Structural characterisation and membrane insertion of M13 procoat, M13 coat and Pf3 coat proteins

Membrane proteins fulfill many central functions in the biological membrane. The insertion process of these proteins and their structure, which are intimately linked to their function, are not yet well understood. As a model we studied three proteins reconstituted into lipid bilayers (which serve as a model for the biological membrane): the major coat proteins of phages Pf3 and M13 and the precursor of the latter, M13 procoat protein, which spans the inner membrane two times and serves as a model for a multi-spanning membrane protein. Whereas Pf3 coat protein can insert into the membrane in its mature form, M13 coat protein needs the signal sequence present in the precursor to insert. A new, simple and efficient purification method has been developed for M13 procoat, M13 and Pf3 coat proteins. Homogenous preparations were obtained in isopropanol/0.l% TFA, where M13 coat protein is found to be dissolved in a monomeric form, and the two other proteins as dimers. The conformations of these particular proteins in different environments have been determined by circular dichroism and infrared spectroscopy. In organic solvents, the proteins adopt a conformation with an average helix content of 90%. In lipid bilayers composed of phospatidylcholine and phosphatidylglycerol lipids, the average helix content is 50% for M13 procoat protein, 60% for M13 coat protein and 75% for Pf3 coat protein. In order to characterize the orientational distribution the orientational order parameter Sα of the protein helices in planar lipid bilayers have been determined by polarized infrared measurements in the amide I spectral range. The helices of the three proteins are oriented preferentially parallel to the membrane normal, with Sα = 0.63 for M13 procoat protein, Sα = 0.58 for Pf3 coat protein and a distinctly higher value of Sα = 0.81 for M13 coat protein. The topology of M13 and Pf3 coat proteins was investigated using limited proteolysis in lipid vesicles with proteinase K combined with mass spectroscopy to analyze the lytic fragments. The C-terminal part of both proteins was found to be inaccessible to proteinase K, only 14 (Pf3) or 15 (M13) residues on the N-terminal were protease accessible from the outside of the vesicles. Furthermore, the standard free energy change, ΔGo, of a membrane-inserting protein with a leader sequence has been determined experimentally for the first time, using M13 procoat protein as an example. The partition coefficient for the distribution of this protein between the aqueous phase and the membrane phase of preformed lipid vesicles yielded a value of Γ = 6.5×105 M-1, corresponding to a ΔGo of -10.4 kcal/mol, based on measurements of the fluorescence energy transfer between the intrinsic tryptophan of the protein and a suitably labeled lipid membrane of POPC. For comparison, the partition coefficient of the M13 coat protein between the aqueous and the POPC lipid bilayer phase was determined to be distinctly lower: Γ = 1×105 M-1 (ΔGo = -9.3 kcal/mol). Proteinase K digestion experiments have been performed, showing that 20% of the procoat protein bound to lipid vesicles spontaneously integrate in a transbilayer form, whereas 80% remain inserted in the interfacial membrane region. By taking together these results, an upper limit for the free energy change of the transmembrane insertion of procoat protein was estimated to be -14.8 kcal/mol. In order to distinguish further the contribution arising from insertion of the procoat protein into the membrane interfacial region from that due to transmembrane insertion, the partition coefficient of a mutant procoat protein OM30R (which contains a positively charged amino acid in its mature hydrophobic segment (exchange of a Val to an Arg residue at position 30)) was determined, yielding Γ = 0.3×105 M-1 (ΔGo = -8.6 kcal/mol). Previously reported in vivo experiments have shown that the OM30R mutant protein is not translocated across Escherichia coli inner membrane, but only binds to the inner surface. The results presented here indicate that although the insertion of the procoat protein into the interfacial region of the lipid bilayer contributes the major part to ΔGo, it is the final energy gain of the interaction of the hydrophobic portions of the folded pre-protein with the lipid chains which drives the transmembrane insertion of the M13 procoat protein. Neither the leader sequence nor the mature coat protein alone yields this free energy gain. For the different proteins investigated here, spontaneous membrane insertion occurs only for fluid lipid bilayers, but not for membranes in the crystalline lipid phase. Furthermore, by using lipid bilayers with negative membrane surface charges, it was shown that both procoat and coat proteins are electrostatically attracted to the surface of the lipid membrane, though only to a small extent, with apparent partition coefficients of the same order of magnitude as for the phosphatidylcholine lipid membrane. This work has yielded new information about the structure and the insertion of the phage coat proteins. The new methods developed in this work might be of general applicability to study the structural dynamics of membrane protein assembly.

Thermodynamics of the Membrane Insertion Process of the M13 Procoat Protein, a Lipid Bilayer Traversing Protein Containing a Leader Sequence

Horst Vogel

For the first time, the std. free energy change, DG Deg, of a membrane-inserting protein with a leader sequence has been detd. exptl., using M13 procoat protein as an example. The partition coeff. for the distribution of the procoat protein between the aq. phase and the membrane phase of preformed lipid vesicles yielded a value of G = 6.5105 M-1, corresponding to a DG Deg of -10.4 kcal/mol, based on measurements of the fluorescence energy transfer between the intrinsic tryptophan of the protein and a suitably labeled lipid membrane of POPC. For comparison, the partition coeff. of the M13 coat protein between the aq. and the POPC lipid bilayer phase was detd. to be distinctly lower: G = 1105 M-1 (DG Deg = -9.3 kcal/mol). Proteinase K digestion expts. have been performed, showing that 20% of the procoat protein bound to lipid vesicles spontaneously integrate in a transbilayer form, whereas 80% remain inserted in the interfacial membrane region. By taking together these results, an upper limit for the free energy change of the transmembrane insertion of procoat protein was estd. to be -14.8 kcal/mol. To distinguish further the contribution arising from insertion of the procoat protein into the membrane interfacial region from that due to transmembrane insertion, the partition coeff. of the mutant procoat protein OM30R [which contains a pos. charged amino acid in its mature hydrophobic segment (exchange of a Val to an Arg residue at position 30)] was detd., yielding G = 0.3*105 M-1 (DG Deg = -8.6 kcal/mol). Previously reported in vivo expts. have shown that the OM30R mutant protein is not translocated across Escherichia coli membranes but only binds to the inner surface. The results presented here indicate that although the insertion of the procoat protein into the interfacial region of the lipid bilayer contributes the major part to DG Deg, it is the final energy gain of the interaction of the hydrophobic portions of the folded pre-protein with the lipid chains which drives the transmembrane insertion of the M13 procoat protein. Neither the leader sequence nor the mature coat protein alone yields this free energy gain. For the different proteins investigated here, spontaneous membrane insertion occurs only for fluid lipid bilayers, but not for membranes in the cryst. lipid phase. Furthermore, by using lipid bilayers with neg. membrane surface charges, it was shown that both procoat and coat proteins are electrostatically attracted to the surface of the lipid membrane, though only to a small extent, with apparent partition coeffs. of the same order of magnitude as for the phosphatidylcholine lipid membrane. [on SciFinder (R)]

1996

Influence of the protein environment on spectroscopy and ultrafast dynamics of retinal in bacteriorhodopsin

Selma Schenkl

The environment is important for the exact course of a chemical reaction. As an example of the strong influence of the environment on the reaction, this work studies the isomerization reaction of the chromophore retinal in the binding pocket of the protein bacteriorhodopsin. Three selected distance scales with reference to the chromophore are addressed: The distant protein surface at a length scale of 3-5 nm, the fuzzy environment of the binding pocket (1-2 nm) and the immediate neighborhood represented by the amino acid tryptophan Trp86 (5 Å). First, static absorption and fluorescence spectroscopies are applied to three dimensionally crystallized bacteriorhodopsin. An especially adapted set-up was developed for each task. The analysis of data is carried out in comparison with the measured spectra of the native protein membrane in solution. While the absorption spectrum shows a broadening on the high-energy side, the fluorescence spectrum deviates in the general shape of that measured in solution. The synoptic analysis of all spectra reveals the existence of three spectroscopically distinct species in the crystal: BR490 (absorption maximum at 490 nm) with a relative contribution of 28%, BR570 (native spectrum of solution, 68%), and BR610 ("blue membrane", 4%). BR490 appears particularly in the additional fluorescence band at 550 nm and is assigned to the dehydrated species of bacteriorhodopsin. The presence of that particular species indicates the suppression of rehydration in a partially dehydrated crystal and shows that the three dimensional arrangement hinders water diffusion. A simple model, close domains are assumed to form, eventually suppressing free water diffusion in a crystal. The lack of water on the protein surface modifies the protonation states of the amino acids in the binding pocket and therefore the optical properties of the retinal. The chromophore actually reacts on the alteration of its distant environment upon incorporation in the protein crystal. The second distance scale - the fuzzy environment - is addressed by a time-integrated fluorescence spectroscopy on native bacteriorhodopsin as function of the excitation wavelength (430 nm to 650 nm). The optimized experimental set-up guaranteed that the fluorescence of only the excited state I460 contributed. The measured spectra show maxima at 740 nm, and exhibit a Stokes shift of 5000 cm-1, independent of the excitation wavelength. The similarity of the fluorescence excitation spectrum with the spectrum of absorbed photons excludes energy-dependent loss channels. However, the spectra show a growing asymmetric broadening on the high-energy side with decreasing excitation wavelength. The additional fluorescence originates from vibrational hot states, also supported by the decomposition by Gaussian functions. A comparison with the fluorescence spectrum of blue membranes shows that the low-energy part also arises from vibrational hot states. Consequently, the first fast intramolecular vibrational energy relaxation does not entirely distribute the access-energy to other modes. The remaining energy is found in a quasi-static occupation of vibrational modes. The subsequent second vibrational relaxation — probably not only involving the retinal but also the protein — takes place on a time scale similar to that of the isomerization. The fast isomerization reaction prevents dissipation of energy relaxation of the excited state of the retinal into the protein environment. On a third distance scale, femtosecond spectroscopy in the UV offers a direct view into the electrostatic interaction of the chromophore with its immediate neighborhood. For the first time, the retinal isomerization was studied within the spectral window of the tryptophan absorption from 265 nm to 310 nm. For this, a set-up adapted to UV wavelengths was realized, basing on non-linear optics. The developed single-shot detection system yields a sensitivity of 10-5 in optical density. In the transient absorption measurements, a time resolution of 90 fs was achieved. At short probe wavelengths (265 nm - 294 nm), the measured transients show first a fast reduction of the absorption which subsequently recovers on three time scales (380 fs, 3 ps, > 16 ps). With increasing probe wavelength an induced transient absorption becomes dominant (282 nm - 294 nm). It has a rise time of 280 fs, and decays with a time constant of 4.3 ps. With further increasing probe wavelength the absorption signal decays faster. In response to the complex signature of the transients, an iterative and model-independent transient-decomposition is introduced. A set of three basis elements were identified: one bleach, and two absorption transients. The two induced absorption transients are assigned to retinal. The dynamics of the excited state (I460) in the first retinal-transient is described by two time constants (280 fs and 1 ps). The fast time constant leads to the photoproduct, while the slower one leads back to the ground state, presumably by internal conversion. The 250 fs delayed onset of the second transient (photo-intermediate J) is connected to a wave packet motion in the excited state. This delayed onset of the transient was observed for the first time. It demands a rise time of the J photo-intermediate of only 280 fs. This contrasts common estimates of 500 fs given in literature. For the first time, the temporal behavior of the permanent dipole moment of retinal is observed experimentally. Its evolution is imprinted in the dominant bleach feature (265 nm - 294 nm), originating from tryptophan Trp86. In the excited state, the permanent dipole moment increases strongly within the first 250 fs, and decays exponentially afterwards, following the formation of the photoproduct. However, the related time constant of 380 fs is slightly greater than that of 280 fs of the photoproduct J. This discrepancy may indicate a remaining long-lived polarization of the binding pocket. In brief, by using the intrinsic tryptophan as a probe, the local evolution of the electric field during the isomerization reaction was investigated. Indeed the isomerization reaction is reflected in the immediate environment. The variety of optical spectroscopy provides methods especially adapted for studying the influences of the environment on a chemical reaction. The results achieved here highlight the importance of these influences.

EPFL2004

A Biochemical and Biophysical Investigation of 5-HT3 Receptor Stability

Menno Berend Tol

The 5-hydroxytryptamine 3 receptor (5-HT3R) is a member of the pentameric ligand-gated ion channel (pLGIC) family, that plays an important role in fast signal transduction and cell-cell communication in synapses: They convert a chemical signal from a neurotransmitter into the electrical signal that represents the action potential. Activation of 5-HT3R with serotonin triggers a range of molecular reorganizations that lead to channel opening and subsequent membrane depolarization. Because of their role, pLGICs are involved in a wide range of diseases and disorders and are therefore important drug targets. A typical pLGIC is composed of a β -sheet rich extracellular domain (ECD) where ligand binding takes place, a transmembrane domain that is composed of four α-helices (TM1-TM4). In vertebrates pLGICs often contain a third intracellular domain (ICD), located between TM3 and TM4. The 5-HT3R is active as a homopentameric receptor of five identical A subunits, or as a heteropentamer containing one or more of several subunits (B to E) together with an A subunit. The 5-HT3 receptor is naturally located in the cell membrane in low amounts. For in vitro experiments such as biophysical investigation, the receptor has to be overproduced and purified in a detergent-solubilized state. Therefore, a robust and scalable expression system for homo- and heteropentameric 5-HT3 receptors was developed, building upon a tetracycline inducible cell line and Strep-tag affinity purification technology. Production of solubilized and purified 5-HT3R is well suited for use in the structural and functional characterization of the receptor. The stability of the 5-HT3 receptor is an important parameter during structural and functional experimentation. Using thermal unfolding the stability of 5-HT3R was investigated in plasma membranes as well as during detergent-extraction, purification and reconstitution into artificial lipid bilayers. A large loss in thermostability was found that correlates with the loss of the lipid bilayer during membrane solubilization and purification. Thermal unfolding of 5-HT3R occurred in consecutive steps at distinct protein locations: First a loss of ligand binding is detected, followed by formation of different transient low oligomeric states of receptor pentamers, followed by partial unfolding of helical parts of the protein, which finally leads to the formation large receptor aggregates. It was also found that structural destabilization of the receptor in detergents could be partially reversed by reconstituting the receptor into lipid bilayers. Thermal unfolding leads to the irreversible formation of aggregates which is known to prevent effective refolding. Therefore, an further investigation of 5-HT3R was made by unfolding the receptor in urea and sodium dodecyl sulfate (SDS). The results indicate iii iv ABSTRACT that, unlike thermal unfolding, unfolding in urea and SDS does not result in the formation of aggregates. Unfolding by urea shows a 50% loss of helical content while keeping the characteristic pentamer intact. Contrastingly, unfolding by SDS shows dissociation of the pentamer, but no noticeable change in secondary structure. Still, refolding from urea and SDS proved to be impossible. Two weak fluorophores, crystal violet (CrV) and ethidium bromide (EtBr), bind to the homologous nicotinic acetylcholine receptor (nAChR). Because the fluorescence of these compounds is also sensitive towards their environment they can be used as a molecular beacon for the functional state of a receptor. When applied to 5-HT3R, it was found that CrV and EtBr bind with micromolar affinity to the desensitized state of the receptor – similar to binding reported for the nAChR. It appeared that binding of CrV or EtBr to the 5-HT3R induces a certain functional state (resting, open or desensitized). Because no detectable change in fluorescence occurs, this prevents their use as molecular beacons. Still, non-competitive binding to the 5-HT3R was little reported on before and could be an important target in pharmacological research. The ICD of the 5-HT3R is predicted to contain a stretch of ∼60 disordered or flexible residues which might be involved in subunit assembly and membrane trafficking. These unstructured regions of a 5-HT3R were probed using limited proteolysis. Thereby two distinct fragments were formed that remain tightly associated with each other, while a small stretch of 35 residues between TM3 and TM4 was removed. Furthermore, it was shown that the thermal stability of the helical core is unchanged compared to untreated 5-HT3R, but that the extracellular ligand-binding domain is very sensitive to cleavage in the ICD. By probing the 5-HT3R with limited proteolysis a rigid core was identified, indicating the important role of the transmembrane domain for holding together the pLGIC scaffold. The results presented here contribute a significant body of knowledge to membrane proteins in general and to the 5-HT3 receptor in particular, upon which further research can be based leading to advances in the fields of biochemistry, biophysics and pharmacology.

EPFL2012