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MUD transcript:  09-12-99

Primary Structure of Proteins

Course room(s): PPS 

15:59:27  ClareS connects.

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16:01:43  SarahL connects.
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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.
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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.
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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.
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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.
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16:37:33  AliceB says "yes, I think so"
16:37:34  SarahL connects.
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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.
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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.
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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.