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Gallery

The example images are all based on the structure of the Ras p21 protein (Ras, for short) determined by NMR spectroscopy (Kraulis et al 1994). For simplicity, the hydrogen atoms have been stripped from the coordinate file ras.pdb, which is used in all example input files. The example input files are available in the distribution directory molscript/examples.

General example images

Image (small JPEG) In other formats Input file
ras_std PostScript
Raster3D (SGI)
Raster3D (JPEG)
VRML 2.0
VRML 2.0 gzipped
EPS
SGI
JPEG (large)
PNG
GIF

ras_std.in

The secondary structure colouring is the default from MolAuto.

ras_rmsd PostScript
Raster3D (SGI)
Raster3D (JPEG)
VRML 2.0
SGI
JPEG (large)

ras_rmsd.in

The same as above, but with colouring according to RMSD of the atoms, by setting the residuecolour... b-factor and colourparts parameters. Notice that the colours vary over the secondary structure elements.

ras_shiny VRML 2.0
SGI
JPEG (large)
PNG

ras_shiny.in

The secondary structure colouring is the default from MolAuto. The specularcolour parameter has been set to white, and the shininess of the atoms increased to 0.6.

ras_cyl PostScript
VRML 2.0
VRML 2.0 gzipped
JPEG (large)
GIF

ras_cyl.in

Cylinders for helices, and colouring according to secondary structure type; highlighting loops involved in ligand binding and conformational variability.

ras_gdp Raster3D (SGI)
Raster3D (JPEG)
VRML 2.0
VRML 2.0 gzipped
JPEG (large)

ras_gdp.in

Closeup of the GDP molecule and some interacting residues. Some labels are shown and some interactions are shown schematically.

VRML example images

A set of VRML files and HTML text organized into frames show some possibilities of how to use VRML for description of protein structures, involving anchors. Also an example showing the use of the level-of-detail (LOD) construct.

MolAuto example images

These images were generated directly from the PDB data set via the MolAuto program, which produces first-approximation input files from a PDB file. It should be noted that the view orientation is not very good; MolAuto does not transform the coordinates in any way.

Command-line options Image (small JPEG) Files
[none: default] molauto PostScript
VRML 2.0
VRML 2.0 gzipped
JPEG (large)
-nice -cpk molauto nice PostScript
VRML 2.0
VRML 2.0 gzipped
JPEG (large)

The Ras p21 protein

The Ras p21 protein is a central component in the cell-signalling system that transmits extra-cellular growth signals via cell membrane receptors, via a cascade of signalling molecules into the nucleus. It is present in many cell types, and several forms of cancer are associated with a mutated form of the protein, where it is locked in a growth-promoting state.

Ras p21 is an enzyme; it hydrolyzes GTP (guanosine triphosphate) to GDP (guanosine diphosphate); it is a GTPase. The protein exists in vivo as a ternary complex with one magnesium ion (Mg) and GDP (or GTP).

The function of Ras is to act as a molecular switch with two possible states, on or off. In the GTP-bound form it is active, and binds to certain other proteins called effectors. The effectors transmit the growth signal further down the signal transduction cascade. This is how Ras p21 transmits the growth signal to the rest of the molecular machinery in the cell.

The signal is switched off by hydrolysis of the GTP to GDP. Ras is fairly inefficient as an enzyme in itself, but its catalytic rate is considerably enhanced by interaction with certain other proteins, such as Ras-GAP (GTPase Activating Protein). Other molecules are responsible for activating Ras by promoting exchange of the GDP molecule for a GTP molecule, as a response to extra-cellular signals.

In many of the cancer-associated mutants of the Ras p21 protein, the ability to hydrolyse GTP is impaired. The active GTP form of the protein is therefore not converted into the inactive GDP form as fast as it should, so the growth signal is transmitted for too long. This contributes to the uncontrolled cellular growth which is characteristic of tumours.

The Ras p21 protein is also the prototypical representative for a large class of signalling proteins called the small GTPases. Other proteins in this family are Rho and Rab.

The Ras p21 structure

The 3D structure of Ras p21 used in these example images was determined by heteronuclear multidimensional NMR spectroscopy, as described in:

Kraulis P.J., Domaille P.J., Campbell-Burk S.L., Van Aken T., & Laue E.D.
Solution structure and dynamics of Ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy.
Biochemistry (1994) vol 33, pp 3515-3531. PubMed PMID:8142349

The RSCB Protein Data Bank (PDB) code for the coordinate set used in these example images is 1CRQ, which contains the minimized average structure. All hydrogen atoms were stripped from the coordinate file before use, for simplicity.

The 40 individual structures are available in two separate PDB data sets with 20 structures each: 1CRR and 1CRP.

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