The structure groups and shading facility provide an extremely powerful and flexible set of tools for integrating sequence information with structural information. The facility is flexible enough to allow the user to display almost any kind of information as color codes along the sequence. Such states can include the obvious secondary structure state of the residue in the three dimensional structure. Less obvious properties like the solvent accessible surface area of the residue or its side chain can also be displayed. The fraction of the side chain in a polar environment is another characteristic that is sometime informative.
One of the most powerful kinds of integration of structure and sequence information allows the user to visually examine the variation in structure or some structural property that occurs as the sequence varies in a series of homologous proteins. This same display allows the user to adjust the alignment based on information derived from the varying structures of a series of homologous proteins.
Alternatively, you can have several copies of the same sequence in the alignment by adding additional copies with different names through the sequence import facility. Remember that each copy must have its own distinct name. These copies of the same sequence can all be highlighted using a different property. This allows you to easily visualize possible correlation of properties or of properties with sequence or structure.
Another use for multiple copies of a single sequence in the alignment is to contrast predictions of structure and properties with that observed in an experimentally determined three dimensional structure.
A wide spread use of the structure shading is to project the structure or properties from a sequence of known structure onto sequences whose structures have not be experimentally determined. This is accomplished by combining the structure shading facility with the group facility. At the same time you use the structure shading dialogue to associate a structure file with a specific sequence in the alignment you can designate that sequence as the master sequence of a structural group. This allows you to associate several sequences with a single structure file. These associated sequences will be shaded with the same colors in the same column of the alignment as the master sequence regardless of the sequence residue present in thhat position of the sequence. Thus this is essentially a low resolution homology modeling facility.
All of these features can be combined into a very informative display for studying structure-function relationships in the following procedure. First, associate a structure file with each sequence in your alignment whose structure has been determined by X-ray crystallography or NMR. Make these sequences the master sequence for a group of the most closely related sequences in the alignment. Ideally the sequences within each group should have common biochemical properties such as substrate specificity, while different groups can have different substrate specificities. Use the sequence editing facility to put sequences in the same group on adjacent rows of the alignment. Put the group master sequence at the top of each group. Then set the display mode to differences mode and make sure this is applied to all of the groups.
This yields a display with all of the group master sequences, that is the sequences with known structures, displayed with all of their residues. The other sequences in each group have a dot displayed where they have the same sequence residue as the group master. Sequence residues that are different from the group master sequence are shown. This highlights substitutions within each group that are presumably successful site directed mutagenesis experiments performed by nature. Differences between groups may be associated with the change in substrate specificity or other property.
It can be very helpful to have exactly the same alignment in a second window highlighted in group contrast mode. This combination of displays can be a very powerful tool for examining structure-function relationships by integrating a large amount of information in an easy to comprehend format and presentation.