BioMoo From 19th Mar 99

ClareS turns the ClareS_recorder on.

ClareS says "go ahead - we're recording now"

JohnN says "What is the empirical data about structures adopted bypolyglyine?"

JohnN says "Sorry you know what I mean"

ClareS says "sorry, exactly what do you mean - physical evidence like diffractioin patterns?"
ClareS . o O ( diffraction, of couse )
ClareS can't type

ClareS says "there are fibre diffraction patterns of poly-glycine, from decades ago"

ClareS says "collagen (with Gly every third position) has a very unusual triple-helical structure"

JohnN says " Wouldn't the possibility of h-bonding to an external solvent affect the structure it adopted"

ClareS says "yes, but that's true with every biological macromolecule: proteins don't exist (or at least don't function) in vacuo"

JohnN says "and a helical structure would be more easily stabilised by internal h-bonds?"

JohnN says " Can we make any generalisations about the genetic codefrom the variations in it between mitochondria, chloroplastsand protozoa? Are we able to learn anything about how the code evolved?"

ClareS says "sorry for delay in answering..."

ClareS says "yes, a helical structure is stabilised by internal h-bonds - that's why it's *so* stable"
David.cavanaugh finds his way in.

ClareS says "of course, a beta-strand is unstable on its own but very stable when it is connected into a beta sheet"

ClareS [to david.cavanaugh] hi

JohnN says "Hi David.cavanaugh"
David.cavanaugh hi clare
David.cavanaugh hi john

ClareS [to david.cavanaugh] you can catch up with what we have been talking about on the transcript - the march19tape
ClareS . o O ( yesterday's tape is here as well )

David.cavanaugh says "good I'll e-mail it to myself"
ClareS . o O ( this is a *much* better line, everyone should try working at midnight GMT )

David.cavanaugh it's 515pm here

JohnN says "the line might be good - not the brain or the typing!"

ClareS [to david.cavanaugh] very civilised, it's 23
ClareS props her eyelashes open with matchsticks and carries on

ClareS says "John had just asked a question about the genetic code, which I was thinking hard about..."

David.cavanaugh says "I had occasion to look through previous PPS course material and there's some good stuff which has come up missing."

ClareS says "you mean material in the previous courses which we don't link to anymore?"

JohnN says " I'll keep asking while you think and maybe we'll be able to get going - Apart from transport of nascent proteinsacross the ER and the use of clathrin coated vesicles, are any other transport mechanismsknown in detail. What is known about transportof proteins across the inner membrane of mitochondria?"

David.cavanaugh says "I mean stuff that's been excluded for whatever reason"

ClareS says "usually we have to take links out when they break - usually if it's external material which the owner removes"

ClareS says "we have no control over other people's material"

ClareS says "if there's anything you particularly wish to see let us know & we'll try to find an equivalent, contact the original author or write our own..."
ClareS . o O ( all good feedback... )

JohnN says " I recently tried to get through to the Trieste link we were given (to stuff on bioinformatics) and was told the address didn't exist - could it just be that the line was down? the link worked a few days earlier?"

ClareS says "it could easily be that the line was down"

ClareS says "I know that Trieste site and it's very unlikely that the material's vanished"
ClareS wonders what the distance is between Trieste & Kosovo

JohnN says " Interesting thought"

David.cavanaugh says "PPS'96 Kurt Berndt helix&sheet; PS'95 Beta Hairpin, Alpha helix& geometry part 2; Protein Degradation resource, Keith Wilkinson@ Emory Univerity"

JohnN says " Has the sequence of events involved in targeting cathepsin been fairly fully worked out?"

ClareS says "could you see the material by following links from the previous courses?"

David.cavanaugh says "yes"

ClareS says "could you email me the URLs? We'll have a look and think hard about reinstating these resources"

David.cavanaugh says "OK"

ClareS says "so the material is still *there*, it must have been removed for other reasons"

David.cavanaugh says "I would think so."

ClareS [to JohnN] I guess so (re cathepsin sequence of events) tho' I'm not very sure

JohnN says "thanks"

David.cavanaugh says "Cathepsin seemed to be a trick question in the self assessment."

ClareS says "there wasn't anything about it in the course material ;)"

JohnN says "Looking at Genbank I came across mention of ASN.1 as an alternative format to .pdb - is it very new or are the implications of the format not worked out yet?"

David.cavanaugh says "The Protein degradation resource I mentioned is *excellent*"

JohnN [to David.cavanaugh] Thanks David I'll have a look.

ClareS says "so, I guess you could easily call it a trick question.. but there's plenty of david, can you paste the URL *here*? Then everyone will see it on the transcript"

ClareS blushes (
ClareS . o O ( two sentences at once )

David.cavanaugh says "I'm using an integrated web browser i/f, so I'll send it to the discussion list"

ClareS says "the first, which I didn't finish was meant to end ".. but there's plenty of stuff on the Web" - I suppose it's late (here), that's some excuse"

ClareS [to david.cavanaugh] thanks - that'll be useful

ClareS says "PDB format is the *standard* format for 3D structures of molecules (now) - but there are others which are used from time to time"

ClareS says "the only *new* one isn't ASN.1 - it's something called mmCIF (macromolecular crystallographic information file) and that is mostly used by crystallographers"

ClareS says "there are rather more regularly used file formats for sequences"

JohnN says " I got the impression that ASN.1 would be helpful for correlating information between different structures?"

JohnN says "Is mmCIF readable by PC?"

ClareS says "it depends whether the software you have can read the file format"

JohnN says "What software reads it?"

ClareS says "I'm very sorry, I can't remember the details of the ASN.1 file format, I'll have to look it up and email you - is that OK?"

ClareS says "re the mmCIF format, really only software used in solving structures"

JohnN says "Fine - its nice to be able to air questions -"

David.cavanaugh says ""Here it is: http://www.biochem.emory.ed/PROTDEG/HOME.HTML. Protein degridation resource."

ClareS says "I *think* that you can look at a mmCIF file of a protein structure from its main PDB page - but I can't remember for sure"

ClareS [to david.cavanaugh] thanks!

ClareS [to david.cavanaugh] I presume you mean .edu, not .ed?

David.cavanaugh says "Yes. it s/b .edu"

JohnN says " On the quiz I didn't know the doubling time for gnebank gene sequences - is it increasing rapidly?"
ClareS will certainly check it out

ClareS says "every 18 months"
ClareS can mention answers to the quiz here as it is entirely anonymous

ClareS says "did you enjoy the quiz? did either of you try out last year's one, on the amino acids?"

David.cavanaugh says "One of the self assessment questions was in regards to transmebrane domains, has this problem been understood to the extent software algorithms may be implemented ?"

JohnN says " Yes, it was comforting to know some answers for a change"

David.cavanaugh says "I did last years quiz, and it was interesting."

JohnN says "I found quite a few quizes from past years and they were helpfull"

ClareS says "there are software algorithms to predict transmembrane segments, in fact these have been around for some time"

ClareS says "the simplest just look at hydrophobicity"

David.cavanaugh says "Speaking of old resources, the HTML tape here on the BioMOO was informative."

ClareS says "some others try to predict helix topology as well as location, on the basis that the inner surface of a transmembrane helix is usually slightly more hydrophilic than the outer surface"

JohnN says " Is the common length of reverse turns fairly predictable (ie short)?"

ClareS says "one good example of a program for this is TopPred"

David.cavanaugh says "The reason I ask is that I read somewhere recently, this was a problem for database searches for transmembrane domains, which is why I ask." ClareS [to JohnN]: yes: at least, it's a matter of terminology - if the loop isn't short it stroctly speaking isn't a "reverse turn" at all, just a loop joining two strands

ClareS [to david.cavanaugh] well.. these programs aren't 100% accurate. They're more accurate than secondary structure prediction, but that's not saying very much

David.cavanaugh says "When you say the inner portion of the helix is slightly hydrophillic, are you speaking of possible R groups like Glycine ?"

ClareS says "usually a program will predict the number and approximate location of transmembrane helices correctly, but not the precise location on a residue-by-residue basis"

ClareS says "Gly is not a good choice as it's not often found in helices, but yes, intermediate polarity residues plus a few hydrophilic ones"

ClareS says "sometimes you even get a charged residue in a transmembrane helix - that will almost invariably be facing towards the centre of the pore between the helices and will interact either with another residue or with a potential ligand to neutralise the charge"

ClareS says "but you need to have a majority of hydrophobics to stabilise the helix in the membrane, that's why I specified "slightly" hydrophilic"

David.cavanaugh says "In one resource I found from previous PPS links, the author mentioned attempts to use Fourier transform analysis, using AA similarities or hydrophobicity scales, to characterize proteins. Did this work ever go anywhere, or was it just a curiousity ?"

JohnN says " is the full range of possibilities of AA to neutralise charge used ? -e.g. is Glu as common as Asp pointing into the *hole*?"

ClareS says "one program of the type I mentioned just now uses just that technique to predict (with hydrophobicity) to predict which face of a helix will face the hydrophilic environment "

ClareS says "it's written by Dan Donnelly, who used to work in the same department as me (Leeds Uni., early 90s) but unfortunately I can't remember its name"

ClareS [to JohnN] I literally don't think that enough data exists to answer that question

David.cavanaugh says "Protein structure resource from PPS '96 by Kurt Berndt."

JohnN says "Are techniques to crystallise them advancing only very slowly?"

ClareS [to JohnN] yes - they are *very* difficult to crystallise as they are not stable in aqueous solution.

ClareS says "there are quite a lot of structures of proteins which are anchored to membranes in vivo (by a single helix) but usually with the transmembrane helix removed"

ClareS says "electron diffraction is sometimes used, but this gives low resolution structures"

ClareS [to david.cavanaugh] thanks for that URL

JohnN says " this must be a major challenge - presumably the number and interest in such proteins is vast"

David.cavanaugh says "Have alternate solvent systems been used besides water?"

ClareS says "sometimes detergents, but even this is not easy"

JohnN [to Thinks] JohnN is slowly falling off his perch

ClareS says "there is a whole chapter on membrane proteins in Branden & Tooze, which provides an excellent introduction to the area: particularly the new edition"

JohnN says "I just got that - looks like many hours of fun!"

ClareS says "I am very sorry - this has been a fascinating conversation but I am beginning to fall asleep! I will really have to go very soon" ClareS [to JohnN]: yes, it's excellent. I will be reviewing it for "Biochemical Education"

David.cavanaugh says "On a lighter note, does the counter-ion in the PPS meeting room do anything anymore?"

JohnN says " Is Attwood's ' Introduction to bioinformatics' at the right level for the course do youknow?"

ClareS says "re: counter-ion: it never did anything apart from annoy people (IMHO ;)"

ClareS says "I know Terri Attwood well so will have to be careful what I say! Yes, it's a very good book but probably has too much detail if all you want is the amount of bioinformatics in the PPS course"

JohnN says "Is it aimed at undergraduates?"

ClareS says "final year undergraduates, possibly. Not the earlier years"

JohnN says "I'll have a look - I could do with some 'lecture' type input in that area as I'm new to it."

ClareS says "I am also writing a textbook on bioinfo - but I don't think it'll be out until 2000"

David.cavanaugh says "In the old days of chemistry, the concept of Lewis acids was widely used, is it a concept which has found any relavence to protein structure and function ?"

ClareS says "not that I have ever come across, but don't take that as gospel"

JohnN says "I'm falling asleep...,. I'll wave goodnight"
(JohnN has disconnected.)

David.cavanaugh says "How about AA to metal cation stability constants ?"

David.cavanaugh says "That's my last question for the night. :)"

ClareS says "I'm falling asleep too... I'd prefer to answer that one by email as well. Please email me to remind me if it doesn't appear!"
David.cavanaugh waves goodnight then ...
ClareS turns the ClareS_recorder off.