Refining membrane penetration by a combination of steady-state and time-resolved depth-dependent fluorescence quenching

Accurate determination of the depth of membrane penetration of a fluorescent probe, attached to a lipid, protein, or other macromolecule of interest, using depth-dependent quenching methodology is complicated by thermal motion in the lipid bilayer. Here, we suggest that a combination of steady-state and time-resolved measurements can be used to generate a static quenching profile that reduces the contribution from transverse diffusion occurring during the excited-state lifetime. This procedure results in narrower quenching profiles, compared with those obtained by traditional measurements, and thus improves precision in determination of the underlying depth distribution of the probe.     

Measuring membrane penetration with depth-dependent fluorescence quenching: Distribution analysis is coming of age

Depth-dependent fluorescence quenching by lipid-attached quenchers (e.g., bromine atoms and doxyl groups) is an important tool for determining the penetration of proteins and peptides into lipid bilayers. Extracting quantitative information and accurate calculations of the depth of the fluorophore are complicated by thermal disorder, resulting in broad distributions of the transverse positions of both quenchers and fluorophores. Twenty-one years ago a methodology called distribution analysis (DA) was introduced, based on the emerging view of the complexity of the transverse organization of lipid bilayer structure. The method is aimed at extracting quantitative information on membrane penetration, such as position and width of fluorophore's distribution along the depth coordinate and its exposure to the lipid phase. Here we review recent progress in refining the DA method and illustrate its applications to protein–membrane interactions. We demonstrate how basic assumptions of the DA approach can be validated using molecular dynamics simulations and how the precision of depth determination is improved by applying a new protocol based on a combination of steady-state and time-resolved fluorescence quenching. Using the example of the MPER fragment of the membrane-spanning domain of the HIV-1 gp41 fusion protein, we illustrate how DA applications and computer simulations can be used together to reveal the molecular organization of a protein–membrane complex. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.     

Protein fluorescence quenching by small molecules: protein penetration versus solvent exposure

Experiments were done to test the thesis that acrylamide and similar small molecules can penetrate into proteins on a nanosecond time scale. The approach taken was to measure the pattern of fluorescence quenching exhibited by quenching molecules differing in molecular character (size, polarity, charge) when these are directed against protein tryptophans that cover the whole range of tryptophan accessibility. If quenching involves protein penetration and internal quencher migration, one expects that larger quenchers and more polar quenchers should display lesser quenching. In fact, no significant dependence on quencher character was found. For proteins that display measurable quenching, the disparate quenchers studied display very similar quenching rate constants when directed against any particular protein tryptophan. For several proteins having tryptophans known to be buried, no quenching occurs. These results are not consistent with the view that the kinds of small molecules studied can quite generally penetrate into and diffuse about within proteins at near-diffusion-limited rates. Rather the results suggest that when quenching is observed, the pathway involves encounters with tryptophans that are partially exposed at the protein surface. Available crystallographic results support this conclusion.     

Depth profiling in membranes by fluorescence quenching

Membrane penetration depth is an important parameter in relation to membrane structure and organization. A methodology has been developed to analyze the membrane penetration depths of fluorescent molecules or groups utilizing differential fluorescence quenching caused by membrane embedded spin-label probes located at different depths. The method involves determination of the parallax in the apparent location of fluorophores, detected when quenching by phospholipids spin-labelled at two different depths is compared. By use of relatively simple algebraic expressions, the method allows calculation of depth in å. This method has been used to determine the location of fluorophores in NBD-labelled lipids and anthroyloxy-labelled fatty acids in model membranes and of the membrane embedded tryptophan residues in the reconstituted nicotinic acetylcholine receptor.     

The penetration of local anesthetics into the red blood cell membrane as studied by fluorescence quenching.

The local anesthetics procaine and tetracaine were found to quench the fluorescence of the probes N-octadecyl naphthyl-2-amine 6-sulfonic acid and 12-(9-anthroyl)stearic acid in the presence of erythrocyte membranes. This quenching was shown to be due to the aromatic amine of the procaine and tetracaine molecules. Lidocaine, an active anesthetic that does not contain an aromatic amine in the same position as does procaine and tetracaine did not quench either of the fluorophores. The preferential quenching of the fluorescent probes by procaine and tetracaine indicated a greater accessibility of tetracaine than of procaine to the hydrocarbon region of the membrane and a greater accessibility of procaine than of tetracaine at the membrane's surface. The addition of calcium was found to reverse the quenching of 12-(9-anthroyl)stearic acid by tetracaine in the presence of red cell membranes.     

Liposomal membranes. XIV. Fusion of liposomal membranes induced by polyisoprenoids as monitored by fluorescence quenching method

Fusion of the single-walled liposomes of egg phosphatidylcholine as induced by the polyisoprenoids such as solanesol, trans-ethyl decaprenoate (EDP), coenzyme Q10, and dolichol has been investigated adopting the fluorescence quenching method. Relative efficiency of the polyisoprenoids employed on the induced fusion of liposomes was a sequence of solanesol less than or equal to EDP much less than CoQ10, dolichol, which was consistent with the result previously obtained by the dye-release method.     

Statistical thermodynamic analysis of peptide and protein insertion into lipid membranes.

A statistical thermodynamic approach is used to analyze the various contributions to the free energy change associated with the insertion of proteins and protein fragments into lipid bilayers. The partition coefficient that determines the equilibrium distribution of proteins between the membrane and the solution is expressed as the ratio between the partition functions of the protein in the two phases. It is shown that when all of the relevant degrees of freedom (i.e., those that change their character upon insertion into the membrane) can be treated classically, the partition coefficient is fully determined by the ratio of the configurational integrals and thus does not involve any mass-dependent factors, a conclusion that is also valid for related processes such as protein adsorption on a membrane surface or substrate binding to proteins. The partition coefficient, and hence the transfer free energy, depend only on the potential energy of the protein in the membrane. Expressing this potential as a sum of a "static" term, corresponding to the equilibrium (minimal free energy) configuration of the protein in the membrane, and a "dynamical" term representing fluctuations around the equilibrium configuration, we show that the static term contains the "solvation" and "lipid perturbation" contributions to the transfer free energy. The dynamical term is responsible for the "immobilization" free energy, reflecting the loss of translational and rotational entropy of the protein upon incorporation into the membrane. Based on a recent molecular theory of lipid-protein interactions, the lipid perturbation and immobilization contributions are then expressed in terms of the elastic deformation free energy resulting from the perturbation of the lipid environment by the foreign (protein) inclusion. The model is formulated for cylindrically shaped proteins, and numerical estimates are given for the insertion of an alpha-helical peptide into a lipid bilayer. The immobilization free energy is shown to be considerably smaller than in previous estimates of this quantity, and the origin of the difference is discussed in detail.     

Intrinsic tryptophan fluorescence of membranes of GH3 pituitary cells: quenching by thyrotropin-releasing hormone.

The intrinsic tryptophan fluorescence of membranes prepared from the GH₃ strain of hormone-producing pituitary cells was monitored by spectrofluorometry. Membranes of GH₃ cells have specific receptors which bind thyrotropin-releasing hormone (TRH). When TRH binds to GH₃ membranes there is quenching of tryptophan fluorescence. The kinetics of the change in fluorescence of GH₃ membranes and of TRH binding are similar. In addition, the concentration of TRH required to produce a half-maximum change in fluorescence is 10 nM, and that required for half-maximum binding of TRH to receptors is 11 nM. Inactive TRH analogs which do not bind to TRH receptors likewise do not alter GH₃ membrane fluorescence, and a pituitary cell strain which lacks TRH receptors does not change membrane fluorescence on incubation with TRH. We conclude that the TRH-receptor interaction in GH₃ membranes is associated with a change in membrane conformation that is readily measured by differential spectrofluorometry.     

Calibration of the parallax fluorescence quenching method for determination of membrane penetration depth: refinement and comparison of quenching by spin-labeled and brominated lipids.

We previously introduced the "parallax" method, which uses fluorescence quenching by spin-labeled lipids in order to measure the depth of molecules within a membrane [Chattopadhyay, A., & London, E. (1987) Biochemistry 26, 39-45]. In this report the accuracy of this method is established by comparison of spin-label quenching to that obtained using brominated lipids. To accomplish this, the fluorescent molecules used were a fatty acid labeled with a carbazole buried deeply within the acyl chain region of the membrane, an acyl-Trp with the Trp residue residing near the polar membrane region, and cytochrome b5, which has Trp residues in its membrane-inserted region. The depths calculated from the amount of bromine quenching agreed with those determined using parallax analysis. This indicates that the depth reported by parallax analysis is accurate and that the spin labels residue very close to their predicted locations in the membrane. Furthermore, there was good agreement when parallax analysis was applied both to quenching by brominated and spin-labeled molecules, suggesting that the analysis is valid in both cases. The effect that different distributions and motions of fluorophores and quenchers would have on parallax analysis was also examined. For uniform distributions of quenchers or fluorophores over a range of depths, it was found that the analysis reports the average fluorophore depth. In addition, experimental data suggest that motional effects do not significantly alter the measured depths. This is consistent with the motions during the short excited state lifetime of the fluorophores being relatively small and/or relatively isotropic.     

Transverse distribution of alpha-tocopherol in bilayer membranes studied by fluorescence quenching

The fluorescence properties of alpha-tocopherol in a range of solvents and in micelles and membrane vesicles have been measured. In solvents the fluorescence decay was fitted by a single exponential. In bilayer membranes of dipalmitoylphosphatidylcholine or egg phosphatidylcholine the fluorescence decay was more accurately fitted as a double exponential. This may indicate that alpha-tocopherol occupies two or more sites in such membranes. Depth-dependent quenching of alpha-tocopherol fluorescence by acrylamide and some doxyl stearates has also been studied. The results confirm that in gel-phase lipid the chromanol group has a transverse distribution close to the head-group region of the lipid. In fluid phase lipid in the presence of buffer the results indicate there is more penetration of the chromanol group into the bilayer.     

Examination of tubulin-nucleotide interactions by protein fluorescence quenching measurements

The fluorescence emission spectrum of bovine brain tubulin is quenched upon binding of GTP, GMPP(NH)P, or GMPP(CH₂)P to the tubulin·GDP complex. At saturating levels of GTP or its nonhydrolyzable β-γ analogues, the partially quenched spectrum is virtually identical, suggesting that a similar conformational state is attained in each case. Titrations with each ligand yielded dissociation constants of 0.8, 3, and 3μM for GTP, GMPP(NH)P, and GMPP(CH₂)P; in all cases the stoichiometry is essentially one molecule of nucleotide per dimer. It is concluded that GDP and GTP stabilize different conformations and that the nonhydrolyzable analogues mimic the binding of GTP. This may be related to the ability of GMPP(NH)P and GMPP(CH₂)P to maintain a pre-assembly conformation similar to tubulin·GTP.     

Monitoring protein conformational changes by quenching of intrinsic fluorescence

The quenching of intrinsic fluorescence of human serum albumin and pigeon liver malic enzyme by acrylamide was studied after the proteins were denatured to different stages. The progress of protein denaturation induced by guanidine hydrochloride was accompanied by increasing of effective dynamic quenching constant which provides a convenient parameter for monitoring protein conformational change.     

Static and dynamic quenching of protein fluorescence. II. lysozyme.

The fluorescence parameters—lifetime, relative quantum yield, wavelength of maximum fluorescence intensity, half-width, and polarization—of 0.01% lysozyme were measured at 15°C in aqueous solution, in glycerol–water mixtures (0–90% v/v glycerol), in aqueous urea (0–8M) solutions, and in aqueous guanidine hydrochloride (0–6.4M) solutions. The changes in the static and dynamic quenching of lysozyme fluorescence, monitored by the quantum yield and lifetime measurements, were correlated with the other fluorescence parameters and compared with our earlier results with bovine serum albumin. The results were interpreted in terms of induced conformational changes. The various perturbants altered the fluorescence parameters of lysozyme and bovine serum albumin very differently. The differences were shown to be entirely consistent with our earlier conclusion that bovine serum albumin fluorophores are nonsurface residues and with the conclusion of others that lysozyme fluorophores are surface residues. Unlike their effects on bovine serum albumin, urea and guanidine hydrochloride affect lysozyme structure quite differently, both in nature and degree. We have suggested that the affect of urea on lysozyme fluorescence is an indirect result of reduction in the size of the cleft brought about by the structure-breaking action of urea on water in the cleft. 4M Urea is sufficient for this reaction. Large decreases in the polarization of the fluorescence of lysozyme in the 0.8–1.6M and 3.2–4.8M guanidine hydrochloride ranges demonstrated two guanidine hydrochloride-induced conformation changes. A red shift of the fluorescence maximum to 354 nm indicated that the second transition completely exposes all fluorescing tryptophan residues of lysozyme to mobile solvent water. However, even 6.4M guanidine hydrochloride did not completely unravel the lysozyme molecule at 15°C, as evidenced by its failure to cause any of the tyrosine residues to become fluorescent.     

Preferential lipid association and mode of penetration of apocytochrome c in mixed model membranes as monitored by tryptophanyl fluorescence quenching using brominated phospholipids

The fluorescence of the single tryptophan residue at position 59 in apocytochrome c, the biosynthetic precursor of the inner mitochondrial membrane protein cytochrome c, was studied in small unilamellar vesicles composed of phosphatidylserine (PS) and phosphatidylcholine (PC) with or without specifically Br-labelled acyl chains at the sn-2 position. The protein has a very high affinity for PS-containing vesicles (dissociation constant Kd less than 1 microM). From the relative quenching efficiency by the brominated phospholipids, it could be concluded that the protein specifically associates with the PS component in mixed vesicles and that maximal quenching occurred with phospholipids in which the bromine was present at the 6,7-position of the 2-acyl chain suggesting that (part of) the bound protein penetrates 7-8 A deep into the hydrophobic core of the bilayer.     

Penetration of dioxygen into proteins studied by quenching of phosphorescence and fluorescence

Experiments were done to measure the ability of dioxygen to collisionally quench the phosphorescent and fluorescent tryptophans in alcohol dehydrogenase and alkaline phosphatase. In all cases, luminescence is quenched with rate constants close to 1 x 10(9) M-1 s-1. The rate of reaching the buried tryptophans is little affected by solvent viscosity due to added glycerol. Quenching by dioxygen is not due to a protein-opening reaction. It appears to be rate limited by internal protein diffusion rather than at the entry step. Dioxygen appears to enter the proteins directly, as in liquidlike diffusion, rather than through transiently forming channels that are only present a small fraction of the time. A high-pressure oxygen system is described that considerably facilitates fluorescence quenching experiments.     

The location of protein in serum lipoproteins: a fluorescence quenching study.

Quenching of the tryptophan fluorescence of pig serum HDL3 and LDL2 lipoproteins by iodide and succinimide has been used to estimate the accessibility of the fluorophores to the solvent and, by inference, the location of the protein in the macromolecular complexes. At least 80% of the protein is thought to be located at or near the surface in both lipoproteins but its accessibility is hindered especially in LDL2. A difference in surface topography in the two lipoproteins is suggested with the protein in LDL2 more buried in lipid and further away from the charged phospholipid polar groups than in HDL3. A refined treatment of the quenching data has been developed to take account of the heterogeneity of quenching sites found in the lipoproteins.     

The transverse organisation of ubiquinones in mitochondrial membranes as determined by fluorescence quenching

The transverse organisation of ubiquinone in mitochondrial membranes was investigated by quenching a set of fluorescent fatty acids. We show that the fluorescent moiety of the probes is located at a graded series of depths in the mitochondrial membrane. The probes sense the characteristics of the lipid phase and do not significantly perturb mitochondrial function as measured by the respiratory control ratio and the ADP/O ratio. The anthroyloxy fatty acids are readily quenched by ubiquinone-10. A recently developed method in the analysis of quenching data was used to obtain the subvolume of the membrane within which the quenching interactions are confined. The results indicate that ubiquinone-10 is restricted to two sites in the transverse plane of the membrane: one near the surface and the other close to the bilayer centre. The implications of these findings for the two-pool model of ubiquinone organisation are discussed.Abbreviations n-AS n-(9-anthroyloxy) stearic acids (n=6,9,12) - n-AP n-(9-anthroyloxy) palmitic acids (n=2,16) - n-AF n-(9-anthroyloxy) fatty acids (n=2,6,9,12,16) - n nitroxide stearic acids (n=5,16) - UQ _n ubiquinone-n (n=4,6,10) - HBHM heavy beet heart mitochondria