MUD transcript: 13-06-00
Protein Tertiary Structure II
Course room(s): PPS
22:01:16 ClareS connects.
SarahL PPS HTTP 11m 31s 11m 31s
MichaelS PPS HTTP 20s 20s
ClareS PPS HTTP 0s 0s
22:01:19 MichaelS says " Hi Sarah.No one else arrived, I see."
22:01:24 ClareS says "Hi"
22:01:43 ClareS says "... so far... it's only just 23:00"
22:01:46 MichaelS says " Hi Clare."
22:02:31 ClareS says "I suggest we wait a few minutes before starting... and you know people always arrive late"
22:02:46 MichaelS says "really enjoyed the latest set of material. The beta helix in particular look amazing!"
22:05:58 ClareS says "it *is* an impressive structure"
22:06:38 SarahL says "I was just wondering about my assign ment haven't received it back yet"
22:10:09 ClareS says (to SarahL) "who is your tutor?"
22:11:02 SarahL says "my computer is alittle bit slow tonight (as usual), my tutor is Beayrice Gorinsky"
22:12:40 ClareS says "I was talking to Beatrice about this today, she has been tied up with marking exams but has promised me she'll do this soon"
22:13:05 ClareS says "I will remind her"
22:14:18 ClareS says "It is slow for me too tonight, this may be why more aren't here"
22:14:35 SarahL says "I would appreciate it back soon although the longer it is left the less use the feed back is as the questions fade out of my memory"e"
22:15:26 ClareS says "you can always remind yourself of the questions, they are still there on the website"
22:17:14 SarahL says "the current work is very interesting and I am finding my newly bought copy of Brandon and Tooze very useful and surprisingly easy to read!"
22:17:37 ClareS says "see http://pps9900.cryst.bbk.ac.uk/course/self-assess/saq2.html"
22:18:15 ClareS says "and our model answers... at http://pps9900.cryst.bbk.ac.uk/course/self-assess/saqa2000_2.html"
22:18:41 ClareS says "do either of you have a particular question you'd like to discuss?"
22:21:16 ClareS looks round expectantly
22:22:08 ClareS says "have you managed to work right through the section yet?"
22:22:10 MichaelS says "As I was revising the material, I was interested in the discussion about the singly vs doubly-wound beat structures. There seems to be little connection between the structure presented ( I assume they ar ecrystals) and the schematics."
22:22:59 ClareS says (to MichaelS) "could you type up the URL so we can find the page you're concerned with easily?"
22:22:59 SarahL says "i have been reading about beta barrels such as retinol binding protein and how retinal fits into the barrel what about jelly rolls do they have a space to bind a protein or not"
22:23:45 ClareS says (to SarahL) "retinol binding protein doesn't bind a protein -- just a small hydrophobic molecule"
22:23:56 ClareS says "(retinal is certainly a good example)"
22:24:24 ClareS says "and no, other types of barrel, such as jelly rolls, don't have enough space to bind anything in the interior"
22:24:39 ClareS says "their binding sites are at one end or the other"
22:26:07 SarahL says "ok a small molecule is what i ment I also ment to type retinol"
22:26:32 ClareS says "yes but retinal is also bound to proteins in this family"
22:27:41 ClareS just crashed Netscape...
22:28:52 SarahL says " would that be a specific binding protein such as retinal binding protein or are they able to bind similar smalll molecules"n"
22:29:20 ClareS is now looking at the all-beta page...
22:29:51 ClareS says "many of these proteins (they are called lipocalins) bind similar small molecules with different specificities"
22:31:07 ClareS says "have you had a change to look at Darren Flower's review of these proteins? It's linked from the course material"
22:31:45 ClareS says "http://www.biochemj.org/bj/318/0001/bj3180001.htm -- there's a link to a version in PDF format from there"
22:32:08 ClareS says "(change=chance, sorry)"
22:32:36 SarahL says "they have to he hydrophobic presumably, yes I have printed of f Darren flowers paper"
22:32:40 MichaelS says "I'm just scanning through it now."
22:33:27 ClareS says "yes, they are largely hydrophobic"
22:34:32 SarahL says "but I haven't read it yet"
22:35:21 ClareS says "it's worth reading, tho' very dense especially if you're not used to reading full scientific papers"
22:35:35 MichaelS says "Isee what you mean about them not being able to bind anything inside the structure."
22:36:57 SarahL says "oh I am use to reading papers I just haven't had a chance yet"
22:38:20 ClareS blushes
22:38:53 ClareS says (to MichaelS) "I assume you're talking about the other types of beta barrel"
22:39:19 ClareS says "there is one type of all beta protein with a wider pore than the lipocalins -- porin"
22:41:15 ClareS just crashed Netscape again
22:41:44 ClareS says "porin is a membrane protein with (as its name implies) a wide port"
22:43:26 MichaelS says "I'm lookingat it now. I assume the extended region and helix act a the *gate* through the pore."
22:43:56 ClareS says "(port=pore, sorry for more typos)"
22:44:32 SarahL says "are you looking at colicin A"
22:46:35 MichaelS says "nately, I can only look at the .gif of porin, as I failed to download the pdb file:-("
22:46:52 ClareS says "there is a lovely picture of porin (looking down the pore) at ftp://www.expasy.ch/databases/swiss-3dimage/IMAGES/JPEG/3POR_porin_1.jpg"
22:48:35 SarahL says "i have all my work in a folder i know that paper is alittle out dated but i find the pages easier to turn!"
22:48:41 MichaelS says "I'm just getting the colicin image. The pore doesn't look as large as that of porin."
22:49:07 ClareS says "there is a lovely picture of porin (looking down the pore) at ftp://www.expasy.ch/databases/swiss-3dimage/IMAGES/JPEG/3POR_porin_1.jpg"
22:49:17 MichaelS says "It's one of the antibiotics that inserts into the cell wall, and make the target leak, right?"
22:49:45 ClareS says (to MichaelS) "you can download the structure of porin from its pdb entry hereL http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3por"
22:50:55 MichaelS says "Thanks. I just finished getting it from ExPasy"
22:51:44 ClareS is now looking up colicin -- you're right (but I had forgotten it)
22:52:20 MichaelS says "I assume there isn't any way that we can get some distance information such as the size of the pore via RasMol, is there?"
22:53:02 ClareS says "PDB entry 1col is the pore forming domain only, its pore is certainly smaller"
22:53:26 ClareS says "you need a molecular modelling program wher you can measure"
22:53:49 ClareS says "that should be, in which you can measure interatomic distances"
22:54:00 SarahL says "i have the expasy picturenow"
22:55:28 ClareS says "rasmol 2.6 doesn't. I can't remember whether rasmol 2.7 does"
22:55:53 MichaelS says "I just re-read the notes about colA (always a good idea;-)), and it undergoes conformastional change. That would be beacuse it is almost all helices. I guess they will interact with the phospholipids, expand, and hey presto, one leaking bacterium."
22:56:27 ClareS says "there are a few free programs that will allow you to do this - I believe that SwissPDBviewer does this"
22:57:10 MichaelS says "Thanks again; I'll have a look see."
22:58:03 ClareS says "SwissPDB viewer is slightly harder to install on a PC than rasmol"
22:58:39 ClareS says "it's intriguing that porin and colicin have such similar functions, given that one is a necessary protein and the other a toxin"
22:58:53 SarahL says "How does colicin a direct itself into the membrane is it attracted by the hydrophillic outside?e"
22:59:00 ClareS says "... and that one is all-alpha and the other all-beta"
22:59:14 MichaelS says "Ah, I have a Mac. I'll let you know if it goes on."
22:59:25 ClareS says "I'm going to have to look that one up!"
23:00:06 ClareS says "I think that SwissPDBviewer does work on macs (speaking from memory) but it must depend on the spec of the mac in question"
23:02:14 ClareS says "It's getting late, and my Netscape has crashed 3x in the last 15 minutes, so I suggest we close the meeting soon"
23:02:31 ClareS says "does anyone have any last burning questions?"
23:02:34 MichaelS says "the notes say that the pore is 1.7 to 2.5 nm. That seems to be a rather large pore."
23:02:59 ClareS says "remember, there is always to-morrow's meeting"
23:03:17 MichaelS says "Apart from a sneak peek at the projects, ;-) no."
23:04:54 SarahL says "thankyou very much that was a very interesting session, may be difficult to9 make it tomorrow "
23:05:12 ClareS says "the projects will be up by the end of the month"
23:05:50 MichaelS says "Good night Clare, Sarah."
23:05:54 ClareS says "it was certainly an interesting discussion in spite of there being so few of you -- thanks for making it so"
23:07:53 SarahL says "goodnight Clare and Michael"
23:08:12 ClareS says "goodnight"
23:08:24 MichaelS disconnects.