Optimization of IPG strip equilibration for the basic membrane protein mABC1

Many proteins with extreme physical properties, including basic and acidic proteins, membrane proteins, and very large proteins, present specific challenges to 2‐DE separation. Using a pressure‐blotting approach, we demonstrate that a basic integral membrane protein, mitochondrial ATP‐binding cassette protein 1 (mABC1), focuses in the IPG strip, but fails to enter into the 2‐D SDS‐PAGE gel. Through modifying the equilibration conditions between the IPG strip and 2nd dimension, we demonstrate that only by increasing both the volume (from 3 to 6 mL for a 7‐cm strip) and SDS concentration (from 2 to 10%) of the equilibration buffer is migration of mABC1 into the 2nd dimension achieved. While 2‐DE remains one of the core separation technologies of proteomic analysis, proteins that are extremely basic, hydrophobic, or of large mass present significant challenges to 2‐DE separation due to aggregation, oxidation, precipitation, and the physical limitations of the 1‐D IPG strip (for recent reviews, see [1–7]). Since the advent of commercially available IPG strips, numerous groups have experimented with IEF conditions using various detergents alone or in combination [8], alternative denaturants [9], and thiol oxidation agents [10] to improve protein focusing. Effective 2‐DE separation of membrane proteins has been affected dramatically by these advances in protein solubilization, as well as improvements in isolation of membranes, delipidation, and active in‐gel rehydration [11, for recent reviews see 4, 5, 7]. Since the development of commercially available basic IPG strips, the most significant advance in the separation of basic proteins has been the introduction of hydroxyethyldisulfides, either alone or in combination with DTT [10]. While hydrophobic proteins were once virtually absent from the 2‐D gel, and basic proteins were only visible as dense streaks, now many groups are undertaking large‐scale analyses of membranes and basic proteins. Using this base of experimental tools, we embarked on a proteomic analysis of cardiac mitochondrial membranes, hoping to combine the knowledge gained from ongoing targeted protein chemistry and molecular biology studies with a broader‐based proteomic analysis. Of particular interest is the inner mitochondrial membrane protein mABC1 (mitochondrial ATP‐binding cassette protein 1), which may play a significant role in cardioprotection as part of the mitochondrial ATP‐sensitive potassium channels [12–14]. Therefore, in designing our 2‐DE approach, it was crucial to ensure that mABC1 is focused, observable, and quantifiable, despite being an integral membrane protein of p I 9.37.