studies of conformational exchange dynamics in microcrystalline ubiquitin are discussed

Intermolecular interactions and protein dynamics by solid-state NMR spectroscopy

Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site-specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small-amplitude overall anisotropic motion sampling the interaction interface in the complex

Subunit Mobility and the Chaperone Activity of Recombinant αB-Crystallin

The comparison of the chaperone-like activity of native and covalently cross-linked human αB-crystallins has confirmed the important role of the subunit mobility in the chaperoning mechanism. Our data clearly demonstrate that the chaperone-like activity of α-crystallin is not only a surface phenomenon as was suggested by some researchers

Studying Dynamics by Magic-Angle Spinning Solid-State NMR Spectroscopy: Principles and Applications to Biomolecules

International audienceMagic-angle spinning solid-state NMR spectroscopy is an important technique to study mo- lecular structure, dynamics and interactions, and is rapidly gaining importance in biomolecu- lar sciences. Here we provide an overview of experimental approaches to study molecular dy- namics by MAS solid-state NMR, with an emphasis on the underlying theoretical concepts and differences of MAS solid-state NMR compared to solution-state NMR. The theoretical foundations of nuclear spin relaxation are revisited, focusing on the particularities of spin re- laxation in solid samples under magic-angle spinning. We discuss the range of validity of Redfield theory, as well as the inherent multi-exponential behavior of relaxation in solids. Ex- perimental challenges for measuring relaxation parameters in MAS solid-state NMR and a few recently proposed relaxation approaches are discussed, which provide information about time scales and amplitudes of motions ranging from picoseconds to milliseconds. We also discuss the theoretical basis and experimental measurements of anisotropic interactions (chemical-shift anisotropies, dipolar and quadrupolar couplings), which give direct infor- mation about the amplitude of motions. The potential of combining relaxation data with such measurements of dynamically-averaged anisotropic interactions is discussed. Although the focus of this review is on the theoretical foundations of dynamics studies rather than their ap- plication, we close by discussing a small number of recent dynamics studies, where the dy- namic properties of proteins in crystals are compared to those in solution

The trehalose coating effect on the internal protein dynamics

15N and 13C NMR experiments were applied to conduct a comparative study of a cold shock protein (Csp) in two states - lyophilized powder and a protein embedded in a glassy trehalose matrix. Both samples were studied at various levels of rehydration. The experiments used (measuring relaxation rates R 1 and R 1ρ, motionally averaged dipolar couplings and solid state exchange method detecting reorientation of the chemical shift anisotropy tensor) allow obtaining abundant information on the protein structural features and internal motions in a range of correlation times from nanoseconds to seconds. The main results are: (a) the trehalose coating makes the protein structure more native in comparison with the dehydrated lyophilized powder, however, trehalose still cannot remove all non-native hydrogen bonds which are present in a dehydrated protein; (b) trehalose has an appreciable effect on the internal dynamics: the motion of the backbone N-H groups in the nanosecond and microsecond time scales becomes slower while the motional amplitude remains constant; (c) upon adding water to the Csp-trehalose mixture, water molecules accumulate around proteins forming a layer between the protein surface and the trehalose matrix. The protein dynamics become faster, however, not as fast as in the fully hydrated state; (d) the hydration response of dynamics of the NH and CH(CH 2) groups in a protein is qualitatively different: upon increasing protein hydration, the correlation times of the N-H motions become shorter and the amplitude remains stable, and for CH(CH 2) groups the motional amplitude increases and the correlation times do not change. This can be explained by a different ability of the NH and CH(CH 2) groups to form hydrogen bonds. © the Owner Societies 2012

Quality of colonoscopy in an emerging country: A prospective, multicentre study in Russia

Background: The quality of colonoscopy has been related to a higher risk of interval cancer, and this issue has been addressed extensively in developed countries. The aim of our study was to explore the main quality indicators of colonoscopy in a large emerging country. Methods: Consecutive patients referred for colonoscopy in 14 centres were prospectively included between July and October 2014. Before colonoscopy, several clinical and demographic variables were collected. Main quality indicators (i.e. caecal intubation rate, (advanced) adenoma detection rate, rate of adequate cleansing and sedation) were collected. Data were analysed at per patient and per centre level (only for those with at least 100 cases). Factors associated with caecal intubation rate and adenoma detection rate were explored at multivariate analysis. Results: A total of 8829 (males: 35%; mean age: 57 + 14 years) patients were included, with 11 centres enrolling at least 100 patients. Screening (including non-alarm symptoms) accounted for 59% (5188/8829) of the indications. Sedation and split preparation were used in 26% (2294/8829) and 25% (2187/8829) of the patients. Caecal intubation was achieved in 7616 patients (86%), and it was ≥85% in 8/11 (73%) centres. Adenoma detection rate was 18% (1550/8829), and it was higher than 20% in five (45%) centres, whilst it was lower than 10% in four (33%) centres. At multivariate analysis, age (OR: 1.020, 95% CI: 1.015–1.024), male sex (OR: 1.2, 95% CI: 1.1–1.3), alarm symptoms (OR: 1.8, 95% CI: 1.7–2), split preparation (OR: 1.4, 95% CI: 1.2–1.6), caecal intubation rate (OR: 1.6, 95% CI: 1.3–1.9) and withdrawal time measurement (OR: 1.2, 95% CI: 1.6–2.1) were predictors of a higher adenoma detection rate, while adequate preparation (OR: 3.4: 95% CI: 2.9–3.9) and sedation (OR: 1.3; 95% CI: 1.1–1.6) were the strongest predictors of caecal intubation rate. Conclusions: According to our study, there is a substantial intercentre variability in the main quality indicators. Overall, the caecal intubation rate appears to be acceptable in most centres, whilst the overall level of adenoma detection appears low, with less than half of the centres being higher than 20%. Educational and quality assurance programs, including higher rates of sedation and split regimen of preparation, may be necessary to increase the key quality indicators

Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility index quantify differences within backbone flexibility, whereas changes in the cooperativity correlation quantify differences within pairwise mechanical couplings. Regardless of metric, the same general conclusions are drawn. That is, small structural perturbations introduced by single point mutations have a frequent and pronounced affect on lysozyme flexibility that can extend over long distances. Specifically, an appreciable change occurs in backbone flexibility for 48% of the residues, and a change in cooperativity occurs in 42% of residue pairs. The average distance from mutation to a site with a change in flexibility is 17–20 Å. Interestingly, the frequency and scale of the changes within single point mutant structures are generally larger than those observed in the hen egg white lysozyme (HEWL) ortholog, which shares 61% sequence identity with human lysozyme. For example, point mutations often lead to substantial flexibility increases within the β-subdomain, which is consistent with experimental results indicating that it is the nucleation site for amyloid formation. However, β-subdomain flexibility within the human and HEWL orthologs is more similar despite the lowered sequence identity. These results suggest compensating mutations in HEWL reestablish desired properties