Early Picosecond Events in the Photocycle of Bacteriorhodopsin

The primary processes of the photochemical cycle of light-adapted bacteriorhodopsin (BR) were studied by various experimental techniques with a time resolution of 5 × 10^-13 s. The following results were obtained. (a) After optical excitation the first excited singlet state S₁ of bacteriorhodopsin is observed via its fluorescence and absorption properties. The population of the excited singlet state decays with a lifetime τ₁ of ~0.7 ps (430 ± 50 fs) (52). (b) With the same time constant the first ground-state intermediate J builds up. Its absorption spectrum is red-shifted relative to the spectrum of BR by ~30 nm. (c) The second photoproduct K, which appears with a time constant of τ₂ = 5 ps shows a red-shift of 20 nm, relative to the peak of BR. Its absorption remains constant for the observation time of 300 ps. (d) Upon suspending bacteriorhodopsin in D₂O and deuterating the retinal Schiff base at its nitrogen (lysine 216), the same photoproducts J and K are observed. The relaxation time constants τ₁ and τ₂ remain unchanged upon deuteration within the experimental accuracy of 20%.     

Charge Motion during the Photocycle of Bacteriorhodopsin

The function of bacteriorhodopsin in Halobacterium salinarum is to pump protons from the internal side of the plasma membrane to the external after light excitation, thereby building up electrochemical energy. This energy is transduced into biological energy forms. This review deals with one of the methods elaborated for recording the charge transfer inside the protein. In this method the current produced in oriented purple membrane containing bacteriorhodopsin is measured. It is shown that this method might be applied not only to correlate charge motion with the photocycle reactions but also for general problems like effect of water, electric field, and different ions and buffers for the functioning of proteins.     

Tuning the Photocycle Kinetics of Bacteriorhodopsin in Lipid Nanodiscs

Monodisperse lipid nanodiscs are particularly suitable for characterizing membrane protein in near-native environment. To study the lipid-composition dependence of photocycle kinetics of bacteriorhodopsin (bR), transient absorption spectroscopy was utilized to monitor the evolution of the photocycle intermediates of bR reconstituted in nanodiscs composed of different ratios of the zwitterionic lipid (DMPC, dimyristoyl phosphatidylcholine; DOPC, dioleoyl phosphatidylcholine) to the negatively charged lipid (DOPG, dioleoyl phosphatidylglycerol; DMPG, dimyristoyl phosphatidylglycerol). The characterization of ion-exchange chromatography showed that the negative surface charge of nanodiscs increased as the content of DOPG or DMPG was increased. The steady-state absorption contours of the light-adapted monomeric bR in nanodiscs composed of different lipid ratios exhibited highly similar absorption features of the retinal moiety at 560 nm, referring to the conservation of the tertiary structure of bR in nanodiscs of different lipid compositions. In addition, transient absorption contours showed that the photocycle kinetics of bR was significantly retarded and the transient populations of intermediates N and O were decreased as the content of DMPG or DOPG was reduced. This observation could be attributed to the negatively charged lipid heads of DMPG and DOPG, exhibiting similar proton relay capability as the native phosphatidylglycerol (PG) analog lipids in the purple membrane. In this work, we not only demonstrated the usefulness of nanodiscs as a membrane-mimicking system, but also showed that the surrounding lipids play a crucial role in altering the biological functions, e.g., the ion translocation kinetics of the transmembrane proteins.     

Structural Changes in the N and N′ States of the Bacteriorhodopsin Photocycle

The bacteriorhodopsin transport cycle includes protonation of the retinal Schiff base by Asp⁹⁶ (M→N reaction) and reprotonation of Asp⁹⁶ from the cytoplasmic surface (N→N′ reaction). We measured distance changes between pairs of spin-labeled structural elements of interest, and in general observed larger overall structural changes in the N state compared with the N′ state. The distance between the C-D loop and E-F interhelical loops in A103R1/M163R1 increased ∼6 Å in the N state and ∼3 Å in the N′ state. The opposite trend of distance changes in V101R1/A168R1 and L100R1/T170R1 supports counterclockwise rotation of helix F in the N but not the N′ state. Small distance increases were observed in S169R1/S226R1, but little change was seen in G106R1/G155R1. Taking earlier published EPR data into account, we suggest that structural changes of the E-F loop occur first, and then helices F and G begin to move together in the late M state. These motions then reach their maximum amplitude in the N state, evidently to facilitate the release of a proton from Asp⁹⁶ and the formation of a proton-conduction pathway from Asp⁹⁶ to the Schiff base. The structural changes reverse their directions and decay in the N′ state.     

Structure Changes upon Deprotonation of the Proton Release Group in the Bacteriorhodopsin Photocycle

In the photocycle of bacteriorhodopsin at pH 7, a proton is ejected to the extracellular medium during the protonation of Asp-85 upon formation of the M intermediate. The group that releases the ejected proton does not become reprotonated until the prephotolysis state is restored from the N and O intermediates. In contrast, at acidic pH, this proton release group remains protonated to the end of the cycle. Time-resolved Fourier transform infrared measurements obtained at pH 5 and 7 were fitted to obtain spectra of kinetic intermediates, from which the spectra of M and N/O versus unphotolyzed state were calculated. Vibrational features that appear in both M and N/O spectra at pH 7, but not at pH 5, are attributable to deprotonation from the proton release group and resulting structural alterations. Our results agree with the earlier conclusion that this group is a protonated internal water cluster, and provide a stronger experimental basis for this assignment. A decrease in local polarity at the N-C bond of the side chain of Lys-216 resulting from deprotonation of this water cluster may be responsible for the increase in the proton affinity of Asp-85 through M and N/O, which is crucial for maintaining the directionality of proton pumping.     

The Photocycle of Bacteriorhodopsin in the Two-Dimensional Orthorombic Crystal Form of Purple Membrane

Laser flash photolysis and low-temperature absorption studies of the photocycle of orthorhombic purple membrane (o-PM) reveal the existence of the same K, L, and M intermediates as found in the native hexagonal purple membrane (h-PM). However, the 0 intermediate is missing in the o-PM. The absorption spectrum of the K intermediate of o-PM is blueshifted by ~15 nm relative to the K intermediate found in the hexagonal purple membrane. The decay relaxation time constants of M in the o-PM are higher by more than an order of magnitude than the corresponding relaxation time constants in the h-PM. Similarly to the h-PM, the decay of M depends on the pulse width of excitation. The time-independent anisotropy factor obtained in photoselection studies of the M intermediate demonstrates the complete immobility of bacteriorhodopsin (bR) within the o-PM matrix. The same anisotropy factor of 0.3 obtained for o-PM and for h-PM suggests that in both crystalline lattices the transition moment of the retinal chromophore has similar angles with the plane of the membrane. The dependence of the decay kinetics of M on its occupancy may suggest the existence of kinetic coupling between neighboring bR molecules.     

Importance of Lipids for Bacteriorhodopsin Structure, Photocycle, and Function

This review begins with a brief history of early studies on the involvement of lipids in certain bacteriorhodopsin (BR) properties. Such properties include the regulation of the pK for the purple to blue transition caused by deionization, and the reformation of trimers from monomers after exposure of the purple membrane to Triton X-100. Most of the review is devoted to newer studies which indicate an important role for the neutral lipid squalene in the functional stability of the fast-decaying M-intermediate, for its decay through a pathway involving the O-intermediate, and for the regulation of the relative amounts of slow-decaying and fast-decaying forms of M. Participation of a peripheral acidic amino acid in the overall expression of fast-decaying M is also discussed. Initial studies suggest that the acidic amino acid may be Asp36 and/or Asp38.     

Influence of the Charge at D85 on the Initial Steps in the Photocycle of Bacteriorhodopsin

Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.     

Infrared Methods for Monitoring the Protonation State of Carboxylic Amino Acids in the Photocycle of Bacteriorhodopsin

This review deals with the role of carboxylic amino acids in the proton-transport activity of bacteriorhodopsin. The main focus is on the infrared data, which allow direct monitoring of the protonation/deprotonation of specific residues during the proton movement in the course of the photocycle. Additional attention is paid to the potential use of carboxylic acids in proteins as internal sensors, based on the sensitivity of their IR frequencies to the immediate environment.     

Photo-sensitized Isomerization of Retinal by Dyes

THE initial reaction following absorption of light in the retina is the isomerization of the 11-cis retinal chromophore of the visual pigment¹. Isolated 11cis retinal will undergo the same isomerization to the all-trans form when excited by light of wavelength shorter than about 450 nm and this reaction can be sensitized to light of longer wavelengths by the addition of trace amounts of iodine to the solution².     

细菌视紫红质光循环中间体M412的动力学初探

采用紫外可见吸收光谱技术和闪光光解技术,初步观察了细菌视紫红质(BR)分子在宽pH范围(2.1～12.3)内的特征吸收峰以及M412的相对浓度和M412的慢成分半衰期的变化,并对其结构和光循环功能进行了讨论.紫外可见吸收光谱实验结果显示:pH=5.0～10.0时,BR最大特征吸收峰值约为568 nm;pH＜5.0时,BR最大特征吸收峰发生红移;pH＞10.0时,BR最大特征吸收峰发生蓝移.闪光动力学光谱结果显示:pH为7.3～9.5时,M412的相对浓度(M0)基本稳定在0.038左右;pH＜7.3时,M0逐渐减小;pH＞9.5时,M0明显上升,在pH=11.8时达到最大值0.1355,随后又快速下降.pH为2.1～7.3时,M412的慢成分半衰期(ts1/2)值在(4.1±1.1)ms左右;pH＞7.3时,ts1/2值急剧延长到40 677.4 ms.推测在高pH条件下,BR分子的光循环有新的路径和机理.     

番茄红素热处理异构化方法研究

番茄红素在受热的情况下会发生反式异构体(all-trans)向顺式异构体(cis-isomers)的转化。本文研究了乙酸乙酯热回流、微波法及超声-微波协同法对番茄红素异构化的影响。结果表明:乙酸乙酯热回流处理后,6%番茄红素油树脂中顺式异构体占比高于90%番茄红素中顺式异构体占比;氮气保护对番茄红素的异构化无明显保护作用;微波对番茄红素异构化有较强的促进作用,处理5 h后顺式占比可以高达54.7%,但超声-微波协同法对番茄红素异构化的影响与微波单独使用时无明显变化。所以微波是较好的番茄红素热处理异构化方法。     

W86F/W86A突变对细菌视紫红质光循环影响的差异性分析

细菌视紫红质(bacteriorhodopsin,bR)是一种光驱受体蛋白,每个活性单元由3个单体组成,每个单体由一分子视蛋白和一分子的视黄醛发色团共价结合而成,其功能为从胞内向胞外定向传输质子,利用形成的质子浓度梯度将光能转化为化学能.光照后视黄醛发色团构型发生all-trans向13-cis转变,蛋白的构象也随之发生了一系列具有稳定中间态的变化并驱动质子的定向传递.为探讨bR视黄醛键合区保守性氨基酸色氨酸86 (Tryptop-han86,w86)对其光循环中间态和质子泵功能的影响,本研究采用定点突变技术将W86突变为侧链大小不同的F86和A86,通过原位紫外-可见光吸收光谱、闪光光解光谱、pH滴定、固体核磁共振等技术手段,探究W86F和W86A突变对bR光循环及质子泵功能影响差异性的分子机制.结果 表明,W86F和W86A突变均造成了bR暗适应状态下视黄醛顺反异构平衡向顺式构型占优的方向移动,且W86F突变可造成反式构型的完全消失.此外,无论是W86F还是W86A突变都造成了蛋白光循环中间态的减弱且衰减延长,以及质子泵功能减弱,但影响机制各有所不同,这可能与这两个突变对视黄醛多烯链上电子云的分布以及周围残基造成的扰动程度不同有关.     

Retinal-Protein Interactions in Halorhodopsin from Natronomonas pharaonis: Binding and Retinal Thermal Isomerization Catalysis

Halorhodopsin from Natronomonas pharaonis (NpHR) is a member of the retinal protein group and serves as a light-driven chloride pump in which chloride ions are transported through the membrane following light absorption by the retinal chromophore. In this study, we examined two main issues: (1) factors controlling the binding of the retinal chromophore to the NpHR opsin and (2) the ability of the NpHR opsin to catalyze the thermal isomerization of retinal isomers. We have revealed that the reconstitution process of pharaonis HR (NpHR) pigment from its apoprotein and all-trans retinal depends on the pH, and the process has a pK_a of 5.8 ± 0.1. It was proposed that this pK_a is associated with the pK_a of the lysine residue that binds the retinal chromophore (Lys256). The pigment formation is regulated by the concentration of sodium chloride, and the maximum yield was observed at 3.7 M NaCl. The low yield of pigment in a lower concentration of NaCl (< 3 M) may be due to an altered conformation adopted by the apomembrane, which is not capable of forming the pigment. Unexpectedly and unlike the apomembrane of bacteriorhodopsin, NpHR opsin produces pigments with 11-cis retinal and 9-cis retinal owing to the thermal isomerization of these retinal isomers to all-trans retinal. The isomerization rate depends on the pH, and it is faster at a higher pH. The pK_a value of the isomerization process is similar to the pK_a of the binding process of these retinals, which suggests that Lys256 is also involved in the isomerization process. The isomerization is independent of the sodium chloride concentration. However, in the absence of sodium chloride, the apoprotein adopts such a conformation, which does not prevent the isomerization of retinal, but it prevents a covalent bond formation with the lysine residue. The rate and the thermodynamic parameter analysis of the retinal isomerization by NpHR apoprotein led to the conclusion that the apomembrane catalyzes the isomerization via a triplet mechanism.     

M145F/F146M突变对光受体蛋白细菌视紫红质和古紫质4光循环的影响 *

古紫质4(archaerhodopsin 4,aR4)与细菌视紫质(bacteriorhodopsin,bR)同属于盐杆菌科,同源性59%,均为光驱质子泵。其功能是在光照条件下将质子由胞内泵到胞外形成跨膜质子梯度,该梯度差被膜上另外一种蛋白ATP合成酶用于ATP的合成,从而完成光能向生物能的转化。aR4和bR具有相似的光循环过程,但质子传递时序不同,aR4是先从胞内吸收质子再将质子释放到胞外,而bR恰好相反。甲硫氨酸-145是位于bR视黄醛发色团键合区的一个重要残基,对其光循环有着重要的影响,而在aR4中处在相应位置上的苯丙氨酸-146是其视黄醛键合区与bR唯一不相同的残基。因此通过定点突变,采用紫外可见吸收光谱、动力学光谱、质子泵功能检测、低温透射红外光谱等手段对比分析研究M145F和F146M单点突变对bR和aR4光循环造成的影响,有助于深入理解aR4结构与功能的关系。研究结果表明,M145F突变造成了bR光循环L的丢失和质子泵功能的减弱,而F146M突变并未对aR4的光循环造成显著影响,且突变后aR4质子释放时序没有反转,表明该位置上的残基在两个体系中的作用不尽相同。     

细菌视紫红质光循环中间体M412的动力学初探

采用紫外可见吸收光谱技术和闪光光解技术,初步观察了细菌视紫红质(BR)分子在宽pH范围（2.1～12.3）内的特征吸收峰以及M₄₁₂的相对浓度和M₄₁₂的慢成分半衰期的变化,并对其结构和光循环功能进行了讨论.紫外可见吸收光谱实验结果显示：pH=5.0～10.0时,BR最大特征吸收峰值约为568 nm;pH＜5.0时,BR最大特征吸收峰发生红移;pH＞10.0时,BR最大特征吸收峰发生蓝移.闪光动力学光谱结果显示：pH为7.3～9.5时,M₄₁₂的相对浓度(M₀)基本稳定在0.038左右;pH＜7.3时,M₀逐渐减小;pH＞9.5时,M₀明显上升,在pH=11.8时达到最大值0.1355,随后又快速下降.pH为2.1～7.3时,M₄₁₂的慢成分半衰期(t^s_1/2)值在(4.1±1.1)ms左右;pH＞7.3时,t^s_1/2值急剧延长到40 677.4 ms.推测在高pH条件下,BR分子的光循环有新的路径和机理.     

Prohibitin as the Molecular Binding Switch in the Retinal Pigment Epithelium

Previously, our molecular binding study showed that prohibitin interacts with phospholipids, including phosphatidylinositide and cardiolipin. Under stress conditions, prohibitin interacts with cardiolipin as a retrograde response to activate mitochondrial proliferation. The lipid-binding switch mechanism of prohibitin with phosphatidylinositol-3,4,5-triphosphate and cardiolipin may suggest the role of prohibitin effects on energy metabolism and age-related diseases. The current study examined the region-specific expressions of prohibitin with respect to the retina and retinal pigment epithelium (RPE) in age-related macular degeneration (AMD). A detailed understanding of prohibitin binding with lipids, nucleotides, and proteins shown in the current study may suggest how molecular interactions control apoptosis and how we can intervene against the apoptotic pathway in AMD. Our data imply that decreased prohibitin in the peripheral RPE is a significant step leading to mitochondrial dysfunction that may promote AMD progression.     

Substituents at the C13 Position of Retinal and Their Influence on the Function of Bacteriorhodopsin

Retinal analogues in which the 13-methyl group is replaced by H, C₂H₅, CF₃, and OCH₃ residues are studied by means of quantumchemical modified neglect of diatomic overlap-correlated version (MNDOC) calculations. The analogues are suitable to test the stereochemical mechanism of proton pumping in bacteriorhodopsin. The results explain the proton-pumping activities of bacterio-opsin reconstituted with these analogues and elucidate the decisive role of retinal's ground-state intramolecular properties in the pump cycle of bacteriorhodopsin.     

Factors That Differentiate the H-bond Strengths of Water Near the Schiff Bases in Bacteriorhodopsin and Anabaena Sensory Rhodopsin

Bacteriorhodopsin (BR) functions as a light-driven proton pump, whereas Anabaena sensory rhodopsin (ASR) is believed to function as a photosensor despite the high similarity in their protein sequences. In Fourier transform infrared (FTIR) spectroscopic studies, the lowest O-D stretch for D₂O was observed at ∼2200 cm⁻¹ in BR but was significantly higher in ASR (>2500 cm⁻¹), which was previously attributed to a water molecule near the Schiff base (W402) that is H-bonded to Asp-85 in BR and Asp-75 in ASR. We investigated the factors that differentiate the lowest O-D stretches of W402 in BR and ASR. Quantum mechanical/molecular mechanical calculations reproduced the H-bond geometries of the crystal structures, and the calculated O-D stretching frequencies were corroborated by the FTIR band assignments. The potential energy profiles indicate that the smaller O-D stretching frequency in BR originates from the significantly higher pK_a(Asp-85) in BR relative to the pK_a(Asp-75) in ASR, which were calculated to be 1.5 and −5.1, respectively. The difference is mostly due to the influences of Ala-53, Arg-82, Glu-194–Glu-204, and Asp-212 on pK_a(Asp-85) in BR and the corresponding residues Ser-47, Arg-72, Ser-188-Asp-198, and Pro-206 on pK_a(Asp-75) in ASR. Because these residues participate in proton transfer pathways in BR but not in ASR, the presence of a strongly H-bonded water molecule near the Schiff base ultimately results from the proton-pumping activity in BR.     

Regeneration of Bacteriorhodopsin from Thermally Unfolded Bacterio-Opsin and All-trans Retinal 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 °C after incubation of bO within the temperature range of 35–75 °C indicate that irreversible thermal unfolding begins at 50 °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 °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.