Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)by Carl White, Alex Nixon, Neil A. Bradbury

Journal of Visualized Experiments


Journal of Visualized Experiments

Copyright © 2015 Journal of Visualized Experiments April 2015 | 98 | e52509 | Page 1 of 10

Video Article

Determining Membrane Protein Topology Using Fluorescence Protease

Protection (FPP)

Carl White1, Alex Nixon1, Neil A. Bradbury1 1Department of Physiology and Biophysics, Chicago Medical School

Correspondence to: Neil A. Bradbury at


DOI: doi:10.3791/52509

Keywords: Cellular Biology, Issue 98, Membrane protein, topology, GFP, fluorescence assay, protease, proteolysis, Digitonin

Date Published: 4/20/2015

Citation: White, C., Nixon, A., Bradbury, N.A. Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP). J. Vis. Exp. (98), e52509, doi:10.3791/52509 (2015).


The correct topology and orientation of integral membrane proteins are essential for their proper function, yet such information has not been established for many membrane proteins. A simple technique called fluorescence protease protection (FPP) is presented, which permits the determination of membrane protein topology in living cells. This technique has numerous advantages over other methods for determining protein topology, in that it does not require the availability of multiple antibodies against various domains of the membrane protein, does not require large amounts of protein, and can be performed on living cells. The FPP method employs the spatially confined actions of proteases on the degradation of green fluorescent protein (GFP) tagged membrane proteins to determine their membrane topology and orientation. This simple approach is applicable to a wide variety of cell types, and can be used to determine membrane protein orientation in various subcellular organelles such as the mitochondria, Golgi, endoplasmic reticulum and components of the endosomal/recycling system. Membrane proteins, tagged on either the N-termini or C-termini with a GFP fusion, are expressed in a cell of interest, which is subject to selective permeabilization using the detergent digitonin. Digitonin has the ability to permeabilize the plasma membrane, while leaving intracellular organelles intact. GFP moieties exposed to the cytosol can be selectively degraded through the application of protease, whereas GFP moieties present in the lumen of organelles are protected from the protease and remain intact. The FPP assay is straightforward, and results can be obtained rapidly.

Video Link

The video component of this article can be found at


The plasma membranes, as well as the numerous intracellular membranes, serve as barriers separating two aqueous compartments. In the case of the plasma membrane, the separation is between the outside and inside of the cell; for intracellular organelles it is between the cytoplasm and the organelle lumen. For example, the endoplasmic reticulum (ER) membrane separates an oxidizing environment within the lumen of the ER from a cytosolic reducing environment1. Membrane proteins are synthesized on ER-associated ribosomes, and achieve their final topology within the ER membrane2. The acquisition of appropriate membrane orientation and topology for proteins is critical for their normal function. Correct topology allows relevant domains of membrane proteins to interact with their binding partners, it allows critical post-translational modifications to occur, and in the case of plasma membrane proteins, allows the cell to interact with and respond to its environment. To fully appreciate the function of a membrane protein, it is clearly imperative to know how that protein is oriented with respect to the membrane within which it resides, i.e., its membrane topology. In addition to acquisition of basic scientific knowledge, understanding the topology of a membrane protein and which aspects of a protein surface are exposed to different environments has marked clinical implications since membrane proteins comprise the majority of pharmacological targets3. Until recently, approaches to determining membrane protein topology have required considerable investment in time and money or have required reagents that are difficult to come by.

Both experimental and in silico approaches have been employed to determine the membrane topology of proteins residing within the plasma membrane. Since the first predictions of membrane spanning domains based on the evaluated hydrophobicity of individual amino acids3, numerous predictive algorithms are now available on the internet, and simply require knowledge of the protein’s amino acid sequence. However, assumptions are often central to such modeling programs, assumptions that can lead to incorrect assignments of topology4,5. Moreover, while these computer-based predictions can tentatively assign membrane spanning regions, they do not always determine whether the amino or carboxy termini of proteins are in the cytoplasm, organelle lumen or cell exterior. Even with increased computational power, and the use of machine-learning algorithms6, such data is still a model, and must be validated using experimentally acquired data. Direct experimental determination of membrane topology has been undertaken using panels of monoclonal antibodies with known epitopes distributed throughout the protein, where assessment of their immunoreactivity has been made before and after cell permeabilization. This approach requires a set of antibodies, which may not be available for the protein of interest.

An alternative strategy is to engineer epitope tags such as myc or hemagglutinin (HA) into various locations throughout the protein, again followed by determination of immunoreactivity before and after membrane permeabilization. In addition to immunogenic tags, enzymatic tags (including alkaline phosphatase, β-galactosidase, or β-lactamase) and chemical modifications such as cysteine scanning have all been employed

Journal of Visualized Experiments