Interaction stabilizing tertiary structure of bacteriorhodopsin studied by denaturation experiments

Identification of Cell-Attachment Factors Derived from Green Algal Cells Disrupted by Sonication in Fabrication of Cell Plastics

Cell plastics which are composed of unicellular green algal cells have been proposed in previous studies. While unicellular green algae can be freely arranged using fabrication processes, a matrix is required to attach the cells together. To date, although the cell contents collected from Chlamydomonas reinhardtii show the possibility of attaching cells, but it is unclear which components can be considered attachment factors. Therefore, in this study, C. reinhardtii cells were disrupted with sonication, and the components were separated and purified with hexane. The cell plastics with only 0.5 wt% of intermediate showed similar mechanical properties to those with 17 wt% and 25 wt% of cell components that were untreated with hexane, meaning that the purified intermediates could function as matrices. The purified intermediate was composed of approximately 60 wt% of protein as the main component, and proteomic analysis was performed to survey the main proteins that remained after hexane treatment. The protein compositions of the cell content and purified intermediate were compared via proteomic analysis, revealing that the existing ratios of 532 proteins were increased in the purified intermediate rather than in the cell content. In particular, the outer structure of each of the 49 proteins-the intensity of which was increased by over 10 times-had characteristically random coil conformations, containing ratios of proline and alanine. The information could suggest a matrix of cell plastics, inspiring the possibility to endow the cell plastics with more properties and functions.

Regeneration of Bacteriorhodopsin from Thermally Unfolded Bacterio-Opsin and All-transRetinal at High Temperatures

The temperature dependence of regeneration of bacteriorhodopsin (bR) from its apoprotein, bacterio-opsin (bO), and all-trans retinal was investigated using two different procedures to probe the structural properties of bO at high temperatures. Regeneration experiments performed at 25 degrees C after incubation of bO within the temperature range of 35-75 degrees C indicate that irreversible thermal unfolding begins at 50 degrees C. When bO is incubated for one hour and mixed with retinal at the same elevated temperatures, however, a greater extent of regeneration to bR occurs, even at temperatures ranging from 50 to 65 degrees C. These experimental results indicate that regeneration of bR occurs from thermally unfolded bO and suggest dynamic structural fluctuation of bO in the unfolded state.

Heterogeneity in Regeneration of Bacteriorhodopsin from Bacterio-Opsin and All-transRetinal at High Temperatures: Implications for Dynamic Structural Fluctuations

Measurements of regeneration kinetics were performed in order to investigate the regeneration mechanisms of bacteriorhodopsin (bR) from thermally unfolded bacterio-opsin (bO) and all-trans retinal. Regeneration kinetics data were successfully fitted to a single exponential function when regeneration was performed at 25 degrees C after incubation at high temperatures. Conversely, the process of regeneration after the addition of retinal to bO at high temperatures occurred at two different rate constants. These findings strongly suggest that the slower regeneration of bR at high temperatures occurs as a result of dynamic structural fluctuation of bO, whereas the faster process corresponds to regeneration from bO, which retains a native structure capable of retinal binding.

Solution NMR of membrane proteins: practice and challenges

This review focuses upon the application of solution NMR methods to multispan integral membrane proteins, particularly with respect to determination of global folds by this approach. Practical methods are described along with the special difficulties that confront the application of solution NMR to proteins that dwell in the netherworld of the lipid bilayer.

The cell cycle associated protein, HTm4, is expressed in differentiating cellsof the hematopoietic and central nervous system in mice

HTm4 is a member of a newly defined family of human and murine proteins, the MS4 (membrane-spanning four) protein group, which has a distinctive four-transmembrane structure. MS4 protein functions include roles as cell surface signaling receptors and intracellular adapter proteins. We have previously demonstrated that HTm4 regulates the function of the KAP phosphatase, a key regulator of cell cycle progression. In humans, the expression of HTm4 is largely restricted to cells of the hematopoietic lineage, possibly reflecting a causal role for this molecule in differentiation/proliferation of hematopoietic lineage cells. In this study, we show that, like the human homologue, murine HTm4 is also predominantly a hematopoietic protein with distinctive expression patterns in developing murine embryos and in adult animals. In addition, we observed that murine HTm4 is highly expressed in the developing and adult murine nervous system, suggesting a previously unrecognized role in central and peripheral nervous system development.

Thr-90 plays a vital role in the structure and function of bacteriorhodopsin

The role of Thr-90 in the bacteriorhodopsin structure and function was investigated by its replacement with Ala and Val. The mutant D115A was also studied because Asp-115 in helix D forms a hydrogen bond with Thr-90 in helix C. Differential scanning calorimetry showed a decreased thermal stability of all three mutants, with T90A being the least stable. Light-dark adaptation of T90A was found to be abnormal and salt-dependent. Proton transport monitored using pyranine signals was approximately 10% of wild type for T90A, 20% for T90V, and 50% for D115A. At neutral or alkaline pH, the M rise of these mutants was faster than that of wild type, whereas M decay was slower in T90A. Overall, Fourier transform infrared (FTIR) difference spectra of T90A were strongly pH-dependent. Spectra recorded on films adjusted at the same pH at 243 or 277 K, dry or wet, showed similar features. The D115A and T90V FTIR spectra were closer to WT, showing minor structural differences. The band at 1734 cm(-1) of the deconvoluted FTIR spectrum, corresponding to the carboxylate of Asp-115, was absent in all mutants. In conclusion, Thr-90 plays a critical role in maintaining the operative location and structure of helix C through three complementary interactions, namely an interhelical hydrogen bond with Asp-115, an intrahelical hydrogen bond with the peptide carbonyl oxygen of Trp-86, and a steric contact with the retinal. The interactions established by Thr-90 emerge as a general feature of archaeal rhodopsin proteins.

The laser-induced blue state of bacteriorhodopsin: mechanistic and color regulatory roles of protein-protein interactions, protein-lipid interactions, and metal ions

In this paper we characterize the mechanistic roles of the crystalline purple membrane (PM) lattice, the earliest bacteriorhodopsin (BR) photocycle intermediates, and divalent cations in the conversion of PM to laser-induced blue membrane (LIBM; lambda(max)= 605 nm) upon irradiation with intense 532 nm pulses by contrasting the photoconversion of PM with that of monomeric BR solubilized in reduced Triton X-100 detergent. Monomeric BR forms a previously unreported colorless monomer photoproduct which lacks a chromophore band in the visible region but manifests a new band centered near 360 nm similar to the 360 nm band in LIBM. The 360 nm band in both LIBM and colorless monomer originates from a Schiff base-reduced retinyl chromophore which remains covalently linked to bacterioopsin. Both the PM-->LIBM and monomer-->colorless monomer photoconversions are mediated by similar biphotonic mechanisms, indicating that the photochemistry is localized within single BR monomers and is not influenced by BR-BR interactions. The excessively large two-photon absorptivities (> or =10(6) cm(4) s molecule(-1) photon(-1)) of these photoconversions, the temporal and spectral characteristics of pulses which generate LIBM in high yield, and an action spectrum for the PM-->LIBM photoconversion all indicate that the PM-->LIBM and Mon-->CMon photoconversions are both mediated by a sequential biphotonic mechanism in which is the intermediate which absorbs the second photon. The purple-->blue color change results from subsequent conformational perturbations of the PM lattice which induce the removal of Ca(2+) and Mg(2+) ions from the PM surface.

A novel measure characterized by a polar energy surface approximation for recognition and classification of transmembrane protein structures

A new theoretical method has been developed for recognition and classification of membrane proteins. The method is based on computation of a polar energy surface that can reveal characteristic interaction patterns for individual helices even if crystal or NMR structure coordinates are not available. A protein with N transmembrane helices is described as a set of N vectors that are derived from a Fourier analysis of this polar energy surface computed for each helix. We then derive a polarity difference score (PDS) for any two proteins computed as the root mean square deviation between the respective vector coordinate sets. The score was found to correlate with the degree of structural similarity between the following three protein families for which tertiary structures have been determined: bacteriorhodopsin, rhodopsin, and the cytochrome c oxidase III subunit.

A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle

We developed a method of predicting the tertiary structures of seven transmembrane helical proteins in triangle lattice models, assuming that the configuration of helices is stabilized by polar interactions. Triangle lattice models having 12 or 11 nearest neighbor pairs were used as general templates of a seven-helix system, then the orientation angles of all helices were varied at intervals of 15 degrees. The polar interaction energy for all possible positions of each helix was estimated using the calculated polar indices of transmembrane helices. An automated system was constructed and applied to bacteriorhodopsin, a typical membrane protein with seven transmembrane helices. The predicted optimal and actual structures were similar. The top 100 predicted helical configurations indicated that the helix-triangle, CFG, occurred at the highest frequency. In fact, this helix-triangle of bacteriorhodopsin forms an active proton-pumping site, suggesting that the present method can identify functionally important helices in membrane proteins. The possibility of studying the structure change of bacteriorhodopsin during the functional process by this method is discussed, and may serve to explain the experimental structures of photointermediate states.

Light-induced denaturation of bacteriorhodopsin solubilized by octyl-beta-glucoside

The structural stability of bacteriorhodopsin (bR) solubilized by octyl-beta-glucoside was studied by measuring the denaturation kinetics under visible light irradiation and in the dark. The denaturation of bR solubilized by 50 mM octyl-beta-glucoside was very slow at room temperature when it was left in the dark. However, its spontaneous denaturation was accelerated when the solubilized bR was irradiated by visible light. The denaturation kinetics under visible light irradiation and in the dark could be well described by a single decay constant. The activation energy for the denaturation of bR was estimated from the temperature dependence of decay time constants. The activation energy under visible light irradiation was 12.5 kcal/mol, which was much smaller than the corresponding value in the dark, 26.2 kcal/mol. These results strongly suggest that some of the photointermediate states are less stable than the ground state of bR. The critical temperature and the activation energy for denaturation of bR in the solubilized state were much lower than those in the 2D crystalline state. Comparing the denaturation behavior in the 2D crystalline state and that in the octyl-beta-glucoside-solubilized state, our findings suggest that protein-protein interaction contributes to the stability of this protein.

Spectroscopic analysis of halothane binding to the plasma membrane Ca2+-ATPase

The intrinsic tryptophan (Trp) fluorescence of the plasma membrane Ca2+-ATPase (PMCA) is significantly quenched by halothane, a volatile anesthetic common in clinical practice. It has been proposed that halothane inhibition of the Ca2+-ATPase activity results from conformational changes following anesthetic binding in the enzyme. We have investigated whether the observed quenching reflects halothane binding to PMCA. We have shown that the quenching is dose dependent and saturable and can be fitted to a binding curve with an equilibrium constant K(Hal) = 2.1 mM, a concentration at which the anesthetic approximately half-maximally inhibits the Ca2+-ATPase activity. The relatively low sensitivity of halothane quenching of Trp fluorescence to the concentration of phosphatidylcholine and detergent in the PMCA preparation concurs with the quenching resulting from anesthetic binding in the PMCA molecule. Analysis of the Trp fluorescence quenching by acrylamide indicates that the Trp residues are not considerably exposed to the solvent (Stern-Volmer quenching constant of 2.9 M(-1)) and do not differ significantly in their accessibility to halothane. Other volatile anesthetics, diethyl ether and diisopropyl ether, reduce the quenching caused by halothane in a dose-dependent manner, suggesting halothane displacement from its binding site(s). These observations indicate that halothane quenching of intrinsic Trp fluorescence of PMCA results from anesthetic binding to the protein. The analysis, used as a complementary approach, provides new information to the still rudimentary understanding of the process of anesthetic interaction with membrane proteins.

Protein:protein interactions in the lipid bilayer (review)

At least four different types of interaction between protein transmembrane helices have been described to date. These include the use of charge-pair interactions that can play a positive or negative role in the assembly of multi-subunit complexes such as the T cell receptor, or recruit signal transducing accessory molecules in the case of some Fc receptors. Inter-helix hydrogen bonds have been shown to play an important role in the constitutive activation of certain proto-oncogenes, whereas helix:helix interfaces stabilized solely by van der Waals contacts mediated by non-polar residues also exist. The fourth type of interaction is an inter-chain disulphide linkage which is dependent on a buried charged residue. A role for glycine residues in several of these mechanisms is also suggested. In addition, the use of disulphide mapping to further explore protein:protein interactions within the lipid bilayer is discussed.

A continuum theory for the prediction of lateral and rotational positioning of alpha-helices in membrane proteins: bacteriorhodopsin

We have developed a new method for the prediction of the lateral and the rotational positioning of transmembrane helices, based upon the present status of knowledge about the dominant interaction of the tertiary structure formation. The basic assumption about the interaction is that the interhelix binding is due to the polar interactions and that very short extramembrane loop segments restrict the relative position of the helices. Another assumption is made for the simplification of the prediction that a helix may be regarded as a continuum rod having polar interaction fields around it. The polar interaction field is calculated by a probe helix method, using a copolymer of serine and alanine as probe helices. The lateral position of helices is determined by the strength of the interhelix binding estimated from the polar interaction field together with the length of linking loop segments. The rotational positioning is determined by the polar interaction field, assuming the optimum lateral configuration. The structural change due to the binding of a prosthetic group is calculated, fixing the rotational freedom of a helix that is connected to the prosthetic group. Applying this method to bacteriorhodopsin, the optimum lateral and rotational positioning of transmembrane helices that are very similar to the experimental configuration was obtained. This method was implemented by a software system, which was developed for this work, and automatic calculation became possible for membrane proteins comprised of several transmembrane helices.