Translational and Rotational Motion of C8 Aromatics Adsorbed in Isotropic Porous Media (MOF-5): NMR Studies and MD Simulations

We combined nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation to study xylene behavior in MOF-5, probing the effects of adsorbate geometry in a weakly interacting model isotropic metal organic framework (MOF) system. We employed NMR diffusometry and relaxometry techniques at low field (13 MHz) to quantify the self -diffusion coefficients (Ds) and the longitudinal relaxation times (T-1) of xylenes in MOF-5 as a function of temperature at the saturated loading for each xylene. These "experiments reveal the translational motion activation energies to be 15.3, 19.7, and 21.2 kj mol(-1) and the rotational activation energies to be 47.26, 12.88, and 11.55 for the (p-, m-, o-) xylene isomers, respectively. Paraxylene exhibits faster translational motion, yet shows four times the activation energy barrier for rotational motion vis-a-vis the other isomers. MD simulations performed on these model systems corroborate the findings for paraxylene and suggest that paraxylene has the lower free energy barrier for hopping away from its binding sites, yet has the slowest rotational motion in the plane of the xylene molecule.

Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics

Daniel Abergel, Geoffrey Bodenhausen

Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free approach and reduced spectral density mapping. Comparison of predictions, based on 77 ns molecular dynamics simulations, with the observed relaxation rates gives insight into dynamical properties of the protein and their alteration on ligand binding. Data indicate dynamics changes in the vicinity of the binding site. More interesting is the presence of perturbations located in remote regions of this well-structured globular protein in which no large-amplitude motions are involved. This suggests that delocalized changes in dynamics that occur upon binding could be a general feature of proteintarget interactions. Proteins 2012; (c) 2011 Wiley Periodicals, Inc.

2012

Chemical exchange in proteins

Mariachiara Verde

Nuclear Magnetic Resonance (NMR) spectroscopy offers many ways to investigate dynamic properties of molecules. A wide variety of experimental techniques can probe molecular dynamics on time scales that range from 10-12 to 103 seconds. Many lines of evidence point to the existence of large scale dynamics on milli- to microsecond time scale that are essential to molecular function. Those conformational motions can give rise to chemical exchange effects. So far in the literature two methods have been mainly used to study such processes: CPMG echo trains and R1ρ spin-lock relaxation experiments. The former is suited to investigate processes on the millisecond time scale, whereas R1ρ can probe processes ranging from milliseconds down to ca. microseconds. CPMG and R1ρ studies of the relaxation rates of single quantum (SQ) coherences can be complemented by multiple quantum coherence (MQ) coherences experiments which can provide information whether two (or more) spins are affected simultaneously by chemical exchange. The goal of this thesis is to characterize chemical exchange in proteins by new (Heteronuclear Double Resonance, HDR) and existing (relaxation compensated CPMG) methods. The presence of chemical exchange has been identified in APO-rMUP using the classical CPMG experiment on single quantum 15N magnetization, whereas in HOLO-rMUP no presence of chemical exchange has been found. Most of the thesis is dedicated to the analysis and the application of a new method, HDR, which is designed to determine the cross-relaxation rates between MQ operators. In fact, in heteronuclear systems, correlated chemical exchange contributes to cross-relaxation between MQ coherences 2IxSx and 2IySy. This method, based on MLEV-32 and WALTZ-16 used in double resonance mode, is designed to effectively preserve all relevant MQ coherences simultaneously so that the interconversion between MQ operators can only arise through cross-relaxation. This is an essential requirement if we want to measure, for example, small cross-relaxation rates between MQ operators. We have treated the effects of coherent evolution during the HDR sequences by numerical simulations and Average Hamiltonian Theory (AHT) showing that, under most conditions, the dynamics of MQ coherences is not affected by coherent evolution. This result is proved experimentally on the 15N-1H pair of selectively deuterated tBoc-glycine. The effect of relaxation during HDR sequences leads to an effective relaxation superoperator which is explored by numerical simulations and predicted by Average Liouvillian Theory (ALT). Finally the HDR MLEV-32 sequence is applied to amide 1H-15N pairs in ubiquitin and KIX proteins. In the case of ubiquitin the HDR MLEV-32 experiments and the numerical simulations run with parameters obtained from the literature are in good agreement, suggesting that HDR sequences could be used as a tool to obtain information about the dynamics of the system.

EPFL2009

Dynamic Studies through Control of Relaxation in NMR Spectroscopy

Nicola Salvi

In numerous biological processes that constitute the base of living organisms, protein function is fundamentally related to internal dynamics occurring on μs-ms time scales that can give rise to chemical exchange contributions to relaxation. In a heteronuclear two-spin system (e.g., 1H-15N), correlated motions of the two nuclei induce cross-relaxation between multiple-quantum coherences that can be quantified using new Heteronuclear Double Resonance (HDR) techniques. An analytical model describes the effect of an applied radio-frequency field on the relaxation rate of interest in the presence of fast exchange, providing accurate information on the kinetics of correlated processes. Numerical simulations and experimental results confirm the validity of the model. HDR and more conventional relaxation dispersion techniques are used to characterize the internal dynamics in several biological systems. Motions on similar time scales are detected in the two different binding surfaces in human ubiquitin and in the linker between them (Phe45), suggesting the presence of a possible global motion. Additional applications of HDR give insights into the dynamics occurring in the KID-binding domain (KIX) of the CREB-binding protein. We identified the presence of exchange processes, faster than the one reported by Konrat and coworkers, outside the main helices of KIX. These fast motions are most likely the sign of conformational disorder within the native state, which may promote the transition to the unfolded ensemble. A combination of 15N relaxation rates and magnetization transfer rates are used to provide a qualitative characterization of internal dynamics in Engrailed 2. While contribution of exchange processes in the ms time scale are small, fluctuations at sub-ms timescales are found to occur both in the unstructured part that contains important binding sites for other transcription factors, and at a few restricted locations in the structured homeodomain. Such motions are characterized by 15N R1ρ relaxation dispersion. Our results reveal that the hexapeptide motif is characterized by complex dynamics that may be linked to its physiological function. Moreover, the time scale of motions in the homeodomain is reasonably close to that of the hexapeptide region. It is therefore tempting to suppose that transient contacts occur between the structured and unstructured regions.