BioMOO Transcript for Dec 9th 1998

ClareS turns the ClareS_recorder on.

ClareS says "Welcome to the first PPS tutorial of the 1998-9 course... we are now being recorded ;)"

Gmocz says "Great"

ClareS says "there will, of course, be another session on Friday afternoon at a more sociable time in Europe, at least"
JohnN remains silent

ClareS says "we are here to discuss the first three sections of course material: does anyone have any comments or questions?"
ClareS looks round expectantly

JohnN says "I have some questions, but I'm unsure of starting with them"

ClareS says "go ahead... no question is too trivial. the worst that can happen is that I fail to know the answer ;)"

Gmocz says "Yes. Thr and Ile have two chiral centers Is this relavant to folding at all? other AA has only one"

ClareS says "I must warn you, tho', I'm on dialup from home and don't have
web access. Please explain your questions without direct reference to the web material if you can"

ClareS says "yes, good point (Gly has none)"

JohnN says "Is there a recommended way of getting the best approximation of
a phi or psi angle when using Rasmol, I think I'm only guessing to about 20 degrees at the moment?"

ClareS says "I don't think it's relevant to folding. Only one form is actually present in "real" proteins"
ClareS can never remember which

Gmocz says "What is the most important property of an AA in folding? Size?"

ClareS says "there are several important properties - which is *most* important will depend on the exact situation"

ClareS says "there is a theory which says that the early part of proteing
folding is driven by the hydrophobic residues preferring to be in the core, in contact with each other..."

Gmocz says "I know that one property alone does not determine folding, but which one has the greatest influence in an average size globular protein?"

ClareS says "hydrogen bonds and electrostatic interactions are more important for deciding the fine detail of the folded structure"

ClareS says "so I suppose you could say that hydrophobicity is the most important factor taken overall"

ClareS says "certainly, proteins (peptides) which are too small to form
proper hydrophobic cores can only fold into stable structures in unusual situations..."

ClareS says "... i.e if they can be held together by metal ions or by disulphide bonds"
ClareS hasn't forgotten the question on rasmol and is consulting the manual

Gmocz says "what is (how many kcal/mol) the hydrophobic interectoc interaction's share vs hydrogen bonds?"

JohnN says "Is rasmol used mainly as a teaching tool or does it find applcations in reserch too?"
JohnN ouch

ClareS says "rasmol itself is most often used as a teaching tool. "

ClareS says "it can produce some excellent graphics which are often used in presentations"

Gmocz says "I know some researchers who use it to display the results of their calculations"

ClareS says "and also, in many cases just looking at a structure can tell you a lot - in that sense only it *can* be used in research"

ClareS says "the real difference is that, I suppose, it is defined as a molecular "visualisation" package rather than a molecular "modelling" package"

ClareS says "and for research, of course, you usually also want to do calculations"

JohnN says "So preliminary viewing of a structure would be its main use"

ClareS says "or if you wanted to identify suitable residues for
experimental analysis - say, site directed mutagenesis or the attachment of fluorescent probes - then a display tool such as rasmol would do just fine"

JohnN says "I'd find it useful to look at examples of leftand right handed
disulphide bridges, and of beta and gamma turns, to gain more familiarity
with spotting and identifying them, though I guess we'll see plenty of examples later in the course. "

ClareS says "generally the more you look at structures the more you get a "feel" for them - learn to visualise the 3D structure from the model"

Gmocz says "If we are at SS bonds, can an SS bond introduce knots into the fold?"

ClareS says "there is a group of small proteins with a fold described as a "disulphide knot""

Gmocz says "Can I find some literure on them?"

JohnN says "Do you know what any of the individual proteins with the disluphide knot are called?"

Gmocz says "Sorry for the missplelling"

JohnN says "It's a common problem!"

ClareS says "it's not a real knot, of course: disulphide bonds are the only
cross-links that can be made in proteins, so the main chain can't tangle up like a knot"

ClareS says "but it certainly does look like a knot"

ClareS says "I can't think of any off-hand but you can find them in the SCOP classification database"

Gmocz says "Can anything like a Mobius type ring be formed by SS bonds?"

JohnN says "I have a question about gamma turns. Are they an unusual
feature?In the example given, despite the turn being 'tight' the hydrogen
bond supporting the turn seems quite long and therefore weak,and the general
direction of the polypeptide chai n doesn't seem to change, am I looking at the turn correctly? "

ClareS says "no... (to Mobius ring question)"

ClareS says "gamma turns are certainly more unusual than beta turns"

JohnN says "do they connect major structural elements/"

ClareS says "and they are not calculated automatically by some of the programs that can calculate helices, sheets and beta turns"
JohnN sorry that was supposed to be a question mark

ClareS says "don't worry, it's difficult to type in real time, I make mistakes all the time!"

JohnN says "Are they restricted to terminal strands orlong loops which are not so constrained by major structural elements? "

ClareS [to JohnN] they usually connect major structural elements (I think)

ClareS says "you don't often get tight turns in long surface loops (ie
nowhere near secondary structure elements) - the chain is usually more flexible there"

JohnN says "In our example the gamma turn just seemed to be a *minor* kink in the end of the polypeptide chain?"

Gmocz says ""What percentage are they present in average in secondary structure?"

ClareS [to gmocz] I'm sorry - I don't know exactly.. they are certainly
quite rare

Gmocz says "I know beta turns are much more common, I was just wondering, certanly below 1%"
ClareS will check out that page to-morrow

JohnN says "Is the single hydrogen bond the main factor (apart from the hydrophobic contraints) in maintain such a tight turn ?"

ClareS [to gmocz] are you asking the % of all protein residues that are in
gamma turns, or the % of all residues within secondary structures?

Gmocz says "all residues that are in gamma turns"

ClareS [to gmocz] I'm still not quite sure what you mean, are you asking
what percentage of all protein residues are in gamma turns?

ClareS [to JohnN] you can't really look at a gamma turn in isolation rather
than as part of a structure, the gamma turn will take the chain in a
particular (stable) direction

Gmocz says "Let us say, on average 20-30% of total residues are in alpha
helix, 15-20% in beta sheet, 10-15% in beta turns. Perhaps 1% in gamma turn? Maybe much more less."

ClareS says "I don't know of anyone who's done that particular calculation but I would say certainly less than 1%"

JohnN says "In gamma crystallin it seems to leave the direction of the polypeptide chain much as it was?"

ClareS says "try doing a search for reviews with "gamma turn" as a keyword in Medline or (UK) BIDS"

JohnN says "Can one connect to BIDS without an academic account?"

ClareS [to JohnN] after a bend or kink

JohnN [to ClareS] yes

ClareS [to JohnN] you need a UK academic identifier but you often don't
need a full time UK university affiliation to get one of those

ClareS says "for example, an account at the UK HGMP resource centre or one via the OU will count"

JohnN says "Would membership of the course be enough for me to get such an identifier?"

ClareS says "I will ask David Moss"

JohnN says "I'd be grateful"

Gmocz [to ClareS] was cis configuration of peptide bond other than with Pro
observed in real protein?

ClareS [to gmocz] yes, but very rarely

Gmocz says "Which amino acid?"

ClareS [to gmocz] and unfortunately I can't remember any examples off hand

JohnN says "Does that mean an omega angle of zero?"

ClareS says "it would be in unusual (geometric) situations"

ClareS [to JohnN] yes (as opposed to 180deg for trans)
ClareS notes the limits of an ASCII keyboard ;)

JohnN says "welcome"
ClareS . o O ( if she's one of us she's nearly an hour late )

Gmocz says "Perhaps with unusual amino acids, other than the 20 proteinogenic AA. How many other AA are known approx?"

JohnN says "Presumably that is very rare if it breaks the pi bond overlap of the peptide link?"

ClareS says "there are very, very many "amino acids" - that is, organic compounds with a -NH3 group and a -COO- group"

ClareS says "only the known 20, of course, can be synthesised directly from the DNA"

ClareS says "a few others are created by post-translational modifications"

ClareS says "such as phosphorylation of Ser, Thr or Tyr"

ClareS says "Hydroxyproline is another such modification"

ClareS says "and there are a lot of complex rare examples"

JohnN says "would most of them occur in bacteria, or are they more general?"

ClareS says "they are more general.. life as we know it could not occur without protein phosphorylation for one example!"

JohnN says "Sorry I was meaning the *complex rare examples*"

ClareS says "sorry for assuming you were asking an obvious question! - it's very late (here at least ;)"

ClareS says "they also occur generally (but are not observed very often)"

ClareS says "in Green Fluorescent Protein (found in jellyfish ;) 3 amino acids react together after translation to create a fluorophor"

ClareS says "that's just one example, there are many others"

JohnN says "I am beginning to realise the importance of psi and phi angles,
but how important is measuring them on the course? do we have to be quite proficient? "

Gmocz says "What would be the advantage and disadvantage of using pseudo
angles such as calpa-Calpha or OC-CO to describe secondary structure rather than using the Ramachandran angles?"

ClareS says "I propose to wind up this meeting very soon (and go to sleep ;) so please be thinking of your last questions"

Gmocz says "Thanks, Have a Good Night."

ClareS [to JohnN] you don't need to be able to estimate them exactly - just
to get a general idea (which is often clear from the secondary structure)

JohnN says "It is late, thanks, sleep well."
AlinaO [guest] materializes out of thin air.

ClareS [to gmocz] that's a good question - can I sleep on it and get back
to you?

ClareS [to AlinaO] hi, are you on the PPS course? If so we're just
finishing the meeting

Gmocz says "Sure. I will be happy to hear from you next time"

ClareS [to gmocz] thanks for understanding - it's past midnight UK time

AlinaO [guest] [to Hi] I am a freshman here.

AlinaO [guest] says "See you then!"

ClareS [to AlinaO] you're not on the Birkbeck Principles of Protein
Structure course?

AlinaO [guest] says "I guess I am!"

ClareS says "thanks for asking such interesting questions! and see you next time"

Gmocz says "Bye!"

ClareS [to AlinaO] I'm afraid you've just missed the meeting which started

at 2300GMT

JohnN says "Thanks, see you all next time, good night."

AlinaO [guest] says "When next?"

ClareS [to AlinaO] if you are on the course you should have details in your

ClareS [to AlinaO] what is your full name and where are you from?

AlinaO [guest] says "O.K. I shall check it!"
ClareS turns the ClareS_recorder off.