From 'I' to 'L' and back again: the odyssey of membrane-bound M13 protein.

The major coat protein of the filamentous bacteriophage M13 is a surprising protein because it exists both as a membrane protein and as part of the M13 phage coat during its life cycle. Early studies showed that the phage-bound structure of the coat protein was a continuous I-shaped alpha-helix. However, throughout the years various structural models, both I-shaped and L-shaped, have been proposed for the membrane-bound state of the coat protein. Recently, site-directed labelling approaches have enabled the study of the coat protein under conditions that more closely mimic the in vivo membrane-bound state. Interestingly, the structure that has emerged from this work is I-shaped and similar to the structure in the phage-bound state.

Picosecond kinetics of light harvesting and photoprotective quenching in wild-type and mutant phycobilisomes isolated from the cyanobacterium Synechocystis PCC 6803.

In high light conditions, cyanobacteria dissipate excess absorbed energy as heat in the light-harvesting phycobilisomes (PBs) to protect the photosynthetic system against photodamage. This process requires the binding of the red active form of the Orange Carotenoid Protein (OCP(r)), which can effectively quench the excited state of one of the allophycocyanin bilins. Recently, an in vitro reconstitution system was developed using isolated OCP and isolated PBs from Synechocystis PCC 6803. Here we have used spectrally resolved picosecond fluorescence to study wild-type and two mutated PBs. The results demonstrate that the quenching for all types of PBs takes place on an allophycocyanin bilin emitting at 660 nm (APC(Q)(660)) with a molecular quenching rate that is faster than (1 ps)(-1). Moreover, it is concluded that both the mechanism and the site of quenching are the same in vitro and in vivo. Thus, utilization of the in vitro system should make it possible in the future to elucidate whether the quenching is caused by charge transfer between APC(Q)(660) and OCP or by excitation energy transfer from APC(Q)(660) to the S(1) state of the carotenoid--a distinction that is very hard, if not impossible, to make in vivo.

Site, rate, and mechanism of photoprotective quenching in cyanobacteria.

In cyanobacteria, activation of the Orange Carotenoid Protein (OCP) by intense blue-green light triggers photoprotective thermal dissipation of excess absorbed energy leading to a decrease (quenching) of fluorescence of the light harvesting phycobilisomes and, concomitantly, of the energy arriving to the reaction centers. Using spectrally resolved picosecond fluorescence, we have studied cells of wild-type Synechocystis sp. PCC 6803 and of mutants without and with extra OCP (ΔOCP and OverOCP) both in the unquenched and quenched state. With the use of target analysis, we managed to spectrally resolve seven different pigment pools in the phycobilisomes and photosystems I and II, and to determine the rates of excitation energy transfer between them. In addition, the fraction of quenched phycobilisomes and the rates of charge separation and quenching were resolved. Under our illumination conditions, ∼72% of the phycobilisomes in OverOCP appeared to be substantially quenched. For wild-type cells, this number was only ∼29%. It is revealed that upon OCP activation, a bilin chromophore in the core of the phycobilisome, here called APC(Q)(660), with fluorescence maximum at 660 nm becomes an effective quencher that prevents more than 80% of the excitations in the phycobilisome to reach Photosystems I and II. The quenching rate of its excited state is extremely fast, that is, at least (∼240 ± 60 fs)(-1). It is concluded that the quenching is most likely caused by charge transfer between APC(Q)(660) and the OCP carotenoid hECN in its activated form.

Asymmetric dipping of bacteriophage M13 coat protein with increasing lipid bilayer thickness.

Knowledge about the vertical movement of a protein with respect to the lipid bilayer plane is important to understand protein functionality in the biological membrane. In this work, the vertical displacement of bacteriophage M13 major coat protein in a lipid bilayer is used as a model system to study the molecular details of its anchoring mechanism in a homologue series of lipids with the same polar head group but different hydrophobic chain length. The major coat proteins were reconstituted into 14:1PC, 16:1PC, 18:1PC, 20:1PC, and 22:1PC bilayers, and the fluorescence spectra were measured of the intrinsic tryptophan at position 26 and BADAN attached to an introduced cysteine at position 46, located at the opposite ends of the transmembrane helix. The fluorescence maximum of tryptophan shifted for 700 cm(-1) on going from 14:1PC to 22:1PC, the corresponding shift of the fluorescence maximum of BADAN at position 46 was approximately 10 times less ( approximately 70 cm(-1)). Quenching of fluorescence with the spin label CAT 1 indicates that the tryptophan is becoming progressively inaccessible for the quencher with increasing bilayer thickness, whereas quenching of BADAN attached to the T46C mutant remained approximately unchanged. This supports the idea that the BADAN probe at position 46 remains at the same depth in the bilayer irrespective of its thickness and clearly indicates an asymmetrical nature of the protein dipping in the lipid bilayer. The anchoring strength at the C-terminal domain of the protein (provided by two phenylalanine residues together with four lysine residues) was estimated to be roughly 5 times larger than the anchoring strength of the N-terminal domain.

Conformational studies of peptides representing a segment of TM7 from H+-VO-ATPase in SDS micelles.

The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, positively charged arginine residue located in the center of both peptides has a destabilizing effect on the helical conformation of the SDS-solubilized peptides, leading to beta-sheet formation and subsequent aggregation.

Profiling of dynamics in protein-lipid-water systems: a time-resolved fluorescence study of a model membrane protein with the label BADAN at specific membrane depths.

Profiles of lipid-water bilayer dynamics were determined from picosecond time-resolved fluorescence spectra of membrane-embedded BADAN-labeled M13 coat protein. For this purpose, the protein was labeled at seven key positions. This places the label at well-defined locations from the water phase to the center of the hydrophobic acyl chain region of a phospholipid model membrane, providing us with a nanoscale ruler to map membranes. Analysis of the time-resolved fluorescence spectroscopic data provides the characteristic time constant for the twisting motion of the BADAN label, which is sensitive to the local flexibility of the protein-lipid environment. In addition, we obtain information about the mobility of water molecules at the membrane-water interface. The results provide an unprecedented nanoscale profiling of the dynamics and distribution of water in membrane systems. This information gives clear evidence that the actual barrier of membranes for ions and aqueous solvents is located at the region of carbonyl groups of the acyl chains.

Exploring the structure of the N-terminal domain of CP29 with ultrafast fluorescence spectroscopy.

A high-throughput Förster resonance energy transfer (FRET) study was performed on the approximately 100 amino acids long N-terminal domain of the photosynthetic complex CP29 of higher plants. For this purpose, CP29 was singly mutated along its N-terminal domain, replacing one-by-one native amino acids by a cysteine, which was labeled with a BODIPY fluorescent probe, and reconstituted with the natural pigments of CP9, chlorophylls and xanthophylls. Picosecond fluorescence experiments revealed rapid energy transfer (approximately 20-70 ps) from BODIPY at amino-acid positions 4, 22, 33, 40, 56, 65, 74, 90, and 97 to Chl a molecules in the hydrophobic part of the protein. From the energy transfer times, distances were estimated between label and chlorophyll molecules, using the Förster equation. When the label was attached to amino acids 4, 56, and 97, it was found to be located very close to the protein core (approximately 15 A), whereas labels at positions 15, 22, 33, 40, 65, 74, and 90 were found at somewhat larger distances. It is concluded that the entire N-terminal domain is in close contact with the hydrophobic core and that there is no loop sticking out into the stroma. Most of the results support a recently proposed topological model for the N-terminus of CP29, which was based on electron-spin-resonance measurements on spin-labeled CP29 with and without its natural pigment content. The present results lead to a slight refinement of that model.

Viruses: incredible nanomachines. New advances with filamentous phages.

During recent decades, bacteriophages have been at the cutting edge of new developments in molecular biology, biophysics, and, more recently, bionanotechnology. In particular filamentous viruses, for example bacteriophage M13, have a virion architecture that enables precision building of ordered and defect-free two and three-dimensional structures on a nanometre scale. This could not have been possible without detailed knowledge of coat protein structure and dynamics during the virus reproduction cycle. The results of the spectroscopic studies conducted in our group compellingly demonstrate a critical role of membrane embedment of the protein both during infectious entry of the virus into the host cell and during assembly of the new virion in the host membrane. The protein is effectively embedded in the membrane by a strong C-terminal interfacial anchor, which together with a simple tilt mechanism and a subtle structural adjustment of the extreme end of its N terminus provides favourable thermodynamical association of the protein in the lipid bilayer. This basic physicochemical rule cannot be violated and any new bionanotechnology that will emerge from bacteriophage M13 should take this into account.

Tilt and rotation angles of a transmembrane model peptide as studied by fluorescence spectroscopy.

In this study the membrane orientation of a tryptophan-flanked model peptide, WALP23, was determined by using peptides that were labeled at different positions along the sequence with the environmentally sensitive fluorescent label BADAN. The fluorescence properties, reflecting the local polarity, were used to determine the tilt and rotation angles of the peptide based on an ideal alpha-helix model. For WALP23 inserted in dioleoylphosphatidylcholine (DOPC), an estimated tilt angle of the helix with respect to the bilayer normal of 24 degrees +/- 5 degrees was obtained. When the peptides were inserted into bilayers with different acyl chain lengths or containing different concentrations of cholesterol, small changes in tilt angle were observed as response to hydrophobic mismatch, whereas the rotation angle appeared to be independent of lipid composition. In all cases, the tilt angles were significantly larger than those previously determined from (2)H NMR experiments, supporting recent suggestions that the relatively long timescale of (2)H NMR measurements may result in an underestimation of tilt angles due to partial motional averaging. It is concluded that although the fluorescence technique has a rather low resolution and limited accuracy, it can be used to resolve the discrepancies observed between previous (2)H NMR experiments and molecular-dynamics simulations.

Picosecond fluorescence relaxation spectroscopy of the calcium-discharged photoproteins aequorin and obelin.

Addition of calcium ions to the Ca(2+)-regulated photoproteins, such as aequorin and obelin, produces a blue bioluminescence originating from a fluorescence transition of the protein-bound product, coelenteramide. The kinetics of several transient fluorescent species of the bound coelenteramide is resolved after picosecond-laser excitation and streak camera detection. The initially formed spectral distributions at picosecond-times are broad, evidently comprised of two contributions, one at higher energy (approximately 25,000 cm(-1)) assigned as from the Ca(2+)-discharged photoprotein-bound coelenteramide in its neutral state. This component decays much more rapidly (t(1/2) approximately 2 ps) in the case of the Ca(2+)-discharged obelin than aequorin (t(1/2) approximately 30 ps). The second component at lower energy shows several intermediates in the 150-500 ps times, with a final species having spectral maxima 19 400 cm(-1), bound to Ca(2+)-discharged obelin, and 21 300 cm(-1), bound to Ca(2+)-discharged aequorin, and both have a fluorescence decay lifetime of 4 ns. It is proposed that the rapid kinetics of these fluorescence transients on the picosecond time scale, correspond to times for relaxation of the protein structural environment of the binding cavity.

Temperature dependence of the lipid packing in thylakoid membranes studied by time- and spectrally resolved fluorescence of Merocyanine 540.

The lipid packing of thylakoid membranes is an important factor for photosynthetic performance. However, surprisingly little is known about it and it is generally accepted that the bulk thylakoid lipids adopt the liquid-crystalline phase above -30 degrees C and that a phase transition occurs only above 45 degrees C. In order to obtain information on the nature of the lipid microenvironment and its temperature dependence, steady-state and time-resolved fluorescence measurements were performed on the fluorescence probe Merocyanine 540 (MC540) incorporated in isolated spinach thylakoids and in model lipid systems (dipalmitoyl phosphatidylcholine and dioleoyl phosphatidylethanolamine) adopting different phases. It is demonstrated that the degree and way of incorporation differs for most lipid phases--upon selective excitation at 570 nm, the amplitude of the fluorescence component that corresponds to membrane-incorporated MC540 is about 20% in gel-, 60% in rippled gel-, and 90% in liquid-crystalline and inverted hexagonal phase, respectively. For thylakoids, the data reveal hindered incorporation of MC540 (amplitude about 30% at 7 degrees C) and marked spectral heterogeneity at all temperatures. The incorporation of MC540 in thylakoids strongly depends on temperature. Remarkably, above 25 degrees C MC540 becomes almost completely extruded from the lipid environment, indicating major rearrangements in the membrane.

Efficiency of excitation energy trapping in the green photosynthetic bacterium Chlorobaculum tepidum.

During the millions of years of evolution, photosynthetic organisms have adapted to almost all terrestrial and aquatic habitats, although some environments are obviously more suitable for photosynthesis than others. Photosynthetic organisms living in low-light conditions require on the one hand a large light-harvesting apparatus to absorb as many photons as possible. On the other hand, the excitation trapping time scales with the size of the light-harvesting system, and the longer the distance over which the formed excitations have to be transferred, the larger the probability to lose excitations. Therefore a compromise between photon capture efficiency and excitation trapping efficiency needs to be found. Here we report results on the whole cells of the green sulfur bacterium Chlorobaculum tepidum. Its efficiency of excitation energy transfer and charge separation enables the organism to live in environments with very low illumination. Using fluorescence measurements with picosecond resolution, we estimate that despite a rather large size and complex composition of its light-harvesting apparatus, the quantum efficiency of its photochemistry is around ~87% at 20 °C, ~83% at 45 °C, and about ~81% at 77 K when part of the excitation energy is trapped by low-energy bacteriochlorophyll a molecules. The data are evaluated using target analysis, which provides further insight into the functional organization of the low-light adapted photosynthetic apparatus.

Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment.

The work presented here describes a new and simple method based on site-directed fluorescence labeling using the BADAN label that permits the examination of protein-lipid interactions in great detail. We applied this technique to a membrane-embedded, mainly alpha-helical reference protein, the M13 major coat protein. Using a high-throughput approach, 40 site-specific cysteine mutants were prepared of the 50-residues long protein. The steady-state fluorescence spectra were analyzed using a three-component spectral model that enabled the separation of Stokes shift contributions from water and internal label dynamics, and protein topology. We found that most of the fluorescence originated from BADAN labels that were hydrogen-bonded to water molecules even within the hydrophobic core of the membrane. Our spectral decomposition method revealed the embedment and topology of the labeled protein in the membrane bilayer under various conditions of headgroup charge and lipid chain length, as well as key characteristics of the membrane such as hydration level and local polarity, provided by the local dielectric constant.

Membrane-bound peptides mimicking transmembrane Vph1p helix 7 of yeast V-ATPase: a spectroscopic and polarity mismatch study.

The V-ATPases are a family of ATP-dependent proton pumps, involved in a variety of cellular processes, including bone breakdown. V-ATPase enzymes that are too active in the latter process can result in osteoporosis, and inhibitors of the enzyme could be used to treat this disease. As a first step in studying the structure and function of the membrane-embedded interface at which proton translocation takes place, and its role in V-ATPase inhibition, synthetic peptides P1 and P2 consisting of 25 amino acid residues are presented here that mimic Vph1p helix 7 of yeast V-ATPase. A single mutation R10A between peptide P1 and P2 makes it possible to focus on the role of the essential arginine residue R735 in proton translocation. In the present work, we use a novel combination of spectroscopic techniques, such as CD spectroscopy, tryptophan emission spectra, acrylamide quenching and parallax analysis, and polarity mismatch modeling to characterize the peptides P1 and P2 in lipid bilayer systems. Based on both the spectroscopic experiments and the polarity mismatch modeling, P1 and P2 adopt a similar transmembrane conformation, with a mainly alpha-helical structure in the central part, placing the tryptophan residue at position 12 at a location 4+/-2 A from the centre of the lipid bilayer. Furthermore, the arginine at position 10 in P1 does not have an effect on the bilayer topology of the peptide, showing that the long, flexible side chain of this residue is able to snorkel towards the lipid headgroup region. This large flexibility of R735 might be important for its function in proton translocation in the V-ATPase enzyme.

Spectroscopy and photophysics of self-organized zinc porphyrin nanolayers. 1. Optical spectroscopy of excitonic interactions involving the soret band.

The photophysical properties of excited singlet states of zinc tetra-(p-octylphenyl)-porphyrin in 5-25-nm-thick films spin-coated onto quartz slides have been investigated by optical spectroscopy. Analysis of the polarized absorption spectra using a dipole-dipole exciton model with two mutually perpendicular transition dipole moments per molecule shows that the films are built from linear aggregates, i.e., stacks with a slipped-deck-of-cards configuration. The molecular planes of the porphyrins in the stacks are found to be perpendicularly oriented with respect to the substrate plane. Assuming a value of 2-3 for the dielectric constant of the film, from the excitonic shift, an angle of 44 degrees +/- 3 degrees and an interplanar distance of 0.35-0.36 nm between adjacent porphyrins are calculated, close to the ground-state geometry in solution. The ordering in these films was further investigated by the effects of various solvents and temperature annealing. Spin-coating from toluene as a solvent results in highly ordered films, and annealing of these films has little effect on their absorption spectra. However, spin-coating from chloroform or pyridine or exposure of the films to these solvents in their vapor phases changes their ordering presumably due to incorporation of residual solvent molecules. Annealing yields absorption spectra identical to those of films spin-coated from toluene. The absorption spectra are insensitive to atmospheric moisture, in contrast to those of zinc tetraphenylporphyrin films lacking octyl substituents.

Spectroscopy and photophysics of self-organized zinc porphyrin nanolayers. 2. Transport properties of singlet excitation.

Exciton diffusion has been studied in 5-25-nm-thick films of zinc tetra-(p-octylphenyl)-porphyrin (ZnTOPP) spin-coated onto quartz slides by intentional doping with quenchers using steady-state as well as time-resolved fluorescence spectroscopy. The fluorescence spectra of the films are very similar to those of solutions, indicating emission from localized exciton states. From the dependence of the fluorescence quenching on the quencher concentration and fluorescence lifetime measurements, the exciton diffusion can be concluded to be quasi-one-dimensional with an exciton diffusion length of 9 +/- 3 nm and an intrastack energy-transfer rate constant of 10(11)-10(12) s(-1). From fluorescence anisotropy decay measurements, we conclude that neighboring stacks aggregate in a herringbone structure, forming ordered domains that are randomly oriented in the substrate plane. These measurements indicate an interstack energy-transfer rate constant of (7 +/- 2) x 10(10) s(-1).

Light harvesting and blue-green light induced non-photochemical quenching in two different C-phycocyanin mutants of Synechocystis PCC 6803.

Cyanobacteria are oxygen-evolving photosynthetic organisms that harvest sunlight and convert excitation energy into chemical energy. Most of the light is absorbed by large light harvesting complexes called phycobilisomes (PBs). In high-light conditions, cyanobacteria switch on a photoprotective mechanism called non-photochemical quenching (NPQ): During this process, absorption of blue-green light transforms the inactive orange form of the orange carotenoid protein OCP (OCP(o)) into the red active form OCP(r) that subsequently binds to the PB, resulting in a substantial loss of excitation energy and corresponding decrease of the fluorescence. In wild-type cells, the quenching site is a bilin chomophore that fluoresces at 660 nm and which is called APC(Q)(660). In the present work, we studied NPQ in two different types of mutant cells (CB and CK) that possess significantly truncated PBs, using spectrally resolved picosecond fluorescence spectroscopy. The results are in very good agreement with earlier in vitro experiments on quenched and unquenched PBs, although the fraction of quenched PBs is far lower in vivo. It is also lower than the fraction of PBs that is quenched in wild-type cells, but the site, rate, and location of quenching appear to be very similar.

Time-resolved fluorescence and fluorescence anisotropy of fluorescein-labeled poly(N-isopropylacrylamide) incorporated in polymersomes.

The phase behavior of fluorescein isothiocyanate (FITC) labeled poly(N-isopropylacrylamide) (PNIPAAm) incorporated in polymersomes (Ps) was studied by monitoring the fluorescence lifetime (FL) and the time-resolved fluorescence anisotropy (TRFA) as a function of temperature at pH 7.4. Ps containing FITC-labeled PNIPAAm with a diameter less than 200 nm were prepared by injecting a THF solution of poly(ethylene glycol)-b-poly(d,l-lactide) (mPEG-PDLLA) and FITC tagged PNIPAAm (FITC-N) into phosphate buffered saline (PBS, pH 7.4). Solutions of free FITC (2 µM) and FITC-N (2 µM) in PBS were used as controls. The polarized fluorescence decay curves of FITC were fitted with one rotational correlation time (θ(1)) and the corresponding amplitude (ß(1)), while those for FITC-N were fitted with two rotational correlation times (θ(1,2)) and their corresponding amplitudes (ß(1,2)). Short rotational correlation times, θ(1), correspond with the rotation of the FITC molecule itself, whereas θ(2) corresponds to FITC-segmental rotation. FITC-N encapsulated in Ps (FITC-N/Ps) showed a decrease of the rotational motion upon increasing the temperature. The long rotational correlation time (θ(2)) of FITC-N increased 3 fold, going from 15 to 40 °C, reflecting a reduced rotational mobility. The residual anisotropy (ß(∞)) of FITC-N/Ps at pH 7.4 showed a gradual increase, going from 15 to 25 °C followed by a gradual decrease at higher temperatures. These results are explained by a transition from coil to globule, a gradual increase of intermolecular aggregation, and possibly phase separation and hydrogel formation.

Solubilization of V-ATPase transmembrane peptides by amphipol A8-35.

Two transmembrane peptides encompassing the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae were studied as complexes with APols A8-35 by CD and fluorescence spectroscopy, with the goal to use APols to provide a membrane-mimicking environment for the peptides. CD spectroscopy was used to obtain the overall secondary structure of the peptides, whereas fluorescence spectroscopy provided information about the local environment of their tryptophan residues. The fluorescence results indicate that both peptides are trapped by APols and the CD results that they adopt a beta-sheet conformation. This result is in contrast with previous work that showed that the same peptides are alpha-helical in SDS micelles and organic solvents. These observations are discussed in the context of APol physical-chemical properties and transmembrane peptide structural propensity.

FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein.

A formalism for membrane protein structure determination was developed. This method is based on steady-state FRET data and information about the position of the fluorescence maxima on site-directed fluorescent labeled proteins in combination with global data analysis utilizing simulation-based fitting. The methodology was applied to determine the structural properties of the N-terminal domain of the major coat protein from bacteriophage M13 reconstituted into unilamellar DOPC/DOPG (4:1 mol/mol) vesicles. For our purpose, the cysteine mutants A7C, A9C, N12C, S13C, Q15C, A16C, S17C, and A18C in the N-terminal domain of this protein were produced and specifically labeled with the fluorescence probe AEDANS. The energy transfer data from the natural Trp-26 to AEDANS were analyzed assuming a two-helix protein model. Furthermore, the polarity Stokes shift of the AEDANS fluorescence maxima is taken into account. As a result the orientation and tilt of the N-terminal protein domain with respect to the bilayer interface were obtained, showing for the first time, to our knowledge, an overall alpha-helical protein conformation from amino acid residues 12-46, close to the protein conformation in the intact phage.