D96N Mutant Research Articles

Time-resolved investigation of nanometric cell membrane patches with a mid-infrared laser microscope

The proton pump Bacteriorhodopsin (BR) undergoes repeated photocycles including reversible conformational changes upon visible light illumination. Exploiting the sensitivity of infrared (IR) spectra to the conformation, we have determined the reaction kinetic parameters of the conductive intermediate M for the wild-type protein and for its slow mutant D96N during its photocycle. Time-resolved IR micro-spectroscopy using an in-house developed confocal laser microscope operating in the mid-IR is employed to record absorption changes of 10−4 at wavelengths λ1 = 6.08 μm and λ2 = 6.35 μm, assigned to backbone and retinal structural modifications, respectively. Protein samples were embedded in dried lipid bilayers deposited on ultraflat gold supports to enhance the surface field. The signals were analyzed according to a simplified photocycle model with only two dominant states: the dark-adapted state BR* and the intermediate M. We obtained the excitation and relaxation times of the intermediate M from exponential fits to the absorption change time traces. Our results constitute a first step towards future plasmonic-assisted nanoscale time-resolved mid-IR spectrometers for the characterization of bioelectronic and light-harvesting nanodevices based on BR.

Photoreaction Pathways of Bacteriorhodopsin and Its D96N Mutant as Revealed by in Situ Photoirradiation Solid-State NMR.

Bacteriorhodopsin (BR) functions as a light-driven proton pump that transitions between different states during the photocycle, such as all-trans (AT; BR568) and 13-cis, 15-syn (CS; BR548) state and K, L, M1, M2, N, and O intermediates. In this study, we used in situ photoirradiation 13C solid-state NMR to observe a variety of photo-intermediates and photoreaction pathways in [20-13C]retinal-WT-BR and its mutant [20-13C, 14-13C]retinal-D96N-BR. In WT-BR, the CS state converted to the CS* intermediate under photoirradiation with green light at −20 °C and consequently converted to the AT state in the dark. The AT state converted to the N intermediate under irradiation with green light. In D96N-BR, the CS state was converted to the CS* intermediate at −30 °C and consequently converted to the AT state. Simultaneously, the AT state converted to the M and L intermediates under green light illumination at −30 °C and subsequently converted to the AT state in the dark. The M intermediate was directly excited to the AT state by UV light illumination. We demonstrated that short-lived photo-intermediates could be observed in a stationary state using in situ photoirradiation solid-state NMR spectroscopy for WT-BR and D96N-BR, enabling insight into the light-driven proton pump activity of BR.

Tip-Enhanced Infrared Difference-Nanospectroscopy of the Proton Pump Activity of Bacteriorhodopsin in Single Purple Membrane Patches.

Photosensitive proteins embedded in the cell membrane (about 5 nm thickness) act as photoactivated proton pumps, ion gates, enzymes, or more generally, as initiators of stimuli for the cell activity. They are composed of a protein backbone and a covalently bound cofactor (e.g. the retinal chromophore in bacteriorhodopsin (BR), channelrhodopsin, and other opsins). The light-induced conformational changes of both the cofactor and the protein are at the basis of the physiological functions of photosensitive proteins. Despite the dramatic development of microscopy techniques, investigating conformational changes of proteins at the membrane monolayer level is still a big challenge. Techniques based on atomic force microscopy (AFM) can detect electric currents through protein monolayers and even molecular binding forces in single-protein molecules but not the conformational changes. For the latter, Fourier-transform infrared spectroscopy (FTIR) using difference-spectroscopy mode is typically employed, but it is performed on macroscopic liquid suspensions or thick films containing large amounts of purified photosensitive proteins. In this work, we develop AFM-assisted, tip-enhanced infrared difference-nanospectroscopy to investigate light-induced conformational changes of the bacteriorhodopsin mutant D96N in single submicrometric native purple membrane patches. We obtain a significant improvement compared with the signal-to-noise ratio of standard IR nanospectroscopy techniques by exploiting the field enhancement in the plasmonic nanogap that forms between a gold-coated AFM probe tip and an ultraflat gold surface, as further supported by electromagnetic and thermal simulations. IR difference-spectra in the 1450–1800 cm–1 range are recorded from individual patches as thin as 10 nm, with a diameter of less than 500 nm, well beyond the diffraction limit for FTIR microspectroscopy. We find clear spectroscopic evidence of a branching of the photocycle for BR molecules in direct contact with the gold surfaces, with equal amounts of proteins either following the standard proton-pump photocycle or being trapped in an intermediate state not directly contributing to light-induced proton transport. Our results are particularly relevant for BR-based optoelectronic and energy-harvesting devices, where BR molecular monolayers are put in contact with metal surfaces, and, more generally, for AFM-based IR spectroscopy studies of conformational changes of proteins embedded in intrinsically heterogeneous native cell membranes.

Raman and SERS Spectroscopy of D96N Mutant Bacteriorhodopsin

Effect of silver nanoparticles (AgNPs) on the D96N mutant form of bacteriorhodopsin (BRh-D96N) contained in fragments of purple membranes (PMs) of bacteria Halobacterium salinarum has been analyzed. It has been found that interaction of AgNPs with BRh-D96N in SERS-active spots leads to “freezing” of the protein photocycle. The AgNPs change and then fix the state of BRh-D96N in SERS-active spots. Outside of SERS-active spots, the effect of AgNPs is weaker and is expressed in deceleration of the M-form decay. Thus, the fundamental difference in the influence of AgNPs on the mutant BRh-D96N in comparison with wild-type BRh was found.

Light-controlled spin filtering in bacteriorhodopsin.

The role of the electron spin in chemistry and biology has received much attention recently owing to to the possible electromagnetic field effects on living organisms and the prospect of using molecules in the emerging field of spintronics. Recently the chiral-induced spin selectivity effect was observed by electron transmission through organic molecules. In the present study, we demonstrated the ability to control the spin filtering of electrons by light transmitted through purple membranes containing bacteriorhodopsin (bR) and its D96N mutant. The spin-dependent electrochemical cyclic voltammetry (CV) and chronoamperometric measurements were performed with the membranes deposited on nickel substrates. High spin-dependent electron transmission through the membranes was observed; however, after the samples were illuminated by 532 nm light, the spin filtering in the D96N mutant was dramatically reduced whereas the light did not have any effect on the wild-type bR. Beyond demonstrating spin-dependent electron transmission, this work also provides an interesting insight into the relationship between the structure of proteins and spin filtering by conducting electrons.

Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer

The complex of sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII) mediates negative phototaxis in halobacteria Natronomonas pharaonis. Upon light activation NpSRII triggers, by means of NpHtrII, a signal transduction chain homologous to the two component system in eubacterial chemotaxis. Here we report on the crystal structure of the ground state of the mutant NpSRII-D75N/NpHtrII complex in the space group I212121. Mutations of this aspartic acid in light-driven proton pumps dramatically modify or/and inhibit protein functions. However, in vivo studies show that the similar D75N mutation retains functionality of the NpSRII/NpHtrII complex. The structure provides the molecular basis for the explanation of the unexpected observation that the wild and the mutant complexes display identical physiological response on light excitation.

2P242 In-situ光照射固体NMRによるバクテリオロドプシンD96N変異体の光中間体の捕捉とタンパク質構造変化の解明(18A.光生物:視覚・光受容,ポスター,日本生物物理学会年会第51回(2013年度))

2P242 In-situ光照射固体NMRによるバクテリオロドプシンD96N変異体の光中間体の捕捉とタンパク質構造変化の解明(18A.光生物:視覚・光受容,ポスター,日本生物物理学会年会第51回(2013年度))

The Signal Transfer from the Receptor NpSRII to the Transducer NpHtrII Is Not Hampered by the D75N Mutation

Sensory rhodopsin II ( NpSRII) is a phototaxis receptor of Natronomonas pharaonis that performs its function in complex with its cognate transducer ( NpHtrII). Upon light activation NpSRII triggers by means of NpHtrII a signal transduction chain homologous to the two component system in eubacterial chemotaxis. The D75N mutant of NpSRII, which lacks the blue-shifted M intermediate and therefore exhibits a significantly faster photocycle compared to the wild-type, mediates normal phototaxis responses demonstrating that deprotonation of the Schiff base is not a prerequisite for transducer activation. Using site-directed spin labeling and time resolved electron paramagnetic-resonance spectroscopy, we show that the mechanism revealed for activation of the wild-type complex, namely an outward tilt motion of the cytoplasmic part of the receptor helix F and a concomitant rotation of the transmembrane transducer helix TM2, is also valid for the D75N variant. Apparently, the D75N mutation shifts the ground state conformation of NpSRII-D75N and its cognate transducer into the direction of the signaling state.

Characteristic noise features in light transmission across membrane protein undergoing photocycle

We demonstrate a technique based on noise measurements which can be utilized to study dynamical processes in protein assembly. Direct visualization of dynamics in membrane protein system such as bacteriorhodopsin (bR) upon photostimulation are quite challenging. bR represents a model system where the stimulus-triggered structural dynamics and biological functions are directly correlated. Our method utilizes a pump-probe near field microscopy method in the transmission mode and involves analyzing the transmittance fluctuations from a finite size of molecular assembly. Probability density distributions indicating the effects of finite size and statistical correlations appear as a characteristic frequency distribution in the noise spectra of bR whose origin can be traced to photocycle kinetics. Valuable insight into the molecular processes were obtained from the noise studies of bR and its mutant D96N as a function of external parameters such as temperature, humidity or presence of an additional pump source.

Optical and electric signals from dried oriented purple membrane of bacteriorhodopsins

All the intermediates of the bacteriorhodopsin photocycle are excitable with light of suitable wavelength. This property might regulate the activity in the cells when they are exposed in the nature to high light intensity. On the other hand this property is involved in many applications. In this study the ground state and M intermediate of dried oriented samples of wild-type bacteriorhodopsin and its mutant D96N were excited with 406 nm laser flashes. Substantial M populations were generated with quasi-continuous illumination. The decay of the absorption of M intermediate had three components: their lifetimes were very different for laser flash and quasi-continuous illuminations in cases of both bacteriorhodopsin species. The optical answer for the excitation of M intermediate had a lifetime of 2.2 ms. Electric signals for M excitation had large fast negative components and small positive components in the 100 μs time domain. The results are expected to have important implications for bioelectronic applications of bacteriorhodopsin.

Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide

The early steps in the photocycle of sensory rhodopsin II mutant D75N are investigated in a comprehensive study using femtosecond visible pump/probe spectroscopy. An overall slower response dynamics after photoexcitation is observed compared to wild-type sensory rhodopsin II, which is assigned to changed electrostatics and an altered hydrogen-bonding network within the retinal binding pocket. Furthermore, the influence of azide on the primary reaction is analyzed. The addition of azide accelerates the sub-10 ps dynamics of the D75N mutant nearly to reaction rates found in wild-type. Moreover, a further reaction pathway becomes observable in the investigated time range, which is assigned to a previously described K(1) to K(2) transition. The specific acceleration of the early steps seems to be a unique feature of the D75N mutant as similar azide effects do not emerge in analogous azide measurements of wild-type sensory rhodopsin II, bacteriorhodopsin, and the bacteriorhodopsin mutant D85N.

Excitation of the M intermediates of wild-type bacteriorhodopsin and mutant D96N: temperature dependence of absorbance, electric responses and proton movements

The simplest proton pump known in biological systems, bacteriorhodopsin (bR), is the first ion-transporting membrane protein, the function of which can be described at the atomic level, with the aid of molecular dynamics calculations. To get additional experimental support for the proposed atomic level description of the function of bR, we studied a quasi-stable state of the protein molecule, the so-called M intermediate that plays a crucial role in the proton pumping process. The temperature dependence of the light-induced events occurring in the photocycle of wild-type bacteriorhodopsin and its mutant D96N were followed in detail. Absorbance changes, electric signals generated by charge motion inside the protein, and movement of protons in the protein solution interface either forward (proton release due to excitation of bR) or backward (uptake of protons due to the M excitation: “back-take”) were monitored. The obtained Arrhenius parameters indicate that the proton back-take is triggered by charge rearrangements in the protein similar to the proton release triggered by those during the L → M transition. The time necessary for proton back-take determines the reconstitution time of the bR ground state. The data are expected to be used in theoretical modeling of the bR function. Based on these results, a more detailed photocycle model is established to describe the proton pumping mechanism, implying a formal principle ("domino model") that is expected to hold also for other charge transfer proteins.

Suppressed or recovered intensities analysis in site-directed 13C NMR: Assessment of low-frequency fluctuations in bacteriorhodopsin and D85N mutants revisited

The first proton transfer of bacteriorhodopsin (bR) occurs from the protonated Schiff base to the anionic Asp 85 at the central part of the protein in the L to M states. Low-frequency dynamics accompanied by this process can be revealed by suppressed or recovered intensities (SRI) analysis of site-directed 13C solid-state NMR spectra of 2D crystalline preparations. First of all, we examined a relationship of fluctuation frequencies available from [1- 13C]Val- and [3- 13C]Ala-labeled preparations, by taking the effective correlation time of internal methyl rotations into account. We analyzed the SRI data of [1- 13C]Val-labeled wild-type bR and D85N mutants, as a function of temperature and pH, respectively, based on so-far assigned peaks including newly assigned or revised ones. Global conformational change of the protein backbone, caused by neutralization of the anionic D85 by D85N, can be visualized by characteristic displacement of peaks due to the conformation-dependent 13C chemical shifts. Concomitant dynamics changes if any, with fluctuation frequencies in the order of 10 4 Hz, were evaluated by the decreased peak intensities in the B–C and D–E loops of D85N mutant. The resulting fluctuation frequencies, owing to subsequent, accelerated dynamics changes in the M-like state by deprotonation of the Schiff base at alkaline pH, were successfully evaluated based on the SRI plots as a function of pH, which were varied depending upon the extent of interference of induced fluctuation frequency with frequency of magic angle spinning or escape from such interference. Distinguishing fluctuation frequencies between the higher and lower than 10 4 Hz is now possible, instead of a simple description of the data around 10 4 Hz available from one-point data analysis previously reported.

Efficient Approach to Determine the pKa of the Proton Release Complex in the Photocycle of Retinal Proteins

This work utilizes a photoelectrochemical approach to study the pH dependence of proton release and uptake in the photocycles of two retinal proteins, bacteriorhodopsin (BR) and archaerhodopsin 4 (AR4). By detecting photoinduced potentials that originate from the proton concentration changes (DeltaH(+)) generated by proteins near the indium tin oxide (ITO) electrode, we show that the kinetics of release and uptake can be followed in a broad pH range, and the pK(a) of the proton release complex (PRC) can be easily determined under different conditions. Nonoriented protein films were deposited on the electrode, and photovoltage in an electrochemical cell was detected after illumination with a green flash. The kinetics of proton release and uptake could be measured as light-induced decreases and increases of the photopotential. A kinetic analysis was performed, and a formula describing proton fluxes of wild-type BR and AR4 and D96N mutant of BR was derived. Three componentsfast proton release, slow proton release, and proton uptakewere found in the wild-type retinal proteins; two components, fast and slow proton releases, were found in the D96N mutant. The pH dependence of the fraction of fast release over the whole release was used to determine the pK(a) for proton release in the photocycles of these retinal proteins. Measurements were also performed in conventional buffer solutions and crown ether. The presence of buffer in 10-50 mM concentration did not abolish the light-induced signals, indicating that the electrode response is much less sensitive to buffers than pH-sensitive dyes in a suspension due to a higher protein/buffer ratio near the electrode. This feature enables us to study effects of chemicals with high buffer capacity, and significant effects of buffers and crown ether on proton pumping behaviors of retinal proteins were revealed. In comparison with the classic pH-sensitive dye approach, the photoelectrochemical approach is convenient and efficient for measurements of transient proton concentration changes (DeltaH(+)) generated by a proton pump and thus might be utilized as a powerful tool for the investigation of light-driven proton pumping mechanisms in a wide pH range.

Switch from conventional to distributed kinetics in the bacteriorhodopsin photocycle.

Below 195 K, the bacteriorhodopsin photocycle could not be adequately described with exponential kinetics [Dioumaev, A. K., and Lanyi, J. K. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 9621-9626] but required distributed kinetics, previously found in hemoglobin and myoglobin at temperatures below the vitrification point of the surrounding solvent. The aim of this study is to determine which factors cause the switch from this low-temperature regime to the conventional kinetics observed at ambient temperature. The photocycle was monitored by time-resolved FTIR between 180 and 280 K, using the D96N mutant. Depending on the temperature, decay and temporal redistribution of two or three intermediates (L, M, and N) were observed. Above approximately 245 K, an abrupt change in the kinetic behavior of the photocycle takes place. It does not affect the intermediates present but greatly accelerates their decay. Below approximately 240 K, a kinetic pattern with partial decay that cannot be explained by conventional kinetics, but suggesting distributed kinetics, was dominant, while above approximately 250 K, there were no significant deviations from exponential behavior. The approximately 245 K critical point is >/=10 K below the freezing point of interbilayer water, and we were unable to correlate it with any FTIR-detectable transition of the lipids. Therefore, we attribute the change from distributed to conventional kinetics to a thermodynamic phase transition in the protein. Most probably, it is related to the freezing and thawing of internal fluctuations of the protein, known as the dynamic phase transition, although in bacteriorhodopsin the latter is usually believed to take place at least 15 K below the observed critical temperature of approximately 245 K.

Dynamics Change of Phoborhodopsin and Transducer by Activation: Study Using D75N Mutant of the Receptor by Site‐directed Solid‐state 13C NMR†

Pharaonis phoborhodopsin (ppR or sensory rhodopsin II) is a negative phototaxis receptor of Natronomonas pharaonis, and forms a complex, which transmits the photosignal into cytoplasm, with its cognate transducer (pHtrII). We examined a possible local dynamics change of ppR and its D75N mutant complexed with pHtrII, using solid-state (13)C NMR of [3-(13)C]Ala- and [1-(13)C]Val-labeled preparations. We distinguished Ala C(beta) (13)C signals of relatively static stem (Ala221) in the C-terminus of the receptors from those of flexible tip (Ala228, 234, 236 and 238), utilizing a mutant with truncated C-terminus. The local fluctuation frequency at the C-terminal tip was appreciably decreased when ppR was bound to pHtrII, while it was increased when D75N, that mimics the signaling state because of disrupted salt bridge between C and G helices prerequisite for the signal transfer, was bound to pHtrII. This signal change may be considered with the larger dissociation constant of the complex between pHtrII and M-state of ppR. At the same time, it turned out that fluctuation frequency of cytoplasmic portion of pHtrII is lowered when ppR is replaced by D75N in the complex with pHtrII. This means that the C-terminal tip partly participates in binding with the linker region of pHtrII in the dark, but this portion might be released at the signaling state leading to mutual association of the two transducers in the cytoplasmic regions within the ppR/pHtrII complex.

Photochromic polymer films based on a 14-F bacteriorhodopsin derivative

Spectral and kinetic characteristics were measured for polymer (gelatin) films based on 14-F bacteriorhodopsin (BR), both wild-type (WT) and D96N mutant, to study the peculiarities of photo-induced transformation of the samples. It was demonstrated earlier that incorporation of 14-F retinal into the apomembrane of both 14-F WT and 14-F D96N produces pigments with drastically different photo-induced behavior, regarding the formation and decay of a red-shifted species at 660 nm. However, similar fundamental differences between 14-F WT and 14-F D96N, if embedded into gelatin matrix, were not observed. Results are discussed in the frame of the relationship between the kinetic rates of two photo-induced processes that occur in suspensions and gelatin films of corresponding pigments. These experimental results can possibly be explained by the difference in kinetics for gelatin films and water suspensions. The main factor in altering the kinetics is the relative humidity of gelatin samples. Therefore, the effect of relative humidity on performance of 14-F BR gelatin films, both WT and D96N, was studied. A range of humidity has been defined for each pigment, in which spectral and kinetic characteristics were changed in the desired direction. It was shown that 14-F WT gelatin films may offer a technological advantage relative to those based on 14-F D96N.

1P-254 D85N変異体を用いて解析したバクテリオロドプシンのシッフ塩基部位の水素結合構造(光生物・視覚,光受容(1),第46回日本生物物理学会年会)

1P-254 D85N変異体を用いて解析したバクテリオロドプシンのシッフ塩基部位の水素結合構造(光生物・視覚,光受容(1),第46回日本生物物理学会年会)

Laser-Induced Transient Grating Analysis of Dynamics of Interaction between Sensory Rhodopsin II D75N and the HtrII Transducer

The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (ΔHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates ( K 1– K 4) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the ΔHtrII portion was found to cause a ΔHtrII-dependent increase in volume rising in 8 μs in the K 4 state and a drastic decrease in the diffusion coefficient ( D) of K 4 relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of ΔHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.

Determinants for Dephosphorylation of the RNA Polymerase II C-Terminal Domain by Scp1

Phosphorylation and dephosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) represent a critical regulatory checkpoint for transcription. Transcription initiation requires Fcp1/Scp1-mediated dephosphorylation of phospho-CTD. Fcp1 and Scp1 belong to a family of Mg2+ -dependent phosphoserine (P.Ser)/phosphothreonine (P.Thr)-specific phosphatases. We recently showed that Scp1 is an evolutionarily conserved regulator of neuronal gene silencing. Here, we present the X-ray crystal structures of a dominant-negative form of human Scp1 (D96N mutant) bound to mono- and diphosphorylated peptides encompassing the CTD heptad repeat (Y1S2P3T4S5P6S7). Moreover, kinetic and thermodynamic analyses of Scp1-phospho-CTD peptide complexes support the structures determined. This combined structure-function analysis discloses the residues in Scp1 involved in CTD binding and its preferential dephosphorylation of P.Ser5 of the CTD heptad repeat. Moreover, these results provide a template for the design of specific inhibitors of Scp1 for the study of neuronal stem cell development.