Projects / Programmes
Simulations and structural analysis of protein surface water
| Code |
Science |
Field |
Subfield |
| 1.07.00 |
Natural sciences and mathematics |
Computer intensive methods and applications |
|
| Code |
Science |
Field |
| B120 |
Biomedical sciences |
Molecular biophysics |
| P170 |
Natural sciences and mathematics |
Computer science, numerical analysis, systems, control |
molecular dynamics, parallel computer simulations, empirical atomic force field, protein hydration, protein surface, small angle scattering intensity, numerical analysis, explicit water models, pair correlation functions, water density changes, dipole-dipole interaction
Researchers (2)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
17255 |
Tatjana Karba |
|
Technical associate |
2003 - 2005 |
0 |
| 2. |
13627 |
PhD Franci Merzel |
Computer intensive methods and applications |
Head |
2003 - 2005 |
220 |
Organisations (1)
| no. |
Code |
Research organisation |
City |
Registration number |
No. of publicationsNo. of publications |
| 1. |
0104 |
National Institute of Chemistry |
Ljubljana |
5051592000 |
21,425 |
Abstract
The aim of the proposed work is to develop and apply new algorithms for analysis of the hydration water structure close to the protein surface. Characterization of the physical properties of protein surface hydration water is critical for understanding protein structure, functioning and folding. We will use molecular dynamics simulation techniques to provide further explanation of recent X-ray and neutron solution scattering data that indicate that the density of water on the surface of some solvated proteins is significantly higher than that of bulk water. The results of our previous work show that the simulation-derived scattering profiles for lysozyme are in excellent agreement with experiment. In the simulation the 0.3nm-thick first hydration layer is 15% denser than bulk water. About two-thirds of this increase is due to a geometric contribution (because of the correlation with the protein surface) that would also be present if the water were unperturbed from the bulk. The remaining third arises from modification of the water structure and dynamics, involving approximately equal contributions from shortening of the average water-water O...O distance and an increase in the coordination number. In our previous work we have shown that the density variation in the first hydration shell is determined by electrostatic properties of the protein surface and local surface topography. The mechanisms of these phenomena will be explained by means of simple theoretical models alowing to treat each of the structure determining effects separately. The well-established correlation between denser water and more-parallel water-dipoles alignment suggests an important role of dipole-dipole interaction between neighbouring water molecules as a structure determining factor. The interplay between the dipole-dipole interaction and electric field generated by the protein atoms will be analysed in detail. In addition, the extent of density variations will be compared for different empirical potentilas used for the explicit water model.
