Sandbox2 Eric Martz: Difference between revisions
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<font color="red">This page contains a collaboration between [[User:Eric Martz]] and the [http://consurf.tau.ac.il ConSurf Team]. Please edit this page only if you are a participant in this collaboration. Thank you.</font> | <font color="red">This page contains a collaboration between [[User:Eric Martz]] and the [http://consurf.tau.ac.il ConSurf Team]. Please edit this page only if you are a participant in this collaboration. Thank you.</font> | ||
==Does ConSurf-DB Use Too Many Sequences?== | |||
In ConSurf-DB, I suppose that no single compromise between too many and too few sequences will produce optimal results for all proteins. Nevertheless, I found the following case informative. | |||
I conclude that perhaps we should caution users: ''ConSurf-DB is designed to include a wide range of sequences in its multiple-sequence alignments (MSA) and analyses. Often, the MSA will a include substantial number of sequences for proteins with different functions than the query protein. Consequently, amino acids that are colored as highly conserved are truly highly conserved across a wide range of sequence-similar proteins. However, amino acids that are highly conserved in proteins with the '''same function''' as the query protein may not appear conserved in ConSurf-DB results. In order to identify these residues, examine the sequences gathered by PSI-BLAST in a ConSurf run, and then set the "Maximum Number of Homologues" equal to the number representing proteins of the same function as the query protein. An example of such an analysis is available.'' | |||
The example follows. | |||
I was surprised to notice that Q226 in the alpha chain of MHC class I receives a conservation grade of 4 in ConSurf-DB. Q226 is involved in recognizing the CD8 protein, and the binding of CD8 to MHC class I is crucial to MHC class I's function in stimulating T lymphocytes to respond to foreign peptide antigens presented by MHC class I. | |||
Examining the MSA utilized by ConSurf-DB, I found many proteins other than MHC class I proteins. | |||
==Functional Loop 220-230 in MHC Alpha Chain== | ==Functional Loop 220-230 in MHC Alpha Chain== | ||