Rubredoxin as a paramagnetic relaxation-inducing probe

Almeida, Rui M.; Pauleta, Sofia R.; Moura, Isabel; Moura, José J. G.

doi:10.1016/j.jinorgbio.2009.07.006

Cited by 13 publications

(24 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…28 As mentioned, the presence of 2 equiv of [GdÀDOTAM] 3+ does not induce by itself chemical shift perturbations on the rubredoxin amide resonances larger than 0.02 ppm (data not shown), as expected for the interaction of such a lanthanide probe with an isotropic distribution of its unpaired electrons.…”

Section: 51supporting

confidence: 61%

“…This might be due, as postulated by us and other authors, 28,47 to small conformational rearrangements of the cytochrome upon ligand binding, thus altering the chemical environment of the other heme groups. The lack of line broadening excludes direct binding of the paramagnetic probe in the vicinity of the other heme groups, as the presence of Gd implies that these chemical shifts cannot be due to long-range pseudocontact shifts.…”

Section: Shown) This Results Indicates That There Is No Interaction Bmentioning

confidence: 67%

“…A similar effect on the line width of these two methyls had been observed in the interaction between cytochrome c 3 and FeÀrubredoxin. 28 All other heme methyls resonances remain essentially unchanged in terms of line broadening, though some start to exhibit small shifts (with heme III's M2 being the most striking example).…”

Section: Shown) This Results Indicates That There Is No Interaction Bmentioning

confidence: 99%

See 2 more Smart Citations

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃

et al. 2011

Self Cite

View full text Add to dashboard Cite

ABSTRACT:Two cyclen-derived Gd probes, [GdÀDOTAM] 3+ and [GdÀDOTP] 5À (DOTAM = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetamide; DOTP = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonate)), were assessed as paramagnetic relaxation enhancement (PRE)-inducing probes for characterization of proteinÀprotein interactions. Two proteins, Desulfovibrio gigas rubredoxin and Desulfovibrio gigas cytochrome c 3 , were used as model partners. In a

show abstract

Section: 51supporting

confidence: 61%

Section: Shown) This Results Indicates That There Is No Interaction Bmentioning

confidence: 67%

Section: Shown) This Results Indicates That There Is No Interaction Bmentioning

confidence: 99%

See 1 more Smart Citation

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…Samples consisted of one part of this solution and one part glycerol. Rubredoxin from Desulfovibrio gigas [30,31] was purified according to a previously reported method [32]. To ensure that no other metal forms of rubredoxin, other than iron, were present in the sample, the protein was injected in a 6 ml Resource Q column (GE Biosciences) equilibrated with 10 mM Tris-HCl pH 7.6 buffer and eluted in a linear NaCl gradient (0-500 mM in buffer).…”

Section: Samplesmentioning

confidence: 99%

Continuous-wave EPR at 275GHz: Application to high-spin Fe3+ systems

Mathies

Blok

Disselhorst

et al. 2011

Journal of Magnetic Resonance

View full text Add to dashboard Cite

“…BiGGER has been used in the last decade to obtain structural models of several electron transfer and proteinprotein complexes [8][9][10], in most cases when the threedimensional structures of the proteins involved are available and the residues at the interface are either not known or known only for one of the partners. Although the coordinates used are considered as ''rigid bodies'', the algorithm offers an option called ''soft-docking'' that takes into account the conformational freedom of some of the surface residue side chains, such as lysine, to assist the prediction of the mode of binding of the two proteins.…”

Section: Introductionmentioning

confidence: 99%

The electron transfer complex between nitrous oxide reductase and its electron donors

Dell’Acqua

Moura

et al. 2011

J Biol Inorg Chem

Self Cite

View full text Add to dashboard Cite

Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N 2 OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N 2 OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N 2 OR, or an electrostatic nature, in the case of P. denitrificans N 2 OR and A. cycloclastes N 2 OR. A set of well-conserved residues on the N 2 OR surface were identified as being part of the electron transfer pathway from the redox partner to N 2 OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N 2 OR sequence). Moreover, we built a model for Wolinella succinogenes N 2 OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N 2 OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N 2 OR domain is similar to that found in the other electron transfer complexes.

show abstract

Rubredoxin as a paramagnetic relaxation-inducing probe

Cited by 13 publications

References 56 publications

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃

Continuous-wave EPR at 275GHz: Application to high-spin Fe3+ systems

The electron transfer complex between nitrous oxide reductase and its electron donors

Contact Info

Product

Resources

About

Rubredoxin as a paramagnetic relaxation-inducing probe

Cited by 13 publications

References 56 publications

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec3

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec3

Continuous-wave EPR at 275GHz: Application to high-spin Fe3+ systems

The electron transfer complex between nitrous oxide reductase and its electron donors

Contact Info

Product

Resources

About

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃

Gd(III) Chelates as NMR Probes of Protein–Protein Interactions. Case Study: Rubredoxin and Cytochromec₃