BioMOO Transcript for Dec 11th 1998

ClareS turns the ClareS_recorder on.

Alina [guest] says "not at all."

Klausri says "no I accidentally dropped out closing other windows on my machine"

ClareS says "Welcome to this PPS meeting. As with the one late last Wednesday evening, we will be discussing parts 1-3 of the course material."

ClareS says "would anyone like to start off with a question?"
(AlinaO [guest] has disconnected.)
ClareS looks round expectantly...

Klausri says "I have had problems with connecting Rasmol with explorer but chime seems to work...?"

Alina [guest] says "I am also looking around"

Alina [guest] says "and nothing happens"

Gmocz says "Yes, I would like to my last question from Wednesday which we could not finish"

ClareS [to Klausri] which version of explorer were you using?

ClareS [to gmocz] could you repeat the question - most people here now
weren't here then, and I've forgotten it

Roby says "yep!"

Gmocz says "What would be the advantage or disadvantage to use virtual bond
such as Calpha-Calpha or CO-CO to describe secondary structure rather than using the Ramachandran angles"
ClareS remembers now

ClareS says "people do use this representation to describe protein structures - but not by quoting explicit angles"

Alina [guest] says "Hello!"

Roby [to gmocz] Do you have your own answer to your question or it's just a

ClareS says "if you display the alpha carbon trace of a protein you're
doing just that (but representing the structure graphically instead of listing angles)"

ClareS says "each amino acid is represented by a single "virtual bond" from calpha to calpha"

ClareS says "the advantage is that it is easy to visualise the general form of the structure"

ClareS says "the disadvantage is that the virtual bonds don't represent anything physical"

Gmocz [to Roby] With my limited experience I find to use Calpha virtual
bonds and angles easier to visualise and recognize sec. struct

ClareS says "you're reducing the 2 parameters phi, psi to one and losing
data - and there is no equivalent of the Ramachandran plot for these virtual bonds"

Roby [to gmocz] I see, thanks!

ClareS [to gmocz] does that help?
Alinka [guest] materializes out of thin air.

Gmocz [to ClareS] Of course, thanks

ClareS [to Alinka] Hi

ClareS [to Alinka] we have just been discussing backbone torsion angles in
proteins and the best way to visualise structure

Alinka [guest] says "ah.."
(Alina [guest] has disconnected.)

Gmocz [to ClareS] In your view what is the best way to visualize sec str.
if you do not want to display all details

ClareS says "it is certainly easier to use virtual bonds to visualise secondary structure"

ClareS says "but it is easier still to use the various "ribbon" and "cartoon" representations"

ClareS says "basically this is similar to the virtual bond approach but a
smooth line is drawn through the peptide backbone and then made into a ribbon"

ClareS says "some representations vary the thickness according to the type of secondary structure"

ClareS says "helices are drawn as thicker ribbons or even tubes; beta strands can be shown as arrows with the arrowhead at the C-terminal end"

Gmocz [to ClareS] Thankd, this clarifies the question completely

Alinka [guest] says ""Would you care for a cup of cofee?!"

ClareS says "it is almost impossible to work out secondary structure using an all-atom representation of a protein"

ClareS [to Alinka] I'd love one, thanks

Gmocz [to Alinka] Sure, it is only 5

Alinka [guest] says "I shall boil some water then."

ClareS says "you can see these representations of proteins with Rasmol"

Gmocz says "Another question regarding beta structure: what determines exactly wheter it will be parallel or antiparallel"

ClareS [to gmocz] I'm not exactly sure what you mean

Gmocz [to Roby] I do not know yet it is still dark

Roby says "I think I know the answer"

Roby says "n and c termini are in opposite positions when antiparallel"

Gmocz [to ClareS] does primary structure completely determines it?

ClareS says "whether a sheet is parallel or antiparallel depends on the overall fold of the protein"

ClareS says "as Roby said, the N and C termini are opposite each other in parallel strands"

ClareS says "and in the reverse places in antiparallel ones"

ClareS says "if the chain folds straight back on itself you have two antiparallel strands"

Alinka [guest] says "so both ends are close together"

ClareS says "if it loops back with a long section of coil, or a helix, so
the N terminal end of strand 2 lies opposite the N terminal end of strand 1 you have 2 parallel strands"

Alinka [guest] says "aren't they?"

Gmocz [to ClareS] So if you put a protein in a more hydrophobic medium
where folding changes, can the a parallel sheet be converted into an
antiparallel one if the orientation of the chain changes?

ClareS [to Alinka] with parallel strands the N terminus of each strand is
close together

ClareS [to Alinka] and with antiparallel strands the N terminus of one is
close to the C terminus of the other

ClareS [to gmocz] very unlikely

Alinka [guest] says "thanks"

Gmocz says "I thinks so too"

ClareS [to gmocz] the fold would need to change *completely* essentially by
denaturing the protein

ClareS says "any protein has one active conformation"

ClareS says "sometimes the conformation can change when e.g. a substrate binds but even then the changes take place almost entirely in the loops"

ClareS says "the overall topology (secondary structure pattern) doesn't change"

Gmocz [to ClareS] So, more or less sec str elements move as rigid part
relatively little to each other

ClareS [to gmocz] yes - that's about right

ClareS says "also if you have a lot of similar structures in a protein
family you will find that the secondary structure elements are very much less likely to change than the loops"

ClareS says "ie family members will have the same number of helices and
strands, in the same topology, separated by loops with different lengths and geometry"

Gmocz says "Can a double helix be formed from a single peptide chain in a protein by bending it back and folding on each other?"

Alinka [guest] says " [to Clare]: Could I ask you another question?"

ClareS [to gmocz] forming a bundle of alpha helices - yes, this is common,
but the loops are not as tight as they can be between adjacent strands

ClareS [to Alinka] yes - go ahead

Klausri says "does computor programs exist that can search through e.g. the PDB data base for a particular configuration of secondary structure?"

ClareS [to Klausri] yes, but it's more common to look for a particular
domain structure or fold

Alinka [guest] says "Is the noncompetitive inhibition of SDH with Hg cations reversible or not, e.g. using EDTA?"

ClareS [to Klausri] there are lots of different forms of e.g. a
helix-turn-helix and it's difficult to get a program to distinguish between
them without using other information
(Gmocz has disconnected.)

Roby says "I think it would be useful to employ full names first, and then the acronysm that stands for the name ..."
(Gmocz has connected.)

ClareS [to Alinka] and in any case I think that this question is rather
outside my subject area - I'd help if I could, but I can't...

ClareS says "maybe someone else here can help?"

Alinka [guest] says " SDH = succinylo dehydrogenase"

ClareS [to Alinka] is there a structure known?

Roby [to Alinka] Thanks !

Gmocz [to ClareS] Sorry I was disconnected. What I meant was not a bundle
of helices but an internaal coiled coil. Can that exist from a single chain

Roby says "interesting question"

Alinka [guest] says " I guess it is but I don't have the details."

Klausri [to ClareS] I was thinking of secondary structure of say a
cytokine to look for other proteins that could be expected to bind the same

Alinka [guest] says "SDH is a membrane protein in mitochondria"

Nadia [guest] says "Claire I have a qusetion!"

Alinka [guest] says "Hi Nadia! I am Alina frpm Gdansk, Poland"

Roby [to ClareS] I have a question too ...

Nadia [guest] says "" Hi veveryonHello everyone!"

Nadia [guest] says "oops that idi not come out right!"

Alinka [guest] says "Where are you from?"

Nadia [guest] says " The VSNS course stuff that is refernced in section2,
There was alot og algoriythm stuff that was abit spookey (dynamic
programming) How much of that do we need to understand and will it be covered in the bioinformatics section?"

ClareS [to Klausri] you can certainly look for proteins with a similar fold
to a given one

ClareS [to nadia] you don't need to understand very much of the complex
algorithms - it's enough for you to learn how to use sequence analysis
programs intelligently and understand the output

Nadia [guest] says " Alia I am from Scotland but I liv e in England!"

Klausri [to ClareS] could you please tell me where?

Nadia [guest] says " phew!!"

Alinka [guest] says "Nice to meet you, Nadia!"

ClareS [to Klausri] you will use the SCOP, CATH and FSSP databases later in
the course

ClareS [to Klausri] they are all (of course) on the Web

Nadia [guest] says "Sorry Alina my spelling is not up to much:- bad typing and severe friday afternnoon syndrome!"

Klausri [to ClareS] OK I'll wait till then. Thanks.

Alinka [guest] says "I am new here, Nadia, you know and I don't feel much at home here..."

ClareS says "there's nothing to stop you looking up the databases now..."

ClareS says "try"

Klausri says "I'll try that, thanks for the URL"

ClareS says "but I expect you'll find them more useful after you've studied more of the course and are more used to looking at structures"

Gmocz [to ClareS] Most Xray str determination builds somewhat on previous
data such as bond length, angles etc. Are there completely independent
struct. determinations of proyeins? How many?

Klausri says "You are undoubtfully right but the question stems from a discussion with a collegue yesterday."

ClareS [to gmocz] I don't appear to have answered your question about
coiled coils

ClareS [to gmocz] there are none... Xray crystallography of large molecules
simply doesn't produce enough data to solve structures independently without
any other information

Gmocz [to ClareS] thats OK. I already asked too much.

ClareS [to gmocz] even for the very first structures there was already a
lot of information about the geometry of e.g. amino acids from small
molecule crystallography

ClareS [to gmocz] the leucine zipper is a good example of a coiled coil
protein but that has two chains

Alinka [guest] says "Hi Anarcyz!"
ClareS . o O ( if he's here for the meeting he's 1hr late )

Roby [to ClareS] Is there any relationship among the last letter of the
codon codifying aa and its relative frequency?

Roby [to ClareS] I mean, more possibilities codifying the last letter =
more frequent?

Roby says "i.e. Leucine has at least four possibilities of being coded on the third letter and it is one of the more frequently found aa."

ClareS says "I am not sure but I think it extremely probable"

Gmocz says "One more question. Is J a standard one-letter code for -SS- cystine?"

ClareS says "codon usage is species dependent so there will be some variation"

ClareS [to gmocz] not one I've heard of before today, so I hope not!
Anarcyz [guest] materializes out of thin air.

Roby [to ClareS] If so, any idea about why they have more letters codifying

Gmocz [to ClareS] I saw it in a paper.

ClareS [to gmocz] do you have the reference?

ClareS [to gmocz] it's not *standard* practice, anyway.

ClareS [to anarcyz] Hi
Anarcyz [guest] hi

Gmocz [to ClareS] I do not have it here but I will look for it and e-mail
it to you

ClareS [to anarcyz] the meeting started 1h ago... you can catch up by
reading the transcript but we've neary finished

ClareS [to gmocz] thanks

Roby says "ok !"

ClareS says "are there any more questions? We should really finish quite soon now"

Alinka [guest] says """y"

Roby [to ClareS] maybe the next time, ok?

Roby says "Is it ok to say goodbye right now?"

Alinka [guest] says ""Do we really have to finish yet?"

ClareS [to Roby] staying to the end of meetings isn't compulsory!

ClareS [to Alinka] I'd be happy to carry on informally but I recognise that
some people have to go early & I have other stuff to do so I like to keep
the recorded sessions to about 1h

Roby [to ClareS] I got it !
(Anarcyz [guest] has disconnected.)

Alinka [guest] says "Dear Clare, let me pass on the greetings from my boss Stan"

Klausri says "thanks for now....."

Nadia [guest] says ""bye!"

ClareS [to Alinka] you mean Stan Zolnierowicz? I remember him well
(Nadia [guest] has disconnected.)

Alinka [guest] says "That's ok with me"
ClareS turns the ClareS_recorder off.