Model-free analysis of a thermophilic Fe7S8 protein compared with a mesophilic Fe4S4 protein

Bertini, Ivano; Luchinat, Claudio; Niikura, Yohei; Presenti, Chiara

doi:10.1002/1097-0134(20001001)41:1<75::aid-prot100>3.0.co;2-2

Cited by 10 publications

(3 citation statements)

References 58 publications

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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). The longitudinal electronic relaxation rate at 14.1 tesla used in these calculations was 4 ϫ 10 9 s Ϫ1 , as interpolated from estimates at 11.7 and 17.6 (64) as well as 18.8 tesla (65) reported for blue copper proteins.…”

Section: Methodsmentioning

confidence: 99%

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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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Section: Methodsmentioning

confidence: 99%

“…These data are shown in Fig. 5A and included in 17,42,63, and 93, which were found slightly above the theoretical maximum, were fixed to the maximum value in the Modelfree analysis. 15 N relaxation data for oxidized Synechocystis sp.…”

Section: Signal Assignment-thementioning

confidence: 99%

Backbone Dynamics of Plastocyanin in Both Oxidation States

Bertini¹,

Bryant²,

Ciurli³

et al. 2001

Journal of Biological Chemistry

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“…Moreover, fast motions are, in themselves, important in the activity of a variety of biomolecules 3, 4. Longitudinal relaxation time (T 1 ) measurements are an important probe of these faster timescale motions 5, 6. This method is complementary to Pulsed Field Gradient Spin Echo (PGSE) techniques, enabling the study of overall molecular sizes and local dynamics by the distinct T 1 s displayed by shift-resolved sites 7–9.…”

Section: Introductionmentioning

confidence: 99%

Ultrafast NMR T₁ Relaxation Measurements: Probing Molecular Properties in Real Time

et al. 2013

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The longitudinal relaxation properties of NMR active nuclei carry useful information about the site-specific chemical environments and about the mobility of molecular fragments. Molecular mobility is in turn a key parameter reporting both on stable properties like size, as well as on dynamic ones such as transient interactions and irreversible aggregation. In order to fully investigate the latter, a fast sampling of the relaxation parameters of transiently formed molecular species may be needed. Nevertheless, the acquisition of longitudinal relaxation data is typically slow, being limited by the requirement that the time for which the nucleus relaxes be varied incrementally until a complete build-up curve is generated. Recently a number of single-shot inversion recovery methods have been developed capable of alleviating this need; still, these may be challenged by either spectral resolution restrictions or when coping with very fast relaxing nuclei. Here we present a new experiment to measure the T 1 s of multiple nuclear spins that experience fast longitudinal relaxation, while retaining full high-resolution chemical shift information. Good agreement is observed between T 1 s measured with conventional means and T 1 s measured using the new technique. The method is applied to the real time investigation of the reaction between D-xylose and sodium borate, which is in turn elucidated with the aid of ancillary ultrafast and conventional 2D TOCSY measurements.

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The NMR contribution to protein–protein networking in Fe–S protein maturation

et al. 2018

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Iron–sulfur proteins were among the first class of metalloproteins that were actively studied using NMR spectroscopy tailored to paramagnetic systems. The hyperfine shifts, their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues are an efficient fingerprint of the nature and the oxidation state of the Fe–S cluster. NMR significantly contributed to the analysis of the magnetic coupling patterns and to the understanding of the electronic structure occurring in [2Fe–2S], [3Fe–4S] and [4Fe–4S] clusters bound to proteins. After the first NMR structure of a paramagnetic protein was obtained for the reduced E. halophila HiPIP I, many NMR structures were determined for several Fe–S proteins in different oxidation states. It was found that differences in chemical shifts, in patterns of unobserved residues, in internal mobility and in thermodynamic stability are suitable data to map subtle changes between the two different oxidation states of the protein. Recently, the interaction networks responsible for maturing human mitochondrial and cytosolic Fe–S proteins have been largely characterized by combining solution NMR standard experiments with those tailored to paramagnetic systems. We show here the contribution of solution NMR in providing a detailed molecular view of “Fe–S interactomics”. This contribution was particularly effective when protein–protein interactions are weak and transient, and thus difficult to be characterized at high resolution with other methodologies.

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Model-free analysis of a thermophilic Fe7S8 protein compared with a mesophilic Fe4S4 protein

Cited by 10 publications

References 58 publications

Backbone Dynamics of Plastocyanin in Both Oxidation States

Backbone Dynamics of Plastocyanin in Both Oxidation States

Ultrafast NMR T₁ Relaxation Measurements: Probing Molecular Properties in Real Time

The NMR contribution to protein–protein networking in Fe–S protein maturation

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Model-free analysis of a thermophilic Fe7S8 protein compared with a mesophilic Fe4S4 protein

Cited by 10 publications

References 58 publications

Backbone Dynamics of Plastocyanin in Both Oxidation States

Backbone Dynamics of Plastocyanin in Both Oxidation States

Ultrafast NMR T1 Relaxation Measurements: Probing Molecular Properties in Real Time

The NMR contribution to protein–protein networking in Fe–S protein maturation

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Product

Resources

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Ultrafast NMR T₁ Relaxation Measurements: Probing Molecular Properties in Real Time