The role of Trp and Tyr residues in determining membrane protein structure is particularly interesting because indole and phenol structures combine hydrophobic and polar groups, and it is hard to predict the exact region of the membrane at which their energy would be at a minimum. To determine the depths intrinsically favored by these residues, the locations of membrane-associating Trp and Tyr analogs have been determined using a fluorescence quenching technique able to measure depth at high resolution. They are found to locate at the same depths as Trp and Tyr in membrane proteins, 14-15 A from the bilayer center, which implies an important role for these residues in aligning membrane proteins in precise relationship to the lipid bilayer.

The location of commonly used charged fluorescent membrane probes in membranes was determined in order to: (1) investigate the relationship between the structure of hydrophobic molecules and their depth within membranes; and (2) aid interpretation of experiments in which these fluorescent probes are used to examine membrane structure. Membrane depth was calculated using parallax analysis, a method in which the quenching induced by lipids carrying a nitroxide group at different locations in the membrane is compared. Shallow locations were found for xanthene dyes (fluorescein, eosin, Texas Red and rhodamine) both in free form and when attached either to the headgroup of phospholipids or long hydrocarbon chains. The exact structure of the xanthene and the nature of its linkage to lipid had only a modest effect on membrane location, which ranged between 19 and 24 A from the center of the bilayer in a charged state. Thus, the location of these fluorophores largely reflects their intrinsic properties rather than the nature of the groups to which they are attached. Furthermore, cationic and anionic xanthene derivatives had similar depths, indicating the type of charge does not have a large effect on depth. Consistent with this conclusion, shallow locations were also found for other hydrocarbon chain-linked cationic (acridine orange and styrylpyridinium) and anionic (coumarin, anilinonaphthalenesulfonic acid (ANS), and toluidinylnaphthalenesulfonic acid (TNS)) charged probes. These all located at 16-18 A from the bilayer center. We conclude that both anionic and cationic molecules that are otherwise hydrophobic predominantly occupy shallow locations within the polar headgroup region of the bilayer no matter how hydrophobic the molecule to which they are linked. This depth is significantly shallower than that occupied by most previously studied uncharged polar molecules that locate near the membrane surface. Consistent with this conclusion, a 2-4 A deeper location was found for xanthene probes with no net charge. In other experiments, methods to avoid chemical reactions that can distort the measurement of depth by fluorescence quenching were developed.

The location of anthracene-labeled molecules incorporated into model membranes was measured by fluorescence quenching. The depth of the anthracene group was calculated from the degree of quenching by lipids carrying a nitroxide at different depths, using the parallax analysis (Chattopadhyay & London (1987) Biochemistry 26, 39-45). A series of anthracene derivatives was examined in order to determine what polar functional groups would anchor at the membrane surface, and at what depth anchoring would occur. An anthracene with only a methyl group was not anchored at the membrane surface, but derivatives with polar or charged groups did anchor near the membrane surface as demonstrated by a shallower anthracene depth. Based on anthracene depths, protonated primary amine, secondary amine, and hydroxyl groups appear to be located 15-16 A from the center of the membrane. A quaternary amino locates more shallowly, at 18 A from the bilayer center. A protonated carboxyl group is slightly deeper, at 14 A from the center of the bilayer. Ester groups are found to be weakly anchoring, having a location dependent on the structure of the molecule to which they are attached. In methyl 9-anthracenepropionate, the ester group is located about 13 A from the bilayer center. Anthracene esters attached to cholesterol or cholesterol esters showed various depths. An anthracene ester attached to the tail of cholesterol was located 1-6 A from the center of the bilayer for a cholesterol derivative, but at 12 A from the bilayer center for a cholesterol oleate derivative.(ABSTRACT TRUNCATED AT 250 WORDS)

To understand the relationship between the chemical structure of polar molecules and their membrane location, the behavior of dansyl (dimethylaminonaphthalenesulfonyl) and related polar fluorescent probes was examined. The depth of these probes in lipid bilayers was determined by parallax analysis of fluorescence quenching [Chattopadhyay and London (1987) Biochemistry 26, 39-45; Abrams & London, Biochemistry (1993) 32, 10826-10831]. Quenching was measured for dansyl groups: (1) attached to the polar headgroup of PE, (2) linked to an alkyl chain, (3) attached to the end of a fatty acyl chain, and (4) attached to the polar headgroup of PE via a spacer group. In all cases, the dansyl probes located in the polar headgroup region, 19-21 A from the bilayer center. This shows the dansyl group has a strong tendency to seek a shallow location in the polar headgroup region. The only exception to this pattern was in the case of a dialkylated dansyl, for which two populations were observed. One population was at the polar headgroup level, but the second was deeply buried in the acyl chain region. To see if the polar sulfonamide group of dansyl influences depth, a structurally related probe substituting a thiocarbamoyl linkage, dimethylaminonaphthalenethiocarbamoyl (dantyl)-labeled PE, was synthesized. Dantyl groups were located deeper than dansyl groups, 13-16 A from the bilayer center. There was an even more dramatic difference in depth between dansyl and mansyl (methylanilinonaphthalenesulfonyl) derivatives. Mansyl probes, which have an extra phenyl group relative to dansyl, were found to locate deeply within the acyl chain region of the bilayer (6-7 A from the bilayer center) when attached to the polar headgroup of PE. Thus, the membrane location of polar groups depends strongly on the details of their chemical structure, and it is possible for a polar group to locate both at shallow and deep locations. These results suggest the energy to bury a polar moiety in the hydrophobic part of the bilayer is not prohibitively high. This contrasts to the behavior of charged groups, which appear to be restricted to shallow locations in membranes. In this report, the effect of populations at two different depths on the parallax analysis is also considered.