8.4 Surface calculation
VEGA ZZ can calculate and display some types of
molecular surface trough its 3D engine. It's possible to display some local molecular
properties like hydropathicity, lypophilicity, volume, molecular charges, etc.
VEGA uses two methods to generate the surfaces. For dotted surfaces, it
uses the fast double cubic lattice method implemented in the NSC approach (F.
Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, J. Comput. Chem,
Vol. 16 N3, 273-284, 1995). For solid and mesh surfaces, it uses a method
called marching cubes implemented in the source code provided by Paul
Bourke (for more information, click
here) and it's based on the surface facet approximation to an isosurface
through a scalar field sampled on a rectangular 3D grid.
The surface properties (DEEP, ILM, MEP, MLP and PSA) are
calculated for each dot with the appropriate algorithm.
The DEEP algorithm is very simple: for each dot is calculated its distance from the geometric center of the molecule. This property is useful to color the surface by gradient in order to highlight the deep pockets and the cavities of the molecule.
The ILM method is based on the principle that at equilibrium the solvent molecules will be more probably found near the hydrophilic regions of the solute, while they will be repelled by the more hydrophobic moieties. The method allows the calculation of a global hydropathicity index (ILM) and this property can be also projected on the molecular surface, giving rise to a very detailed local hydropathicity mapping. The computational steps required for the ILM calculation are:
1) Solvatation of the molecule using a
water cluster (see the solvent cluster section).
2) Molecular dynamics (T= 300K, time step = 1 fs). The simulation length is in
function of the system complexity and please remember that the solvent-solute
environment will be at the equilibrium.
3) ILM calculation.
The equation used to calculate the ILM property is the following:
where: dij is the distance between the the solute atom i and the mass center of the water molecule j, na is the number of the solute atoms and ns is the number of water molecules (A. Pedretti, A.M. Villa, L. Villa, G. Vistoli, Internet Journal of Chemistry, Vol. 45 (7), Art. 13, 2000).
The Molecular Electrostatic Potential (MEP) surface is calculated projecting the atomic charge on the surface. The value of each i surface dot is calculated with the following equation:
Where: | ||
Vi | = | projected value on the i surface dot. |
Qj | = | partial charge of the j atom. |
dij | = | distance between the i dot and j atom. |
The Molecular Lipophilicity Potential (MLP) is calculated projecting the Broto-Moreau lipophilicity atomic constants on the molecular surface (P. Gaillard, P.A. Carrupt, B. Testa, A. Boudon, J. C.A.M.D., Vol. 8, 83, 1994)
The Polar Surface Area (PSA) is calculated considering polar and apolar atom surfaces. Apolar are C and H bonded to C. Polar atoms are O, S, H, P and H not bonded to C. These properties are projected on the surfaces using two color codes: blue (apolar surface) and red (polar surface).
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In the New tab of the Surface management window, are placed the controls to calculate a new surface. In the top-right box, you can choose the shape type (Dots, Mesh and Solid) and use the Type field to select the surface type (see the following table), the Probe Rad. field to enter the probe radius and the Density field to enter the surface dot density. This last field could be replaced by the Mesh size, if you select Mesh or Solid surface shape. The probe radius can't be changed for all surface property types.
Type | Description | Probe Rad. |
VdW | Van der Waals Surface accessible to solvent |
Yes |
DEEP | Deep surface | Yes |
MEP | Molecular Electrostatic Potential | No |
MLP | Molecular Lypophilic Potential | No |
ILM | Hydropathicity profile (a water cluster is needed) |
No |
PSA | Polar Surface Area | Yes |
Checking Consider selected atoms only, it's possible calculate the surface of the visible atoms only. At the end of the surface calculation, in the console you can read the area in Ų and the range of values assigned at each point. If you want color the surface by property using a color gradient, you must check the Color by gradient option (see the surface gradient section).
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Dotted surface | |
Mesh surface | ![]() |
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Solid surface | |
Multiple solid sufaces | ![]() |
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Color by atom | |
Color by residue | ![]() |
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Color by chain | |
Color by segment | ![]() |
![]() With the Dot size slider you can change the dot size of a dotted surface. When you select values greater than four, the dots are converted in small spheres. |
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Transparent surface | |
Dotted surface with small spheres | ![]() |
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