Graphics Systems Structures System

Figure 3.18 Secondary structure of matrix metalloproteinase 12 (MMP12) (A) PDB lYCM (structure determined using solution NMR) and (B) PDB IRMZ (structure determined using X-ray crystallography). Visualized using The PyMOL Molecular Graphics System and ChemDraw Ultra, version 10.0. (Printed with permission of Delano Scientific, LLC and CambridgeSoft Corporation.) (See color plate)...

In the fifth step of an X-ray structure determination the electron density map is calculated using the intensities and phase information. This map can be thought of as a true three-dimensional image of the molecule revealed by the X-ray microscope. It is usually displayed as a stereoscopic view on a computer graphics system (Fig. 3-22). It is also often prepared in the form of a series of transparencies mounted on plastic sheets. Each sheet represents a layer, perhaps 0.1 ran thick, with contour lines representing different levels of electron density. 

It is beyond the scope of this little book to cover all the tools available for studying protein structure. I will conclude by listing and briefly describing additional tools, especially ones used in conjunction with modeling on graphics systems. 

Figure 9. The structure of GCAP3 (Stephen et at., 2006). Residues that correspond to pathogenic mutations in GCAP1, the structure of which is unknown, are shown in yellow with the side chains. Ca2+ is shown as yellow spheres. Molecular graphics representations were created with PYMOL (Warren L. DeLano The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA. http //www.pymol.org) (See Colour Plate 9)...

The challenge of how to represent the receptor that is deduced from these results is greatly helped by the use of computer graphics systems. For example, it was used to show the complementarity of molecular surfaces in the crystal structure of the complex between an antibody and lysozyme. The contact area is about 20x20 A. Side chains from one, such as Gin 121 of lysozyme, fit in a depression on the surface of the other protein. Interactions with small antigens, such as phosphorylcholine, have also demonstrated the specificity of the interactions between antibodies and antigens. 

A. 1.1 A useful graphical organizer that represents properties as emergent from the systemic structure which is comprised of elements, rules and boundary/ background space. 

The most popular graphics systems for protein structure research are those manufactured by Evans and Sutherland and by Vector General. These employ a colour vector display system and are linked to a host computer. Manufacturers now provide their own graphic support processor capable of controlling completely the graphics system and of being interfaced to any host computer. The display systems are... 

Fig. 22 The molecular shape of tetramer with a Cn spacer unit shows the minimized structure in the gas phase at absolute zero using a Silicon Graphics system operating with Quanta and CHARMm software...

G2 allows the representation of deep knowledge, analytic and heuristic knowledge, and other aspects required for the implementation of real-time expert systems. Graphics and structured natural language interfaces allow the user to construct knowledge bases of dynamic applications, to test expert system behavior and to validate knowledge bases under various dynamic scenarios. The interactive developer interface allows short development-... 

Figure 2 (a) Ribbon diagram of the monomeric structure of DhiA. For clarity, a-helices are shown in cyan and /3-strands in purple. The location of the active site is indicated by the bound chloride ion, which is shown as a red sphere, (b) A close-up of the active site of DhIA where Asp-124 is covalently modified by a chloroethyl group, which results from the nucleophilic attack of Asp-124 on 1,2-dichloroethane (Figure 3). For clarity, both the chlorine atoms of the chloroethyl group and the displaced chloride ion are shown in yellow. The roles of the key active site residues (Glu-56, Asp-124, Trp-125, Trp-175, Asp-260, and Flis-289) and their interactions are discussed in the text. The figure was prepared with F>yMOL (W. L. DeLano, The PyMOL Molecular Graphics System-, DeLano Scientific San Carlos, CA, USA, 2002, http //www.pymol.org.).

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