Real-time protein NMR spectroscopy and investigation of assisted protein folding

Kumar, Amit; Balbach, Jochen

doi:10.1016/j.bbagen.2014.12.003

Cited by 20 publications

(13 citation statements)

References 112 publications

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“…The results easily draw focus on the induced order in structures, overlooking or underestimating the functional significance of originally disordered regions. Therefore, it is essential to supplement these data by spectroscopic techniques (e.g., CD or NMR) sensitive to the solution structure of the individual interacting partners and to the structural changes on their interactions, as well as to the dynamic nature of the protein structure …”

Section: Discussionmentioning

confidence: 99%

Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study

et al. 2016

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X-ray diffractometry dominates protein studies, as it can provide 3D structures of these diverse macromolecules or their molecular complexes with interacting partners: substrates, inhibitors, and/or cofactors. Here, we show that under cocrystallization conditions the results could reflect induced protein folds instead of the (partially) disordered original structures. The analysis of synchrotron radiation circular dichroism spectra revealed that the Im7 immunity protein stabilizes the native-like solution structure of unfolded NColE7 nuclease mutants via complex formation. This is consistent with the fact that among the several available crystal structures with its inhibitor or substrate, all NColE7 structures are virtually the same. Our results draw attention to the possible structural consequence of protein modifications, which is often hidden by compensational effects of intermolecular interactions. The growing evidence on the importance of protein intrinsic disorder thus, demands more extensive complementary experiments in solution phase with the unligated form of the protein of interest.

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Section: Discussionmentioning

confidence: 99%

Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study

et al. 2016

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“…For very slow processes (i.e. processes occurring over time scales longer than seconds) it is possible to follow dynamics in real-time with NMR (Kumar & Balbach, 2015). This approach requires a perturbation of the system in order to get an experimentally observable signal.…”

Section: Methods For Quantifying Dynamics By Nmr Spectroscopymentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

149

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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“…Proline isomerization is invisible to most biochemical methods, however, NMR provides a powerful probe for this structural interconversion, and RT-NMR recently elucidated a role for proline isomerization in gene-3-protein (G3P) in filamentous phage infection [38]. The application of RT-NMR to monitor proline isomerization in protein folding studies was recently reviewed by Kumar and Balbach [39].…”

Section: Proline Isomerizationmentioning

confidence: 98%

“…RT-NMR has been used in several studies of protein folding and assembly processes, including the aforementioned work on proline isomerization [39,40]. Here, we highlight RT-NMR approaches that exploit the selective incorporation of 19 F fluorine to monitor protein folding and aggregation events [41], as well as ubiquitin chain assembly and disassembly, both in reconstituted ubiquitination systems and cell extracts [42].…”

Section: Real-time Nmr Monitoring Of Protein Folding and Assemblymentioning

confidence: 99%

Real-time NMR monitoring of biological activities in complex physiological environments

Smith

Marshall

Theillet

et al. 2015

Current Opinion in Structural Biology

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Real-time protein NMR spectroscopy and investigation of assisted protein folding

Cited by 20 publications

References 112 publications

Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study

Intrinsic protein disorder could be overlooked in cocrystallization conditions: An SRCD case study

Protein dynamics and function from solution state NMR spectroscopy

Real-time NMR monitoring of biological activities in complex physiological environments

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