Exploring Uniform, Dual, and Dynamic Topologies of Membrane Proteins by Substituted Cysteine Accessibility Method (SCAM™)

A described simple and advanced protocol for Substituted Cysteine Accessibility Method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform or identify and quantify the degree of mixed topology or establish transmembrane assembly dynamics from relatively static experimental data such as endpoint topologies of membrane proteins. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at the time by cysteine residue, and the orientation with respect to the membrane is evaluated by using a pair of membrane-impermeable non-detectable and detectable thiol-reactive labeling reagents. For the most water-exposed cysteine residues in proteins, the thiol pKa lies in the range of 8-9, and formation of cysteinyl thiolate ions is optimum in aqueous rather in a nonpolar environment. These features and the ease of specific chemical modification with thiol reagents are central to SCAM™. Membrane side-specific sulfhydryl labeling allows to discriminate "exposed, protected or dynamic" cysteines strategically "implanted" at desired positions throughout cysteine less target protein template. The strategy described is widely used to map the topology of membrane protein and establish its transmembrane dynamics in intact cells of both diderm (two-membraned) Gram-negative and monoderm (one-membraned) Gram-positive bacteria, cell-derived oriented membrane vesicles, and proteoliposomes.

Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins

Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort. Here, we report novel XL-MS-based topology data for 17 integral membrane proteins (Akr1p, Fks1p, Gas1p, Ggc1p, Gpt2p, Ifa38p, Ist2p, Lag1p, Pet9p, Pma1p, Por1p, Sct1p, Sec61p, Slc1p, Spf1p, Vph1p, Ybt1p).

Mapping of Membrane Protein Topology by Substituted Cysteine Accessibility Method (SCAM™)

A described simple and advanced protocol for the substituted-cysteine accessibility method as applied to transmembrane (TM) orientation (SCAM™) permits a topology analysis of proteins in their native state and can be universally adapted to any membrane system to either systematically map an uniform topology or identify and quantify the degree of mixed topology. In this approach, noncritical individual amino acids that are thought to reside in the putative extracellular or intracellular loops of a membrane protein are replaced one at a time by cysteine residue, and the orientation with respect to the membrane is evaluated using a pair of membrane-impermeable nondetectable and detectable thiol-reactive labeling reagents.

The active site of yeast phosphatidylinositol synthase Pis1 is facing the cytosol

Five yeast enzymes synthesizing various glycerophospholipids belong to the CDP-alcohol phosphatidyltransferase (CAPT) superfamily. They only share the so-called CAPT motif, which forms the active site of all these enzymes. Bioinformatic tools predict the CAPT motif of phosphatidylinositol synthase Pis1 as either ER luminal or cytosolic. To investigate the membrane topology of Pis1, unique cysteine residues were introduced into either native or a Cys-free form of Pis1 and their accessibility to the small, membrane permeating alkylating reagent N-ethylmaleimide (NEM) and mass tagged, non-permeating maleimides, in the presence and absence of non-denaturing detergents, was monitored. The results clearly point to a cytosolic location of the CAPT motif. Pis1 is highly sensitive to non-denaturing detergent, and low concentrations (0.05%) of dodecylmaltoside change the accessibility of single substituted Cys in the active site of an otherwise cysteine free version of Pis1. Slightly higher detergent concentrations inactivate the enzyme. Removal of the ER retrieval sequence from (wt) Pis1 enhances its activity, again suggesting an influence of the lipid environment. The central 84% of the Pis1 sequence can be aligned and fitted onto the 6 transmembrane helices of two recently crystallized archaeal members of the CAPT family. Results delineate the accessibility of different parts of Pis1 in their natural context and allow to critically evaluate the performance of different cysteine accessibility methods. Overall the results show that cytosolically made inositol and CDP-diacylglycerol can access the active site of the yeast PI synthase Pis1 from the cytosolic side and that Pis1 structure is strongly affected by mild detergents.

Topology of the yeast Ras converting enzyme as inferred from cysteine accessibility studies

The Ras converting enzyme (Rce1p) is an endoprotease that is involved in the post-translational processing of the Ras GTPases and other isoprenylated proteins. Its role in Ras biosynthesis marks Rce1p as an anticancer target. By assessing the chemical accessibility of cysteine residues substituted throughout the Saccharomyces cerevisiae Rce1p sequence, we have determined that yeast Rce1p has eight segments that are protected from chemical modification. Notably, the three residues that are essential for yeast Rce1p function (E156, H194, and H248) are all chemically inaccessible and associated with separate protected segments. By specifically assessing the chemical reactivity and glycosylation potential of the NH2 and COOH termini of Rce1p, we further demonstrate that Rce1p has an odd number of transmembrane spans. Substantial evidence that the most NH2-terminal segment functions as a transmembrane segment with the extreme NH2 terminus projecting into the endoplasmic reticulum (ER) lumen is presented. Because each of the remaining seven segments is too short to contain two spans and is flanked by chemically reactive positions, we infer that these segments are not transmembrane segments but rather represent compact structural features and/or hydrophobic loops that penetrate but do not fully span the bilayer (i.e., re-entrant helices). We thus propose a topological model in which yeast Rce1p contains a single transmembrane helix localized at its extreme NH2 terminus and one or more re-entrant helices and/or compact structural domains that populate the cytosolic face of the ER membrane. Lastly, we demonstrate that the natural cysteine residues of Rce1p are chemically inaccessible and fully dispensable for in vivo enzyme activity, formally eliminating the possibility of a cysteine-based enzymatic mechanism for this protease.

Membrane topology of yeast alkaline ceramidase YPC1

Ypc1p (yeast phyto-ceramidase 1) and Ydc1p (yeast dihydroceramidase 1) are alkaline ceramide hydrolases that reside in the ER (endoplasmic reticulum). Ypc1p can catalyse the reverse reaction, i.e. the condensation of non-esterified fatty acids with phytosphingosine or dihydrosphingosine and overexpression of YPC1 or YDC1 can provide enough ceramide synthesis to rescue the viability of cells lacking the normal acyl-CoA-dependent ceramide synthases. To better understand the coexistence of acyl-CoA-dependent ceramide synthases and ceramidases in the ER we investigated the membrane topology of Ypc1p by probing the cysteine residue accessibility of natural and substituted cysteines with membrane non-permeating mass-tagged probes. The N- and C-terminal ends of Ypc1p are oriented towards the lumen and cytosol respectively. Two of the five natural cysteines, Cys27 and Cys219, are essential for enzymatic activity and form a disulfide bridge. The data allow the inference that all of the amino acids of Ypc1p that are conserved in the Pfam PF05875 ceramidase motif and the CREST {alkaline ceramidase, PAQR [progestin and adipoQ (adiponectin) receptor] receptor, Per1 (protein processing in the ER 1), SID-1 (sister disjunction 1) and TMEM8 (transmembrane protein 8)} superfamily are located in or near the ER lumen. Microsomal assays using a lysine residue-specific reagent show that the reverse ceramidase activity can only be blocked when the reagent has access to Ypc1p from the lumenal side. Overall the data suggest that the active site of Ypc1p resides at the lumenal side of the ER membrane.