Time-resolved multidimensional NMR with non-uniform sampling

Mayzel, Maxim; Rosenlow, Joakim; Isaksson, Linnéa; Orekhov, Vladislav Yu.

doi:10.1007/s10858-013-9811-1

Cited by 94 publications

(89 citation statements)

References 66 publications

(88 reference statements)

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“…to the standard experiment, were sampled using non-uniform sampling, and the standard data set were reconstructed by multi-dimensional decomposition co-processing (co-MDD) [88]. The extracted exchange parameters were comparable to the ones obtained from the standard experiments, which confirmed the performance of the experiment.…”

Section: Paper IIIsupporting

confidence: 54%

Improved Methods for Characterization of Protein Dynamics by NMR spectroscopy and Studies of the EphB2 Kinase Domain

Ahlner¹

2015

Linköping Studies in Science and Technology. Dissertations

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Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins.To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the software also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multiv dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at Cα positions in proteins, using the CPMG relaxation dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals.To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of E...

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Section: Paper IIIsupporting

confidence: 54%

Improved Methods for Characterization of Protein Dynamics by NMR spectroscopy and Studies of the EphB2 Kinase Domain

Ahlner¹

2015

Linköping Studies in Science and Technology. Dissertations

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“…Fine resolution in reaction time implies fast acquisition rates, which in turn limit the resolution attainable in indirectly-detected spectral dimensions. These issues have recently been addressed in a multidimensional TR NMR study [81] that employed NUS to acquire BEST-TROSY (Bandselective Excitation Short-Transient) type 3D HNCO data, increasing resolution in the spectral dimension while maintaining high time resolution for the kinetic process. The implementation of BEST-TROSY provided a further enhancement in resolution and sensitivity.…”

Section: Fast Nmr Methodsmentioning

confidence: 99%

Applications of high dimensionality experiments to biomolecular NMR

Nowakowski

Saxena

Staněk

et al. 2015

Progress in Nuclear Magnetic Resonance Spectroscopy

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“…In combination with non-uniform sampling schemes, fast-pulsing acquisitions, and simultaneous spectral processing routines, RT-NMR experiments will likely enable advanced profiling of post-translational protein modification reactions in the future, as exemplified by real-time 3D NMR approaches to monitor tyrosine phosphorylation of CD79b, with a 'time resolution' of less than 10 minutes (i.e. the time requirements for a single NMR spectrum) [21]. The works by Cordier et al and Theillet et al also provide detailed mathematical equations and fitting procedures to derive quantitative kinetic parameters of multi-site phosphorylation reactions from such RT-NMR measurements [13 ,16 ].…”

Section: Current Opinion In Structural Biologymentioning

confidence: 99%