Kinetic analysis of the thermal stability of the photosynthetic reaction center from Rhodobacter sphaeroides

Probing the energy barriers and stages of membrane protein unfolding using solid-state NMR spectroscopy

Understanding how the amino acid sequence dictates protein structure and defines its stability is a fundamental problem in molecular biology. It is especially challenging for membrane proteins that reside in the complex environment of a lipid bilayer. Here, we obtain an atomic-level picture of the thermally induced unfolding of a membrane-embedded α-helical protein, human aquaporin 1, using solid-state nuclear magnetic resonance spectroscopy. Our data reveal the hierarchical two-step pathway that begins with unfolding of a structured extracellular loop and proceeds to an intermediate state with a native-like helical packing. In the second step, the transmembrane domain unravels as a single unit, resulting in a heterogeneous misfolded state with high helical content but with nonnative helical packing. Our results show the importance of loops for the kinetic stabilization of the whole membrane protein structure and support the three-stage membrane protein folding model.

Purification and preparation of Rhodobacter sphaeroides reaction centers for photocurrent measurements and atomic force microscopy characterization

The formation of defined surfaces consisting of photosynthetic reaction centers (RCs) in biohybrid solar cells is challenging. Here, we start with the production of engineered RCs for oriented binding. RCs are deposited onto gold electrodes, and 6-mercapto-1-hexanol (MCH) is used to displace multilayers and non-specifically adsorbed RCs. The resulting electrode surfaces are analyzed for photocurrent generation using an intensity-modulated light and lock-in amplifier. Atomic force microscopy (AFM) is used to characterize the surface and the formation of RC structural assemblies.

For complete details on the use and execution of this profile, please refer to Jun et al. (2021).

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Express and purify RC membrane proteins from Rhodobacter sphaeroides

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Deposit RCs and MCH on gold electrodes for formation of structural assemblies

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Measure RC photocurrents with an intensity-modulated LED and lock-in detection

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Prepare single crystal gold electrodes for AFM of RCs and image processing

Effect of Detergents and Osmolytes on Thermal Stability of Native and Mutant Rhodobacter sphaeroides Reaction Centers

Photosynthetic reaction center (RC) of the purple bacterium Rhodobacter sphaeroides is one of the most well-studied transmembrane pigment-protein complexes. It is a relatively stable protein with established conditions for its isolation from membranes, purification, and storage. However, it has been shown that some amino acid substitutions can affect stability of the RC, which results in a decrease of the RCs yield during its isolation and purification, disturbs spectral properties of the RCs during storage, and can lead to sample heterogeneity. To optimize conditions for studying mutant RCs, the effect of various detergents and osmolytes on thermal stability of the complex was examined. It was shown that trehalose and, to a lesser extent, sucrose, maltose, and hydroxyectoin at 1 M concentration slow down thermal denaturation of RCs. Sodium cholate was found to have significant stabilizing effect on the structure of native and genetically modified RCs. The use of sodium cholate as a detergent has several advantages and can be recommended for the storage and investigation of the unstable mutant membrane complexes of purple bacteria in long-term experiments.

The effect of some antiseptic drugs on the energy transfer in chromatophore photosynthetic membranes of purple non-sulfur bacteria Rhodobacter sphaeroides

Chromatophores of purple non-sulfur bacteria (PNSB) are invaginations of the cytoplasmic membrane that contain a relatively simple system of light-harvesting protein-pigment complexes, a photosynthetic reaction center (RC), a cytochrome complex, and ATP synthase, which transform light energy into the energy of synthesized ATP. The high content of negatively charged phosphatidylglycerol (PG) and cardiolipin (CL) in PNSB chromatophore membranes makes these structures potential targets that bind cationic antiseptics. We used the methods of stationary and kinetic fluorescence spectroscopy to study the effect of some cationic antiseptics (chlorhexidine, picloxydine, miramistin, and octenidine at concentrations up to 100 μM) on the spectral and kinetic characteristics of the components of the photosynthetic apparatus of Rhodobacter sphaeroides chromatophores. Here we present the experimental data on the reduced efficiency of light energy conversion in the chromatophore membranes isolated from the photosynthetic bacterium Rb. sphaeroides in the presence of cationic antiseptics. The addition of antiseptics did not affect the energy transfer between the light-harvesting LH1 complex and reaction center (RC). However, it significantly reduced the efficiency of the interaction between the LH2 and LH1 complexes. The effect was maximal with 100 μM octenidine. It has been proved that molecules of cationic antiseptics, which apparently bind to the heads of negatively charged cardiolipin molecules located in the rings of light-harvesting pigments on the cytoplasmic surface of the chromatophores, can disturb the optimal conditions for efficient energy migration in chromatophore membranes.

Optimizing the linker length for fusing an alcohol dehydrogenase with a cyclohexanone monooxygenase

The use of enzymes in organic synthesis is highly appealing due their remarkably high chemo-, regio- and enantioselectivity. Nevertheless, for biosynthetic routes to be industrially useful, the enzymes must fulfill several requirements. Particularly, in case of cofactor-dependent enzymes self-sufficient systems are highly valuable. This can be achieved by fusing enzymes with complementary cofactor dependency. Such bifunctional enzymes are also relatively easy to handle, may enhance stability, and promote product intermediate channeling. However, usually the characteristics of the linker, fusing the target enzymes, are not thoroughly evaluated. A poor linker design can lead to detrimental effects on expression levels, enzyme stability and/or enzyme performance. In this chapter, the effect of the length of a glycine-rich linker was explored for the case study of ɛ-caprolactone synthesis through an alcohol dehydrogenase-cyclohexanone monooxygenase fusion system. The procedure includes cloning of linker variants, expression analysis, determination of thermostability and effect on activity and conversion levels of 15 variants of different linker sizes. The protocols can also be used for the creation of other protein-protein fusions.

Spectral and Photochemical Properties of Rhodobacter sphaeroides R-26 Reaction Center Films in Vacuum

Using absorption spectroscopy in the visible/near-IR and mid-IR regions, spectral and photochemical properties of isolated reaction centers (RCs) from Rhodobacter sphaeroides R-26 were studied in dried films on the inorganic support surface (quartz or CaF₂ plates) under vacuum dehydration conditions (10^-2 or 7·10^-5 mm Hg). Three detergents, N,N-dimethyldodecylamine N-oxide (LDAO), Triton X-100 (TX100), and n-dodecyl-β-D-maltoside (DM), were tested for their ability to stabilize the RC-detergent complexes in the vacuum-dried state. It was shown that in the presence of LDAO, RC complexes underwent destruction in vacuum. In contrast, DM provided an environment that minimized irreversible disruptive changes in the RCs in vacuum. The effects of vacuum dehydration on the RC-DM films included a small increase in the content of α-helices in the RC protein, a short-wavelength reversible shift in the optical transitions of pigments, and minor changes in the electronic structure of the P⁺ dimer. The films retained their photochemical activity upon excitation with high-intensity light (200 mW/cm²). TX100 also helped to maintain spectral and functional properties of the RCs in vacuum; however, in this case, the stabilizing effect was less pronounced than in the presence of DM, especially, at high detergent concentrations. The results are discussed within the framework of a model suggesting that the detergent-protein interactions and the properties of detergent micelles play a dominant role in maintaining the structure of the RCs upon vacuum dehydration of the RC complexes. The obtained data can be useful for developing hybrid photoconverting systems based on bacterial RCs.

Temperature dependence of photosynthetic reaction centre activity in Rhodospirillum rubrum

The influence of temperature on photosynthetic reactions was investigated by a combination of time-resolved bacteriochlorophyll fluorescence, steady-state and differential absorption spectroscopy, and polarographic respiration measurements in intact cells of purple non-sulphur bacterium Rhodospirillum rubrum. Using variable bacteriochlorophyll fluorescence, it was found that the electron-transport activity increased with the increasing temperature up to 41 °C. The fast and medium components of the fluorescence decay kinetics followed the ideal Arrhenius equation. The calculated activation energy for the fast component was E_a1 = 16 kJ mol^-1, while that of the medium component was more than double, with E_a2 = 38 kJ mol^-1. At temperatures between 41 and 59 °C, the electron transport was gradually, irreversibly inhibited. Interestingly, the primary charge separation remained fully competent from 20 to 59 °C as documented by both BChl fluorescence and differential absorption spectroscopy of the P₈₇₀⁺ signal. At temperatures above 60 °C, the primary photochemistry became reversibly inhibited, which was manifested by an increase in minimal fluorescence, F₀, whereas maximal fluorescence, F_M, slowly declined. Finally, above 71 °C, the photosynthetic complexes began to disassemble as seen in the decline of all fluorometric parameters and the disappearance of the LH1 absorption band at 880 nm. The extended optimal temperature of photosynthetic reaction centre in a model species of Rhodospirillales adds on the evidence that the good thermostability of the photosynthetic reaction centres is present across all Alphaproteobacteria.

Hybrid complexes of photosynthetic reaction centers and quantum dots in various matrices: resistance to UV irradiation and heating

The effects of ultraviolet (UV) irradiation (up to 0.6 J/cm²) and heating (65 °C, 20 min) on the absorption spectra and electron transfer in dehydrated film samples of photosynthetic reaction centers (RCs) from purple bacterium Rhodobacter (Rb.) sphaeroides, as well as in hybrid structures consisting of RCs and quantum dots (QDs), have been studied. The samples were placed in organic matrices containing the stabilizers of protein structure-polyvinyl alcohol (PVA) and trehalose. UV irradiation led to partially irreversible oxidation of some RCs, as well as to transformation of some fraction of the bacteriochlorophyll (BChl) molecules into bacteriopheophytin (BPheo) molecules. In addition, UV irradiation causes degradation of some BChl molecules that is accompanied by formation of 3-acetyl-chlorophyll a molecules. Finally, UV irradiation destroys the RCs carotenoid molecules. The incorporation of RCs into organic matrices reduced pheophytinization. Trehalose was especially efficient in reducing the damage to the carotenoid and BChl molecules caused by UV irradiation. Hybrid films containing RC + QD were more stable to pheophytinization upon UV irradiation. However, the presence of QDs in films did not affect the processes of carotenoid destruction. The efficiency of the electronic excitation energy transfer from QD to P865 also did not change under UV irradiation. Heating led to dramatic destruction of the RCs structure and bacteriochlorins acquired the properties of unbound molecules. Trehalose provided strong protection against destruction of the RCs and hybrid (RC + QD) complexes.

The Peptidisc, a simple method for stabilizing membrane proteins in detergent-free solution

Membrane proteins are difficult to work with due to their insolubility in aqueous solution and quite often their poor stability in detergent micelles. Here, we present the peptidisc for their facile capture into water-soluble particles. Unlike the nanodisc, which requires scaffold proteins of different lengths and precise amounts of matching lipids, reconstitution of detergent solubilized proteins in peptidisc only requires a short amphipathic bi-helical peptide (NSP_r) and no extra lipids. Multiple copies of the peptide wrap around to shield the membrane-exposed part of the target protein. We demonstrate the effectiveness of this ‘one size fits all’ method using five different membrane protein assemblies (MalFGK₂, FhuA, SecYEG, OmpF, BRC) during ‘on-column’, ‘in-gel’, and ‘on-bead’ reconstitution embedded within the membrane protein purification protocol. The peptidisc method is rapid and cost-effective, and it may emerge as a universal tool for high-throughput stabilization of membrane proteins to advance modern biological studies.

Surrounding every living cell is a biological membrane that is largely impermeable to water-soluble molecules. This hydrophobic (or “water-hating”) barrier preserves the contents of the cell and also regulates how the cell interacts with its environment. This latter function is critical and relies on a class of proteins that are embedded within the membrane and are also hydrophobic.

The hydrophobic nature of membrane proteins is however inconvenient for biochemical studies which usually take place in water-based solutions. Therefore, membrane proteins are under-represented in biological research compared to the water-soluble ones, even though roughly one quarter of a cell’s proteins are membrane proteins. Researchers have developed a few tricks to keep membrane proteins soluble after they have been extracted from the membrane. An old but popular technique makes use of detergents, which are chemicals with opposing hydrophobic and hydrophilic properties (hydrophilic literally means “water-loving”). However, even mild detergents can damage membrane proteins and will sometimes lead to experimental artifacts. More recent tricks to stabilize membrane proteins without detergents have been described but remain laborious, costly or difficult to perform.

To overcome these limitations, Carlson et al. developed a simple method to stabilize membrane proteins without detergent. Called the “peptidisc”, the method uses multiple copies of a unique peptide – a short sequence of the building blocks of protein – that had been redesigned to have optimal hydrophobic and hydrophilic properties. The idea was that the peptides would wrap around the hydrophobic parts of the membrane protein, and shield them from the watery solution. Indeed, when Carlson et al. mixed this peptide with five different membrane proteins from bacteria, all were perfectly soluble and functional without detergent. The ideal ratio of peptide needed to form a peptidisc around each membrane protein was reached automatically, without having to test many different conditions. This indicates that the peptidisc acts like a “one size fits all” scaffold.

The peptidisc is a new tool that will allow more researchers, including those who are not expert biochemists, to study membrane proteins. This will yield a better understanding of the structure of a cell’s membrane and how it interacts with the environment. Since the approach is both simple and easy to apply, more membrane proteins can now also be included in high-throughput searches for potential new drugs for various medical conditions.

Heterologous Production of the Photosynthetic Reaction Center and Light Harvesting 1 Complexes of the Thermophile Thermochromatium tepidum in the Mesophile Rhodobacter sphaeroides and Thermal Stability of a Hybrid Core Complex

The photosynthetic complexes of the thermophile Thermochromatium tepidum are of considerable interest in biohybrid solar cell applications because of the ability of thermophilic proteins to tolerate elevated temperatures. Synthetic operons encoding reaction center (RC) and light harvesting 1 (LH1) pigment-protein complexes of T. tepidum were expressed in the mesophile Rhodobacter sphaeroides The T. tepidum RC (TRC) was assembled and was found to be functional with the addition of menadione to populate the Q_A pocket. The production of T. tepidum LH1 (TLH1) was increased by selection of a phototrophy-capable mutant after UV irradiation mutagenesis, which yielded a hybrid RC-TLH1 core complex consisting of the R. sphaeroides RC and T. tepidum TLH1, confirmed by the absorbance peak of TLH1 at 915 nm. Affinity chromatography partial purification and subsequent sucrose gradient analysis of the hybrid RC-TLH1 core complex indicated that this core complex assembled as a monomer. Furthermore, the RC-TLH1 hybrid core complex was more tolerant of a temperature of 70°C than the R. sphaeroides RC-LH1 core complexes in both the dimeric and monomeric forms; after 1 h, the hybrid complex retained 58% of the initial starting value, compared to values of 11% and 53% for the R. sphaeroides RC-LH1 dimer and monomer forms, respectively.IMPORTANCE This work is important because it is a new approach to bioengineering of photosynthesis proteins for potential use in biophotovoltaic solar energy capture. The work establishes a proof of principle for future biohybrid solar cell applications.

Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures

The data provide information in support of the research article, “Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures” [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt–PEG phase separation.

Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures

Mixtures of neutral salts and polyethylene glycol are used for various purposes in biological studies. Although the effects of each component of the mixtures are theoretically well investigated, comprehension of their integrated effects remains insufficient. In this work, their roles and effects as a precipitant were clarified by studying dependence of precipitation curves on salt concentration for integral membrane protein/detergent particles of different physicochemical properties. The dependence of precipitation curves was reasonably related to intermolecular interactions among relevant molecules such as protein, detergent and polyethylene glycol by considering their physicochemical properties. The obtained relationships are useful as basic information to learn the early stage of biological macromolecular associations.

Dehydration affects the electronic structure of the primary electron donor in bacterial photosynthetic reaction centers: evidence from visible-NIR and light-induced difference FTIR spectroscopy

The photosynthetic reaction center (RC) is a membrane pigment-protein complex that catalyzes the initial charge separation reactions of photosynthesis. Following photoexcitation, the RC undergoes conformational relaxations which stabilize the charge-separated state. Dehydration of the complex inhibits its conformational dynamics, providing a useful tool to gain insights into the relaxational processes. We analyzed the effects of dehydration on the electronic structure of the primary electron donor P, as probed by visible-NIR and light-induced FTIR difference spectroscopy, in RC films equilibrated at different relative humidities r. Previous FTIR and ENDOR spectroscopic studies revealed that P, an excitonically coupled dimer of bacteriochlorophylls, can be switched between two conformations, P866 and P850, which differ in the extent of delocalization of the unpaired electron between the two bacteriochlorophyll moieties (PL and PM) of the photo-oxidized radical P(+). We found that dehydration (at r = 11%) shifts the optical Qy band of P from 866 to 850-845 nm, a large part of the effect occurring already at r = 76%. Such a dehydration weakens light-induced difference FTIR marker bands, which probe the delocalization of charge distribution within the P(+) dimer (the electronic band of P(+) at 2700 cm(-1), and the associated phase-phonon vibrational modes at around 1300, 1480, and 1550 cm(-1)). From the analysis of the P(+) keto C[double bond, length as m-dash]O bands at 1703 and 1713-15 cm(-1), we inferred that dehydration induces a stronger localization of the unpaired electron on PL(+). The observed charge redistribution is discussed in relation to the dielectric relaxation of the photoexcited RC on a long (10(2) s) time scale.

Bacterial reaction centers purified with styrene maleic acid copolymer retain native membrane functional properties and display enhanced stability

Integral membrane proteins often present daunting challenges for biophysical characterization, a fundamental issue being how to select a surfactant that will optimally preserve the individual structure and functional properties of a given membrane protein. Bacterial reaction centers offer a rare opportunity to compare the properties of an integral membrane protein in different artificial lipid/surfactant environments with those in the native bilayer. Here, we demonstrate that reaction centers purified using a styrene maleic acid copolymer remain associated with a complement of native lipids and do not display the modified functional properties that typically result from detergent solubilization. Direct comparisons show that reaction centers are more stable in this copolymer/lipid environment than in a detergent micelle or even in the native membrane, suggesting a promising new route to exploitation of such photovoltaic integral membrane proteins in device applications.

Kinetics and thermodynamics of membrane protein folding

Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

Simple screening method for improving membrane protein thermostability

Biochemical and biophysical analysis on integral membrane proteins often requires monodisperse and stable protein samples. Here we describe a method to characterize protein thermostability by measuring its melting temperature in detergent using analytical size-exclusion chromatography. This quantitative method can be used to screen for compounds and conditions that stabilize the protein. With this technique we were able to assess and improve the thermostability of several membrane proteins. These conditions were in turn used to assist purification, to identify protein ligand and to improve crystal quality.

Practical considerations of membrane protein instability during purification and crystallisation

Crystallisation of integral membranes requires milligrams of purified protein in a homogeneous, monodisperse state, and crucially, the membrane protein must also be fully functional and stable. The stability of membrane proteins in solution is dependent on the type of detergents used, but unfortunately the use of the most stabilising detergent can often decrease the probability of obtaining crystals that diffract to high resolution, especially of small membrane proteins. A number of strategies have been developed to facilitate the purification of membrane proteins in a functional form, which have led to new possibilities for structure determination.

The petite purple photosynthetic powerpack

Photoreaction centres are Nature's solar batteries. These nanometre-scale power producers are responsible for transducing the energy of sunlight into a form that can be used by biological systems, thereby powering most of the biological activity on the planet. Although to the layman the word 'photosynthesis' is usually associated with green plants, much of our understanding of the molecular basis of biological transduction of light energy has come from studies of purple photosynthetic bacteria. Their RCs (reaction centres) and attendant light-harvesting complexes have been subjected to an intensive spectroscopic scrutiny, coupled with genetic manipulation and structural studies, that has revealed many of the molecular and mechanistic details of biological energy transfer, electron transfer and coupled proton translocation. This review provides a short overview of the structure and mechanism of the purple bacterial RC, focusing in the main on the most heavily studied complex from Rhodobacter sphaeroides.

Structural responses to cavity-creating mutations in an integral membrane protein

X-ray crystallography has been used to investigate the extent of structural changes in mutants of the purple bacterial reaction center that assemble without a particular ubiquinone or bacteriopheophytin cofactor. In the case of the bacteriopheophytin-exclusion mutant, in which Ala M149 was replaced by Trp (AM149W), the quality of protein crystals was improved over that seen in previous work by minimizing illumination, time, and temperature during the purification protocol and carrying out crystal growth at 4 degrees C after overnight incubation at 18 degrees C. The X-ray crystal structure of the AM149W mutant, determined to a resolution of 2.2 A, showed very little change in protein structure despite the absence of the bacteriopheophytin cofactor. Changes in the electron density map in the region of the cofactor binding site could be accounted for by changes in the conformation of the phytol side chains of adjacent cofactors and the presence of a buried water molecule. Residues lining the vacated binding pocket did not show any significant changes in conformation or increases in disorder as assessed through crystallographic atomic displacement parameters (B-factors). The X-ray crystal structure of a reaction center lacking the primary acceptor ubiquinone through mutation of Ala M248 to Trp (AM248W) was also determined, to a resolution of 2.8 A. Again, despite the absence of an internal cofactor only very minor changes in protein structure were observed. This is in contrast to a previous report on a reaction center lacking this ubiquinone through mutation of Ala M260 to Trp (AM260W) where more extensive changes in structure were apparent. All three mutant reaction centers showed a decrease in thermal stability when housed in the native membrane, but this decrease was smaller for the AM260W mutant than the AM248W complex, possibly due to beneficial effects of the observed changes in protein structure. The lack of major changes in protein structure despite the absence of large internal cofactors is discussed in terms of protein rigidity, the protective influence of the adaptable membrane environment, and the role of small molecules and ions as packing material in the internal cavities created by this type of mutation.