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Stafford K.A.,Columbia University | Ferrage F.,CNRS Biomolecules Laboratory | Cho J.-H.,Texas A&M University | Palmer A.G.,Columbia University
Journal of the American Chemical Society

Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H. © 2013 American Chemical Society. Source

Combined use of cross-polarization and magic-angle spinning in the middle of the seventies has opened a new era of high-resolution solid-state NMR spectroscopy. Cross-polarization procedure is commonly used to obtain a shorter measuring time and to investigate or exploit one nucleous by means of the other nucleous involved in the polarization transfer. An extended family of cross-polarization experiments including constant time cross-polarization approach, cross-polarization inversion and indirect observation of proton spin system is reviewed and illustrated with applications to a large range of solids. © 2015 Elsevier Inc. Source

Kurzbach D.,CNRS Biomolecules Laboratory
Protein Science

A methodological framework is presented for the graph theoretical interpretation of NMR data of protein interactions. The proposed analysis generalizes the idea of network representations of protein structures by expanding it to protein interactions. This approach is based on regularization of residue-resolved NMR relaxation times and chemical shift data and subsequent construction of an adjacency matrix that represents the underlying protein interaction as a graph or network. The network nodes represent protein residues. Two nodes are connected if two residues are functionally correlated during the protein interaction event. The analysis of the resulting network enables the quantification of the importance of each amino acid of a protein for its interactions. Furthermore, the determination of the pattern of correlations between residues yields insights into the functional architecture of an interaction. This is of special interest for intrinsically disordered proteins, since the structural (three-dimensional) architecture of these proteins and their complexes is difficult to determine. The power of the proposed methodology is demonstrated at the example of the interaction between the intrinsically disordered protein osteopontin and its natural ligand heparin. © 2016 The Protein Society. Source

Calligari P.,International School for Advanced Studies | Abergel D.,CNRS Biomolecules Laboratory
Journal of Physical Chemistry B

Fluctuations of NMR resonance frequency shifts and their relation with protein exchanging conformations are usually analyzed in terms of simple two-site jump processes. However, this description is unable to account for the presence of multiple time scale dynamics. In this work, we present an alternative model for the interpretation of the stochastic processes underlying these fluctuations of resonance frequencies. Time correlation functions of 15N amide chemical shifts computed from molecular dynamics simulations (MD) were analyzed in terms of a transiently fractional diffusion process. The analysis of MD trajectories spanning dramatically different time scales (∼200 ns and 1 ms [ Shaw, D. E.; Science 2010, 330, 341-346 ]) allowed us to show that our model could capture the multiple scale structure of chemical shift fluctuations. Moreover, the predicted exchange contribution Rex to the NMR transverse relaxation rate is in qualitative agreement with experimental results. These observations suggest that the proposed fractional diffusion model may provide significative improvement to the analysis of NMR dispersion experiments. © 2014 American Chemical Society. Source

Ferrage F.,CNRS Biomolecules Laboratory
Methods in Molecular Biology

Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dynamics used by NMR spectroscopists. It provides the general characteristics of hydrodynamics as well as internal motions on subnanosecond, micro- and millisecond timescales of a biomolecule. Here, we present a full protocol to perform and analyze a series of experiments to measure the 15N longitudinal relaxation rate, the 15N transverse relaxation rate under an echo train or a single echo, the 15N- 1H dipolar cross-relaxation rate, as well as the longitudinal and transverse cross-relaxation rates due to the cross-correlation of the nitrogen-15 chemical shift anisotropy and the dipolar coupling with the adjacent proton. These rates can be employed to carry out model-free analyses and can be used to quantify accurately the contribution of chemical exchange to transverse relaxation. © 2012 Springer Science+Business Media, LLC. Source

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