scholarly journals Determination of Protein Structural Ensembles by Hybrid-Resolution SAXS Restrained Molecular Dynamics

2020 ◽  
Vol 16 (4) ◽  
pp. 2825-2834 ◽  
Author(s):  
Cristina Paissoni ◽  
Alexander Jussupow ◽  
Carlo Camilloni
Keyword(s):  
Molecular Dynamics ◽  
Structural Ensembles ◽  
Restrained Molecular Dynamics

scholarly journals Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion protein, by1H NMR and restrained molecular dynamics

1999 ◽  
Vol 266 (3) ◽  
pp. 1192-1201 ◽  
Author(s):  
Enzio Ragg ◽  
Fabrizio Tagliavini ◽  
Paolo Malesani ◽  
Luca Monticelli ◽  
Orso Bugiani ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Prion Protein ◽  
Solution Conformations ◽  
Restrained Molecular Dynamics

Determination of the conformation of d(GGAAATTTCC)2 in solution by use of proton NMR and restrained molecular dynamics

Biochemistry ◽  
1990 ◽  
Vol 29 (31) ◽  
pp. 7214-7222 ◽  
Author(s):  
Masato Katahira ◽  
Hiromu Sugeta ◽  
Yoshimasa Kyogoku ◽  
Satoshi Fujii
Keyword(s):  
Molecular Dynamics ◽  
Proton Nmr ◽  
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.

Determination of the Stress Distribution at the Interface Metal-Oxide: Numerical and Theoretical Considerations

2005 ◽  
Vol 237-240 ◽  
pp. 145-150 ◽  
Author(s):  
Sébastien Garruchet ◽  
A. Hasnaoui ◽  
Olivier Politano ◽  
Tony Montesin ◽  
J. Marcos Salazar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Stress Distribution ◽  
Oxide Film ◽  
Metal Oxide ◽  
Reaction Kinetics ◽  
Analytical Model ◽  
Equilibrium Thermodynamics ◽  
Theoretical Considerations ◽  
Molecular Dynamics Results

In this paper we give a brief presentation of the approaches we have recently developed on the oxidation of metals. Firstly, we present an analytical model based on non-equilibrium thermodynamics to describe the reaction kinetics present during the oxidation of a metal. Secondly, we present the molecular dynamics results obtained with a code specially tailored to study the oxidation and growth of an oxide film of aluminium. Our simulations present an excellent agreement with experimental results.

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