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Re: [sbml-multi] StateFeature and BindingSite
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From: Bill H. <wi...@la...> - 2009-09-23 17:11:14
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Multi enthusiasts, I think I follow what Nic wrote below in response to my query about StateFeature and BindingSite. I want to make sure I understand, and if I do, then I want to make a suggestion for a new multi extension. Consider the following rule, which is written in BioNetGen language (BNGL) or kappa, which is essentially the same as BNGL: Mol1(binding_site1~state1)+Mol2(binding_site2)<-> Mol1(binding_site1~state1!1).Mol2(binding_site2!1) This "rule" says that molecules "Mol1" and "Mol2" associate via a chemical bond between "binding_site1" and "binding_site2." Moreover, binding_site1 has a state, which is called "state1," and binding_site1 must be in state1 for the bond to form between binding_site1 and binding_site2. I hope I have done a good job of explaining what this rule means - let me know if I need to clarify anything. Anyway, as you can see from this rule, we think of molecules as having components (which can be binding sites) and we think of components as having states. If I understand correctly, according to the conventions of multi, binding sites do not have states; only molecules (or more precisely speciesTypes) have states. The important point is that multi does not associate states with binding sites. Do I understand correctly? If I understand correctly, then we cannot encode the rule above using multi. Instead, we would have to encode a different, but functionally equivalent rule: Mol1(binding_site1,feature~state1)+Mol2(binding_site2)<- >Mol1(binding_site1!1,feature~state1).Mol2(binding_site2!1) In this new rule, there is a StateFeature, "feature," associated with Mol1 that is assigned the state "state1." This is fine in that the new rule will behave the same as the first rule, i.e., the two rules are functionally equivalent. (I hope that makes sense.) However, there is some loss of information, information that is useful for annotation purposes. In the new rule, we have no idea that "feature" is associated with "binding_site1," which would be the case if "binding_site1" is an ITAM and "feature" is the phosphorylation status of the ITAM. The important point is that a StateFeature can be related to a BindingSite. I think it is useful to record relationships between StateFeatures and BindingSites for annotation purposes at least. On the basis of the prolegomena, I propose that a new multi attribute be introduced, which can perhaps be called "belongsTo" or "associatedWith," that can be used to record relationships between StateFeatures and BindingSites. The attribute could be optional. Thoughts? --Bill On Sep 22, 2009, at 3:39 PM, Nicolas Le novère wrote: > Hi Bill, > > Bill Hlavacek wrote: > >> I am concerned about how to represent a "binding site" that has >> multiple states. An example of binding site with multiple states is >> the ITAM in the alpha or beta chain of the B cell antigen receptor, >> which is a docking site for certain proteins that contain an SH2 >> domain, such as the protein tyrosine kinases Lyn and Syk. Such an >> ITAM is a docking site for Lyn when it is singly phosphorylated and a >> docking site for Syk when it is doubly phosphorylated. It is not >> reactive with either Lyn or Syk when it is NOT phosphorylated. The >> examples of BindingSite usage at the wiki do not account for this >> type >> of case, and it is not clear to me how it would be done. > > What you describe is not in fact a binding site with several states. A > binding site can be bound or unbound. What you describe is a species > type > that contains a binding site, that can be bound or unbound, and a > state > feature that represents the phosphorylation state of two amino-acid > residues. The binding reactions are then affected by the states of the > residues. What you need to do is to create: > > 1) a reaction representing the binding of B cell antigen receptor > with Lyn > 2) a reaction representing the binding of B cell antigen receptor > with Syk > > A rule on reaction 1) restricts it to take place only when the state > feature is monophosphorylated and a rule on reaction 2) restricts it > to > take place only when the state feature is biphosphorylated. > > Best. > > -- > Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome- > Trust > Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel: > +441223494521 > Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nle...@ho...(NOT > email) > http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/ > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9-12, 2009. Register > now! > http://p.sf.net/sfu/devconf > _______________________________________________ > Sbml-multi mailing list > Sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-multi William S. Hlavacek, Ph.D. Theoretical Biology and Biophysics Group Theoretical Division Mail Stop K710 Drop Point 03041003U Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-665-1355 Fax: 505-665-3493 E-mail: wi...@la... http://www.t6.lanl.gov/wish/ |