pps logo Main Index Course Material Noticeboard
Technology Discussion Lists MUD Transcripts

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.