Bioinformatics Exercise 2 - Cell Biology Promotion

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Oct 1, 2013 (3 years and 8 months ago)

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Introductory molecular biology computing and bioinformatics
for
Molecular Mechanisms of Development.

Barcelona 2006
.

Exercise Set 2



1.

Retrieve the sequence for human microtubule associated protein 1B (MAP
B1) with accession number P46821. Determine the

expected molecular
weight (MW) and isoelectric point (pI) of this protein.

2.

Analyse MAP 1B using “Blocks” (Use FingerPrints and follow “search by
user query sequence”). Decide if it is likely that MAP B1 will share
structure
-
function relationships with e
ither Neuromodulin or HMG1a.

3.

Analyse MAP 1B with “FingerPRINTScan (FPScan). Contrast the results
with those obtained with BLOCKS, are any of the descriptions of likely
structure
-
function relationships the same?

4.

Analyse the protein sequence of MAP 1B us
ing Pfam. Do the position of
the “repeats” match those found with BLOCKS. What conclusions can you
draw about which repeats are likely to be “real”?

5.

Select the sequence for Frankensteinin 1 from the course home page and
predict the molecular weight (MW)
and isoelectric point (pI). Go on to
repeat the analyses that you have just performed with BLOCKS,
FingerPRINTScan and Pfam. Once again, decide if there is any
consensus amongst these the results regarding the likely structure
-
function relationships enco
ded in this sequnce.

6.

Analyse the sequences for both MAP 1B and Frankensteinin 1 using
Scansite. Are any of the potential phosphorylation sites also sites where
“phosphoprotein” interaction domains” would seek to bind. What does this
tell you?

7.

Repeat the
analysis both MAP 1B and Frankensteinin 1 using
Phosphobase (NetPhos). Can you decide if any of the phosphorylation
sites are the same as those identified by Scansite. If yes, what might this
imply?


Geraint Thomas

Department of Physiology,

UCL

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