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MUD transcript:  02-08-00

Protein Interactions; Projects

Course room(s): PPS 

15:00:26  ClareS connects.

ClareS       PPS          HTTP         0s       0s
AttilaR      PPS          HTTP        19s      19s
VijayK       PPS          HTTP        18s      18s
15:00:31  ClareS says "Hi"
15:00:37  AttilaR says "Hello, everyone!"
15:00:49  MichaelS connects.
ClareS       PPS          HTTP        23s      18s
AttilaR      PPS          HTTP        42s      12s
VijayK       PPS          HTTP        41s      41s
MichaelS     PPS          HTTP         0s       0s
15:01:01  ClareS says "I wasn't sure whether everyone knew exactly when we would be starting... I hope it will be soon"
15:01:12  VijayK says "Hello"
15:01:26  ClareS says "I suggest we wait around for a few minutes for latecomers, tho'"
15:01:39  MichaelS says " Hello all"
15:05:06  ClareS says "OK; let's start now"
15:05:21  ClareS says "I hope that you've all chosen your projects"
15:05:51  AttilaR says "Yes, I have chosen."
15:06:02  ClareS says "are you all happy with your project choices and with the procedure... is there anything to discuss there or shall we start straight on with section 12?"
15:06:38  VijayK says "We can discuss a bit of both if possible"
15:07:19  ClareS says "of course... I'm just wondering where you'd like to start"
15:07:31  AttilaR says "I have written my choice yesterday to You, I don't know, whether it has arrived or not."
15:09:03  VijayK says "Section 12 appears quite straight forward. The problem thpough is one needs to now more in depth to be able to discuss. But the refreshing of chapter 7 was useful."
15:09:28  ClareS says (to AttilaR) "yes, I've received your choice -- it's fine, you can go ahead"
15:09:38  MichaelS disconnects.
ClareS       PPS          HTTP     9m 12s      10s
AttilaR      PPS          HTTP     9m 31s    2m 7s
VijayK       PPS          HTTP     9m 30s      35s
15:10:01  AttilaR says "I think, lecture 12 was the one of the most exciting ones during the course."
15:10:06  ClareS says "have you had a chance to look at the new self assessment page? I hope that that will help your revision"
15:10:36  VijayK says "I did post my choice last week"
15:11:23  VijayK says "Yes! And I will look again"
15:11:55  ClareS says (to VijayK) "yes, I have received your choice too"
15:12:28  ClareS says (to AttilaR) "I'm very pleased to hear that... I wrote it ;)  Is there anything you don't understand in that material?"
15:15:47  ClareS says "in this section, at the very end of the course, we begin to talk much more about the function of proteins..."
15:15:59  ClareS says ".. and how structure relates to function"
15:16:10  VijayK says "In the section Serine Proteases part 1 three kinds of homologies were pointed out"
15:16:34  ClareS says (to VijayK) "yes..."
15:17:04  ClareS has finally found the serine protease material
15:17:28  VijayK says "Inthe section Serine proteases part 1, 3 kinds of homologies were mentioned, sequence hom., residues on the surface , and buried residues. How are the last to dteremined?"
15:17:55  VijayK says "Last two Imean"
15:18:03  ClareS says "I have just been told that I will have to leave this computer at 5pm, this is an advance warning to think of your questions fast!"
15:19:05  AttilaR says "I found the most interesting the hemoglobin, and the muscle proteins, I am very proud, that a Hungarian man, Szentgyorgyi made such important discoveries. But the quaternary structure is also very interesting, it turned out that before reading this lecture I had bad imagination about the structure of hemoglobin"
15:19:34  ClareS says "there is actually quite an important mistake in this page! (serine proteases I mean)"
15:19:49  ClareS didn't write that page
15:20:13  ClareS says "it talks about percentage homology but it should have said similarity or identity"
15:20:40  ClareS says "Homologous just means evolutionarily related. Proteins are either homologous or they're not"
15:21:03  ClareS says "tho' you can talk about distant homologues"
15:21:46  ClareS says "what is meant here is that 50% of the residues in any pair of these proteins will be identical"
15:22:49  ClareS says "then it is easy to calculate percentages based on surface or buried residues alone, you only include one or the other category"
15:23:07  ClareS says "is this clear?"
15:23:08  VijayK says "hence similarity or identity at the surface residue level or buried residues is structural evaluation I think"
15:23:31  AttilaR says "The overall similarity can be determined, I think only from the sequence comparisons, but for the two other categories, which is asked requires the precise structure or very good structure predicting programmes."
15:24:24  VijayK says "can you nmae some good predicting programs/"
15:25:39  AttilaR says "You can find some very good possibilities under the SWISSPROT/database, http://www.expasy.ch. There are quite a wide range of them."
15:25:44  ClareS says (to AttilaR) "yes, that's right. You almost always find buried resides much more strongly conserved than surface ones"
15:26:17  VijayK says "Thanks Clare ans Attila"
15:26:25  ClareS says "you can only evaluate identity for a group of structurally conserved residues if you know the structures"
15:27:16  ClareS says "homology modelling programs are very good at predicting a fold if a close relative is known but not yet much good at predicting details of active sites"
15:27:40  ClareS says (to VijayK) "do you mean programs for homology modelling?"
15:27:46  VijayK says "I anm going back to section 7 - I see that hydrophobicity is calibrated as Kcalmol-1 per methylene group. I do not understand this"
15:30:00  ClareS says (to VijayK) "can you type in the URL of that section of course material, please?"
15:30:04  VijayK says "yes for homology modelling"
15:30:38  ClareS says (to AttilaR) "you're right, if you look at the ExPASy page you will see links to SwissPDBViewer and SwissModel"
15:31:27  ClareS says "SwissPDBViewer is a viewing and modelling package that is much more complex than Rasmol but still free, unlike e.g. Insight or Sybyl"
15:31:44  ClareS says "it is harder to install and learn than Rasmol, tho'"
15:31:48  AttilaR says "This is I think, the free energy change, when you change the environment of the protein from a polar to a nonpolar material, or vice versa."
15:32:00  ClareS says "SwissModel is a server for homology modelling"
15:32:43  ClareS says "you submit your protein sequence and it will find homologs and generate a model"
15:33:05  ClareS says "its only disadvantage is that it is nothing like as flexible as the expensive packages"
15:33:49  VijayK says ""
15:35:04  ClareS says "that is a very strange URL, it would be easier to use the site outside Hotmail if you can"
15:36:14  ClareS says "I think I have the page now, it's Hydrophobic Interactions within section 7?"
15:36:44  VijayK says "http://pps9900.cryst.bbk.ac.uk/ppscore/section7/hydroph.html"
15:37:39  VijayK says "See pargraph 1"
15:38:15  ClareS says "yes, the energy value quoted is the amount of energy lost when one methyl group is folded into the interior of the protein"
15:38:55  VijayK says "That makes sense to me now. Thank you"
15:39:15  ClareS is pleased that it now makes sense
15:40:41  ClareS says "there is usually a trade-off between program functionality and price; the programs on the Geneva site are certainly some of the best free ones"
15:43:13  ClareS says "do you have any more questions (including on the projects)? I now have less than 15 minutes before I will have to leave this computer"
15:44:29  ClareS says (to AttilaR) "do you have any questions or comments on the haemoglobin material?"
15:46:25  ClareS looks round expectantly
15:46:48  AttilaR says (to ClareS) "No, thank You, now everything is clear for me about the hemoglobin. The only problem was, that the usual books cannot make us feel the structural symmetry so strongly as the rasMol, for example."
15:47:45  ClareS says "yes, it is always a great help to be able to look at the molecules in three dimensions"
15:48:06  VijayK says "What is the difference between an oligimer and a multimer"
15:48:22  ClareS says "this is particularly so for symmetry as this is quite complicated to see"
15:48:50  ClareS says "just a matter of scale -- oligo means few, multi means many"
15:49:31  ClareS says "an oligopeptide is a chain a few amino acids long -- a protein is a multipeptide"
15:49:40  ClareS says "(a word that is never used)"
15:50:18  VijayK says "often one comes across the two terms oligopeptides and polypeptides"
15:50:54  ClareS says "with protein complexes the words tend to be used interchangeably because there are hardly any known structures where more than "a few" chains associate"
15:51:27  ClareS says "polypeptide can be used for any number of peptide units greater than 1, it doesn't imply few or many"
15:52:46  VijayK says "What is the smallest lenght knowm for a functional protein and the largest"
15:53:00  AttilaR says "the hsp60 forms oligomers of 14 molecules. I think, this , the proteasome and the ribosome are the bigger oligomers or multimers in the cell."
15:53:17  AttilaR says "I meant the biggest"
15:54:02  ClareS says "the estructures"
15:54:28  ClareS says "I meant the 3D structures of these enormous complexes are not yet known at atomic resolution"
15:54:36  VijayK says "This is very useful to know for me.Thank you"
15:54:55  ClareS says "re largest and smallest lengths, it depends what you mean by "protein""
15:55:20  ClareS says "there are some very short peptides that have biological functions but they do not fold into specific shapes"
15:55:52  ClareS says "people tend to refer to anything less than something between 50 and 100 residues as an oligopeptide (a category that includes insulin)"
15:56:09  VijayK says "I guess the term protein can mean  just a sequence of amino acids with structure but no function2"
15:56:34  ClareS says "but insulin, like some other moderate sized peptides does fold into a specific shape, it is stabilised with disulphide bonds"
15:57:04  ClareS says "I don't know what the biggest is, you could probably find out from the protein sequence databases"
15:57:54  ClareS says "I'm going to have to go in a couple of minutes.. sorry to cut it short"
15:58:13  ClareS says "you could always come back to-morrow"
15:58:27  ClareS says "(propping your eyelids open with matchsticks)"
15:58:53  AttilaR says "I think, this has been a very interesting session. Thank You for everybody."
15:59:40  ClareS says "sorry to cut it short, best of luck with the projects, see you to-morrow 11pm/midnight??"
15:59:48  ClareS waves and leaves
15:59:51  VijayK says "Well its time to go"
16:00:04  AttilaR says "Goodbye!"
16:01:22  AttilaR disconnects.