## Abstract Several molecular dynamics simulations were performed on three proteins—bovine apo‐calbindin D9K, human interleukin‐4 R88Q mutant, and domain IIA of __bacillus subtilis__ glucose permease—with each of the AMBER94, CHARMM22, and OPLS‐AA force fields as implemented in CHARMM. Structural a
Calculation of Protein-Polymer Force Fields Using Molecular Dynamics
✍ Scribed by William G. Pitt; Daniel R. Weaver
- Publisher
- Elsevier Science
- Year
- 1997
- Tongue
- English
- Weight
- 325 KB
- Volume
- 185
- Category
- Article
- ISSN
- 0021-9797
No coin nor oath required. For personal study only.
✦ Synopsis
Molecular dynamics simulations were performed to determine gradient of U is known as the force function F and describes the force field of attraction between Leu-enkephalin and a model the forces interacting within the configuration. Various popolyethylene surface. Four separate rotational orientations of the tential functions have been developed for atoms, some mopolypeptide were simulated. During the simulations the surface lecular groups, and a few small molecules, but not for comatoms were held static, but the water atoms were dynamic. Some plex molecules such as polymers or proteins. If such a potensimulations were studied employing restricted dynamics of the tial or force function was available for a polymer-protein polypeptide in which only the five backbone a-carbon atoms held pair, it would be useful in predicting interaction energy, immobile. For an orientation with oxygen atoms toward the PE adsorption energy, and even the probability of adsorption of surface the force between the enkephalin and the surface was repulsive and was approaching zero as the separation reached 8 a particular conformation or orientation of the protein.
A ˚. The maximum repulsive force reached 8 kcal/mole/A ˚at 2.7 A ˚This paper presents the development of interaction force separation. For an orientation with hydrophobic groups toward fields and potentials for crystalline polyethylene and leucine the PE, the force was attractive with a minimum in the force enkephalin, a small pentapeptide. Subsequent papers will field of 4 kcal/mole/A ˚at 2.3 A ˚. Two other orientations were also discuss the use of the force fields to predict the probability investigated. The results of the MD simulations indicated that the of adsorption of various orientations and the prediction of force between enkephalin and PE in the region 0 õ z õ 9.5 A ˚adsorption rates.
was mostly a function of the separation distance and the orientation angle of enkephalin with respect to the surface.
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