× Didn't find what you were looking for? Ask a question
Top Posters
Since Sunday
5
o
5
4
m
4
b
4
x
4
a
4
l
4
t
4
S
4
m
3
s
3
New Topic  
charlane charlane
wrote...
Posts: 2
Rep: 0 0
9 years ago
1. Integral glycoprotein sequence, 195mer (Note amino acid sequence is broken into segments
containing 10 amino acids for ease in counting):
ZQMHNSDMGN (10) TKERYFLLVI (20) TLIFSFTILV (30) VAVYRASSRG[GFP] (40)
KHSDQRGDYF (50) FFIIILLLTS (60) VVVTAILYKE (70) S[BFP]NKHMYLSGG (80)
IAASTAAFGI (90) GLGGYKNED[BFP]L (100) KHWAIFFFFI (110) LVVVGALII (120)
GYEESQNSRE (130) NMRYIFHLPG (140) TTQNDDPPRN (150) TREKHNTSNT (160)
DESHMNQPPP (170) SSDHDKNPQT (180) YWYTSEKPLG (190) FKEEQ
Experimental comments:
A. Exposing the native membrane to an α-N-amino fluorescent labeling agent, demonstrated NO
retention of fluorescence within this specific membrane protein.
B. Exposing the native membrane to cyanogen bromide (CnBr), we were able to isolate a peptide
fragment that was carbohydrate positive.
C. Exposing the native membrane to tryptic digestion, we were NOT able to isolate a peptide
fragment that was carbohydrate positive.
D. The membrane protein DID NOT demonstrate FRET when exposed to 300 nm
Questions:
(i) Indicate the areas of sequence which would represent transmembrane spanning domains in a
native lipid bilayer
(ii) Draw a cartoon of the predicted transmembrane protein as it would be found in a native lipid
bilayer member – label all features (N- and C-termini), including carbohydrate positioning and
cleave sites used in defining protein orientation.
(iii) Draw a representative hydropathy plot for the above protein – Indicate the probable exit
points from
Read 1642 times
1 Reply

Related Topics

Replies
wrote...
9 years ago
You are going to have to put in some work on this one. I will meet you half way.

(i) areas of the sequence which represent the transmembrane spanning domains will be hydrophobic. So look for repeats of hydrophobic amino acids.

(ii) So If you have say for example 5 (I am just giving example here) segments that contains amino acids that are hydrophobic, that means that this transmembrane protein will cross the membrane five times. I am not sure how to tell if it is N or C terminus tho.

(iii) Take a look at this example (http://www.whatislife.com/reader/channels/Image100.gif)

- the x axis will have amino acid numbers. Looks like you have 195 AA. So you label the x axis from 1 to 195. The y axis is the hydropathy index. The middle will be labeled with 0 and the top should be labeled with (+3) and the bottom should be labeled with (-3). All the y axis is telling you is whether the amino acid segment is hydrophobic or hydrophilic. Hydrophobic amino acids will go on the positive side (top) and hydrophilic amino acid will go on the negative side (bottom). This may sound confusing but look at the image.
- So if amino acids 100 - 110 are hydrophobic, they would go above the x axis. if amino acids 140 - 150 are hydrophilic then they would go below x axis. Again these are just example, I don't have the time right now to look at the sequences and tell you what is hydrophobic and what is hydrophilic. But it isn't hard, just takes some time. Let me know if you need more help.
New Topic      
Explore
Post your homework questions and get free online help from our incredible volunteers
  976 People Browsing
Related Images
  
 119
  
 71
  
 160
Your Opinion
Do you believe in global warming?
Votes: 370