Comparative Skeletal Muscle Proteomics Using Two-Dimensional Gel Electrophoresis

Abstract

The pioneering work by Patrick H. O'Farrell established two-dimensional gel electrophoresis as one of the most important high-resolution protein separation techniques of modern biochemistry (Journal of Biological Chemistry1975, 250, 4007-4021). The application of two-dimensional gel electrophoresis has played a key role in the systematic identification and detailed characterization of the protein constituents of skeletal muscles. Protein changes during myogenesis, muscle maturation, fibre type specification, physiological muscle adaptations and natural muscle aging were studied in depth by the original O'Farrell method or slightly modified gel electrophoretic techniques. Over the last 40 years, the combined usage of isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension has been successfully employed in several hundred published studies on gel-based skeletal muscle biochemistry. This review focuses on normal and physiologically challenged skeletal muscle tissues and outlines key findings from mass spectrometry-based muscle proteomics, which was instrumental in the identification of several thousand individual protein isoforms following gel electrophoretic separation. These muscle-associated protein species belong to the diverse group of regulatory and contractile proteins of the acto-myosin apparatus that forms the sarcomere, cytoskeletal proteins, metabolic enzymes and transporters, signaling proteins, ion-handling proteins, molecular chaperones and extracellular matrix proteins.

Keywords: difference in-gel electrophoresis; isoelectric focusing; mass spectrometry; muscle fiber type; muscle plasticity; muscle proteomics; muscular atrophy; polyacrylamide gel electrophoresis; protein separation; skeletal muscle.

Figure 1

Summary of the number of publication entries with the keywords “two-dimensional gel electrophoresis” and “skeletal muscle” registered with the PubMed databank of the US National Library of Medicine ranging from 1976 to 2015.

Figure 2

Overview of protein classes from skeletal muscle tissue that can be separated by routine two-dimensional gel electrophoresis using isoelectric focusing in the first dimension and sodium dodecyl sulfate polyacrylamide slab gel electrophoresis in the second dimension. Abbreviations used: ACT, actin; MBP, myosin binding protein; MLC, myosin light chain; MyHC, myosin heavy chain; TM, tropomyosin; Tn, troponin.

Figure 3

Overview of proteomic approaches routinely used in the profiling of skeletal muscle proteins following separation by two-dimensional gel electrophoresis. Abbreviations used: DIGE, difference in-gel electrophoresis; GE, gel electrophoresis; IEF, isoelectric focusing; NR/RED, non-reducing/reducing; PAGE, polyacrylamide gel electrophoresis.

Figure 4

Fluorescence two-dimensional difference in-gel electrophoretic analysis of aging skeletal muscle (Sample A: Young muscle; Sample B: Aged muscle). Abbreviations used: DIGE, difference in-gel electrophoresis; GE, gel electrophoresis; IEF, isoelectric focusing; PAGE, polyacrylamide gel electrophoresis.