scholarly journals Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems

2016 ◽  
Vol 85 (1) ◽  
pp. 155-176 ◽  
Author(s):  
Clay A. Foster ◽  
Ann H. West
Keyword(s):  
Molecular Dynamics ◽  
Signaling Systems ◽  
Two Component ◽  
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.

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

Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

Biochemistry ◽  
1993 ◽  
Vol 32 (47) ◽  
pp. 12612-12623 ◽  
Author(s):  
John Santa Lucia ◽  
Douglas H. Turner
Keyword(s):  
Molecular Dynamics ◽  
Restrained Molecular Dynamics
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