1eky
From Proteopedia
(New page: 200px<br /><applet load="1eky" size="450" color="white" frame="true" align="right" spinBox="true" caption="1eky" /> '''MODEL STRUCTURE FROM NON-NOE BASED NMR STRUC...) |
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| - | [[Image:1eky.jpg|left|200px]]<br /><applet load="1eky" size=" | + | [[Image:1eky.jpg|left|200px]]<br /><applet load="1eky" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1eky" /> | caption="1eky" /> | ||
'''MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION'''<br /> | '''MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Orientational and novel long-range order restraints available from | + | Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation. |
==About this Structure== | ==About this Structure== | ||
| - | 1EKY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus] with HEM as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1EKY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Rhodobacter_capsulatus Rhodobacter capsulatus] with <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EKY OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Blackledge, M.]] | [[Category: Blackledge, M.]] | ||
| - | [[Category: Hus, J | + | [[Category: Hus, J C.]] |
[[Category: Marion, D.]] | [[Category: Marion, D.]] | ||
[[Category: HEM]] | [[Category: HEM]] | ||
[[Category: four helix bundle]] | [[Category: four helix bundle]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:28:50 2008'' |
Revision as of 10:28, 21 February 2008
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MODEL STRUCTURE FROM NON-NOE BASED NMR STRUCTURE CALCULATION
Overview
Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from the nuclear Overhauser effect. By exploiting the complementary geometric dependence of paramagnetic pseudocontact shifts and the recently proposed Curie-dipolar cross correlated relaxation effect, in combination with orientational constraints derived from residual dipolar coupling, autorelaxation rate ratios and secondary structure constraints, it is possible to define uniquely the fold and refine the tertiary structure of the protein (0.73 A backbone rmsd for 82/129 amino acid residues) starting from random atomic Cartesian coordinates. The structure calculation protocol, developed using specific models to describe the novel constraint interactions, is robust, requiring no precise a priori estimation of the various interaction strengths, and provides unambiguous convergence based only on the value of the target function. Tensor eigenvalues and their component orientations are allowed to float freely, and are thus simultaneously determined, and found to converge, during the structure calculation.
About this Structure
1EKY is a Single protein structure of sequence from Rhodobacter capsulatus with as ligand. Full crystallographic information is available from OCA.
Reference
De novo determination of protein structure by NMR using orientational and long-range order restraints., Hus JC, Marion D, Blackledge M, J Mol Biol. 2000 May 19;298(5):927-36. PMID:10801359
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