Protein cleavage strategies for an improved analysis of the membrane proteome

Proteome Science
Frank Fischer, Ansgar Poetsch

Abstract

Membrane proteins still remain elusive in proteomic studies. This is in part due to the distribution of the amino acids lysine and arginine, which are less frequent in integral membrane proteins and almost absent in transmembrane helices. As these amino acids are cleavage targets for the commonly used protease trypsin, alternative cleavage conditions, which should improve membrane protein analysis, were tested by in silico digestion for the three organisms Saccharomyces cerevisiae, Halobacterium sp. NRC-1, and Corynebacterium glutamicum as hallmarks for eukaryotes, archea and eubacteria. For the membrane proteomes from all three analyzed organisms, we identified cleavage conditions that achieve better sequence and proteome coverage than trypsin. Greater improvement was obtained for bacteria than for yeast, which was attributed to differences in protein size and GRAVY. It was demonstrated for bacteriorhodopsin that the in silico predictions agree well with the experimental observations. For all three examined organisms, it was found that a combination of chymotrypsin and staphylococcal peptidase I gave significantly better results than trypsin. As some of the improved cleavage conditions are not more elaborate than trypsin diges...Continue Reading

References

May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Jun 25, 1998·Electrophoresis·D FenyöB T Chait
Jan 5, 2002·Journal of the American Society for Mass Spectrometry·Kenneth C Parker
Oct 19, 2002·Science·Adrian Cho, Dennis Normile
Nov 16, 2002·Analytical Chemistry·Michael J MacCossJohn R Yates
Nov 21, 2002·Protein Science : a Publication of the Protein Society·Chien Peter ChenBurkhard Rost
Apr 15, 2003·Nature Biotechnology·Christine C WuJohn R Yates
Nov 25, 2003·Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences·Yasuhiro Kashino
Mar 31, 2004·Rapid Communications in Mass Spectrometry : RCM·Piotr SuderJerzy Silberring
Feb 18, 2005·Proteomics·Daniela SchluesenerAnsgar Poetsch

❮ Previous
Next ❯

Citations

Feb 26, 2011·Applied Microbiology and Biotechnology·Bianca PorteusJohn P Bowman
Jul 14, 2010·Amino Acids·Bjoern MeyerMichael Karas
Jan 31, 2013·Proteome Science·Ja KoziolJe Schnitzer
Feb 11, 2010·Future Microbiology·Steffen Rupp
Apr 13, 2013·Cellular and Molecular Life Sciences : CMLS·Armand G Ngounou WetieCostel C Darie
Sep 26, 2013·International Journal of Proteomics·Hercules MouraJohn R Barr
May 12, 2012·The Biochemical Journal·Jay J Thelen, Ján A Miernyk
May 8, 2008·Molecular & Cellular Proteomics : MCP·Susanne WolffDörte Becher
Mar 31, 2011·Molecular & Cellular Proteomics : MCP·M V JagannadhamHeramb M Kulkarni
Jun 16, 2010·Molecular & Cellular Proteomics : MCP·Noelle M Griffin, Jan E Schnitzer
Apr 12, 2012·Molecular & Cellular Proteomics : MCP·Christian TrötschelAnsgar Poetsch
Feb 1, 2011·Arthritis and Rheumatism·Ann K RosenthalBassam T Wakim
Dec 11, 2014·Proteomics·Christian Trötschel, Ansgar Poetsch
Jan 30, 2019·Expert Opinion on Drug Delivery·Lin-Yan WanJiang-Feng Wu
Mar 21, 2009·Journal of Separation Science·Caterina TemporiniGabriella Massolini
Dec 2, 2009·Proteomics·Benjamin FränzelDirk Andreas Wolters
Dec 28, 2019·The EMBO Journal·Christian TrötschelU Benjamin Kaupp
Jun 19, 2013·Mass Spectrometry Reviews·Elien VandermarliereLennart Martens
Jul 30, 2011·Proteomics·Gianluca MaddaloDaniel O Daley
Sep 10, 2008·Proteomics·Ansgar Poetsch, Dirk Wolters
Feb 25, 2015·The Journal of Pharmacy and Pharmacology·Christopher R DunstonHelen R Griffiths
Jul 21, 2017·NPJ Systems Biology and Applications·Derek Croote, Stephen R Quake
Nov 2, 2014·Photosynthesis Research·Natalia BattchikovaEva-Mari Aro
Nov 14, 2019·International Journal of Molecular Sciences·Delphine VincentGerman Spangenberg
Jan 1, 2009·Molecular & Cellular Proteomics : MCP·Benjamin RietschelAnsgar Poetsch
Feb 3, 2021·Journal of Proteome Research·Vidur KailashMichael R Hoopmann
Mar 1, 2018·Comprehensive Reviews in Food Science and Food Safety·Olga Luisa TavanoRoberto Fernandez-Lafuente
May 21, 2008·Journal of Proteome Research·Wilma DormeyerJeroen Krijgsveld
Apr 8, 2009·Journal of Proteome Research·Mio IwasakiYasushi Ishihama
Jun 15, 2010·Journal of Proteome Research·Nadia TaouatasShabaz Mohammed
Jan 6, 2018·Journal of Proteome Research·Mariana I CostaMaría I Giménez
May 12, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Han-Yuan LiuSusan Daniel

❮ Previous
Next ❯

Methods Mentioned

BETA
glycosylation
electrophoresis

Software Mentioned

MudPIT
Expasy PeptideCutter
BioPerl
PERL
Mascot
tryspin
TMHMM

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.