Introduction to 'Explore the Mechanism'
'Explore the Mechanism' is a tutorial which introduces you to parts of Rubisco's structure known to be important for the reaction mechanism. It takes you on a journey which begins with the substrate RuBP. After examining the changes this substrate undergoes, our vision expands to consider the influence of the amino acids which make up the active site. We then view the striking changes in conformation of the subunit to which the active site belongs. The tutorial concludes by looking at interactions of the two L subunits which enclose the active site, briefly commenting on the influence of the S subunit, influence which, while probably highly significant, is not yet well understood. The current mechanism may not be perfect, but it is extremely sophisticated. Classical chemical techniques followed by site directed mutagenesis experiments and then high resolution X-ray diffraction studies now provide very tight constraints indeed.
In an attempt to make the tutorial more PC friendly I have edited
original files from the protein databank; the full files are too big
for my PC to handle comfortably! The origin of my
pdb data files is usually indicated,
but be aware that some displays contain data from more than one
I have divided the material into twelve sections and especially in the case of the early sections, it is best to complete the section before quitting. As an aid to navigation around the tutorial, at the start of each section you will find a link to the 'right panel index' which will appear in the right hand frame.
The tutorial begins with an 'Overview'. This 'Overview' is inherently rather sketchy, but before launching into the next section I suggest that you come to terms with it to get some idea of what is going on. You will have access to two formulations of the proposed mechanism. These will appear in separate windows and I suggest that use them to see where we are in the overall reaction. Smaller more easily digested portions of formulation 1 will appear from time to time. To avoid over-complicating an already complex story, formulation 2 will not appear in the frame: It is accessible from the separate window. Where I think it will help, I point out differences in detail between the two. Formulation 2 is particularly helpful in understanding electron movement and stereochemistry.
When you have finished exploring the mechanism, you may find it interesting to explore some of the web sites and references I have provided.
One final point: If you find the colour scheme annoying it is easy to change it on any display to cpk by using the right mouse click to 'select all' and then 'Colour, Atom.By Scheme, Element cpk'. If you explore the right mouse button over the Jmol display, you'll find many other options.