[ccp4bb] Fwd: Delivery Status Notification (Failure)
Dear CCP4BB members Sorry for off topic, i had question related to dispersity of proteins of my interest, i am working on DNA binding protein, having PI around 9 to 10,Initially protein was remaining stable at high salt, but was not able to concentrate more than 1mg/ml, after using 50mm Arg, 50mm Glutamate i overcome the solubility and concentrating problem but problem now is that my protein is remaining polydisperse, so i want to try different additives, i had tried some detergents and chaotropic agent,pH ranges.but it didnt help, so any suggestions to bring my protein in monodisperse state that will be really helpful...thanks for your suggestions in advance -- Arpit Mishra
[ccp4bb] CASP10: Call for structure prediction targets
Dear colleagues, This is a follow up to our earlier message, requesting prediction targets for CASP10. First THANK YOU to those who came forward with targets -- really much appreciated, and has helped get this CASP off to a great start. We now have over 70 targets released. Second, please send more targets! There is still a month of the prediction season to run, and the first batch of targets is all used up. The details of what is needed and so on are below -- just like in the earlier message. Again, thanks to the structural biology community for all your help, in this and previous CASPs (1): /CASP10 organizers: Torsten Schwede, Andriy Kryshtafovych, Anna Tramontano, Krzysztof Fidelis and John Moult./ *The specifics:* We need all sorts of targets but in particular: 1. (More than ever) novel folds and membrane protein targets -- even with the extended collection season provided by CASP ROLL (http://predictioncenter.org/casprol/index.cgi) there will be still a shortage. This round there are some interesting methods developments for ab initio modeling, and it is important to be able to decisively evaluate their effectiveness. 2. A diversity of comparative modeling targets. Cases where the there is fairly high sequence identity (30-50%) between the target structure and an available template are valuable for testing the degree to which model accuracy can approach that of experiment, particularly in functionally critical regions. Cases with lower sequence identity to template, right down to undetectable, are valuable for testing the ability of the methods to detect remote homologs, to overcome challenging alignment difficulties, to make use of multiple templates, and to build regions of the structure not obviously available from a template. 3. Targets containing significant amounts of disordered structure, so as to test the ability of methods to identify these regions. Disorder identified by absence of density in crystallography is current the main source and very useful, but its important to have cases where the nature of the disorder has been established by other means, such as NMR. 4. Some targets will also be used to test methods of structure refinement. In these cases, the best model received for a target will be released to the refinement community, who will subsequently submit new models. This too is an area where there have been some exciting developments in the last year, so we are hoping for significant progress. Refinement targets are selected based on the nature of the errors in the initial models. Because of the extended process, these targets need to be available for longer before release of the experimental structure. The time table is similar to other CASPs: The prediction season opened at the beginning of May, and will run until the end of July. We are releasing targets continuously throughout that period, as evenly spaced as possible, aiming for about 100 targets altogether. Each target will be available for prediction for a period of three weeks, although in some cases we request a longer period to allow it to be used to test refinement methods. It is of course important that there not be any kind of public release of the experimental structure (including things like pictures on web pages or abstracts) until after the predictions for that target are closed. As many of you know, it's fairly simple, with just two things to bear in mind. First, because of the timing framework, there needs to be at least a month between the submission date and any release of the structure. Second, we ideally need the experimental co-ordinates by the beginning of August and definitely by the end of August, so that the predictions can be assessed. At that point, they can be kept confidential if necessary, though we would like to provide them to predictors of your structure at the beginning of November at the latest, so that can see how well they have done. Participants would also usually like to be able to show slides and discuss their predictions at the meeting at the beginning of December. So, if you have any thing suitable, we would be most grateful if you would go to the target entry page: http://www.predictioncenter.org/casp10/targets_submission.cgi 1. 'Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction.' Kryshtafovych A et al. PROTEINS 2011;79 Suppl 10:6-20. doi: 10.1002/prot.23196. Epub 2011 Oct 21.
Re: [ccp4bb] Fwd: Delivery Status Notification (Failure)
Add DNA? Also, polydispersity is not great for crystallization but may not be the end of the world :) Artem On Mon, Jun 18, 2012 at 4:52 AM, Arpit Mishra ar...@igib.in wrote: Dear CCP4BB members Sorry for off topic, i had question related to dispersity of proteins of my interest, i am working on DNA binding protein, having PI around 9 to 10,Initially protein was remaining stable at high salt, but was not able to concentrate more than 1mg/ml, after using 50mm Arg, 50mm Glutamate i overcome the solubility and concentrating problem but problem now is that my protein is remaining polydisperse, so i want to try different additives, i had tried some detergents and chaotropic agent,pH ranges.but it didnt help, so any suggestions to bring my protein in monodisperse state that will be really helpful...thanks for your suggestions in advance -- Arpit Mishra
Re: [ccp4bb] pROBLEM IN RUNNING dm
Well - I guess you need to check the input mtz file. do mtzdmo this.mtz and check that the columns you have selected are present and have non-zero values. You need a FOM there. Eleanor On 14 Jun 2012, at 12:58, Appu kumar wrote: Hello Dear all I am trying running dm (density modification) programe for density modification, but it giving error complaining about density map. It says, dm: (WFO) No density in map! Check input FOM present and nonzero. Please suggest me how to overcome this problem. I am density modification with SAD data , but dm giving error. Your help will be much appreciated. Thank you Appu
Re: [ccp4bb] do you think it is interesting?
Wow, that's very cool! Can you divulge what the function of the protein is? One thinks of some kind of mechanical spring... JPK On Mon, Jun 18, 2012 at 8:49 AM, anna anna marmottalb...@gmail.com wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] do you think it is interesting?
Certainly it's interesting, but I think your description is inaccurate. Endless linear polymers - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] do you think it is interesting?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim On 06/18/12 16:21, David Schuller wrote: Certainly it's interesting, but I think your description is inaccurate. Endless linear polymers - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP o034eyZnadpwyQRGXI4FV9w= =Q5GJ -END PGP SIGNATURE-
Re: [ccp4bb] do you think it is interesting?
how about greek-protomers-bands (aka GPB) :-) Nice picture, you can make decorative art with it and sell it. Jürgen On Jun 18, 2012, at 10:43 AM, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim On 06/18/12 16:21, David Schuller wrote: Certainly it's interesting, but I think your description is inaccurate. Endless linear polymers - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP o034eyZnadpwyQRGXI4FV9w= =Q5GJ -END PGP SIGNATURE- .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] do you think it is interesting?
On 06/18/12 10:43, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. I didn't invent the term multimer, it has been in use for some decades. And I am writing English, not Latin or Greek. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] badly behaved DNA binder
Try adding DNA then dialyzing to low salt (in some microdialyer). = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Mon, 18 Jun 2012 15:22:46 +0530 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Arpit Mishra ar...@igib.in) Subject: [ccp4bb] Fwd: Delivery Status Notification (Failure) To: CCP4BB@JISCMAIL.AC.UK Dear CCP4BB members Sorry for off topic, i had question related to dispersity of proteins of my interest, i am working on DNA binding protein, having PI around 9 to 10,Initially protein was remaining stable at high salt, but was not able to concentrate more than 1mg/ml, after using 50mm Arg, 50mm Glutamate i overcome the solubility and concentrating problem but problem now is that my protein is remaining polydisperse, so i want to try different additives, i had tried some detergents and chaotropic agent,pH ranges.but it didnt help, so any suggestions to bring my protein in monodisperse state that will be really helpful...thanks for your suggestions in advance -- Arpit Mishra
Re: [ccp4bb] Question on Symmetry Axis Notation Convention
James,
The IUCr report that Ethan referred to distinguishes carefully between
a symmetry element and a symmetry operation. A symmetry element
corresponds to a set of coaxial rotation or screw axes (assuming we're
limiting the discussion to enantiomorphic space groups) in a unit cell
related by allowed origin shifts, as shown in the space group diagram.
A symmetry element set consists of a number of symmetry operations
(i.e. the operations are the members of the set). To distinguish
symmetry operations from element sets, the symbol for all element sets
starts with the letter 'E' (for 'element').
So space group P2_1 consists of two symmetry element sets: 'E1' and
'E2_1' which together form a group obeying the usual group rules. The
symmetry element set 'E2_1' (two-fold screw axis) is a set with 4
symmetry operations as members: the defining '2_1' operation plus 3
other coaxial 2_1 operations related by origin shifts. Note that the
identity operation 1 is not a member of the E2_1 set, contrary to what
you might think, i.e. E2_1 is indeed a set, not a group (the identity
operation 1 is the only member of the element set E1).
This might seem like a lot redundancy at first sight, until you
consider higher order axes; so for example the symmetry element set
'E4_1' (4-fold screw axis) contains the 3 operations '4_1' and '4_1^2'
and '4_1^3' (where e.g. the operation '4_1^n' is the operation '4_1'
repeated n times in succession) plus other coaxial 4_1^n operations
related by origin shifts. Note that '4_1^2' is NOT the same as '4_2'
similarly for the other 'power' operations. In fact the set 'E4_2'
which represents the 4_2 axis in space groups P4_2, P4_2 2_1 2 etc.
contains the operations 4_2, 4_2^2, 4_2^3 plus other coaxial 4_2 axes
related by origin shifts.
Now to get back to your question, a 2-fold screw axis parallel to the
a axis would be E2_1 parallel to (100). Unfortunately the IUCr
report doesn't seem to suggest a symbol for parallel to so you'll
have to be inventive: parallel bars ('||') being the usual symbol for
this relationship would seem the obvious choice. So the whole symbol
then becomes 'E2_1 || (100)'. On the other hand, if you want to
symbolise a symmetry operation the most concise notation would seem to
be the usual (1/2+x,1-y,-z), or whatever.
Cheers
-- Ian
On 14 June 2012 20:06, James Stroud xtald...@gmail.com wrote:
Hello All,
I would like to discuss symmetry axes, but I'm not sure what the notation
convention is. For example, I'd like to say something about a 2(1) along the
x-axis, but the phrase the 2(1) symmetry axis along x is a bit cumbersome
to repeat many times or to put in a table. So I'd like a shorthand, maybe
something like x(2_1) (where the preceding _ means that the 1 is
subscript. Another way I like is x_{2(1)} (where the curly braces mean that
all of 2(1) is subscript).
Does anyone know what the convention is or if there is one?
Thanks in advance for any help.
James
Re: [ccp4bb] do you think it is interesting?
I have been curious and suspicious for a long time about multimer: I always assumed it to be a more homey substitute for oligomer, as there seems to me to be no difference in usage, and certainly not in the etymological sense. I have often heard it used by non-experts who don't know exactly the meaning of the prefix oligo- but do know multi-, so they feel more comfortable I think. But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? JPK On Mon, Jun 18, 2012 at 9:48 AM, David Schuller dj...@cornell.edu wrote: On 06/18/12 10:43, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. I didn't invent the term multimer, it has been in use for some decades. And I am writing English, not Latin or Greek. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] do you think it is interesting?
Of course, oligomer (pure Greek) usually does that kind of job, but not in this specific case, since oligo means few and in this case we have endless chains. I can only think of the neologism myriomer for this particular case, if you want to stick to Greek. Myrioi can mean 1 or countless, depending on where you accent the word! If that catches on, remember you (probably) saw it here first! Cheers, Emmanuel - Original Message - From: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, June 18, 2012 5:43 PM Subject: Re: [ccp4bb] do you think it is interesting? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim On 06/18/12 16:21, David Schuller wrote: Certainly it's interesting, but I think your description is inaccurate. Endless linear polymers - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP o034eyZnadpwyQRGXI4FV9w= =Q5GJ -END PGP SIGNATURE-
Re: [ccp4bb] do you think it is interesting?
On 18/06/2012, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim Oligomer, surely, from Gk 'oligos' meaning 'a few'? -- Ian
Re: [ccp4bb] do you think it is interesting?
On 06/18/12 11:17, Jacob Keller wrote: But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] do you think it is interesting?
I love myriomer, but what's wrong with boring old polymer? JPK On Mon, Jun 18, 2012 at 10:27 AM, Emmanuel Saridakis esari...@chem.demokritos.gr wrote: Of course, oligomer (pure Greek) usually does that kind of job, but not in this specific case, since oligo means few and in this case we have endless chains. I can only think of the neologism myriomer for this particular case, if you want to stick to Greek. Myrioi can mean 1 or countless, depending on where you accent the word! If that catches on, remember you (probably) saw it here first! Cheers, Emmanuel - Original Message - From: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, June 18, 2012 5:43 PM Subject: Re: [ccp4bb] do you think it is interesting? -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. Cheers, Tim On 06/18/12 16:21, David Schuller wrote: Certainly it's interesting, but I think your description is inaccurate. Endless linear polymers - Each monomer is a polymer, but a collection of monomers is called a multimer, not a polymer. I don't suppose there are any knots? That would be really interesting. On 06/18/12 09:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP3z51UxlJ7aRr7hoRAqviAKDJXxXkeOE3Z0M14+RT8dznQhpD3gCcDKEP o034eyZnadpwyQRGXI4FV9w= =Q5GJ -END PGP SIGNATURE- -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] do you think it is interesting?
Okay, I wiki'd it, and according to them seems you're right: it says they are typically connected by covalent chemical bonds. So either we revert to the etymological use of polymer, or move onward to myriomer! (assuming the cross-bred multimer is out of the question!) JPK On Mon, Jun 18, 2012 at 10:37 AM, David Schuller dj...@cornell.edu wrote: On 06/18/12 11:17, Jacob Keller wrote: But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] do you think it is interesting?
isn't a polymer considered a poly-multimer of undefined size ? And you use multi once you run out with your greek naming scheme say when icosahedron ? Jürgen P.S. where are all those greeks to shed some light on us ? On Jun 18, 2012, at 11:48 AM, Jacob Keller wrote: Okay, I wiki'd it, and according to them seems you're right: it says they are typically connected by covalent chemical bonds. So either we revert to the etymological use of polymer, or move onward to myriomer! (assuming the cross-bred multimer is out of the question!) JPK On Mon, Jun 18, 2012 at 10:37 AM, David Schuller dj...@cornell.edumailto:dj...@cornell.edu wrote: On 06/18/12 11:17, Jacob Keller wrote: But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edumailto:schul...@cornell.edu -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu *** .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] do you think it is interesting?
If the original poster could engineer a few disulfides or other covalent linkages in there, I would drop my objections, and be even more impressed. On 06/18/12 11:48, Jacob Keller wrote: Okay, I wiki'd it, and according to them seems you're right: it says they are typically connected by covalent chemical bonds. So either we revert to the etymological use of polymer, or move onward to myriomer! (assuming the cross-bred multimer is out of the question!) JPK On Mon, Jun 18, 2012 at 10:37 AM, David Schullerdj...@cornell.edu wrote: On 06/18/12 11:17, Jacob Keller wrote: But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] do you think it is interesting?
If we are to strictly adhere to polymer as describing few, then were do we stand with DNA/RNA being described as a polymer - a long polymer made up from repeating units of nucleotides, as has been used in textbooks for ages?! Is DNA/RNA too now a myriomer? Cale
Re: [ccp4bb] do you think it is interesting?
Hi Anna, Interesting assembly. What is the function of your protein? Is it known if your protein forms a fibril-like assembly in solution? Moreover, can your crystal packing be indexed higher symmetry space group? Cheers, Shiva On Mon, Jun 18, 2012 at 9:03 AM, David Schuller dj...@cornell.edu wrote: If the original poster could engineer a few disulfides or other covalent linkages in there, I would drop my objections, and be even more impressed. On 06/18/12 11:48, Jacob Keller wrote: Okay, I wiki'd it, and according to them seems you're right: it says they are typically connected by covalent chemical bonds. So either we revert to the etymological use of polymer, or move onward to myriomer! (assuming the cross-bred multimer is out of the question!) JPK On Mon, Jun 18, 2012 at 10:37 AM, David Schullerdj...@cornell.edu wrote: On 06/18/12 11:17, Jacob Keller wrote: But anyway, what is wrong with calling her structures polymers? Is there a subtle covalent insinuation to polymer? subtle? No, it's not subtle. -- ==**==** === All Things Serve the Beam ==**==** === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- ==**==** === All Things Serve the Beam ==**==** === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] do you think it is interesting?
2012/6/18 Tim Gruene t...@shelx.uni-ac.gwdg.de: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [...] of monomers is called a multimer, not a polymer. [...] shiver - what a terrible mixture of languages. 'multi-' has got latin origin, whereas both poly and mer have got greek origin, and I don't think one should mix these. Please!!! think of a different _GREEK_ syllable to express what you describe as 'multimer'. In fact this is quite common. Automobile, for example comes from greek autos plus latin mobilis.
Re: [ccp4bb] do you think it is interesting?
This may be somethng similar Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure. Spinelli S, Desmyter A, Frenken L, Verrips T, Tegoni M, Cambillau C. FEBS Lett. 2004 Apr 23;564(1-2):35-40. Remy Loris Vrije Universiteit Brussel On 18/06/12 15:49, anna anna wrote: Hi all! I'd like your opinion about a structure I solved. Apart from protein structure itself, I think that my protein xtallized in an odd way! The biological unit is a dimer while the asymmetric unit is a tetramer (red cartoon in the figure) resulting from domain swapping between two dimers. The strange thing is that swapping connects infinite monomers and, rather than a xtal, my diffracting object seems a multilayer of endless linear polymers, a kind of papyrus with greek fret-like fibers. The figure shows the orientation of the polymers in each layer. I'd like to know if some of you have already seen a similar pattern or it is weird as I think! I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. All suggestions are welcome!! Cheers, Anna
Re: [ccp4bb] do you think it is interesting?
I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. There are a variety of domain swapped crystal structures out there, but at least the two I'm most familiar with are regarded as being crystallization artifacts. I think I recall seeing examples where domain swapping was biologically relevant, but my impression is most are red herrings. In the poster child of plaque formation, prion protein formed cys-cross linked domain swapped dimers in some crystals. http://www.nature.com/nsmb/journal/v8/n9/abs/nsb0901-770.html However, using PAGE DLS it was later shown that prion has no preference for dimers when you break down Infectious fibrils. Cross linked dimers definitely out. Any subunits ruled out, in fact. http://www.nature.com/nature/journal/v437/n7056/abs/nature03989.html RNaseA is another example, and isn't even a disease associated molecule. Similarly to how we've found that many/most proteins may be converted to amyloid forms by harsh enough conditions, I think some will domain swap, and some authors have pursued domain swapping heavily with RNaseA a as a model for amyloid formation. RNaseA will swap in major and minor conformations even, though not in the same crystal. Still, that's the first thing you need for an infinite series, is two compatible/simultaneous swapping points. Now, I do think domain swapping, particularly an infinite chain, can be interesting from a bioengineering or biophysical level, if that is what you are interested in. I just want to say that there is a high bar to showing biochemical relevance in the sense of holding any physiological implications. Alexander D. Scouras Postdoctoral Fellow Alber Lab, QB3 University of California, Berkeley
Re: [ccp4bb] do you think it is interesting?
I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. A good example of domain swaps involved in disease-associated polymerisation is the polymerisation of serpins; while there is still some debate about whether this mechanism is actually what happens in patients in vivo, the formation of polymers via domain swapping is becoming widely accepted as the new paradigm. Relevant references include: Nature. 2008 Oct 30;455(7217):1255-8. Epub 2008 Oct 15. Crystal structure of a stable dimer reveals the molecular basis of serpin polymerization. Yamasaki M, Li W, Johnson DJ, Huntington JA. PMID: 18923394 EMBO Rep. 2011 Sep 30;12(10):1011-7. doi: 10.1038/embor.2011.171. Molecular basis of α1-antitrypsin deficiency revealed by the structure of a domain-swapped trimer. Yamasaki M, Sendall TJ, Pearce MC, Whisstock JC, Huntington JA. PMID: 21909074 Interestingly enough they don't rely on disulfide formation (normal polymers fall apart on an SDS gel but not a native gel), but they can be engineered to include disulfides which render the polymers stable to SDS (on a non-reducing gel). This was actually a really useful tool in determining exactly which domains of a given molecule swapped into their neighbour during polymerisation. Best Regards Tom
Re: [ccp4bb] do you think it is interesting?
On Monday, June 18, 2012 02:06:46 pm Alexander Scouras wrote: I'm further racking my brain to figure out a biological implication of this behaviour, I thought something like plaque formation but I can't find support in literature. There are a variety of domain swapped crystal structures out there, but at least the two I'm most familiar with are regarded as being crystallization artifacts. I think I recall seeing examples where domain swapping was biologically relevant, but my impression is most are red herrings. You might be interested in the following paper, which describes domain-swapped (domain exchange) dimerization as a control mechanism for kinases. Activation segment dimerization: a mechanism for kinase autophosphorylation of non-consensus sites. Pike, A.C.W., Rellos, P., Niesen, F.H., Turnbull, A., Oliver, A.W., Parker, S.A., Turk, B.E., Pearl, L.H., Knapp, S., Journal: (2008) Embo J. 27: 704 But these are specifically dimeric. Unlike the case posted here, there is not a second non-swapped interface that would allow formation of an infinite chain. Ethan In the poster child of plaque formation, prion protein formed cys-cross linked domain swapped dimers in some crystals. http://www.nature.com/nsmb/journal/v8/n9/abs/nsb0901-770.html However, using PAGE DLS it was later shown that prion has no preference for dimers when you break down Infectious fibrils. Cross linked dimers definitely out. Any subunits ruled out, in fact. http://www.nature.com/nature/journal/v437/n7056/abs/nature03989.html RNaseA is another example, and isn't even a disease associated molecule. Similarly to how we've found that many/most proteins may be converted to amyloid forms by harsh enough conditions, I think some will domain swap, and some authors have pursued domain swapping heavily with RNaseA a as a model for amyloid formation. RNaseA will swap in major and minor conformations even, though not in the same crystal. Still, that's the first thing you need for an infinite series, is two compatible/simultaneous swapping points. Now, I do think domain swapping, particularly an infinite chain, can be interesting from a bioengineering or biophysical level, if that is what you are interested in. I just want to say that there is a high bar to showing biochemical relevance in the sense of holding any physiological implications. Alexander D. Scouras Postdoctoral Fellow Alber Lab, QB3 University of California, Berkeley -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] do you think it is interesting?
Hi Anna, Your structure and description remind me very much of our domain-swapped crystal structure of trp repressor, also an infinite lattice. One more example to add to the many that have been pointed out by others. http://www.pdb.org/pdb/explore.do?structureId=1MI7 Cheers, Cathy Lawson
