If I'm not wrong, part of the course is also to put up a home page
for the assigned amino acid of your group.
There are already some very extensive home pages on amino acids
(http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids.html made my
bookmarks list!) so our pages should be something special !
I was thinking that it would be a nice idea to see in which proteins your
amino acids plays an important or even crucial role. This could be done
using the Prosite database (motif database) for a start.
For my own amino acid (K, lysine) I know that it plays an important
role in binding the phosphate of ATP (or NTP) in ATP binding proteins (like
the ATP synthase and adenylate cyclase) and is part of the ATP-A motif
GxxxxGKT (Also called the Walker A loop). This is just from the top of my
head, but there must be more.
I'm not sure if for every amino acid you can assign an important or crucial
role but we can try !
The relation ship of amino acids could also be highlighted.
All the different matrices which are used in multiple alignments (PAM250,
BlosumXX and what do you have) could be discussed.
Multiple alignments are used by many of us but do we all understand the theory ?
Maybe this is something for a homepage of its own (or maybe there
is already something like this ?)
Sincerely, Thon de Boer
+======================================================================+
! A.P.N. de Boer | eMail : deboer@bio.vu.nl !
! | Phone : +31-204447183/+31-206811519 !
! BioCentrum IMBW, Amsterdam | Fax : +31-204447123/+31-206811519 !
! Vrije Universiteit |_______________PPS Course______________!
! De Boelelaan 1087 | BioMOO name : deboer !
! 1081 HV Amsterdam | Assigned AA group : K (Lysine) !
! The Netherlands | Assigned Protein : 2ACT !
! | ACTINIDIN (SULFHYDRYL PROTEINASE) !
+======================================================================+