Related ArticlesStructure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics.
J Mol Biol. 1995 Feb 3;245(5):661-81
Authors: Blackledge MJ, Medvedeva S, Poncin M, Guerlesquin F, Bruschi M, Marion D
The solution structure of Desulfovibrio vulgaris Hildenborough (DvH) ferrocytochrome c553 has been determined by nuclear magnetic resonance spectroscopy and combined simulated annealing/high temperature restrained molecular dynamics calculations. This three-stage protocol consists of an initial determination of overall fold from randomised co-ordinates, followed by a 20 picosecond exploratory stage, during which the non-bonded terms are simplified to facilitate as broad a sampling of conformational space as possible, and a 26 picosecond refinement stage, using the full AMBER force field. This latter stage systematically improved the energetic and convergence characteristics of the ensemble, while still satisfying the experimental restraints. Forty structures have been obtained from a total of 875 distance constraints for this protein of 79 amino acid residues. The root-mean-square deviation over all residues with respect to the mean is 0.70(+/- 0.12)A for the backbone (N, C alpha and C') atoms. Two conformations of the turn motif at the solvent/heme cleft interface have been identified, both fulfilling the experimental data and having equally viable energetic characteristics. The stability of the ensemble and the dynamic characteristics have been further investigated by subjecting ten of the structures to constraint-free molecular dynamics calculations (130 picoseconds) in vacuo. The structures were found to be stable to within 1.5 A of the initial backbone conformation. Comparison with the dynamic behaviour of the restrained molecular dynamics calculations has been used to identify regions of inherent flexibility in the molecule.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Structure of the lipodepsipeptide syringomycin E in phospholipids and sodium dodecylsulphate micelle studied by circular dichroism, NMR spectroscopy and molecular dynamics.
Biochim Biophys Acta. 2011 Sep;1808(9):2102-10
Authors: Anselmi M, Eliseo T, Zanetti-Polzi L, Fullone MR, Fogliano V, Di Nola A, Paci M, Grgurina I
Abstract
Syringomycin E (SRE) is a member of a...
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[NMR paper] Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP1 studied
Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP1 studied by NMR relaxation.
Related Articles Refined solution structure and backbone dynamics of 15N-labeled C12A-p8MTCP1 studied by NMR relaxation.
J Biomol NMR. 1999 Dec;15(4):271-88
Authors: Barthe P, Chiche L, Declerck N, Delsuc MA, Lefèvre JF, Malliavin T, Mispelter J, Stern MH, Lhoste JM, Roumestand C
MTCP1 (for Mature-T-Cell Proliferation) was the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The...
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[NMR paper] Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR
Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR and restrained simulated annealing.
Related Articles Solution structure of horse heart ferrocytochrome c determined by high-resolution NMR and restrained simulated annealing.
Biochemistry. 1994 May 31;33(21):6408-17
Authors: Qi PX, Di Stefano DL, Wand AJ
A model for the solution structure of horse heart ferrocytochrome c has been determined by nuclear magnetic resonance spectroscopy combined with hybrid distance geometry-simulated annealing calculations....
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[NMR paper] Two-dimensional NMR studies of the flavin binding site of Desulfovibrio vulgaris flav
Two-dimensional NMR studies of the flavin binding site of Desulfovibrio vulgaris flavodoxin in its three redox states.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Two-dimensional NMR studies of the flavin binding site of Desulfovibrio vulgaris flavodoxin in its three redox states.
Arch Biochem Biophys. 1994 Nov 1;314(2):291-300
Authors: Peelen S, Vervoort J
The riboflavin 5'-monophosphate (FMN) binding site of Desulfovibrio vulgaris flavodoxin in the diamagnetic...
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[NMR paper] Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibr
Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Overexpression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR.
Eur J Biochem. 1993 Dec 1;218(2):293-301
...
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[NMR paper] Homonuclear and heteronuclear NMR studies of oxidized Desulfovibrio vulgaris flavodox
Homonuclear and heteronuclear NMR studies of oxidized Desulfovibrio vulgaris flavodoxin. Sequential assignments and identification of secondary structure elements.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Homonuclear and heteronuclear NMR studies of oxidized Desulfovibrio vulgaris flavodoxin. Sequential assignments and identification of secondary structure elements.
Eur J Biochem. 1993 Apr 1;213(1):167-84
Authors: Knauf MA, Löhr F,...
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[NMR paper] Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NM
Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Structural studies of Desulfovibrio vulgaris ferrocytochrome c3 by two-dimensional NMR.
Eur J Biochem. 1992 Dec 15;210(3):931-6
Authors: Turner DL, Salgueiro CA, LeGall J, Xavier AV
Two-dimensional NMR has been used to make specific assignments for the four haems in Desulfovibrio vulgaris...
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[NMR paper] Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytoch
Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytochrome c3 by 2D-NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytochrome c3 by 2D-NMR.
FEBS Lett. 1992 Dec 14;314(2):155-8
Authors: Salgueiro CA, Turner DL, Santos H, LeGall J, Xavier AV
Using 2D-NMR the four haems of Desulfovibrio vulgaris (Hildenborough) cytochrome c3 within the X-ray structure were...