MUD transcript: 09-12-99
Primary Structure of Proteins
Course room(s): PPS
15:59:27 ClareS connects.
15:59:27
ClareS PPS HTTP 0s 0s
16:01:43 SarahL connects.
16:01:43
ClareS PPS HTTP 2m 16s 41s
Wizard Void HTTP 1m 21s 15s
SarahL PPS HTTP 0s 0s
16:04:08 SarahL says "Hi Clare how are you, I just managed to get home in time to log in, although I have to go at$.45pm"
16:04:19 KevinO connects.
16:04:19
ClareS PPS HTTP 4m 52s 3m 17s
Wizard Void HTTP 3m 57s 1m 4s
SarahL PPS HTTP 2m 36s 11s
KevinO PPS HTTP 0s 0s
16:05:11 ClareS says "Hi -- I had hoped that a few more people would arrive on time, but I guess we should get going..."
16:05:24 ClareS says "... expecially as Sarah has to leave quite soon"
16:05:34 ClareS says "How are you finding the course so far?"
16:06:25 KevinO says "fine"
16:07:01 PeterW connects.
16:07:01
ClareS PPS HTTP 7m 34s 1m 22s
Wizard Void HTTP 6m 39s 1m 26s
SarahL PPS HTTP 5m 18s 2m 53s
KevinO PPS HTTP 2m 42s 12s
PeterW PPS HTTP 0s 0s
16:07:55 ClareS says (to peterw) "Hi - welcome"
16:08:08 ClareS says (to peterw) "Welcome!"
16:08:12 SarahL says "I'm really enjoying the course so far, most of the work is revision for me , but I love the chemical mime, I am still referring to Stryer though. I feel that stryer is like the Biochemists Bible!"
16:08:27 ClareS says (to peterw) "any problems with the course so far?"
16:08:50 ClareS says (to sarahl) "enjoy it while it lasts, it gets harder soon!"
16:09:22 ClareS says "we try to start quite slowly, so that any students who have problems with the technology are easily able to catch up"
16:09:24 AliceB connects.
16:09:24
AliceB PPS Telnet 0s 0s
ClareS PPS HTTP 9m 57s 2s
Wizard Void HTTP 9m 2s 2m 8s
SarahL PPS HTTP 7m 41s 1m 12s
KevinO PPS HTTP 5m 5s 58s
PeterW PPS HTTP 2m 23s 2m 23s
16:09:45 ClareS says (to sarahl) "Yes, stryer is an excellent textbook"
16:10:14 ClareS says "talking of textbooks, has anyone here used Branden & Tooze - the bible of protein structure"
16:10:22 SarahL says "I was anticipating it getting harder, it most probably will!"
16:12:01 ClareS says "that's further on than we are in the course but I'm sure you can cope!"
16:12:36 ClareS says "this book is a very clear introduction to the subject, with some lovely diagrams"
16:13:03 ClareS says "have you all managed to set up Rasmol, and are any of you also using Chime?"
16:13:21 PeterW says "..ClareS No problems really trying to grasp some of the chemistry"
16:14:03 AliceB says "I have only managed to set up Chime: Ras mol"
16:14:20 ClareS says (to kevino) "we will be linking to those kinemages from the next section"
16:14:29 AliceB says "doesn't seem to launch from Internet Explorer 4"
16:14:48 ClareS says "sometimes it is difficult to set up chime and rasmol on the same computer"
16:15:29 ClareS says (to kevino) "these programs are designed to do slightly different things"
16:15:47 ClareS says (to kevino) "these programs are designed to do slightly different things"
16:16:19 ClareS says "rasmol and chime are for displaying molecules (only) and use PDB files of atomic coordinates"
16:16:39 ClareS says "kinemages are interactive diagrams that can be used for many things and they have their own file format"
16:17:18 ClareS says "we don't insist that everyone uses chime as it isn't available for unix macnines"
16:17:27 ClareS says "(machines)"
16:17:34 ClareS can't type
16:19:09 ClareS says "does anyone have a particular problem or query they'd like to discuss here?"
16:20:25 ClareS says (to kevino) "go ahead.."
16:24:09 ClareS was in another window... sorry :(
16:24:40 ClareS says (to kevino) "yes, these are the surfaces where the two forces are in equilibrium"
16:25:04 ClareS says "you *can* think of them as "hard" surfaces, but this is very much a first order approximation"
16:25:40 ClareS says "this is the so-called "hard sphere potential" - in reality, of course, the boundaries of atoms are much "fuzzier""
16:26:02 ClareS says "there is a whole unit on molecular forces later in the course"
16:27:12 ClareS says "in this we describe forces like the Lennard-Jones potential that describe attraction / repulsion in terms of distance from the centre of an atom"
16:29:34 ClareS says "can you remember the context in which you are offered the other type of surface by rasmol?"
16:31:07 ClareS says (to kevino) "..and which version of rasmol are you using?"
16:31:57 ClareS says "in version 2.6 you can get a solvent accessible surface"
16:32:29 ClareS says "you set the value of the parameter "solvent" to be true and then use the dots command"
16:32:54 ClareS says "do you (all) know what I mean by solvent accessible surface?"
16:33:10 SarahL says "this sounds different from what I have installed I think that I have got Chime"
16:33:25 AliceB says "no"
16:33:56 ClareS says (to sarahl) "very likely - if your molecules appear in your web browser window, you have Chime installed"
16:34:02 ClareS says "OK"
16:34:26 ClareS says "a solvent accessible surface is the surface that is accessible to solvent molecules"
16:34:59 ClareS says "you think of the "shape" of the molecule that a water molecule would "see" if it was close to the protein"
16:35:22 ClareS says "i.e. a solvent accessible surface has no sharp edges..."
16:35:51 ClareS says "... and no very tight crevices, as a water molecule wouldn't be able to enter a very narrow cleft"
16:36:12 ClareS says "is that making sense?"
16:37:14 PeterW says "yes .. sort of"
16:37:23 SarahL disconnects.
16:37:23
AliceB PPS Telnet 27m 59s 3m 58s
ClareS PPS HTTP 37m 56s 1m 11s
Wizard Void HTTP 37m 1s 8m 1s
KevinO PPS HTTP 33m 4s 14s
PeterW PPS HTTP 30m 22s 9s
16:37:33 AliceB says "yes, I think so"
16:37:34 SarahL connects.
16:37:34
AliceB PPS Telnet 28m 10s 1s
ClareS PPS HTTP 38m 7s 1m 22s
Wizard Void HTTP 37m 12s 8m 12s
SarahL PPS HTTP 0s 0s
KevinO PPS HTTP 33m 15s 25s
PeterW PPS HTTP 30m 33s 20s
16:39:01 ClareS says (to kevino) "that's true - some parts of the "surface" of molecules will actually be inaccessible to all other molecules"
16:39:08 SarahL says "I got disconnected for some reason"
16:39:28 ClareS says "and, of course, there are many "cavities" in proteins that are too tight for a drug molecule to fit in"
16:39:44 ClareS says (to sarahl) "don't worry, that often happens"
16:45:56 ClareS says "was my explanation of solvent accessible surfaces helpful?"
16:47:02 ClareS is wondering if there are any more questions...
16:47:33 KevinO shakes his head
16:48:08 PeterW says (to ClareS) "a question"
16:50:41 SarahL disconnects.
16:50:41
AliceB PPS Telnet 41m 17s 4s
ClareS PPS HTTP 51m 14s 3m 39s
Wizard Void HTTP 50m 19s 5m 53s
KevinO PPS HTTP 46m 22s 3m 8s
PeterW PPS HTTP 43m 40s 2m 33s
16:51:03 ClareS says (to peterw) "go ahead"
16:52:13 PeterW says (to ClareS) "why is proline listed as aliphatic in some of the notes and not in others ?"
16:52:47 JohnP connects.
16:52:47
AliceB PPS Telnet 43m 23s 54s
ClareS PPS HTTP 53m 20s 1m 44s
Wizard Void HTTP 52m 25s 12s
JohnP PPS HTTP 0s 0s
KevinO PPS HTTP 48m 28s 5m 14s
PeterW PPS HTTP 45m 46s 34s
16:54:07 ClareS says "I think because it depends on the exact definition of the word "aliphatic""
16:54:47 ClareS says "an aliphatic amino acid is one with a non-polar, non-aromatic side chain (composed of CH2 groups etc)"
16:55:20 ClareS says "proline counts, officially, within this definition - it has no polar or other unusual groups and no aromatic rings"
16:56:09 ClareS says "but its defining feature is not its chemical structure but that covalent bond between the side & main chains"
16:56:43 ClareS says "so it is, actually, very different from amino acids like L, I, V, containing hydrocarbon chains with no links"
16:57:25 ClareS says "personally I would be most likely to class proline on its own, but to a certain extent it's a matter of tasts"
16:57:34 ClareS says "(taste)"
16:57:42 ClareS says "is that clear?"
16:58:24 ClareS says "it underlies the fact that some classification schemes are not very clear-cut"
16:58:28 PeterW says (to ClareS) "I understand that.. but was just wondering about the definition. thanks"
16:58:30 KevinO nods vigourously
16:59:03 ClareS says "for example, which amino acids are described as "hydrophilic" and which as "hydrophobic" depends on where the line is drawn"
16:59:11 ClareS says (to johnp) "welcome!"
16:59:19 ClareS says (to johnp) "welcome!"
17:00:48 JohnP says "hi clare"
17:01:12 ClareS says (to johnp) "how are you getting on with the course so far?"
17:01:45 JohnP says "alright actually, i seem to be able to download the programs through default but they work fine"
17:02:37 ClareS says (to johnp) "excellent!"
17:02:48 ClareS says (to johnp) "excellent!"
17:02:57 KevinO says "bye all, lunch beckons!"
17:03:15 JohnP says "how important is Toozes book for all this Clare"
17:03:19 ClareS says "actually I would like to go fairly soon (within the next 10 minutes or so) so are there any last miniute questions?#"
17:03:56 ClareS says (to johnp) "I talked a bit about this at the beginning - it's an excellent textbook but I suppose it's not essential"
17:04:15 ClareS says "all the really essential stuff will be on the web"
17:04:22 PeterW waves goodbye
17:04:36 JohnP says "do you think i should put it on my Christmas list?"
17:05:05 ClareS says "if you don't mind spending Christmas reading about protein structure ;)"
17:05:32 JohnP says "cheers Clare, sorry for my late arrival"
17:05:51 KevinO disconnects.