Visualizing Regions of Conservation in 3D Protein Structures

Dark regions show conservation in the catalytic site of enolase.
Regions of evolutionary conservation or variability (lower or higher than average mutation rates, respectively) can be visualized on a 3D protein structure by applying a color scheme based upon a multiple sequence alignment. Such regions generally signal clusters of residues of crucial functional importance. In December, 2001, Glaser, Ben-Tal, Pupko and Martz released the ConSurf Server, where you will find a Gallery of exemplary results. ConSurf automatically generates a multiple protein sequence alignment (or accepts one you have made), then automatically generates a phylogenetic tree, and applies colors representing the resulting grades of conservation for each residue to the 3D protein structure. The results are displayed in Protein Explorer.

Earlier, beginning in 2000, Protein Explorer offered MSA3D, which accepts a user-provided multiple protein sequence alignment, and uses it to color the 3D protein structure. MSA3D simply divides residues into 3 categories: identical, similar, and different.

ConSurf is much easier to use than MSA3D, because it is completely automatic and provides everything needed at a single site. More importantly, the algorithms employed by ConSurf are much more sophisticated. For nearly all purposes, ConSurf is superior to MSA3D. Therefore we strongly recommend that you use ConSurf to visualize regions of conservation in 3D protein structures.

The documentation below, describing MSA3D, is now mostly of historical interest. Protein Explorer's MSA3D routines remain available in case they are useful for specialized purposes.

Protein Explorer's Multiple Sequence Alignment in 3D (MSA3D): Enolase

A multiple protein sequence alignment was prepared for enolase. Protein Explorer's MSA3D feature then assigned colors to represent identity, similarity, or difference of the aligned amino acids, shown in Protein Explorer's alignment listing. The alignment includes eubacteria, archebacteria, and eukaryotes (Drosophila, yeast, and human). Despite this enormous span of evolutionary time, all of the residues in the catalytic site pocket are identical. (The catalytic site is marked by the red sulfate ion that happens to be bound there in this structure, 4enl.)

If you have Chime installed, you can see this molecule rotate in an interactive window. If not, downloading Chime and installing it takes only a few minutes.

The links and buttons in the snapshot below don't work since this is just a snapshot.
Thanks to Paul Stothard for major portions of the MSA3D code, and to Garry Duncan for providing this alignment.

How do you find MSA3D after you start Protein Explorer? If you start Protein Explorer from the special link below, you'll see a link to MSA3D immediately. Most other links to Protein Explorer will first give you a FirstView description. From FirstView, click "Explore More", and there you'll see a link to "Advanced Explorer", where you'll see MSA3D on the menu. The enolase alignment is a built-in demonstration in MSA3D.

This special Enolase-MSA3D link starts Protein Explorer, loads enolase, then automatically changes from FirstView directly to Advanced Explorer, where the MSA3D link will be evident.

A detailed tutorial is provided on how to construct an alignment and use it to color a molecule of interest with MSA3D.