Molecular model of a barley xyloglucan endotransglucosylase (HvXET5) enzyme. The electrostatic potential is mapped onto molecular surface of HvXET5. The deep substrate-binding cleft contains conserved catalytic amino acid residues with a bound hexasaccharide acceptor substrate (sticks).The Figure was prepared with APBS (Adaptive Poisson-Boltzmann Solver) implemented in PyMol.

The 3D models of a cotton chitinase-like protein (magenta) and the template barley chitinase (cyan), are very similar with only three non-matching loop regions in the cotton protein (yellow arrows). The overall geometry of the active site cleft is also conserved, but its detailed shape was changed so that the cotton chitinase-like protein was predicted to have chitin-binding activity but lack hydrolytic activity. White arrows indicate NH2- and COOH- termini of the proteins. The Figure was prepared with PyMol.

Protein modelling using SAPAC supercomputers and Stereo 3D Workstations

A./Prof. Maria Hrmova, Australian Centre for Plant Functional Genomics (ACPFG)

Protein modelling provides techniques whereby the three-dimensional structure and biological function of a protein molecule can be identified. Associate Professor Maria Hrmova from the Australian Centre for Plant Functional Genomics and the University of Adelaide solves the structures of agriculturally significant grass proteins for research into improving crop resistance to abiotic stress.

We first take the reflection file generated through X-Ray Crystallographic processes and use the CCP4 and CNS programs to calculate the initial structural factors and electron density maps. These calculations can be computationally intensive and running this software on SAPAC facilities has significantly reduced processing time.

We then associate the electron density map to chemical information, evaluating and refining the initial data supplied. Software such as PyMol, XtalView and SPDBViewer are used to view the protein model and to assess its accuracy. We use a stereo three-dimensional workstation specification developed by SAPAC to perceive the protein model in three-dimensional orientation. A stereo three-dimensional display is essential to precisely annotate the position of the object in three-dimensional cartesian space.

Stereo visualisation makes it possible to precisely interpret the electron density map with respect to its structural features like backbone or ligands and how these features relate to each other. Interactions between these and other components, such as those between protein and DNA or protein and carbohydrate can then be modelled to help determine the precise biological role of the protein in the organism.

The SAPAC visualisation workstation has supplied the necessary tools: workstation graphics card, high-end CRT monitor, emitter, glasses and was pre-installed with Linux and open source visualisation software.

All molecular 3D models and images by Maria Hrmova.