Model Building using Crystallographic Data

Consider a proposed mechanism and build a model, using crystallographic data if available, from the active site outwards. Choose important protein residues, substrates, intermediates and products, water molecules involved in the mechanism, etc., knowing that the validity of the results will depend critically on these choices. 

Rather than manual model building, it is possible to use a database approach to build a starting structure from homologous structural fragments taken from the crystallographic protein data bank.37 The main use of this technique is that it can be used during the earliest investigations of a molecule when adequate NMR may not yet be available. 

CAMSEQ/M provides the user with the capability to input complete molecular structures from the internal (disk) data base, to input cartesian or crystallographic coordinates, or to use a "joystick" controlled model-building system. In addition, a molecule may be constructed from one or more substructures with substituents attached using the joystick model-builder routines. Data input is therefore quite flexible, and the user is guided through every step by the program. 

Many catalytically important oxide materials, such as ceria, are crystalline at (catalytic) operating temperatures and therefore a model of the crystal structure can be generated using symmetry operators. These symmetry operators, which have been introduced into many simulation codes (such as GULP), can be used to build the atomistic model using pertinent crystallographic data. This includes the... 

The isoenzymes of phosphoglycerate kinase (PGK, EC 2.7.2.3) from barley leaves have been purified in this laboratory and used to raise antisera (1). These antisera were used to isolate the wheat cDNAs, specific for each isoenzyme, which have since been sequenced (2 ). The derived amino acid sequences have been used to build models for the structures of both isoenzymes on an Evans and Sutherland graphics station. The co-ordinates obtained from the x-ray crystallographic studies of the yeast structure, which have been deposited in the Brookhaven protein data bank, have been used as a template (3). 

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