Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: Towards developing an MDCK protein database
Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20–30% of eukaryotic genomes, a detailed characterisation of their encoded proteins is underrepresented, due, to their low copy number and the inher...
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Published in | Proteomics (Weinheim) Vol. 11; no. 7; pp. 1238 - 1253 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
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Weinheim
WILEY-VCH Verlag
01.04.2011
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Abstract | Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20–30% of eukaryotic genomes, a detailed characterisation of their encoded proteins is underrepresented, due, to their low copy number and the inherent difficulties in their isolation and purification as a consequence of their high hydrophobicity. We describe here a strategy that combines two orthogonal methods to isolate and purify PM proteins from Madin Darby canine kidney (MDCK) cells. In this two‐step method, we first used cationic colloidal silica (CCS) to isolate adherent (Ad) and non‐adherent (nAd) PM fractions, and then subjected each fraction to Triton X‐114 (TX‐114) phase partitioning to further enrich for hydrophobic proteins. While CCS alone identified 255/757 (34%) membrane proteins, CCS/TX‐114 in combination yielded 453/745 (61%). Strikingly, of those proteins unique to CCS/TX‐114, 277/393 (70%) had membrane annotation. Further characterisation of the CCS/TX‐114 data set using Uniprot and transmembrane hidden Markov model revealed that 306/745 (41%) contained one or more transmembrane domains (TMDs), including proteins with 25 and 17 TMDs. Of the remaining proteins in the data set, 69/439 (16%) are known to contain lipid modifications. Of all membrane proteins identified, 93 had PM origin, including proteins that mediate cell adhesion, modulate transmembrane ion transport, and cell–cell communication. These studies reveal that the application of CCS to first isolate Ad and nAd PM fractions, followed by their detergent‐phase TX‐114 partitioning, to be a powerful method to isolate low‐abundance PM proteins, and a useful adjunct for in‐depth cell surface proteome analyses. |
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AbstractList | Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20–30% of eukaryotic genomes, a detailed characterisation of their encoded proteins is underrepresented, due, to their low copy number and the inherent difficulties in their isolation and purification as a consequence of their high hydrophobicity. We describe here a strategy that combines two orthogonal methods to isolate and purify PM proteins from Madin Darby canine kidney (MDCK) cells. In this two‐step method, we first used cationic colloidal silica (CCS) to isolate adherent (Ad) and non‐adherent (nAd) PM fractions, and then subjected each fraction to Triton X‐114 (TX‐114) phase partitioning to further enrich for hydrophobic proteins. While CCS alone identified 255/757 (34%) membrane proteins, CCS/TX‐114 in combination yielded 453/745 (61%). Strikingly, of those proteins unique to CCS/TX‐114, 277/393 (70%) had membrane annotation. Further characterisation of the CCS/TX‐114 data set using Uniprot and transmembrane hidden Markov model revealed that 306/745 (41%) contained one or more transmembrane domains (TMDs), including proteins with 25 and 17 TMDs. Of the remaining proteins in the data set, 69/439 (16%) are known to contain lipid modifications. Of all membrane proteins identified, 93 had PM origin, including proteins that mediate cell adhesion, modulate transmembrane ion transport, and cell–cell communication. These studies reveal that the application of CCS to first isolate Ad and nAd PM fractions, followed by their detergent‐phase TX‐114 partitioning, to be a powerful method to isolate low‐abundance PM proteins, and a useful adjunct for in‐depth cell surface proteome analyses. Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20-30% of eukaryotic genomes, a detailed characterisation of their encoded proteins is underrepresented, due, to their low copy number and the inherent difficulties in their isolation and purification as a consequence of their high hydrophobicity. We describe here a strategy that combines two orthogonal methods to isolate and purify PM proteins from Madin Darby canine kidney (MDCK) cells. In this two-step method, we first used cationic colloidal silica (CCS) to isolate adherent (Ad) and non-adherent (nAd) PM fractions, and then subjected each fraction to Triton X-114 (TX-114) phase partitioning to further enrich for hydrophobic proteins. While CCS alone identified 255/757 (34%) membrane proteins, CCS/TX-114 in combination yielded 453/745 (61%). Strikingly, of those proteins unique to CCS/TX-114, 277/393 (70%) had membrane annotation. Further characterisation of the CCS/TX-114 data set using Uniprot and transmembrane hidden Markov model revealed that 306/745 (41%) contained one or more transmembrane domains (TMDs), including proteins with 25 and 17 TMDs. Of the remaining proteins in the data set, 69/439 (16%) are known to contain lipid modifications. Of all membrane proteins identified, 93 had PM origin, including proteins that mediate cell adhesion, modulate transmembrane ion transport, and cell-cell communication. These studies reveal that the application of CCS to first isolate Ad and nAd PM fractions, followed by their detergent-phase TX-114 partitioning, to be a powerful method to isolate low-abundance PM proteins, and a useful adjunct for in-depth cell surface proteome analyses. [PUBLICATION ABSTRACT] |
Author | Kapp, Eugene A. Moritz, Robert L. Mathias, Rommel A. Mathivanan, Suresh Simpson, Richard J. Goode, Robert J. A. Chen, Yuan-Shou Zhu, Hong-Jian |
Author_xml | – sequence: 1 givenname: Rommel A. surname: Mathias fullname: Mathias, Rommel A. organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 2 givenname: Yuan-Shou surname: Chen fullname: Chen, Yuan-Shou organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 3 givenname: Robert J. A. surname: Goode fullname: Goode, Robert J. A. organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 4 givenname: Eugene A. surname: Kapp fullname: Kapp, Eugene A. organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 5 givenname: Suresh surname: Mathivanan fullname: Mathivanan, Suresh organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 6 givenname: Robert L. surname: Moritz fullname: Moritz, Robert L. organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia – sequence: 7 givenname: Hong-Jian surname: Zhu fullname: Zhu, Hong-Jian organization: Department of Surgery (RMH), The University of Melbourne, Parkville, Victoria, Australia – sequence: 8 givenname: Richard J. surname: Simpson fullname: Simpson, Richard J. email: Richard.Simpson@ludwig.edu.au organization: Ludwig Institute for Cancer Research, Parkville, Victoria, Australia |
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Keywords | Membrane protein Purification Plasma membrane Proteomics Database Cell biology Isolation Cationic colloidal silica MDCK Triton X-114 |
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Snippet | Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20–30%... Plasma membrane (PM) proteins are attractive therapeutic targets because of their accessibility to drugs. Although genes encoding PM proteins represent 20-30%... |
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Title | Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: Towards developing an MDCK protein database |
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