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Ishima, Rieko; Torchia, Dennis A.

doi:10.1038/78963

Cited by 506 publications

(328 citation statements)

References 64 publications

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“…These figures translate into an average error margin of ±1.5 times the black symbol size, and ±1.0 times the red symbol size. Table 1 Best-fit parameters, listed under "output", obtained with combined fitting of 16 relaxation rates (8 relaxation rates including 2 H T 1 and T 2 acquired at 9.4, 11.7, 14.1 and 18.8 T T, and 6 relaxation rates associated with the three rank 2 coherences acquired at 11.7 and 14.1 T) measured at 25 °C for methyl A50, using the input parameters shown under "input" (rows [1][2][3][4][5][6] Table 2 Combined fitting of 10 relaxation rates ( 2 H T 1 , T 2 and the three relaxation rates associated with the rank 2 coherences) acquired at 11.7 and 14.1 T, 25 °C for the depicted methyl groups. The data under "MF" were taken from ref.…”

Section: Schematic Representing Trends In Srls and S Axismentioning

confidence: 99%

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

et al. 2007

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Protein dynamics is intimately related to biological function. Core dynamics is usually studied with 2 H spin relaxation of the 13 CDH 2 group, analyzed traditionally with the model-free (MF) approach. We showed recently that MF is oversimplified in several respects. This includes the assumption that the local motion of the dynamic probe and the global motion of the protein are decoupled, the local geometry is simple, and the local ordering has axial symmetry. Because of these simplifications MF has yielded a puzzling picture where the methyl rotation axis is moving rapidly with amplitudes ranging from nearly complete disorder to nearly complete order in tightly packed protein cores. Our conclusions emerged from applying to methyl dynamics in proteins the slowly relaxing local structure (SRLS) approach of Polimeno and Freed (J. Phys. Chem. 1995, 99, 1099), which can be considered the generalization of MF, with all the simplifications mentioned above removed. The SRLS picture derived here for the B1 immunoglobulin binding domain of peptostreptococcal protein L, studied over the temperature range of 15 − 45 °C, is fundamentally different from the MF picture. Thus, methyl dynamics is characterized structurally by rhombic local potentials with varying symmetries, and dynamically by tenfold slower rates of local motion. On average potential rhombicity decreases, mode-coupling increases and the rate of local motion increases with increasing temperature. The average activation energy for local motion is 2.0 ± 0.2 kcal/mol. Mode-coupling affects the analysis even at 15 o C. The accuracy of the results is improved by including in the experimental data set relaxation rates associated with rank 2 coherences. Keywords slowly relaxing local structure; methyl dynamics in proteins; NMR spin relaxation in proteins

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Section: Schematic Representing Trends In Srls and S Axismentioning

confidence: 99%

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

et al. 2007

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“…The S 2 values were calculated using a fixed N-H bond length of 1.02 Å and 15 N chemical shift anisotropy ⌬ ϭ Ϫ172 ppm (60). In the case of the Cu(II)-oxidized plastocyanin, the paramagnetic contribution to the experimental R 1 , R 2 , and NOE values was evaluated through the point-dipole approximation according to the Solomon-Bloembergen equations (61) and subtracted from the measured relaxation rates as described previously (62,63).…”

Section: Methodsmentioning

confidence: 99%

Backbone Dynamics of Plastocyanin in Both Oxidation States

Bertini¹,

Bryant²,

Ciurli³

et al. 2001

Journal of Biological Chemistry

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A model-free analysis based on 15 N R 1 , 15 N R 2 , and 15 N-1 H nuclear Overhauser effects was performed on reduced (diamagnetic) and oxidized (paramagnetic) forms of plastocyanin from Synechocystis sp. PCC6803. The protein backbone is rigid, displaying a small degree of mobility in the sub-nanosecond time scale. The loops surrounding the copper ion, involved in physiological electron transfer, feature a higher extent of flexibility in the longer time scale in both redox states, as measured from D 2 O exchange of amide protons and from NH-H 2 O saturation transfer experiments. In contrast to the situation for other electron transfer proteins, no significant difference in the dynamic properties is found between the two redox forms. A solution structure was also determined for the reduced plastocyanin and compared with the solution structure of the oxidized form in order to assess possible structural changes related to the copper ion redox state. Within the attained resolution, the structure of the reduced plastocyanin is indistinguishable from that of the oxidized form, even though small chemical shift differences are observed. The present characterization provides information on both the structural and dynamic behavior of blue copper proteins in solution that is useful to understand further the role(s) of protein dynamics in electron transfer processes.

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“…Protein conformations as shown by x-ray crystallography or nuclear magnetic resonance spectroscopy are virtually dynamic entities over various time ranges in solution (1,2). Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3)(4)(5).…”

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confidence: 99%

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

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NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residuebased conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP ؉ reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP ؉ )-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD r values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD r values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP ؉ -binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP ؉ -binding domain at pD r 8.0, the daytime pH in chloroplasts, than at pD r 6.0 is likely to be involved in the increased binding of NADP ؉ for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.Protein conformations as shown by x-ray crystallography or nuclear magnetic resonance spectroscopy are virtually dynamic entities over various time ranges in solution (1, 2). Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3-5). The hydrogen/deuterium (H/D) 4 exchange of amide protons in backbones has become an important way to address the motions of a protein from small or relatively large scale motions involved in biological functions such as binding of a substrate or releasing a product to much more large scale motions like a global unfolding process (4, 6). Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7). For many globular proteins, this approach has identified protected cores, which are often composed of secondary structures buried inside the molecules and the cooperative interactions with partner molecules (4, 8), leading to allostery (9). Detailed analyses of exchanges in the native state of cytochrome c in the presence of various concentrations of denaturants suggested a pathway to unfolding, in which groups of secondary structural elements (i.e. foldons) are unfolded sequentially through distin...

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Cited by 506 publications

References 64 publications

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

Backbone Dynamics of Plastocyanin in Both Oxidation States

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

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Cited by 506 publications

References 64 publications

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of 2H Spin Relaxation

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of 2H Spin Relaxation

Backbone Dynamics of Plastocyanin in Both Oxidation States

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

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An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation

An Improved Picture of Methyl Dynamics in Proteins from Slowly Relaxing Local Structure Analysis of ²H Spin Relaxation