BioMoo Held on the 6th Mar. 1998

ClareS turns the ClareS_recorder on.

Stewart [guest] says "?""

ClareS says "The floor is yours this morning/afternoon/whatever - we can discuss whatever you like"

Okoh [guest] materializes out of thin air.

ClareS . o O ( as long as it features in the course so far )


ClareS says "does anyone have anything particular they'd like to start with?"

Stewart [guest] says "nio i just dropped""

Stewart [guest] says "with bad spelling""

BMD says "Yes"

ClareS [to BMD] go on?

BMD says "I have not yet figured out how to visualise 'handedness' in spiral structures."

ClareS [to BMD] as in the alpha helix?

Okoh [guest] says "hello everyone this okoh a pps student! do tell me if please if i am getting through..."

BMD says "Structures like helices that is."

Patricia [to okoh] You're getting through.

ClareS [to okoh] yes, you are getting through loud and clear, welcome!

Jim Pitts [to okoh] Yes you are

ClareS [to BMD] well... I found it comes with practice ;) so keep working on it.

ClareS says "does anyone have any more specific advice?"

Patricia [to BMD] Start with the amino terminal at the beginning

Patricia [to Clare] That is right, isn't it?

ClareS [to BMD] it's a case of learning to "see" in 3 dimensions from a 1-dimensional computer screen

BMD [to Patricia] Yes?

ClareS [to Patricia] yes

Okoh [guest] says "this is my first time on this meeting i am glad at long last i could finally get through"

Patricia [to BMD] Yes. And using Rasmol and using plastic chemical models.

ClareS [to okoh] I am very pleased that you are finally able to join us

Stewart [guest] says "does anyone have a simple way of accessing Rasmol?"

Okoh [guest] says "thanks alot for your help"

ClareS says "Yes, it may go somewhat against the spirit of the course to say so, but plastic models certainly do help you learn to visualise in 3 dimensions"

Jim Pitts [to BMD] winding string around a cylinder can help ie in a left-handed or right handed way

ClareS [to stewart] Rasmol can be freely downloaded from the net

ClareS can't remember the URL

Stewart [guest] says "does anyone know the uURL for rasmol?"

Patricia [to Stewart All] I'm looking for it.

Stewart [guest] says "thanks""

BMD says "Why should alpha helices be right handed usually, is the left handed one less stable?"

ClareS is looking for that URL too, on a slow 486

ClareS [to BMD] yes - it's due to the "handedness" of the amino acids - a left-handed helix will give steric clashes

ClareS [to BMD] as far as I can remember the clashes are with residues 1 turn apart so very short stretches of L-handed helix (< 1 turn) are possible

ClareS [to Jim Pitts] can you confirm that, please?

ClareS . o O ( or anyone? )

BMD says "Why should it be so, is it due to the side chain torsion angles?"

ClareS says "it's due to the basic geometry of the amino acid residues"

Jim Pitts [to BMD] The beta carbon position clashes with the carbonyl oxygen if it is not right handed

ClareS says "if you get hold of a kit of 3D models and build a few amino acids it would help"

Okoh [guest] says "in relation to the steric clashes is there know means by which such can be corrected in nature, because say for instance in modelling you can do energy minimization"

ClareS [to okoh] steric clashes can be partly corrected, but even so, the left-handed form of an alpha helix is significantly less stable than the right-handed one

ClareS says "(i.e. it is of higher energy)"

Jim Pitts [to BMD] so in glycine the hydrogen allows for close contact in both right and left alpha helices and can therefore be located in any region of the Ramachadran plot

BMD says "Taking the side chains in gauche(+)?"

ClareS says "so, presumably, one could build a stable left-handed helix out of poly-glycine"

Stewart [guest] says "any joy yet on the rasmol front?"

Jim Pitts [to ClareS] that is right

ClareS says ""

Okoh [guest] says "just wondering what serious job can one really do with rasmol"

Stewart [guest] says "thank you ver much."

ClareS says "there are links there to rasmol sites in Edinburgh (UK) and Geneva (Switzerland)"

ClareS [to stewart] where are you based?

Stewart [guest] says "dundee,Scotland"

Stewart [guest] says "what about you?"

ClareS [to stewart] so the Edinburgh site will be best for you, no doubt ;)

ClareS [to okoh] It depends what you mean by "serious job"...

Claudia finds her way in.

ClareS [to okoh] Rasmol is *not* a molecular modelling program

ClareS [to claudia] Welcome - you can catch up with what we have been saying by typing "read mar6tape" (no quotes)

BMD says "Is there a freeware molecular editor?"

ClareS [to okoh] Rasmol is excellent for viewing, displaying, presenting and teaching / learning about molecular structures

Okoh [guest] says "thanks clare,precisely that was what i meant by serious job modelling"

ClareS [to okoh] it can't be used for *modelling*

ClareS [to okoh] although if all you want to do is examine molecular structures to get a handle on function (measure binding sites etc.) that's OK

Patricia [to Clare] I have a question about #20 on the self assessment quiz.

ClareS [to BMD] I don't know of one, unfortunately

Okoh [guest] says "in a sense,rasmol can only be use to view already existing structure that is what you mean?.Anyway, can it be used to download a pdb files"

ClareS [to BMD] IsisDraw is a freeware *2-D* molecular editor, and it can export structures into 3D format

BMD says "What is the closest one can get to a reasonably priced, flexible molecular editor?"

ClareS [to okoh] download files from the PDB, you mean?

Okoh [guest] says "yes"

BMD says "Really?, Where can I find it?"

ClareS can't remember

Stewart [guest] says "stewbkfer sorry raving incoherently."

Jim Pitts [to Patricia]

Stewart [guest] says "i would quite like to find it too."

BMD says "Hello everyone..did a search and found"

ClareS [to BMD] thanks... you got there much faster than this extremely slow 486

Claudia says ", Hi everyone, I have just finished to read what you said so far. Sorry for delay."

Jim Pitts [to Patricia]

BMD says "Try also"

Claudia says " ClareS, Thank you for your help"

ClareS has found an extreme number of Japanese sites in Japanese with AltaVista

BMD says "Don't worry..the first one I found is in german with a rather spiffing background!"

Claudia says ", I would be interested in a molecular modelling program, above all for the project for the course. "

ClareS [to claudia] you shouldn't *need* to use modelling programs for the project

Stewart [guest] says "are there any free 3-d molecular editors........hopefully"

BMD says "So ISISDraw would be the equivalent of plastic component models of atoms which can be manipulated and constructed, right?"

Patricia [to BMD] Clare mentioned the URL Jim Pitts, A URL for ISIS/DRAW http

Okoh [guest] says "i was wondering if one could ask some other question apart from bioinformatics"

ClareS [to BMD] no... the equivalent of a drawing program for organic chemistry only, I'm afraid, but with limited facilities to convert 2-D sketches to 3-D models. Still very useful

ClareS [to okoh] yes.. go on?

BMD [to ClareS] Thanks.

ClareS says "there are some nice examples of what IsisDraw can produce on"

Patricia [to ClareS] Making *.gif files from RasMol can be interesting, useful.

ClareS agrees with Patricia

ClareS says "Rasmol is actually one of the easiest ways of producing images of molecules suitable for displaying on web pages"

ClareS [to okoh] what is your question?

BMD [to ClareS] What is meant exactly by a nucleation centre for protein folding?

Okoh [guest] says "is cd only good for secondary structure determination, what are other method that could be use to correlate cd results"

ClareS [to Patricia] was it you who mentioned you had a question about the self-assessment questions a while back?

Patricia [to Clare] Yes. A couple of questions

ClareS [to BMD] that's beyond the scope of the course this far... but very briefly it's a point where the protein starts folding, usually a secondary structure element or elements

ClareS [to Patricia] go ahead?

Okoh [guest] says "nte cd as in circular dicroism spectroscopy"

Patricia [to Clare] #20 mentions asymmetric beta carbons on amino acids,

Patricia [to ClareS] I found threonine, serine, and proline.......that's 3, not 2. OK?

ClareS has just found the question

Patricia [to ClareS] I just found out that proline's beta carbon is not asymmetric.

BMD says "I don't have a copy of the question here, could you paste it on screen, pls?"

Jim Pitts [to Patricia] you need three different groups around the carbon, you do not have that in proline see http

ClareS says "You're looking for tetrahedral carbon atoms with four different substitutents... Thr is one and there's one other (not Ser or Pro)"


20. Two of the twenty amino acid residues which occur in proteins have          

    side groups which contain asymmetric carbons. Which are they and what       

    is the R/S classification of each asymmetric centre?                        


Patricia [to itts]

Jim Pitts [to Patricia] Isoleucine and thr

ClareS was wondering if we were allowed to mention the *answers* (heavy hints being, of course, UK)

ClareS . o O ( OK.. not just for those from the UK ;) )

ClareS can't type

Patricia groans

Claudia says "ClareS, I see. Do you mean I must not use it or do you think I can use it as a help tool for my purpose?"

ClareS [to claudia] I'm sorry... what possible help tool are you talking about?

Stewart [guest] smiles

ClareS says "I expect to finish the "formal" part of this meeting before *very long*, now, so please start thinking if you have any final things you'd like to discuss"

BMD says "Torsion angles phi & psi: they can be + or -, with respect to what?"

Patricia [to ClareS] Question #3, the principles underlying side chain conformations....

Claudia says "ClareS, I thought of dealing my project with the building of a hypothetical protein able to bind a very hydrophobic molecule."

Patricia [to ClareS] The question is not clear to me.

ClareS [to BMD] phi and psi.. different conventions have been used over the years. As far as there is a consensus now, phi & psi etc. run from -180 to +180 degrees

BMD says "With respect to what?"

ClareS says "Zero is when the atoms are eclipsed: ie. if you have 4 atoms ABCD, then looking down the BC bond A will lie approximately on top of D"

ClareS [to Patricia] I admit that question is not particularly clearly worded...

JudyH says "I am not clear about q3 too, is it about torsion angles ?"

Patricia [to ClareS] Help......

ClareS [to Patricia] it means, what principles determine what conformations are allowed and what are not

MAZ [guest] finds its way in.

ClareS [to JudyH] yes, in terms of torsion angles

ClareS [to MAZ] Hi.. are you here for the PPS meeting?

Patricia [to ClareS] Then we can discuss, as part of answer, why phi, psi?

BMD says "So in the peptide bond ABCD are O C N and H, right?"

MAZ [guest] says "AR"

Stewart [guest] says "maz is part of my class at diundee we are exploring web sites"

BMD says " not C C N and C."

ClareS [to BMD] yes, and in this case the torsion angle is omega and it is 0 for a cis amino acid

ClareS . o O ( which in principle is usually proline )

ClareS . o O ( in practice (i.e. in real protein structures) is more what I intended to say )

Stewart [guest] says "bye thanks for your help"

(Stewart [guest] has disconnected.)

Okoh [guest] says "taking hydrophobicity of protein into account can one incorprate energy with potential energy function?"

BMD says "Are -180 and 180 the same, therefore...and again what is - and what is +?"

ClareS says "-180 and 180 are, of course, the same"

AlanR finds his way in.

MAZ [guest] says "EXIT"

(MAZ [guest] has disconnected.)

ClareS says "AlanR is a former colleague of mine, from when I was a postdoc at Leeds"

AlanR goes up.

BMD says "The +/- question is pivotal for the Ramachandran plot."

Jim Pitts says "As far as question 3 is conserned may be of help"

ClareS says "I can't remember how the convention is defined (it is just a convention) but all (or almost all) programs are now defining the Ramachandran plot in the same way"

ClareS says "so if you measure a torsion angle in an alpha helix (or anywhere for that matter) in Rasmol, and again in Insight or another package, you'll get the same answer..."

Jim Pitts says "See for Ramachandran info"

Patricia [to ClareS] How do you measure a torsion angle in RasMol?

ClareS says "... and if you are measuring phi or psi, you will find that that angle fits in the "alpha helix" part of the ramachandran plot"

Jim Pitts says " covers the convention for the peptide bond"

BMD says "So, is there a Ramachandran plot for every polypeptide or is it a kind of survey of possible secondary structure motifs?"

Patricia [to ClareS] Could you suggest a reference for question 12, about glycine and conservation during evolution?

ClareS says "You can construct a Ramachandran plot for any polypeptide - that will just plot phi against psi for every residue in the polypeptide"

ClareS says "if you do this for a large number of proteins you will find the points clustering in specified regions, the largest referring to alpha helix and beta strand"

ClareS says "in fact, if you are solving a crystal structure and you find that a residue other than Gly or Pro lies outside a well defined region, this *may* (but may not) indicate a problem"

Jim Pitts [to BMD] it shows allowed and disallowed regions originally derived from dipeptide analysis for the energy of different conformations, you can of course plot the data from any solved structure to give an individual fingerprint plot

Okoh [guest] says "exit"

Jim Pitts [to Patricia] the question is asking abouut the important structural role glycine plays and often this needs to be conserved

ClareS has been reading the Rasmol manyal online

(Okoh [guest] has disconnected.)

ClareS says "you can measure torsion angles in Rasmol, but you need to use the command line interface - type "set picking torsion", then pick (with the mouse) four atoms"

Patricia [to ClareS] OK....

ClareS says "Does anyone have a final question before we wind up?"

BMD says "Thank you all."

ClareS says "Good luck with the exercises: we're looking forward to receiving your answers"

Patricia [to ClareS] The time frame for the answers is.....?

ClareS says "it's in the mail message I sent out (I think)"

JudyH says "when do we need to mail them in, haven't got very far yet:)"

Patricia [to ClareS] OK and Thanks again

ClareS says "we want them in on Mon. Mar 16"

ClareS says "so there is still a reasonable amount of time left"

Patricia [to ClareS] They are interesting questions.......and a limit of 100 words each.

ClareS says "approximate limit, we're not going to carp at 104 words ;)"

Patricia sighs

ClareS says "it's not *that* bad... is it?"

Patricia [to ClareS] It's not "bad. It's interesting...there's so much on every detail.

(BMD has disconnected.)

ClareS is happy now )

ClareS turns the ClareS_recorder off.