ClareS turns the ClareS_recorder on.

ClareS says "Testing recorder and tape""

ClareS turns the ClareS_recorder off.

ClareS turns the ClareS_recorder on.

ClareS says "Welcome to the first PPS BioMOO meeting of 1998"

ClareS says "We will be discussing section 4, Protein Synthesis"

ClareS says "Jim Pitts from Birkbeck, whpo is here, knows more about this subject than I do ;)"

ClareS says "and I hope that we will be joined by Henry Brzeski later. He wrote some of this material"

ClareS says "so, to start with, do any of you have any questions ion this section..."

ClareS says "or or an issue to raise for more general discussion?"

Claudia finds her way in.

BMD says "Yes..."

BMD says "I am not sure how ribosomes provide their motive force to move along mRNA strands."

ClareS says "I don't know the answer to that one either.... Jim?"

BMD says "I know that GTP hydrolysis is involved, but that does not take me very far."

Claudia says ", Hello"


(Claudia has disconnected.)

ClareS [to claudia] welcome to the meeting

Henryb finds his way in.

ClareS . o O ( Ah. Here's Henry. )

ClareS [to henryb] Welcome - glad you can make it

Henryb says "hello everybody. Sorry I'm late. Real live tutorial .... with bodies!!!"

ClareS grins

ClareS [to henryb] you have only missed a few minutes.

(Claudia has connected.)

ClareS [to henryb] I have just been asked a question I can't answer

ClareS [to henryb] can you help?

Henryb says "The easy answer to that is the energy comes from the hydrolysis of GTP. Unfortunately that is probably not what the questioner wanted to know. The question of how the mechanics work is, as far as I know, still not worked out. "

ClareS says "thanks, Henry"

ClareS says "I don't feel quite as ignorant for not knowing now ;)"

BMD says "tRNAs seem to be entering and leaving the ribosome at an incredible rate, is that simple diffusion, or is there a motor somewhere in there too?"

Henryb says "I'm not sre that I am an expert on protein synthesis but I will help where I can. As far as I know they simply enter by diffusion. However, I am surew that the binding site is quite precise as all tRNAs have the same 3D shape and so must be

able to bind to the A site quite specifically."

ClareS says "that certainly makes sense"

BMD  is very grateful.

ClareS says "Have you all managed to try out the Rasmol / Chime exercises from Henry's material on Transcription?"

Pawel [guest] says "Yes"

Claudia says ", Not yet, unfortunately."

Pawel [guest] says "But I have another guestion - what is total energetic cost of one amino acid connection in Procaryota and what is in Eucaryota ?"

Pawel [guest] says "In another way - what kind of organisms are most "ergonomical" ?"

ClareS says "think Interesting question..."

Pawel [guest] says "Sorry, should be economical..."

NickyM says ""in answer to Rasmol exercises, I couldn't get a spin menu on my PowerMac""

Henryb [to Pawel] Coupling of amino acids to tRNAs proceed via the same enzymic mechanism in prokaryotes and eukaryotes

ClareS says "I don't think that the "economy" of an organism can be measured trictly from protein synthesis"

Henryb [to Pawel] ribosome steps are the same in prokaryotes and eukaryotes. therefore I think the energetic cost is the same in both organisms

ClareS says "you will ned to consider organism size, metabolic rate, etc"

ClareS [to NickyM] thanks for the question

ClareS says "does anyone else use a Mac - and if so, have they experienced the same problem (no spin menu)"

Henryb [to NickyM] do you mean you can't set the molecule spinning? or do you mean that the spinning molecule is not visible?

ClareS . o O ( there are no Macs at Birkbeck )

BMD says "I do not have the spin option on my RasMol either."

ClareS [to BMD] what hardware platform are you using?

BMD says "IBM PC"

NickyM says ""I can spin the molecule using the mouse, but noy from a seperate menu with rotation options, speeds etc""

NickyM says ""Perhaps this is a PC version thing""

BMD says "I concur with NickyM"

ClareS [to BMD] Win 3.1 or 95?

BMD says " 95"

ClareS says "and which version of Rasmol?"

BMD says "2.6"

Henryb [to NickyM] you can spin molecules with PCs. what do you get on your short menu (I don't know how you acess a short menu on a mac!)

ClareS has no rasmol on this machine & is trying to work entirely from memory (

ClareS says "if any of you are using version 2.5 of rasmol I would recommend you to obtain version 2.6"

Henryb says "sorry everybody I Have been using chime for so long I have forgotten all about rasmol. Forget the question about short menus it was to do with chime!"

ClareS understands now...

NickyM says ""There is only 1 menu I can find on my Mac, using Rasmol v.2.6, and the options part gives everything but spin""

ClareS [to henryb] don't worry about it. A very common mistake tomake

ClareS says "there is only one menu bar on the versions I use - 2.6 for SGI and Win95"

NickyM says ""perhaps it doesn't matter, I CAN rotate the molecule but not set up a spin dialogue box. Is this important?""

(Claudia has disconnected.)

Henryb says "I think I remember that you have to do this via the command line. I am looking for it but have not found it yet. I will let you know if I am sucessful"

ClareS says "you can certainly set a molecule spinning via the command line, which means you can put it in a script"

NickyM says ""Thanks""

ClareS says "I would like to remind you all of the excellent Rasmol manual & other documentation"

(Pepi has disconnected.)

Pawel [guest] says "I have version 2.6 on Win95 and the command window has the bug - it does not have Close and Resize buttons."

ClareS [to Pawel] you are sure you have the latest version? I've certainly not seen that particular bug

Pawel [guest] says "But it is the only bugI found"

Pawel [guest] says "Yes, I'm sure, it is 2.6."

ClareS [to Pawel] try downloading v.2.6 from a different site if possible & re-installingit

Pawel [guest] says "OK, I'll try it. "

Henryb says "the command line window does not have any buttons on it. It was not designed that way."

The housekeeper arrives to cart claudia off to bed.

Patricia finds her way in.

ClareS [to Patricia] welcome to the meeting

ClareS says "we are discussing bugs and other problems with Rasmol"

Pawel [guest] says "OK, it is finnally only trifle"

Pawel [guest] says "I mean RasMol buttons and not the discussion..."

ClareS smiles

The housekeeper arrives to cart Pepi off to bed.

ClareS says "there are several different ways to do most things in Rasmol"

Pawel [guest] says "Yes ?"

NickyM says "" I have another, different question. In the section on transmembrane proteins, there is a mention of proteins which weave in and out of the membrane. Ihave not heard of this before, is there a link to a diagram or model of this""

ClareS says "i.e. very simply, you can use the command line, a script or often a top line menu"

ClareS [to NickyM] can you give us the URL with the reference, please, so I can look it up?

NickyM says "" somewhere here""

ClareS [to NickyM] thanks

Patricia [to NickyM] I think that there are diagrams of membrane proteins in Branden and Tooze's textbook

ClareS says "Ah - I have it"

ClareS says "I think (I may be wrong) that you have misunderstood the sentence"

ClareS says "the protein chain does not weave in and out of the membrane, in the sense thparts of the chain move in and out of the membrane over time"

ClareS says "(sorry - thparts should read that parts)"

NickyM says ""Thanks, I'll have a hunt in the Textbook.""

ClareS says "instead, parts of the chain are embedded in the membrane, and these transmembrane regions are joined up by loops either in the cytoplasm or the extracellular medium"

ClareS says "for example, rhodopsin has 7 transmembrane regions and some transport proteins have 12"

ClareS [to NickyM] does that make sense?

ClareS says "there *must* be a picture of a transmembrane protein somewhere on the web..."

NickyM says "" Thanks, but only sort of. Unfortunately, I am one of those for whom a picture tells a thousand words""

ClareS says "oh, for a shared whiteboard ;)"

NickyM says "" I will have a hunt""

Pawel [guest] says "What kind of protein chain properties determines their properties to membrane permeabilization ? Is it only the hydrophobicity ?"

Claudia finds her way in.

Claudia says ", Sorry, problem with connection"

ClareS enters "rhodopsin" in Yahoo for want of somehting better to try ;)

BMD [to NickyM] I'd look for diagrams of neuroreceptors, they're usually transmembrane proteins...

BMD [to NickyM] Ion channels should also do quite nicely.

NickyM says ""Thank you Clare and BMD""

BMD smiles benignly.

ClareS says "one of our first PPS students has his project on 7-transmembrane helix proteins *somewhere* on the web"

Henryb says "if you are interested in looking at ion channels then ther is good demo on eric martz' rasmol home page. I will look for the URL"

BMD [to henryb] Many thanks.

ClareS [to Pawel] the most important feature of transmembrane regions in proteins is indeed their hydrophobicity...

JudyH says "I have a question about leucine zippers; why do you think they are always leucine? Wouldn't any hydrophobic aa do the job?"

ClareS says "almost all transmembrane segments are helical, so..."

ClareS says "1) you need stretches of about 20 aas of very high average hydrophobicity (to span the membrane) and 1) I suppose there should be few prolines \"

BMD [to ClareS] I think I read somewhere that the transmembrane region in different molecules may have certain conserved similarities, so much so that computer programs can be used to detect transmembrane proteins in novel sequences.

Henryb says "the channel script is available from and look at 'Lipid bilayers and membrane channels'. You will be able todownload a script which will demonstrate how an ion channel works. Its go


ClareS has found *one* of the things she was looking for...

ClareS says "the bacteriorhodopsin home page, created for the first PPS course by Iddo Friedberg"

ClareS says "(Iddo is now a consultant on the course - you may well have met him here ;)"

Pawel [guest] says "These programs probably simply finds the hydrophobic residues of proper length"

ClareS says ""

Henryb [to JudyH] I suppose what you say is true. There must be something about the size or structure of leucine which makes it particularly suited to its dimerisation role in leucine zippers.

ClareS says "henryb, you're right: I hadn't thought of it before, but there must be. It's an interesting question"

Pawel [guest] says "Are there known the beta-structure tansmembrane regions in proteins ?"

ClareS says "I always assumed it was something to do with its branched structure: but then, why won't Ile or Val do as well?"

ClareS [to Pawel] there is *one* known structure where transmembrane regions are beta strands

Henryb [to Pawel] again I'm no expert on transmembrane proteins but I am fairly sure that some membrane proteins contain a structure known as a beta barrell

Pawel [guest] says "I know, that the defensins, the antimicrobial and cytotoxic peptides can permeabilize the membranes and are almost completely beta-structural molecules"

Pawel [guest] says "But these peptides rather disrupt the membrane"

Patricia [to NickyM]

ClareS says "you can also try looking in the Scop database"

NickyM says ""Thank you Patricia ""

Patricia [to NickyM]

(Claudia has disconnected.)

ClareS says "Scop stands for Structural Classification of Proteins"

ClareS says "the URL is"

ClareS says "to find out what proteins have transmembrane beta folds I type "porin" in the keyword search"

The housekeeper arrives to cart claudia off to bed.

Patricia [to ClareS]

ClareS . o O ( it might do... I'm not sure... )

BMD [to Patricia] I think it does, but it is very much like the case of defensins.

BMD [to Patricia] in the sense that they're not there to stay.

Patricia [to BMD]

Henryb says "I think so to. I think when complement is activated a protein inserts into the cell membrane and punches a hole in it??????"

BMD [to Patricia] their function

BMD [to Patricia] so probably their structure too.

Patricia [to BMD]

Claudia finds her way in.

Pawel [guest] says "The principal (final) effect of defensins and complement (and e.g. lymphotoxins) exposition to membrane is the same - their disruption"

Pawel [guest] says "But in my opinion these proteins are extremely different"

BMD says "So I guess, their transient transmembrane state will not require features similar to more 'permanent' trans.meb. proteins."

Patricia [to BMD]

ClareS agrees

BMD [to Pawel] In what way were you claiming defensins and complement to be different?

Pawel [guest] says "Defensins are small molecules. Theit MW is about 4 kDa"

BMD hmmms...

Pawel [guest] says "But they can form the multimers that can more effectively permeabilize the membrane"

BMD [to Pawel] Which would mean that their multimerisation makes them look more like complement...

Pawel [guest] says "Yes !!! "

Henryb says "Sorry about this folks but I have to leave. This is especially dificult as the discussion is going so well. I'm afraid hunger wins. Bye everybody."

BMD waves.

Pawel [guest] says "To Henry: Bye"

(Henryb has disconnected.)

Claudia says ", Sorry, but connection is too unstable. I must go. "

Claudia says ", Good-bye"

(Claudia has disconnected.)

BMD waves.

Pawel [guest] says "Bye !"

BMD waves.

ClareS says "Thank you very much for taking part in such an interesting discussion"

ClareS says "I will turn the recorder off now"

ClareS turns the ClareS_recorder off.