Change search
ReferencesLink to record
Permanent link

Direct link
Membrane protein shaving with thermolysin can be used to evaluate topology predictors
Show others and affiliations
2013 (English)In: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 13, no 9, 1467-1480 p.Article in journal (Refereed) Published
Abstract [en]

Topology analysis of membrane proteins can be obtained by enzymatic shaving in combination with MS identification of peptides. Ideally, such analysis could provide quite detailed information about the membrane spanning regions. Here, we examine the ability of some shaving enzymes to provide large-scale analysis of membrane proteome topologies. To compare different shaving enzymes, we first analyzed the detected peptides from two over-expressed proteins. Second, we analyzed the peptides from non-over-expressed Escherichia coli membrane proteins with known structure to evaluate the shaving methods. Finally, the identified peptides were used to test the accuracy of a number of topology predictors. At the end we suggest that the usage of thermolysin, an enzyme working at the natural pH of the cell for membrane shaving, is superior because: (i) we detect a similar number of peptides and proteins using thermolysin and trypsin; (ii) thermolysin shaving can be run at a natural pH and (iii) the incubation time is quite short. (iv) Fewer detected peptides from thermolysin shaving originate from the transmembrane regions. Using thermolysin shaving we can also provide a clear separation between the best and the less accurate topology predictors, indicating that using data from shaving can provide valuable information when developing new topology predictors.

Place, publisher, year, edition, pages
2013. Vol. 13, no 9, 1467-1480 p.
Keyword [en]
Bioinformatics, Digestion on-membrane, Mass spectra, Membrane proteins
National Category
Biochemistry and Molecular Biology
URN: urn:nbn:se:kth:diva-123114DOI: 10.1002/pmic.201200517ISI: 000318049800011ScopusID: 2-s2.0-84876490541OAI: diva2:624907
Swedish Research Council, VR-NT 2009-5072 VR-M 2007-3065 VR-NT 2008-3454 2009-698Swedish Foundation for Strategic Research EU, FP7, Seventh Framework Programme, FP7-PEOPLE-2007-1-1-ITN FP7-HEALTH-F4-2007-201924Science for Life Laboratory - a national resource center for high-throughput molecular bioscience

QC 20130603

Available from: 2013-06-03 Created: 2013-06-03 Last updated: 2013-06-03Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Käll, Lukas
By organisation
Gene TechnologyScience for Life Laboratory, SciLifeLab
In the same journal
Biochemistry and Molecular Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 43 hits
ReferencesLink to record
Permanent link

Direct link