Tertiary Structure Biomoo - 10 June 1998

ClareS turns the ClareS_recorder on.

ClareS says "Hi - welcome to this PPS meeting, talking about protein tertiary structure"

NickyM says "Bonjour"

Lizw says ""Hi""

ClareS says "First, I would like to welcome Zev Leifer (Zleifer), one of our consultants. He's in New York in RL"

ZLeifer nods

Patricia [to ZLeifer] RL is...?

ZLeifer [to Patricia] Real Life

ClareS says "this will be the only meeting on this subject (unless anyone is really anxious to fit another one in) - the next set of BioMOOs will be specifically to discuss the Projects"

Patricia Oh.

ClareS [to Patricia] sorry, I should have been more explicit

ClareS [to ZLeifer] thanks ;)

NickyM says "pardon my ignorance - but what is RL"

ClareS says "RL is shorthand for Real Life (i.e. not cyberspace)"

Claudia says "... and AFK...?"

ClareS says "just as AFK, which I used earlier, is shorthand for Away From Keyboard - ie you're logged in but not looking at the screen ;)"

BMD burns his pocket Oxford English Dictionary...

ClareS grins

Patricia {-)

ClareS says "people who use e-conferencing a lot use a lot of these acronyms. No-one else (usually) knows what they mean"

ClareS says "very useful when you're online from home and time is (literally) money ;)"

Claudia says "Is there an acronym list or something similar?"

ClareS says "after that little digression, would anyone like to kick off with a question on protein tertiary structure?"

Lizw says "...and I'm online from home..."

ClareS chooses metaphors carefully

ZLeifer . o O ( perhaps we should append an acronym dictionary to MOO-help. Just a thought... )

ClareS [to lizw] ... and the local time is ...?

Lizw says "a much improved 22.28"

ClareS is sure there's an acronym dictionary around *somewhere*...

Patricia  "Time here is a little after 10 AM."

BMD says "Yes, I would have a query..."

BMD says "I have this sentence from our notes..."

BMD says "Whereas parallel beta-sheets tend to have both faces covered by alpha helices (with 2/3 of the sheet residues taking part in"

BMD says "the interface area), antiparallel beta-sheets are often packed against one beta sheet only (1/3 of the residues in the interface)"

ClareS is listening...

BMD says "What does"antiparallel beta-sheets are often packed against one beta sheet only " mean exactly?"

ClareS [to BMD] could you paste in the URL so I can see that sentence in context?

BMD says "Just hang on.."

BMD says " It's sheet-sheet packing at http://pps98.cryst.bbk.ac.uk/ppscore/section9/9_sheshe.html"

ClareS says "Antiparallel beta sheets are most often found in all-beta structures: barrels or sandwiches"

ClareS says "this is a contrast from parallel beta sheets which are most often found in alpha / beta structures"

ClareS says "if you visualise a beta-barrel..."

ClareS says "it consists of two sheets, stacked against each other"

Ajj says "are we still connected?"

ClareS says "the barrel is distorted and this is sometimes referred to as a "beta-sandwich" instead"

ClareS [to ajj] I'm receiving you loud and clear

ClareS says "so the residues of each strand are in close contact with a strand on the opposite side of the barrel or sandwich"

ClareS [to BMD] are you following this so far?

BMD says "Ok"

BMD says "I have a bit of a problem imagining a beta barrel as a distorted sandwich"

ClareS [to BMD] if you take a barrel and squash it, it gets flatter and flatter.. eventually it's closer to sandwich shaped than barrel shaped.

Patricia  Is it like this ")(", a sandwich, instead of like this "()", a barrel?

Ajj says "so where are the contacts to the opposite face or to neigbor strands"

ClareS [to BMD] in this distorted barrel the residues are closer to those on the opposite side than they would be in a cylindrical barrel

Ajj says "ok"

ClareS [to Patricia] it's more that the distorted barrel is like this () whereas a cylindrical (non distorted) barrel would look more like this O

ClareS [to ajj] there are always contacts to neighbouring strands - the hydrogen bonds which hold adjacent strands of the sheet together

ClareS [to ajj] in a distorted barrel () there are also contacts between residues across the barrel

Ajj says "Yes i see"

ClareS says "some structures contain barrels which are truly barrel shaped - ie there are very few contacts across the barrel"

Patricia says "Oh, OK."

ClareS says "most of these are carrier or transport proteins - ligands bind within or are transported through the core of the barrel"

Patricia says "Would the forces at work on the inside of a "sandwich" be hydrophobic?"

BMD says "So, let's take the structure of glycolate oxidase as an example: are we saying that...."

ClareS says "Lipocalins (eg retinol binding protein) are barrel-shaped transport proteins"

ClareS says "and porin is an example of a transport protein which is a beta-barrel with a very wide pore"

ClareS [to Patricia] yes, predominantly hydrophobic

BMD says "the beta barrel here is made of two beta sheets which are "not distorted"?"

BMD says "Two sheets of four strands each?"

Pepi says "what keeps beta barrels with large pors to colaps into beta sandwiches?"

ClareS says "yes.. GOX is a TIM barrel which is one of the commonest protein folds"

ClareS says "it consists of eight strands, in a parallel beta barrel, surrounded by a second "outer barrel" of eight helices"

ClareS [to Pepi] the transport proteins are held in the barrel shape by their ligands - they tend to distort with no ligands bound

BMD says "So what determines whether the barrel "distorts" or not, the size of the core side chains perhaps?"

ClareS [to Pepi] the porin structure is held in that pore shape by the rest of the cell membrane

ClareS . o O ( at least I assume so ;) )

ClareS says "you can see the structure of porin, with its wide pore, at http://www.biochem.ucl.ac.uk/bsm/pdbsum/2omf/tracel.html"

Patricia says "Could it be the alpha helices on the outside of a parallel sheet beta barrel that keep it from collapsing?"

Claudia says "In what sense the membrane maintains the pore in its shape?"

ClareS [to Patricia] yes - undoubtedly. The alpha/beta barrel architecture is one of the most stable

ClareS says "the porin strands are in contact with phospholipids within the membrane, with many attractive hydrophobic interactions"

Lizw says "Is the alpha-beta barrel very common in transmembrane pore proteins? I mean in contrast with proteins found in other locations? Like, I didn't think that TIM was a transmenbrane protein!"

Patricia says "I cannot seem to get that URL about the porin protein."

ClareS [to lizw] I'm very sorry - I have managed to confuse you totally by talking about two proteins at the same time

Claudia says "This means that in a non hydrophobic environment the pore protein would irremediably loose its shape?"

ClareS says "porin is a transmembrane beta barrel (in fact, porin is *the* transmembrane beta barrel"

ClareS says "TIM Barrels such as GOX are not transmembrane proteins at all; they are alpha/beta barrels"

ClareS says "is that OK?"

Lizw says "Thanks, that helps"

Patricia says "Isn't porin a multimeric pore?"

ClareS [to claudia] the inner pore of the porin is filled with solvent

Claudia says "Thanks"

ClareS [to Patricia] yes, you're right and the contacts between monomers will also help to keep the pore in shale

ClareS . o O ( shale = shape )

ClareS says "page ofer mondial?"

ClareS blushes

ClareS says "I hope that you are all slightly clearer about beta-barrels now: I tried to keep all the threads of the discussion going together without confusing everyone"

ClareS says "that URL I gave you for a porin structure is on the CATH site: have you all had a chance to play with the CATH and SCOP databases?"

BMD nods

ClareS says "there is an immense amount of information there"

Patricia says "It isn't even overwhelming, the amount of information, that is."

ClareS says "it is well laid out, linked and documented; both these sites are invaluable"

ClareS says "I will have to go before very long: are there any more questions?"

Patricia says "Are we to hear about projects soon?"

ClareS says "the projects will be posted on the web before very long - really..."

ClareS says "they should have been up this week, but we have had one or two delays here"

Patricia says "Thanks. "

ClareS says "in the next two meetings (on July 1) we will be discussing specifically all aspects of the projects"

Ajj says "i have asmall technical question"

ClareS . o O ( the titles had *better* be up by then... )

ClareS [to ajj] go on?

Ajj says "i've had to reconfiqure my browser and i can't seem to get rasmol to pick up the script information"

Ajj says "when i tried looking up its application it is rather obscure "

Ajj says "not easily found that is"

ClareS [to ajj] are you using rasmol as a helper application or separately?

Ajj says "either way"

(Patricia has disconnected.)

(Patricia has connected.)

ClareS [to ajj] can you use the scripts with rasmol separate from the browser (ie is it a browser problem)?

Ajj says "i can use rasmol separately"

Ajj says "but i can't seem to load the scripts"

Ajj says "i will view the moleculaes fine but the visualization intended in the scripts is not accessible"

Pepi says "I have the same problem as Ajj, my browser opens ras files in rasmol, but the program skips the script part of the file"

ClareS . o O ( very strange... )

(Patricia has disconnected.)

(BMD has disconnected.)

(Patricia has connected.)

Ajj says "should we send a note to david?"

ClareS [to ajj] could you set out the problem in an email and send it to the technical list? I don't think I can sort it out in a few minutes online

ClareS says "David will no doubt see the message on the list ;)"

Ajj says "ok will do"

Ajj says "thanks "

ClareS [to ajj] thanks, sorry I can't be of more help right now

JudyH says """

JudyH says " I have been having trouble too with scripts ,I have been using Rasmol 2.5"

JudyH says " ""

(Ajj has disconnected.)

ClareS [to JudyH] if you upgrade to version 2.6 it might help

Patricia says "I've been typing in the commands a line at a time. I think there is an easier way by typing "script"?"

JudyH says " "

(Patricia has disconnected.)

JudyH says " ""

Claudia says "I must go now, "see" you soon. Bye."

Pepi says "can anyone see what JudyH is saying (I see only double quotes and blank spaces"

(Claudia has disconnected.)

ClareS has been searching for the rasmol manual online

The housekeeper arrives to cart Patricia off to bed.

The housekeeper arrives to cart BMD off to bed.

ClareS can't see what Judy is saying either

ClareS has found the online rasmol manual it's http

(JudyH has disconnected.)

(Lizw has disconnected.)

ClareS says "this is an excellent hyperlinked guide to rasmol commands"

ClareS says "it has full instructions for reading and *writing* rasmol scripts"

Pepi says "thank you Clare, I'll check again that link."

ClareS says "it is in the States so may be slow from Europe, particularly in the afternoons"

Patricia finds her way in.

ClareS [to Patricia] welcome back.. but we've nearly done ;)

(JudyH has connected.)

ClareS [to Patricia] did you see the URL for the Rasmol manual?

The housekeeper arrives to cart ajj off to bed.

Patricia says "OK. Excuse me, but I got disconnected, somehow. It's been interesting."

Pepi says "no problem, I am usuali connecting to internet during weekends"

ClareS [to Patricia] don't worry about it

JudyH says "can anyone hear me?"

Patricia says "Hmmmmmmmmmm?"

Pepi . o O ( usuali=usualy )

ClareS [to JudyH] yes, I can now

ClareS has a RL meeting to go to now ;)

ClareS says "thanks, everyone, for this lively discussion: it has been most interesting and, I hope, useful"

Pepi says "bye Clare"

Patricia  waves , "Until July 1, then."

ClareS turns the ClareS_recorder off.