A mathematical view on the decoupled sites representation. Martini, J. W. R. & Ullmann, G. M. Journal of Mathematical Biology, 66:477–503, 2012. ![A mathematical view on the decoupled sites representation [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex The decoupled sites representation (DSR) is a theoretical instrument which allows to regard complex pH titration curves of biomolecules with several interacting proton binding sites as composition of isolated, non-interacting sites, each with a standard Henderson–Hasselbalch titration curve. In this work, we present the mathematical framework in which the DSR is embedded and give mathematical proofs for several statements in the periphery of the DSR. These proofs also identify exceptions. To apply the DSR to any molecule, it is necessary to extend the set of binding energies from R to a stripe within C. An important observation in this context is that even positive interaction energies (repulsion) between the binding sites will not guarantee real binding energies in the decoupled system, at least if the molecule has more than four proton binding sites. Moreover, we show that for a given overall titration curve it is not only possible to find a corresponding system with an interaction energy of zero but with any arbitrary fix interaction energy. This result also effects practical work as it shows that for any given titration curve, there is an infinite number of corresponding hypothetical molecules. Furthermore, this implies that—using a common definition of cooperative binding on the level of interaction energies—a meaningful measure of cooperativity between the binding sites cannot be defined solely on the basis of the overall titration. Consequently, all measures of cooperativity based on the overall binding curve do not measure the type of cooperativity commonly defined on the basis of interaction energies. Understanding the DSR mathematically provides the basis of transferring the DSR to biomolecules with different types of interacting ligands, such as protons and electrons, which play an important role within electron transport chains like in photosynthesis.
@article{Martini2012Mathematical,
abstract = {The decoupled sites representation (DSR) is a theoretical instrument which allows to regard complex pH titration curves of biomolecules with several interacting proton binding sites as composition of isolated, non-interacting sites, each with a standard Henderson--Hasselbalch titration curve. In this work, we present the mathematical framework in which the DSR is embedded and give mathematical proofs for several statements in the periphery of the DSR. These proofs also identify exceptions. To apply the DSR to any molecule, it is necessary to extend the set of binding energies from R to a stripe within C. An important observation in this context is that even positive interaction energies (repulsion) between the binding sites will not guarantee real binding energies in the decoupled system, at least if the molecule has more than four proton binding sites. Moreover, we show that for a given overall titration curve it is not only possible to find a corresponding system with an interaction energy of zero but with any arbitrary fix interaction energy. This result also effects practical work as it shows that for any given titration curve, there is an infinite number of corresponding hypothetical molecules. Furthermore, this implies that---using a common definition of cooperative binding on the level of interaction energies---a meaningful measure of cooperativity between the binding sites cannot be defined solely on the basis of the overall titration. Consequently, all measures of cooperativity based on the overall binding curve do not measure the type of cooperativity commonly defined on the basis of interaction energies. Understanding the DSR mathematically provides the basis of transferring the DSR to biomolecules with different types of interacting ligands, such as protons and electrons, which play an important role within electron transport chains like in photosynthesis.},
author = {Martini, Johannes W. R. and Ullmann, G. Matthias},
year = {2012},
title = {A mathematical view on the decoupled sites representation},
url = {http://dx.doi.org/10.1007/s00285-012-0517-x},
keywords = {phd},
pages = {477--503},
volume = {66},
issn = {0303-6812},
journal = {Journal of Mathematical Biology},
doi = {10.1007/s00285-012-0517-x},
howpublished = {refereed}
}
Downloads: 0
{"_id":"nG8u4Dg3u55AxPgrt","bibbaseid":"martini-ullmann-amathematicalviewonthedecoupledsitesrepresentation-2012","downloads":0,"creationDate":"2019-02-26T11:22:36.236Z","title":"A mathematical view on the decoupled sites representation","author_short":["Martini, J. W. R.","Ullmann, G. M."],"year":2012,"bibtype":"article","biburl":"http://www.uni-goettingen.de/de/document/download/9d7c40531010bf5be953ccd9446e47ae.bib/GRK1644BibHomepage.bib","bibdata":{"bibtype":"article","type":"article","abstract":"The decoupled sites representation (DSR) is a theoretical instrument which allows to regard complex pH titration curves of biomolecules with several interacting proton binding sites as composition of isolated, non-interacting sites, each with a standard Henderson–Hasselbalch titration curve. In this work, we present the mathematical framework in which the DSR is embedded and give mathematical proofs for several statements in the periphery of the DSR. These proofs also identify exceptions. To apply the DSR to any molecule, it is necessary to extend the set of binding energies from R to a stripe within C. An important observation in this context is that even positive interaction energies (repulsion) between the binding sites will not guarantee real binding energies in the decoupled system, at least if the molecule has more than four proton binding sites. Moreover, we show that for a given overall titration curve it is not only possible to find a corresponding system with an interaction energy of zero but with any arbitrary fix interaction energy. This result also effects practical work as it shows that for any given titration curve, there is an infinite number of corresponding hypothetical molecules. Furthermore, this implies that—using a common definition of cooperative binding on the level of interaction energies—a meaningful measure of cooperativity between the binding sites cannot be defined solely on the basis of the overall titration. Consequently, all measures of cooperativity based on the overall binding curve do not measure the type of cooperativity commonly defined on the basis of interaction energies. Understanding the DSR mathematically provides the basis of transferring the DSR to biomolecules with different types of interacting ligands, such as protons and electrons, which play an important role within electron transport chains like in photosynthesis.","author":[{"propositions":[],"lastnames":["Martini"],"firstnames":["Johannes","W.","R."],"suffixes":[]},{"propositions":[],"lastnames":["Ullmann"],"firstnames":["G.","Matthias"],"suffixes":[]}],"year":"2012","title":"A mathematical view on the decoupled sites representation","url":"http://dx.doi.org/10.1007/s00285-012-0517-x","keywords":"phd","pages":"477–503","volume":"66","issn":"0303-6812","journal":"Journal of Mathematical Biology","doi":"10.1007/s00285-012-0517-x","howpublished":"refereed","bibtex":"@article{Martini2012Mathematical,\r\n abstract = {The decoupled sites representation (DSR) is a theoretical instrument which allows to regard complex pH titration curves of biomolecules with several interacting proton binding sites as composition of isolated, non-interacting sites, each with a standard Henderson--Hasselbalch titration curve. In this work, we present the mathematical framework in which the DSR is embedded and give mathematical proofs for several statements in the periphery of the DSR. These proofs also identify exceptions. To apply the DSR to any molecule, it is necessary to extend the set of binding energies from R to a stripe within C. An important observation in this context is that even positive interaction energies (repulsion) between the binding sites will not guarantee real binding energies in the decoupled system, at least if the molecule has more than four proton binding sites. Moreover, we show that for a given overall titration curve it is not only possible to find a corresponding system with an interaction energy of zero but with any arbitrary fix interaction energy. This result also effects practical work as it shows that for any given titration curve, there is an infinite number of corresponding hypothetical molecules. Furthermore, this implies that---using a common definition of cooperative binding on the level of interaction energies---a meaningful measure of cooperativity between the binding sites cannot be defined solely on the basis of the overall titration. Consequently, all measures of cooperativity based on the overall binding curve do not measure the type of cooperativity commonly defined on the basis of interaction energies. Understanding the DSR mathematically provides the basis of transferring the DSR to biomolecules with different types of interacting ligands, such as protons and electrons, which play an important role within electron transport chains like in photosynthesis.},\r\n author = {Martini, Johannes W. R. and Ullmann, G. Matthias},\r\n year = {2012},\r\n title = {A mathematical view on the decoupled sites representation},\r\n url = {http://dx.doi.org/10.1007/s00285-012-0517-x},\r\n keywords = {phd},\r\n pages = {477--503},\r\n volume = {66},\r\n issn = {0303-6812},\r\n journal = {Journal of Mathematical Biology},\r\n doi = {10.1007/s00285-012-0517-x},\r\n howpublished = {refereed}\r\n}\r\n\r\n\r\n","author_short":["Martini, J. W. R.","Ullmann, G. M."],"key":"Martini2012Mathematical","id":"Martini2012Mathematical","bibbaseid":"martini-ullmann-amathematicalviewonthedecoupledsitesrepresentation-2012","role":"author","urls":{"Paper":"http://dx.doi.org/10.1007/s00285-012-0517-x"},"keyword":["phd"],"metadata":{"authorlinks":{}},"downloads":0},"search_terms":["mathematical","view","decoupled","sites","representation","martini","ullmann"],"keywords":["phd"],"authorIDs":[],"dataSources":["psxr4mFyE5JDwFLuZ","2w3D54bmLuhpt4TNv","t8S6Y6RWEwDAQHiSQ","cLGdYAfLyvQDgrYmh"]}