Authors: Palma PN, Moura I, LeGall J, Van Beeumen J, Wampler JE, Moura JJ
Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain operating between substrate electron donors and respiratory electron acceptors, in sulfate-reducing bacteria (Desulfovibrio species). The nature and properties of the complex formed between these proteins are revealed by 1H-NMR and molecular modeling approaches. Our previous study with the Desulfovibrio vulgaris proteins [Moura, I., Moura, J.J. G., Santos, M.H., & Xavier, A. V. (1980) Cienc. Biol. (Portugal) 5, 195-197; Stewart, D.E. LeGall, J., Moura, I., Moura, J. J. G., Peck, H.D. Jr., Xavier, A. V., Weiner, P. K., & Wampler, J.E. (1988) Biochemistry 27, 2444-2450] indicated that the complex between cytochrome c3 and flavodoxin could be monitored by changes in the NMR signals of the heme methyl groups of the cytochrome and that the electrostatic surface charge (Coulomb's law) on the two proteins favored interaction between one unique heme of the cytochrome with flavodoxin. If the interaction is indeed driven by the electrostatic complementarity between the acidic flavodoxin and a unique positive region of the cytochrome c3, other homologous proteins from these two families of proteins might be expected to interact similarly. In this study, three homologous Desulfovibrio cytochromes c3 were used, which show a remarkable variation in their individual isoelectric points (ranging from 5.5 to 9.5). On the basis of data obtained from protein-protein titrations followed at specific proton NMR signals (i.e., heme methyl resonances), a binding model for this complex has been developed with evaluation of stoichiometry and binding constants. This binding model involves one site on the cytochromes c3 and two sites on the flavodoxin, with formation of a ternary complex at saturation. In order to understand the potential chemical form of the binding model, a structural model for the hypothetical ternary complex, formed between one molecule of Desulfovibrio salexigens flavodoxin and two molecules of cytochrome c3, is proposed. These molecular models of the complexes were constructed on the basis of complementarity of Coulombic electrostatic surface potentials, using the available X-ray structures of the isolated proteins and, when required, model structures (D. salexigens flavodoxin and Desulfovibrio desulfuricans ATCC 27774 cytochrome c3) predicted by homology modeling.
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR.
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR.
The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-? Structure: Evidence from Solid-State NMR.
J Mol Biol. 2011 Apr 8;
Authors: Kryndushkin DS, Wickner RB, Tycko R
Intracellular fibril formation by Ure2p produces the non-Mendelian genetic element in Saccharomyces cerevisiae, making Ure2p a prion protein. We show that solid-state NMR spectra of full-length Ure2p fibrils, seeded...
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04-19-2011 11:01 PM
[NMR paper] Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
Related Articles Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
Biochemistry. 2005 Aug 9;44(31):10654-68
Authors: Deep S, Im SC, Zuiderweg ER, Waskell L
To identify the binding site for bovine cytochrome b(5) (cyt b(5)) on horse cytochrome c (cyt c), cross-saturation transfer NMR experiments were performed with (2)H- and (15)N-enriched cyt c and unlabeled cyt b(5). In addition, chemical shift changes of the cyt c...
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12-01-2010 06:56 PM
[NMR paper] The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 vis
The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.
Related Articles The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.
Protein Sci. 2005 Mar;14(3):799-811
Authors: Volkov AN, Ferrari D, Worrall JA, Bonvin AM, Ubbink M
The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift...
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Journal club
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11-24-2010 11:14 PM
[NMR paper] Rotational-echo double-resonance NMR-restrained model of the ternary complex of 5-eno
Rotational-echo double-resonance NMR-restrained model of the ternary complex of 5-enolpyruvylshikimate-3-phosphate synthase.
Related Articles Rotational-echo double-resonance NMR-restrained model of the ternary complex of 5-enolpyruvylshikimate-3-phosphate synthase.
J Biomol NMR. 2004 Jan;28(1):11-29
Authors: McDowell LM, Poliks B, Studelska DR, O'Connor RD, Beusen DD, Schaefer J
The 46-kD enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes the condensation of shikimate-3-phosphate (S3P) and phosphoenolpyruvate to form EPSP....
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11-24-2010 09:25 PM
[NMR paper] NMR-based binding screen and structural analysis of the complex formed between alpha-
NMR-based binding screen and structural analysis of the complex formed between alpha-cobratoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica.
Related Articles NMR-based binding screen and structural analysis of the complex formed between alpha-cobratoxin and an 18-mer cognate peptide derived from the alpha 1 subunit of the nicotinic acetylcholine receptor from Torpedo californica.
J Biol Chem. 2002 Oct 4;277(40):37439-45
Authors: Zeng H, Hawrot E
The alpha18-mer...
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11-24-2010 08:58 PM
[NMR paper] Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR an
Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies.
Related Articles Evidence for a ternary complex formed between flavodoxin and cytochrome c3: 1H-NMR and molecular modeling studies.
Biochemistry. 1994 May 31;33(21):6394-407
Authors: Palma PN, Moura I, LeGall J, Van Beeumen J, Wampler JE, Moura JJ
Small electron-transfer proteins such as flavodoxin (16 kDa) and the tetraheme cytochrome c3 (13 kDa) have been used to mimic, in vitro, part of the complex electron-transfer chain...
nmrlearner
Journal club
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08-22-2010 03:33 AM
[Nature network NMR forum] Journal club: structure of the ternary Prp31:15.5K:U4 snRNA complex (1 reply)
Journal club: structure of the ternary Prp31:15.5K:U4 snRNA complex (1 reply)
I would like to start the “journal club” section of the NMR forum by presenting my favorite paper from the recent literature.
The paper (in this weeks issue of Science) is, in my opinion at least, a perfect example of the ability of NMR to contribute to the structural analysis of a challenging RNA-protein complex
I chose this high-impact paper because the combination of biochemistry, NMR, and crystallography on a ternary complex is how I would like to tackle a challenging project that I am...
nmrlearner
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08-21-2010 03:29 PM
A solution model of the complex formed by adrenodoxin and adrenodoxin reductase deter
A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A solution model of the complex formed by adrenodoxin and adrenodoxin reductase determined by paramagnetic NMR spectroscopy.
Biochemistry. 2010 Aug 17;49(32):6846-55
Authors: Keizers PH, Mersinli B, Reinle W, Donauer J, Hiruma Y, Hannemann F, Overhand M, Bernhardt R, Ubbink M
Lanthanide tags offer the opportunity to...