Related ArticlesHeteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex.
Biochemistry. 2000 Mar 14;39(10):2530-7
Authors: Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F
The combination of docking algorithms with NMR data has been developed extensively for the studies of protein-ligand interactions. However, to extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult to access. In the present work, we describe a new approach that combines an ab initio docking calculation and the mapping of an interaction site using chemical shift variation analysis. The cytochrome c553-ferredoxin complex is used as a model of numerous electron-transfer complexes. The 15N-labeling of both molecules has been obtained, and the mapping of the interacting site on each partner, respectively, has been done using HSQC experiments. 1H and 15N chemical shift analysis defines the area of both molecules involved in the recognition interface. Models of the complex were generated by an ab initio docking software, the BiGGER program (bimolecular complex generation with global evaluation and ranking). This program generates a population of protein-protein docked geometries ranked by a scoring function, combining relevant stabilization parameters such as geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We have implemented a new module that includes experimental input (here, NMR mapping of the interacting site) as a filter to select the accurate models. Final structures were energy minimized using the X-PLOR software and then analyzed. The best solution has an interface area (1037.4 A2) falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.
[NMR paper] Synechocystis ferredoxin/ferredoxin-NADP(+)-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking.
Synechocystis ferredoxin/ferredoxin-NADP(+)-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking.
Related Articles Synechocystis ferredoxin/ferredoxin-NADP(+)-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking.
FEBS Lett. 2005 Aug 29;579(21):4585-90
Authors: Palma PN, Lagoutte B, Krippahl L, Moura JJ, Guerlesquin F
Ferredoxin (Fd) and ferredoxin-NADP(+)-reductase (FNR) are two terminal physiological partners of the photosynthetic electron transport chain. Based on a nuclear magnetic resonance...
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12-01-2010 06:56 PM
[NMR paper] Filtering and selection of structural models: combining docking and NMR.
Filtering and selection of structural models: combining docking and NMR.
Related Articles Filtering and selection of structural models: combining docking and NMR.
Proteins. 2003 Oct 1;53(1):18-32
Authors: Dobrodumov A, Gronenborn AM
It is generally accepted that protein structures are more conserved than protein sequences, and 3D structure determination by computer simulations have become an important necessity in the postgenomic area. Despite major successes no robust, fast, and automated ab initio prediction algorithms for deriving accurate...
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[NMR paper] An NMR approach to structural proteomics.
An NMR approach to structural proteomics.
Related Articles An NMR approach to structural proteomics.
Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1825-30
Authors: Yee A, Chang X, Pineda-Lucena A, Wu B, Semesi A, Le B, Ramelot T, Lee GM, Bhattacharyya S, Gutierrez P, Denisov A, Lee CH, Cort JR, Kozlov G, Liao J, Finak G, Chen L, Wishart D, Lee W, McIntosh LP, Gehring K, Kennedy MA, Edwards AM, Arrowsmith CH
The influx of genomic sequence information has led to the concept of structural proteomics, the determination of protein structures on a...
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[NMR paper] A novel approach for assessing macromolecular complexes combining soft-docking calcul
A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
Related Articles A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
Protein Sci. 2001 Oct;10(10):2131-7
Authors: Morelli XJ, Palma PN, Guerlesquin F, Rigby AC
We present a novel and efficient approach for assessing protein-protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data...
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[NMR paper] A structural mode-coupling approach to 15N NMR relaxation in proteins.
A structural mode-coupling approach to 15N NMR relaxation in proteins.
Related Articles A structural mode-coupling approach to 15N NMR relaxation in proteins.
J Am Chem Soc. 2001 Apr 4;123(13):3055-63
Authors: Tugarinov V, Liang Z, Shapiro YE, Freed JH, Meirovitch E
The two-body Slowly Relaxing Local Structure (SRLS) model was applied to (15)N NMR spin relaxation in proteins and compared with the commonly used original and extended model-free (MF) approaches. In MF, the dynamic modes are assumed to be decoupled, local ordering at the N-H sites...
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chemical shift anisotropy (CSA) in model-free approach
Hi !
I have a quite general question about the value used for the CSA while studying protein dynamics of 15N-1H vectors with model-free approach.
In the litterature, we mainly find two values for the CSA (-160 and -172 ppm).
There is, if I understand well, a link between the bond length and the CSA, but everyone seems to agree about using the same value of 1.02 A which should give rise to a mean S2 of 0.85 for secondary structure when combined to a CSA of -172 ppm. When using a CSA of -160 ppm, the mean S2 for secondary structure should slightly rise up from 0.85.
The manuals for...
Heteronuclear NMR and soft docking: an experimental approach for a structural model o
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