Direct 13C-detection for carbonyl relaxation studies of protein dynamics

Pasat, Gabriela; Zintsmaster, John S.; Peng, Jeffrey W.

doi:10.1016/j.jmr.2008.05.003

Cited by 19 publications

(17 citation statements)

References 44 publications

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“…7 Motions of hydrophilic side chains have been investigated with nitrogen-15 [8][9][10][11] and carbon-13 relaxation. [12][13][14] Aromatic side-chain dynamics have been investigated by carbon-13 NMR. 15,16 Yet, most studies of protein side-chain motions focused on aliphatic side chains 17 and have used methyl groups as probes.…”

Section: Introductionmentioning

confidence: 99%

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

et al. 2018

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Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions.

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Section: Introductionmentioning

confidence: 99%

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

et al. 2018

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“…These can in principle be determined through 13 C directdetection experiments, as recently shown in selected applications. [50][51][52][53] Herein, we propose a suite of 13 C direct-detection NMR experiments to determine a variety of observables beyond chemical shifts, providing additional tools for the study of biological macromolecules in general. The exclusively heteronuclear experiments proposed here, tested on the widely characterized protein ubiquitin, are based on the CON pulse scheme, which combines carbonyl direct detection with 15 N chemical shift evolution in the indirect dimension to take advantage of the Provided that 13 C-detected NMR experiments are either preferable or complementary to 1 H detection, we report here tools to determine C a ÀC', C'ÀN, and C a ÀH a residual dipolar couplings on the basis of the CON experiment.…”

Section: Introductionmentioning

confidence: 99%

Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins

et al. 2010

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Provided that (13)C-detected NMR experiments are either preferable or complementary to (1)H detection, we report here tools to determine C(alpha)-C', C'-N, and C(alpha)-H(alpha) residual dipolar couplings on the basis of the CON experiment. The coupling constants determined on ubiquitin are consistent with the subset measured with the (1)H-detected HNCO sequences. Since the utilization of residual dipolar couplings may depend on the mobility of the involved nuclei, we also provide tools to measure longitudinal and transverse relaxation rates of N and C'. This new set of experiments is a further development of a whole strategy based on (13)C direct-detection NMR spectroscopy for the study of biological macromolecules.

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“…4–7 Nonetheless, despite the importance of Asx and Glx residues in enzyme catalysis and substrate binding processes, surprisingly few studies on the side chain dynamics of these residues have been reported. 8–10 Here, we present a 13 C γ/δ relaxation investigation of the side chain amide and carboxyl groups in Asx/Glx residues of E. coli RNase H, by using recently developed NMR relaxation methods. 8 To gain more mechanistic insights, we have compared our experimental findings with the results of molecular dynamics (MD) simulations.…”

mentioning

confidence: 99%

Side Chain Dynamics of Carboxyl and Carbonyl Groups in the Catalytic Function of Escherichia coli Ribonuclease H

et al. 2013

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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 (MD) 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 pre-organized on ps-ns timescales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs – ms timescales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential linebroadening, 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.

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Direct 13C-detection for carbonyl relaxation studies of protein dynamics

Cited by 19 publications

References 44 publications

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations

Exclusively Heteronuclear NMR Experiments to Obtain Structural and Dynamic Information on Proteins

Side Chain Dynamics of Carboxyl and Carbonyl Groups in the Catalytic Function of Escherichia coli Ribonuclease H

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