A Test of the Model-Free Formulas. Effects of Anisotropic Rotational Diffusion and Dimerization

Schurr, J. Michael; Babcock, Hazen P.; Fujimoto, Bryant S.

doi:10.1006/jmrb.1994.1127

Cited by 201 publications

(239 citation statements)

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“…Having both proteins almost equal in mass, the formation of a 1:1 adduct would cause doubling of the molecular mass of the species observed, which implies a doubling of the tumbling correlation time. Anisotropic tumbling of the complex in solution can yield up to an additional 15% increase in this correlation time [55]. In our case, the observed values of s m are sizably larger, indicating the presence of an equilibrium involving adducts of mass larger than the double of each protein.…”

Section: Discussionmentioning

confidence: 45%

“…The second interaction region appears instead to be more susceptible to variations in primary sequence. In our case, the most likely additional binding site comprises helix a 5 (55)(56)(57)(58)(59)(60)(61) and the turn up to residue 64.…”

Section: Comparison With Previous Studiesmentioning

confidence: 76%

“…3A), as both studies find the same region. This comprises helix a 4 (43)(44)(45)(46)(47)(48), part of helix a 5 (55)(56)(57)(58) and part of the strand formed by residues 23-27. The second interaction region appears instead to be more susceptible to variations in primary sequence.…”

Section: Comparison With Previous Studiesmentioning

confidence: 99%

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A further investigation of the cytochrome b 5–cytochrome c complex

et al. 2003

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The interaction of reduced rabbit cytochrome b 5 with reduced yeast iso-1 cytochrome c has been studied through the analysis of 1 H-15 N HSQC spectra, of 15 N longitudinal (R 1 ) and transverse (R 2 ) relaxation rates, and of the solvent exchange rates of protein backbone amides. For the first time, the adduct has been investigated also from the cytochrome c side. The analysis of the NMR data was integrated with docking calculations. The result is that cytochrome b 5 has two negative patches capable of interacting with a single positive surface area of cytochrome c. At low protein concentrations and in equimolar mixture, two different 1:1 adducts are formed. At high concentration and/or with excess cytochrome c, a 2:1 adduct is formed. All the species are in fast exchange on the scale of differences in chemical shift. By comparison with literature data, it appears that the structure of one 1:1 adduct changes with the origin or primary sequence of cytochrome b 5 .

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Section: Discussionmentioning

confidence: 45%

Section: Comparison With Previous Studiesmentioning

confidence: 76%

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A further investigation of the cytochrome b 5–cytochrome c complex

et al. 2003

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“…However, the fitting is not satisfactory since the NOE values calculated with the parameters of this model for internal motion are larger than the experimental values. Although one possible explanation for the unsatisfactory fit of Table 5 could be anisotropic tumbling of the polysaccharide subunit (Schurr et al, 1994;Hricovini & Tori, 1995), we have some evidence indicating that anisotropy is not significant. In model building based on 3 J CH data and NOE data for the polysaccharide of S. mitis J22, we have observed that the orientation of the C1-H1 vectors of residues a, b, g, and f are quite different, so it is likely that these vectors would differ in their orientation with respect to the principal axis of any anisotropic motion [Xu & Bush, 1996 (accompanying paper)].…”

Section: Dynamics Of a Flexible Polysaccharidementioning

confidence: 71%

Dynamics of Uniformly ¹³C-Enriched Cell Wall Polysaccharide of Streptococcus mitis J22 Studied by ¹³C Relaxation Rates

Bush

1996

Biochemistry

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We have studied the dynamics of the motion of a complex polysaccharide having seven sugar residues in the repeating subunit and which is a receptor for lectin interaction in the coaggregation of oral bacteria. Measurements of the longitudinal and the rotating frame relaxation rates and the heteronuclear nuclear Overhauser effects were carried out on a uniformly 13 C-enriched sample using pulse sequences chosen to minimize the effects of 13 C-13 C coupling and cross relaxation. T 1 and T 1F measurements both showed single exponential decay for the anomeric carbon atom resonances of the polysaccharide. The results show the polymer to be highly flexible with a hinge at the (1f6)-linked galactofuranoside residue. Since there is no generally accepted scheme for interpreting polysaccharide dynamics, several different methods of data analysis were used including a reduced spectral density function method as well as several different methods in which a series of isotropically decaying rotational correlation functions are assumed. The different analyses all show that there are differing amounts of internal motion in the different residues of the polysaccharide. One possible interpretation of the data, which uses an extended version of the model-free treatment, indicates that picosecond motion is exhibited to a similar degree by all the residues in addition to a slower motion on the nanosecond time scale whose amplitude is greatest in the hinge region around the (1f6)-linked galactofuranoside residue in the polysaccharide.While the question of the conformation and dynamics of complex polysaccharides has received considerable attention, a number of questions remain concerning the nature and extent of conformational exchange. The notion of flexibility is generally recognized to be important at least for certain oligosaccharide linkages (Rutherford et al., 1993; Poppe & van Halbeek, 1992;Maler et al., 1996; Xu et al., 1996a,b). Although it is accepted that exchange can occur among different conformations of the glycosidic linkage, the kinetics of that exchange remains uncertain. NMR 1 relaxation data provide an experimental approach to this question. Directly detected 13 C T 1 data have been reported for natural abundance sucrose by McCain and Markley (1986) which were interpreted in terms of motion on the picosecond time scale attributed to sugar puckering. An alternative approach in which 13 C T 1 was measured for a series of homologous oligosaccharides was used to show that motion of a polysaccharide can be viewed in terms of a persistence length of some 10-15 sugar units. Polymers longer than this show the same values of T 1 for the central residues regardless of chain length (Benesi & Brant, 1985;Brant et al., 1995). These directly detected 13 C relaxation experiments generally require sufficiently high concentrations of sample that the viscosity of the solution introduces some concentration dependence to the measured relaxation rates.Indirect detection offers an improvement in the sensitivity of relaxation r...

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“…In this case, the rotational diffusion of the protein as a whole modulates the effects of internal dynamics on NMR relaxation, and the spin relaxation rates depend on the orientation of the u(N i H i ) vectors with respect to the principal axes of the protein diffusion tensor. [7,8] For an overall diffusion described by a symmetric top model the correlation function C ii (t) is given in Equation (13), using the conventions used by Daragan and Mayo: [9] C ii ðtÞ¼ X where the symbol D r denotes the three eigenvalues of the overall diffusion tensor and the coefficients x ir, s relate the orientation of the vector u(N i H i ) to the diffusion tensor frame. The expressions of x ir, s are defined by Daragan and Mayo [9] and are reproduced in Table 1.…”

Section: Ementioning

confidence: 99%

Predicting NMR Relaxation Rates in Anisotropically Tumbling Proteins through Networks of Coupled Rotators

2008

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We show that the prediction of 15N relaxation rates in proteins can be extended to systems with anisotropic global rotational diffusion by using a network of coupled rotators (NCR), starting from a three‐dimensional structure. The relaxation rates predicted by this method are confronted in several examples with experiments performed by other groups. The NCR spectral density functions are compared with the results obtained from reduced spectral density mapping. The consequence of the timescales of internal motions on the predicted relaxation rates and the effects of the predicted local anisotropy—present only in the case of anisotropic overall tumbling—on dynamic parameters, are discussed.

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A Test of the Model-Free Formulas. Effects of Anisotropic Rotational Diffusion and Dimerization

Cited by 201 publications

References 0 publications

A further investigation of the cytochrome b 5–cytochrome c complex

A further investigation of the cytochrome b 5–cytochrome c complex

Dynamics of Uniformly ¹³C-Enriched Cell Wall Polysaccharide of Streptococcus mitis J22 Studied by ¹³C Relaxation Rates

Predicting NMR Relaxation Rates in Anisotropically Tumbling Proteins through Networks of Coupled Rotators

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A Test of the Model-Free Formulas. Effects of Anisotropic Rotational Diffusion and Dimerization

Cited by 201 publications

References 0 publications

A further investigation of the cytochrome b 5–cytochrome c complex

A further investigation of the cytochrome b 5–cytochrome c complex

Dynamics of Uniformly 13C-Enriched Cell Wall Polysaccharide of Streptococcus mitis J22 Studied by 13C Relaxation Rates

Predicting NMR Relaxation Rates in Anisotropically Tumbling Proteins through Networks of Coupled Rotators

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Dynamics of Uniformly ¹³C-Enriched Cell Wall Polysaccharide of Streptococcus mitis J22 Studied by ¹³C Relaxation Rates