Practical applications of time-averaged restrained molecular dynamics to ligand-receptor systems: FK506 bound to the Q50R,A95H,K98I triple mutant of FKBP-13

1996 ◽  
Vol 8 (1) ◽  
Author(s):  
ChristopherA. Lepre ◽  
DavidA. Pearlman ◽  
Olga Futer ◽  
DavidJ. Livingston ◽  
JonathanM. Moore
Keyword(s):  
Molecular Dynamics ◽  
Triple Mutant ◽  
Practical Applications ◽  
Restrained Molecular Dynamics

scholarly journals Molecular Dynamics Simulation on the Interaction between Palygorskite Coating and Linear Chain Alkane Base Lubricant

Coatings ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 286
Author(s):  
Jin Zhang ◽  
Lv Yang ◽  
Yue Wang ◽  
Huaichao Wu ◽  
Jiabin Cai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Molecular Diffusion ◽  
Linear Chain ◽  
Interfacial Interaction ◽  
Dynamics Simulation ◽  
Electrostatic Energy ◽  
Experimental Development ◽  
Practical Applications ◽  
Self Diffusion

Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C12, tetradecane C14, hexadecane C16, and octadecane C18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C12 molecule exhibited higher self-diffusion coefficient values than C14, C16 and C18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.

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

REFINED SOLUTION STRUCTURE OF Al3+-THYMULIN COMPLEXES BASED ON RESTRAINED MOLECULAR DYNAMICS CALCULATIONS

1997 ◽  
Vol 20 (12) ◽  
Author(s):  
Jean-Pierre Laussac ◽  
Philippe Arnaud ◽  
Piotr Orlewski ◽  
Manh-Thong Cung
Keyword(s):  
Molecular Dynamics ◽  
Solution Structure ◽  
Molecular Dynamics Calculations ◽  
Restrained Molecular Dynamics
Sign in / Sign up

Export Citation Format

Share Document