Molecular surface color coding

In situations where, either from previous QSAR work or from experimental evidence, it is known or suspected that differences in the reactivity of a set of molecules are attributed primarily to their hydrophobic rather than their electrostatic properties it is probably of more use to compare molecular surfaces that display hydrophobicity or polarity information. Indeed, dotted molecular surfaces color-coded by hydrophobic character have been used very successfully by Hansch and coworkers to rationalize QSARs from several different systems (418,419). This concept has been extended to calculate the hydrophobic field surrounding a molecule by Kellogg and Abraham (420,421 )and utilized in CoMFA studies. 

To display properties on molecular surfaces, two different approaches are applied. One method assigns color codes to each grid point of the surface. The grid points are connected to lines chicken-wire) or to surfaces (solid sphere) and then the color values are interpolated onto a color gradient [200]. The second method projects colored textures onto the surface [202, 203] and is mostly used to display such properties as electrostatic potentials, polarizability, hydrophobidty, and spin density. 

Figure Bll.1.1 represents a 3T3 cell stained with BODIPY FL C5-ceramide (from Molecular Probes), a specific stain for the Golgi apparatus The color coding for the lifetimes is from 0 to 5 ns. The lifetime is coded in color (right upper) and this color-coded lifetime information is mapped onto the intensity surface (upper left) to give the combined lifetime/intensity plot (lower right). The final combined image shows intensity contours (in white), and a lit intensity surface is employed to accentuate the information in a three-dimensional form.

Fig. 5. Three views of the NCP from Harp et al. [31]. (a) Ventral surface view, (b) Side view, (c) View down the molecular pseudo-dyad axis. The histones are represented by Ca ribbon models of the secondary structure elements, and the DNA model indicates the base pairing between complementary strands. The DNA is positioned asymmetrically by one-half base pair on the NCP. This results in a two sides arbitrarily referred to a dorsal and ventral (the surface shown here). The ventral surface of the NCP is best recognized by the extended N-terminal H3 tail protruding to the right. In these images, the pseudo-dyad axis is represented by vertical bars for both the ventral and side view. The pseudo-dyad axis passes through the center of the dyad view orthogonal to the plane of the page, (d) Color code for histone chains in the figures in this chapter. Note the change in hue denoting the two sides of the histone octamer.

In order to visualize the results of MLP calculations for a given set of parameters and molecules, a LipoDyn output file for the molecular surface can be color-coded by the MLP values and displayed in VRML 2.0 format... 

Feldmann and others have developed a series of teaching tools for macromolecular structure using color-coded molecular graphics-derived images 24 28). Connolly and others have improved upon this approach by clearly showing which portions of the protein surface are indeed accessible to a water molecule, as opposed to those portions which are inaccessible, such as in clefts, etc 27). Images based on the Connolly methods directly show those regions of the protein surface which can be expected to interact with other molecules. It provides immediate, comprehensible information about steric complimentarity. 

Fig. 4.1. COSMO surfaces of water and CO2 color coded by the polarization charge density a. Red areas denote strongly negative parts of the molecular surface and hence strongly positive values of a. Deep blue marks denote strongly positive surface regions (strongly negative a) and green denotes nonpolar surface.

The molecular surface concept is not only useful for a representation of the bulkiness and the shape of molecules. These surfaces can also be used as screens for the visualization of many properties by means of color coding techniques. Color coding is a popular means of displaying scalar information on a surface. " " Every three-dimensional scalar or vector field that may be generated on the basis of the position of atomic or molecular fragments can be visualized by color coding on a given surface. 

The comparison of two given molecular surfaces on the basis of curvature can be done interactively by the use of two-dimensional texture maps, with color coding of the two canonical curvatures calculated for different selection distances along the x and y coordinate of the texture map. However, the information from the curvature profile can be further reduced by introducing a surface topography index STI as demonstrated by... 

In the work of Zachmann et al. new approaches to the quantification of surface flexibility have been suggested. The basis data for these approaches are supplied by molecular dynamics (MD) simulations. The methods have been applied to two proteins (PTI and ubiquitin). The calculation and visualization of the local flexibility of molecular surfaces is based on the notion of the solvent accessible surface (SAS), which was introduced by Connolly. For every point on this surface a probability distribution p(r) is calculated in the direction of the surface normal, i.e., the rigid surface is replaced by a soft surface. These probability distributions are well suited for the interactive treatment of molecular entities because the former can be visualized as color coded on the molecular surface although they cannot be directly used for quantitative shape comparisons. In Section IV we show that the p values can form the basis for a fuzzy definition of vaguely defined surfaces and their quantitative comparison. 

H, white O, red). The ball-and stick model is shown inside a computer-generated molecular surface. The surface is color-coded to show how charge ranges from very positive (red) to very negative (blue). 

Color-coded molecular surfaces can provide qualitative or quantitative displays of hydrophobic and hydrophilic regions, neutral and charged amino acid side chains, electrostatic potential, and conformational mobility of side chains (based on the temperature factors from X-ray crystallographic refinement or moelcular dynamics simulation). Color-coding by hydro-... 

Figure 2. Molecular (a), van der Waals (b), and extra radius (c) surfaces of chymotrypsin-tosyl inhibitor complex. The surface is color-coded by hydrophobicity as described in the text red = hydrophobic, blue = hydrophilic, neutral = yellow. The tosyl group is covalently attached to the sidechain hydroxyl of Ser-195. The catalytic triad of His-57, Asp-102, and Ser-195 is shown in green. (The coordinates for this and all other molecules in the following figures are from the Brookhaven Protein Data Bank (14) except where otherwise noted.)... 

Figure 3. Cu. Zn superoxide dismutase—electrostatic potential mapped onto the enzyme s molecular surface to show the highly positive potential around the active site channel (S3). The dots are color-coded by electrostatic potential red, <-21kcal/mol yellow, -21 to -7 kcal/ mol green, -7 to +7 kcal/mol cyan, +7 to 21 kcal/mol blue, > 21 kcal/mol. The bound copper ion is shown by the purple sphere.

Figure 8. Probe map of E. coli dihydrofolate reductase-methotrexate (10) complex. The calculated minimum energy positions for an ammonium probe (blue) and carboxylate oxygen probe (yellow) closely match the experimental positions for the pteridine amino groups and the carboxyl of methotrexate (20,21). The molecular surface of the enzyme is purple, while all bonds are color-coded by atom type carbon = white, nitrogen = blue, oxygen = red, sulfur = yellow. 

Figure 25. Bovine phospholipase A2 with model of benzylacenapthene (12, yellow) binding. The active site molecular surface is color-coded by hydrophobicity as in Figure 2 and the bonds for the enzyme are color-coded by atom type as in Figure 8. The bound Ca+ + ion is shown by the green sphere. 

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