Related ArticlesSOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models suggest a role for side chain flexibility in protein hydrodynamics.
Structure. 2005 May;13(5):723-34
Authors: Rai N, Nöllmann M, Spotorno B, Tassara G, Byron O, Rocco M
Reduced numbers of frictional/scattering centers are essential for tractable hydrodynamic and small-angle scattering data modeling. We present a method for generating medium-resolution models from the atomic coordinates of proteins, basically by using two nonoverlapping spheres of differing radii per residue. The computed rigid-body hydrodynamic parameters of BPTI, RNase A, and lysozyme models were compared with a large database of critically assessed experimental values. Overall, very good results were obtained, but significant discrepancies between X-ray- and NMR-derived models were found. Interestingly, they could be accounted for by properly considering the extent to which highly mobile surface side chains differently affect translational/rotational properties. Models of larger structures, such as fibrinogen fragment D and citrate synthase, also produced consistent results. Foremost among this method's potential applications is the overall conformation and dynamics of modular/multidomain proteins and of supramolecular complexes. The possibility of merging data from high- and low-resolution structures greatly expands its scope.
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
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A Large-scale Comparison of Computational Models on the Residue Flexibility for NMR-derived Proteinss.
A Large-scale Comparison of Computational Models on the Residue Flexibility for NMR-derived Proteinss.
A Large-scale Comparison of Computational Models on the Residue Flexibility for NMR-derived Proteinss.
Protein Pept Lett. 2011 Sep 20;
Authors: Zhang H, Shi H, Hanlon M
Abstract
As an alternative to X-ray crystallography, nuclear magnetic resonance (NMR) has also emerged as the method of choice for studying both protein structure and dynamics in solution. However, little work using computational models such as Gaussian network model...
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09-22-2011 04:25 PM
NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation.
NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation.
NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation.
Biochemistry. 2011 Mar 29;50(12):2123-34
Authors: Roberts AG, Sjögren SE, Fomina N, Vu KT, Almutairi A, Halpert JR
To understand the molecular basis of sequential N-dealkylation by cytochrome P450 2B enzymes, we studied the binding of...
[NMR paper] Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions.
Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions.
Related Articles Bead-linked proteoliposomes: a reconstitution method for nmr analyses of membrane protein-ligand interactions.
J Am Chem Soc. 2005 Aug 31;127(34):12021-7
Authors: Yokogawa M, Takeuchi K, Shimada I
Structural information about the interactions between membrane proteins and their ligands provides insights into the membrane protein functions. A variety of surfactants have been used for structural analyses of membrane...
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12-01-2010 06:56 PM
[NMR paper] High-quality homology models derived from NMR and X-ray structures of E. coli protein
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Related Articles High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Protein Sci. 2005 Jun;14(6):1597-608
Authors: Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T
The structural...
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11-25-2010 08:21 PM
[NMR paper] An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-
An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.
Related Articles An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.
Biochemistry. 1994 May 31;33(21):6424-32
Authors: Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA
A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the...
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08-22-2010 03:33 AM
[NMR paper] An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-
An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.
Related Articles An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2-Fe, 2-S ferredoxin from Pseudomonas.
Biochemistry. 1994 May 31;33(21):6424-32
Authors: Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA
A model for the solution structure of oxidized putidaredoxin (Pdx), a 106-residue globular protein containing a Fe2S2 cluster, has been determined using homonuclear NMR methods. Pdx is the first of the...
SOMO (SOlution MOdeler) differences between X-Ray- and NMR-derived bead models sugges
Linear Mode
