Determining Membrane Protein Topology Using Fluorescence Protease Protection (FPP)

Summary

Here, we present a protocol to determine the orientation and topology of integral membrane proteins in living cells. This simple protocol relies on selective protease sensitivity of chimeras between the protein of interest and GFP.

Abstract

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.

Introduction

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 prot....

Protocol

1. Generation and Validation of Fluorescent Protein Chimeras

1. Append green fluorescent protein (GFP) to the amino or carboxyl termini of the protein of interest using standard recombinant DNA strategies¹³.
   NOTE: Although we have used GFP extensively, other variants such as cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), DsRed and mCherry can be employed. Improvements in fluorophore folding efficiency, brightness and photostability are constantly being made, and investigators should avail themselves of the latest generation constructs.
   1. Confirm correct DNA sequence and ensure that the GFP moiety is in frame with....

Results

Plasma Membrane Permeabilization

Efficient plasma membrane permeabilization is determined by the use of soluble fluorescent proteins (e.g., GFP, DsRed) (Step 4). These proteins, when expressed in cells, are free to diffuse in the cytosol, and are lost when the plasma membrane is permeabilized using digitonin (Figure 2). A complete disappearance of fluorescent signal should occur within 10-60 sec of digitonin application. Confirmation that the protein of inter.......

Discussion

The correct orientation and topology of membrane proteins is essential for their proper function. Despite the importance of understanding membrane protein topology, there are many proteins for which such data is completely lacking. FPP provides an easy and efficient way of determining membrane protein topology, and one that can be performed by most laboratories. The FPP approach affords significant advantages over previous methods for determining protein topology. For example, there is no need to have a panel of multiple.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Digitonin	Calbiochem	300410
Proteinase K	Sigma	P2308
Trypsin	Sigma	T3924
Cav1-GFP	Addgene	44433
pAcGFP-1 Golgi	Clontech	632464
Polylysine	Sigma	P4707
Mounting Media	Dako	cS704