Uniaxial Symmetry Breaking in Bacteriorhodopsin at the Thermal Phase Transition of Lipids of Purple Membranes.

The article correlates between symmetry breaking and phase transition. An analogy, extending from physics to biology, is known to exist between these two topics. Bacteriorhodopsin (bR) as a paradigm of membrane proteins has been used as a case study in the present work. The bR, as the sole protein embedded in what is called a purple membrane (PM), has attracted widespread interest in bionanotechnological applications. The lipids of PM have a crucial role in maintaining the crystal lattice of bR inside PM. For this reason, the present work has been concerned with elucidating the thermal phase transition properties of the PM lipids in orthogonal directions. The results indicated that the axial symmetry of bR exhibits considerable changes occurring at the thermal phase transition of lipids. These changes are brought by an anomaly observed in the time course of orthogonal electric responses during the application of thermal fields on PM. The observed anomaly may bear on symmetry breaking in bR occurring at the phase transition of lipids based on such analogy found between symmetry breaking and phase transition. Lipid-protein interactions may underlie the broken axial symmetry of bR at such lipid thermal transition of PM. Accordingly, thermally perturbed axial symmetry of bR may be of biological relevance relying on the essence of the crystal lattice of bR. Most importantly, a question has to be raised in the present study: Can bR, as a helical protein with broken axial symmetry, affect the symmetry breaking of helical light? This may be of potential technical applications based on a recent discovery that bR breaks the symmetry of helical light.

Detection of bacteriorhodopsin trimeric rotation at thermal phase transitions of purple membrane in suspension.

Bacteriorhodopsin (bR) of purple membrane (PM) is a retinal protein that forms aggregates in the form of trimers constituting, together with archaeal lipids, the crystalline structure of PM. The rotary motion of bR inside PM may be pertinent in understanding the essence of the crystalline lattice. An attempt has been made to determine the rotation of bR trimers which has been found to be detected solely at thermal phase transitions of PM, namely lipid, crystalline lattice and protein melting phase transitions. The temperature dependences of dielectric versus electronic absorption spectra of bR have been determined. The results suggest that the rotation of bR trimers, together with concomitant bending of PM, are most likely brought by structural changes in bR which might be driven by retinal isomerization and mediated by lipid. The rupturing of the lipid-protein contact might consequently lead to rotation of trimers associated with bending, curling or vesicle formation of PM. So the retinal reorientation may underlie the concomitant rotation of trimers. Most importantly, rotation of trimers might play a role, in terms of the essence of the crystalline lattice, in the functional activity of bR and may serve physiological relevance.

Exploring isotropic tendency for the blue membrane containing wild-type bacteriorhodopsin.

Bacteriorhodopsin of purple membrane has wide potential applications in bioelectronics and biophotonic nanodevices. Upon acidification, it turns blue and upon further acidification by HCl, it retains its purple color. The acid-induced structural changes might be correlated to its crystalline structure, which might be mediated by lipids of purple membrane. Therefore, the present study aims at revealing the acidic pH dependence of anisotropic properties of bacteriorhodopsin. The electric impedance has been measured for parallel- and perpendicular-oriented purple membrane, in addition to the randomly-oriented one in the acidic pH range. The results have showed that the electric anisotropy is proportional to the color transitions occurred at low pH with consistent pKa values. It has found that the bacteriorhodopsin, upon turning into blue form, tends to be isotropic within narrow pH region around 2.55, whereas it preserves its anisotropy in its purple form. It is noteworthy that several mutants of bacteriorhodopsin that resemble its blue form became attractive in technical applications such as real-time holographic interferometry and optical data storage. Accordingly, such isotropic tendency might implicate bacteriorhodopsin for further potential technical applications.

Action spectrum for reorientations in bacteriorhodopsin of purple membrane in suspension.

In the present study, the dependency of purple membrane (PM) dielectric responses on the wavelength of light in the range 380-750 nm has showed meaningful changes about the rotation of PM in suspension and about the rotation of bacteriorhodopsin (bR) trimer inside PM, as well. The action spectrum of PM random walk substantiates the existence of two states of bR. One of them (blue edge-state) lies at the blue edge and the other (red edge-state) at the red edge of the visible absorption of bR. The results might bear on correlation of these bands to some bR photocycle intermediates or bR photoproducts. The results implicate the protein-chromophore interactions that eventually underlie protein-lipid interactions. Disrupting the protein-lipid contact during the illumination with light of wavelength in ranges of (410-470 nm) and (610-720 nm) has resulted in emergence of distinct dielectric dispersion at 0.06-0.08 MHz which is comparable to the size of bR trimer or monomer.The work reports on the chromatic adaptation of bR in view of the dielectric spectral parameters of PM. It aimed to explore a correlation seemingly found between the light wavelength and the relaxations of bR trimer inside PM. Changes in rotational diffusion of bR trimer upon blue and red light illumination can influence the three dimensional data storage based on bR, which may implicate bR in bioelectronics.

Nonlinear electric response of the diffuse double layer to an abrupt charge displacement inside a biological membrane.

In order to elucidate the old, still unsolved problem of how the diffuse electric double layer responds to an abrupt, intramolecular charge displacement inside a biological membrane, we investigated the fastest components of the light-induced electric signals of bacteriorhodopsin and its mutants, in numerous ionic and buffer solutions. The obtained data for temperature and solute concentration dependence were interpreted as a consequence of changes in the capacity of the diffuse double layer surrounding the purple membrane. The possible physiological consequences of this so far not demonstrated phenomenon are discussed.

Molecular docking investigation of the binding interactions of macrocyclic inhibitors with HCV NS3 protease and its mutants (R155K, D168A and A156V).

Hepatitis C Virus (HCV) non-structural protein 3 (NS3) protease drug resistance poses serious challenges on the design of an effective treatment. Substrate Envelope Hypothesis, "the substrates of HCV NS3/4A protease have a consensus volume inside the active site called substrate envelope" is used to design potent and specific drugs to overcome this problem. Using molecular docking, we studied the binding interaction of the different inhibitors and protein and evaluated the effect of three different mutations (R155K, D168A and A156V) on the binding of inhibitors. P2-P4 macrocycles of 5A/5B and modified 5A/5B hexapeptide sequences have the best scores against the wild-type protein -204.506 and -206.823 kcal/mole, respectively. Also, charged P2-P4 macrocycles of 3/4A and 4A/4B hexapeptide sequences have low scores with the wild-type protein -200.467 and -203.186 kcal/mole, respectively. R155K mutation greatly affects the conformation of the compounds inside the active site. It inverts its orientations, and this is because the large and free side chain of K155 which restricts the conformation of the large P2-P4 macrocycle. The conformation of charged P2-P4 macrocycle of 3/4A hexapeptide sequence in wild-type, A156V and D168A proteins is nearly equal; while that of charged P2-P4 macrocycle of 4A/4B hexapeptide sequence is different. Nevertheless, these compounds have a slight increase of Van der Waals volume compared to that of substrates, they are potent against mutations and have good scores. Therefore, the suggested drugs can be used as an effective treatment solving HCV NS3/4A protease drug resistance problem.

QSAR analysis and molecular docking simulation of suggested peptidomimetic NS3 protease inhibitors.

Based on the N-terminal hexapeptide product of hydrolysis (EDVVCC) at HCV NS5A/5B junction, three modified groups of compounds are built. The first group contains linear peptides while the second and third groups contain P1-P3 and P2-P4 macrocyclic structures, respectively. Quantitative Structure Activity Relationship (QSAR) characterization and docking simulations are performed in order to investigate the potential of these compounds as HCV NS3/4A protease inhibitors. Based on the QSAR properties, the three most stable compounds due to their lowest total energy are P1-P3 and P2-P4 macrocycles of azahexapeptide sequence (DDIVP vinyl amino cyclopropane) and P2-P4 macrocycle of azahexapeptide sequence (DDIVP norvaline). They also have high surface area, solvent accessible surface area, volume, molar refractivity and polarizabilty. They have moderately low dipole moment and good log P values, as well. The docking scores of the best two P2-P4 macrocycles are just acceptable. The two compounds 5A/5B hexapeptide sequence (DDIVP vinyl amino cyclopropane) and P2-P4 macrocycle of azapentapeptide sequence (DIVP vinyl amino cyclopropane) yielded the best docking scores.

Heterogeneity based on bending of purple membrane containing bacteriorhodopsin.

The first and second derivatives of dielectric spectra have evidenced the existence of two interacting states of purple membrane (PM) that respond differently to the intensity of illuminating light providing, this way, underlying consequences to the heterogeneous behavior of bacteriorhodopsin (bR). It is of particular interest to note that the rotational diffusion coefficient of PM has exhibited non-linearity versus light intensity. The explored non-linearity in electrical properties beers, thereby, on changes in PM size. The non-linear variations in PM bending might initiate, in consequence, variations in the dipole moment (permanent and induced) and dc-conductivity of PM patches. Proposal based on PM bending has been introduced to correlate the light intensity effect to the PM lipid environment. Modulation of the global structure of PM and, in turn, its electrical properties by an external perturbation (e.g., light) could be of interest in biotechnological applications based on optoelectronic properties of bR.

Light adaptation of bacteriorhodopsin correlates with dielectric spectral kinetics in purple membrane.

The retinal protein, bacteriorhodopsin (bR), has several potential bioelectronic applications and it is considered as a model for G-protein coupled receptors. Its electrical parameters, therefore, deserve particular attention. Such parameters could be determined by virtue of studying its dielectric spectrum in the low frequency range (20 Hz-1 MHz). The kinetics of dark-light adaptation of bR is reported in terms of electrical parameters of the purple membrane (PM) containing bR. The data have exhibited sudden pronounced increase in the ac-conductivity, upon illuminating the dark-adapted bR (DA-bR), which may be considered in further implications of bR for biotechnological applications. These changes turned out to be composed of, at least, two growing exponential components: one relatively fast followed by slower one. Their lifetime ratio exhibited decreases with increasing the frequency; meanwhile, their amplitude ratio displayed very exciting behavior at significant frequencies. This may correlate the kinetics of light adaptation to relaxations in PM. Moreover, the light adaptation has been observed to cause initial fast and large decreases in dc-conductivity with subsequent slower and smaller decreases. Changing the conductivity during the time of light adaptation reflects changes in the surface charge of the PM. The lifetimes of these events, therefore, help follow the kinetics of the pathway of conformational changes that might be occurring during light adaptation. The dipole moment (permanent and induced) of PM, in addition to, its size showed one exponential growth of comparable lifetime (approximately 7 min) during the light adaptation. The variation in PM size from dark to light state should be in keeping with that diffusion may influence the three-dimensional data storage in data processing based on bR.

Effect of beta-particles on the retinal chromophore in bacteriorhodopsin of Halobacterium salinarium.

Bacteriorhodopsin (bR) is an attractive intelligent material. Understanding the mechanism of its light-driven proton pumping outward the cell implicates it in many technical applications, particularly, in what is called optical computers, and the biotechnology is waiting for this promised biological molecule. An ionizing radiation source handling could be computerized in radiation fields. The computer containing such biological material will not be out of reach of the fields of ionizing radiation. So it is interesting to report on the working of such biological computer if it is subjected to ionizing radiation. The functional unit in this molecule is retinal chromophore. In the present work, it is interested to assess the functionality of bR through determining the electronic transition dipole moment of its chromophore. Significant changes in the values of the absorption transition dipole moment were noticed at different doses of beta-particles in the range of 0.1-0.3 kGy. Ionizing radiation-induced changes in bR were followed by intrinsic fluorescence spectroscopy. An analysis of the fluorescence data bears on the tertiary structure of bR. The emission spectrum is, however, red shifted with an increase in intensity with the different doses; in the meanwhile, gradual decrease in the visible absorbance has occurred till almost complete loss is attained. This bleaching due to ionizing radiation may offer an alternative way of data processing in such optical devices based on bR. Nevertheless, bR has proofed to be used as a biological indicator of ionizing radiation. However, the potential of bR for use as a biosensor to detect ionizing radiation should be considered.

Changes in the retinal transition dipole moment in bacteriorhodopsin of the purple membrane of Halobacterium Salinarium at the so-called PH(rev).

The chromophore transition dipole moment of light-adapted wild-type bacteriorhodopsin (WT-bR) in suspension is evaluated for pH range of 2.8-12. Significant variations in the transition dipole moment are observed at the so-called pH(rev). The results have reported a value of 11 and 8.5 Debye for chromophore transition dipole moment of the neutral purple and acid blue form of bacteriorhodopsin, respectively. There may be a correlation with the process of reversing the direction of the permanent electric dipole moment, due to the reversal of the surface charge asymmetry, of the purple membrane to its opposite side at that pH(rev).