scholarly journals Structure Determination by Restrained Molecular Dynamics Using NMR Pseudocontact Shifts as Experimentally Determined Constraints

1999 ◽  
Vol 121 (40) ◽  
pp. 9276-9285 ◽  
Author(s):  
Kechuan Tu ◽  
Miriam Gochin
Keyword(s):  
Molecular Dynamics ◽  
Structure Determination ◽  
Pseudocontact Shifts ◽  
Restrained Molecular Dynamics

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

The lanthanide-shifted N.M.R. spectra of some cyclopentadienone-cobalt complexes

1975 ◽  
Vol 28 (8) ◽  
pp. 1681 ◽  
Author(s):  
RS Dickson ◽  
SH Johnson ◽  
ID Rae
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Carbonyl Group ◽  
Structure Determination ◽  
Cobalt Complexes ◽  
Hydrogen Atoms ◽  
Pseudocontact Shifts ◽  
Lone Pairs ◽  
Nuclear Magnetic Resonance Spectra ◽  
Lanthanide Shift Reagents

The effect of the lanthanide shift reagents, Eu(fod)3 and Pr(fod)3, on the nuclear magnetic resonance spectra of some (η4-cyclopentadienone)(η- cyclopentadienyl)cobalt complexes has been investigated as an aid to structure determination in this series. The lanthanides complex with the lone pairs of the carbonyl group. Pseudocontact shifts are observed for hydrogens attached to each ring and for hydrogen atoms in substituents on the cyclopentadienone. With Eu(fod)3, contact shifts are also observed for the cyclopentadienone ring hydrogens.

Exploration of disorder in protein structures by X-ray restrained molecular dynamics

1991 ◽  
Vol 10 (4) ◽  
pp. 340-358 ◽  
Author(s):  
John Kuriyan ◽  
Klara Ösapay ◽  
Stephen K. Burley ◽  
Axel T. Brünger ◽  
Wayne A. Hendrickson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structures ◽  
X Ray ◽  
Restrained Molecular Dynamics

Conformational Studies on Pentagastrin by 2D NMR and Restrained Molecular Dynamics

1995 ◽  
Vol 28 (5) ◽  
pp. 761-772 ◽  
Author(s):  
Weiping Shao ◽  
Sansan Wan ◽  
Jinhua Wei ◽  
Wenxia Tang
Keyword(s):  
Molecular Dynamics ◽  
2D Nmr ◽  
Conformational Studies ◽  
Restrained Molecular Dynamics
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