Effects of codon usage and vector-host combinations on the expression of spinach plastocyanin in Escherichia coli

Reactivity of human antisera to codon optimized SARS-CoV2 viral proteins expressed in Escherichia coli

Objective

The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV2 virus continues to pose a serious threat to public health worldwide. The development of rapid diagnostic kits can assist the Tzu Chi Foundation in supporting global volunteers working to provide relief during the current pandemic.

Materials and Methods

In this study, nucleotide sequences derived from publicly available viral genome data for several domains of the SARS-CoV2 spike and nucleocapsid (N) proteins were chemically synthesized, with codon optimization for Escherichia coli protein expression. No actual viral particles were involved in these experiments. The synthesized sequences were cloned into an E. coli expression system based on pQE80L, and expressed viral proteins were subsequently purified using Ni-affinity chromatography. Western blotting was conducted using human antiviral sera to assess the response of codon-modified viral proteins to COVID-19 patient sera.

Results

N protein was expressed in amounts large enough to support large-scale production. The N-terminal domain, receptor-binding domain (RBD), Region 3, and the S2 domain were expressed in small but sufficient amounts for experiments. Immunoblotting results showed that anti-N IgG and anti-N IgM antibodies were detected in most patient sera, but only 60% of samples reacted with the recombinant RBD and S2 domain expressed by E. coli.

Conclusion

The results indicated that codon-optimized SARS-CoV2 viral proteins can be expressed in E. coli and purified for rapid antibody detection kit preparation, with the codon-optimized N protein, RBD, and S2 protein demonstrating the most potential.

Purification of plastocyanin and cytochrome c6 from plants, green algae, and cyanobacteria

Plastocyanin and cytochrome c6 are widely distributed over the oxygen-evolving photosynthetic organisms. The two proteins are functionally equivalent, but strongly differ in their global electrostatic charge. In fact, they are acidic in eukaryotes, but either neutral or basic in cyanobacteria. Such a difference in their electrostatic features is a critical factor in designing the purification procedure, which must thus be modified and adapted accordingly. This chapter reports the methods for producing (including cell cultures), isolating, and purifying plastocyanin and cytochrome c6--which greatly differ in their isoelectric point--from a number of eukaryotic and prokaryotic organisms.

Oral vaccination with a recombinant Salmonella vaccine vector provokes systemic HIV-1 subtype C Gag-specific CD4+ Th1 and Th2 cell immune responses in mice

BACKGROUND

Recombinant Salmonella vaccine vectors may potentially be used to induce specific CD4+ T cell responses against foreign viral antigens. Such immune responses are required features of vaccines against pathogens such as human immunodeficiency virus type 1 (HIV-1). The aim of this study was to investigate the induction of systemic HIV-1-specific CD4+ T helper (Th) responses in mice after oral immunization with a live attenuated Salmonella vaccine vector that expressed HIV-1 subtype C Gag. Groups of BALB/c mice were vaccinated orally three times (4 weeks apart) with this recombinant Salmonella. At sacrifice, 28 days after the last immunization, systemic CD4+ Th1 and Th2 cytokine responses were evaluated by enzyme-linked immunospot assay and cytometric bead array. HIV-1 Gag-specific IgG1 and IgG2a humoral responses in the serum were determined by enzyme-linked immunosorbent assay.

RESULTS

Mice vaccinated with the recombinant Salmonella elicited both HIV-1-specific Th1 (interferon-gamma (IFN-gamma) and tumour necrosis factor-alpha (TNF-alpha)) and Th2 (interleukin-4 (IL-4) and interleukin-5 (IL-5)) cytokine responses. The vaccine induced 70 (IFN-gamma) spot-forming units (SFUs)/10e(6) splenocytes and 238 IL-4 SFUs/10e(6) splenocytes. Splenocytes from vaccinated mice also produced high levels of Th1 and Th2 cytokines upon stimulation with a Gag CD4 peptide. The levels of IFN-gamma, TNF-alpha, IL-4 and IL-5 were 7.5-, 29.1-, 26.2- and 89.3-fold above the background, respectively. Both HIV-1 Gag-specific IgG1 and IgG2a antibodies were detected in the sera of vaccinated mice.

CONCLUSION

The study highlights the potential of orally-delivered attenuated Salmonella as mucosal vaccine vectors for HIV-1 Subtype C Gag to induce Gag-specific CD4+ Th1 and Th2 cellular immune responses and antibodies which may be important characteristics required for protection against HIV-1 infection.

Mutations in the periplasmic chaperone leading to loss of surface expression of the colonization factor CS6 in enterotoxigenic Escherichia coli (ETEC) clinical isolates

Enterotoxigenic Escherichia coli (ETEC) cause diarrhoea by adhesion to human enterocytes by one or more colonization factors (CFs) and secretion of heat-labile (LT) and/or heat-stable (ST) enterotoxins. Expression of coli surface antigen 6 (CS6) on the bacterial surface, usually associated with ETEC strains that produce ST alone or in combination with LT, is rarely found in strains expressing only LT. However, a number of LT-only strains which are genotypically positive but phenotypically negative for CS6 have been identified. In this study, eight such strains from India and Guinea-Bissau belonging to different clones were analysed. The CS6 operon cssABCD was transcribed but protein analyses suggested that the structural subunits CssA and CssB of CS6 were absent in the periplasm. Most strains contained truncating mutations within the periplasmic chaperone-encoding gene cssC and protein modelling indicated that this severely affected the substrate-binding capacity of the chaperone. A single-nucleotide polymorphism (SNP) (A-->T) in the 5'-untranslated region of cssC distinguished the eight strains from ETEC strains that do express CS6 on the surface and may be a potential marker for ETEC strains containing phenotypically silent cssABCD. The study emphasizes the importance of using both genotypic and phenotypic methods in epidemiological studies of ETEC, e.g. for vaccine development.

Codon bias and heterologous protein expression

The expression of functional proteins in heterologous hosts is a cornerstone of modern biotechnology. Unfortunately, proteins are often difficult to express outside their original context. They might contain codons that are rarely used in the desired host, come from organisms that use non-canonical code or contain expression-limiting regulatory elements within their coding sequence. Improvements in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences to maximize the likelihood of high protein expression. Redesign strategies are discussed here, including modification of translation initiation regions, alteration of mRNA structural elements and use of different codon biases.

Pseudospecificity of the Acidic Patch of Plastocyanin for the Interaction with Cytochrome f

The ionic strength dependence of the physiological electron-transfer reaction of plastocyanins (PCus) from a range of sources with a eukaryotic cytochrome f (cyt f) has been studied. The presence of an acidic patch on the surface of PCu is key to this interaction in higher plants, but minor modifications in this surface region have a limited effect. Surprisingly, a similarly small influence results from the repositioning of the acidic patch (as in the fern PCu). The only requirement of a plant PCu to ensure efficient interaction with its cyt f is the presence of acidic residues on the periphery of the protein's hydrophobic patch.

The crystal structure of the spinach plastocyanin double mutant G8D/L12E gives insight into its low reactivity towards photosystem 1 and cytochrome f

Plastocyanin (Pc) is a copper-containing protein, which functions as an electron carrier between the cytochrome b(6)f and photosystem 1 (PS1) complexes in the photosynthetic electron transfer (ET) chain. The ET is mediated by His87 situated in the hydrophobic surface in the north region of Pc. Also situated in this region is Leu12, which mutated to other amino acids severely disturbs the ET from cytochrome f and to PS1, indicating the importance of the hydrophobic surface. The crystal structure of the Pc double mutant G8D/L12E has been determined to 2.0 A resolution, with a crystallographic R-factor of 18.3% (R(free)=23.2%). A comparison with the wild-type structure reveals that structural differences are limited to the sites of the mutations. In particular, there is a small but significant change in the hydrophobic surface close to His87. Evidently, this leads to a mismatch in the reactive complex with the redox partners. For PS1 this results in a 20 times weaker binding and an eightfold slower ET as determined by kinetic measurements. The mutations that have been introduced do not affect the optical absorption spectrum. However, there is a small change in the EPR spectrum, which can be related to changes in the copper coordination geometry.

Thermal denaturation of spinach plastocyanin: effect of copper site oxidation state and molecular oxygen

The thermal denaturation of the cupredoxin plastocyanin (PC) from spinach has been studied with the aim of improving the understanding of factors involved in the conformational stability of antiparallel beta-sheet proteins. Studies using differential scanning calorimetry have been complemented with nuclear magnetic resonance spectroscopy, absorbance spectroscopy, dynamic light scattering, and mass spectrometry in elucidation of the effect of the copper-site oxidation state on the irreversible thermal denaturation process. Our results indicate that copper-catalyzed oxidation of the metal-ligating cysteine is the sole factor resulting in thermal irreversibility. However, this can be prevented in reduced protein by the removal of molecular oxygen. Application of a two-state equilibrium transition model to the folding process thus allowed the extraction of thermodynamic parameters for the reduced protein (Delta(trs)H = 494 kJ mol(-1), DeltaH(vH) = 343 kJ mol(-1), and T(m) = 71 degrees C). However, anaerobically denatured oxidized protein and all aerobically denatured species undergo covalent modification as a result of the copper-catalyzed oxidation of the metal-ligating cysteine residue resulting in the formation of both oxidized monomers and disulfide-linked dimers. On the basis of these results, a general mechanism for the irreversible thermal denaturation of cupredoxins is proposed. The results presented here also indicate that PC, as opposed to the previously characterized homologous protein azurin, unfolds via at least one significantly populated intermediate state (DeltaH(vH)/Delta(trs)H = 0.7) despite the almost identical native state topologies of these proteins. These findings will aid the characterization of the stability of PC and other cupredoxins and possibly of all cysteine-ligating metal-binding proteins.

Strong associations between gene function and codon usage

The association between codon usage and gene function was analyzed in the complete genomes of Eschericia coli, Bacillus subtilis, Lactococcus lactis and Campylobacter jejuni, using the functional annotation provided by NCBI. Two distinctly different ways of quantifying codon usage were used in the analysis. By using contingency tables it was found that for most amino acids a highly significant association with gene function exists for all species, indicating that codon usage at the level of individual amino acids is generally closely coordinated with gene function. By computing the effective number of codons in the annotated genes and comparing the median values in groups of different gene functions it was shown for all species that codon bias gene by gene also differs.

Effects of codon usage versus putative 5'-mRNA structure on the expression of Fusarium solani cutinase in the Escherichia coli cytoplasm

Matching the codon usage of recombinant genes to that of the expression host is a common strategy for increasing the expression of heterologous proteins in bacteria. However, while developing a cytoplasmic expression system for Fusarium solani cutinase in Escherichia coli, we found that altering codons to those preferred by E. coli led to significantly lower expression compared to the wild-type fungal gene, despite the presence of several rare E. coli codons in the fungal sequence. On the other hand, expression in the E. coli periplasm using a bacterial PhoA leader sequence resulted in high levels of expression for both the E. coli optimized and wild-type constructs. Sequence swapping experiments as well as calculations of predicted mRNA secondary structure provided support for the hypothesis that differential cytoplasmic expression of the E. coli optimized versus wild-type cutinase genes is due to differences in 5(') mRNA secondary structures. In particular, our results indicate that increased stability of 5(') mRNA secondary structures in the E. coli optimized transcript prevents efficient translation initiation in the absence of the phoA leader sequence. These results underscore the idea that potential 5(') mRNA secondary structures should be considered along with codon usage when designing a synthetic gene for high level expression in E. coli.

Effects of pH on kinetics of the structural rearrangement that gates the electron-transfer reaction between zinc cytochrome c and plastocyanin: Analysis of protonation states in a diprotein complex

Electron transfer from zinc cytochrome c to copper(II)plastocyanin in the electrostatically- stabilized complex [Crnogorac MM, Shen C, Young S Hansson O, Kostic NM (1996) Biochemistry 35, 16465?74]. We study this rearrangement in four complexes Zncyt/pc(II), which zinc cytochrome c makes with the wild-type form and the single mutants Asp42Asn, Glu59Gln, and Glu60Gln of plastocyanin. The rate constant for the rearrangement, kF differs for the four forms of plastocyanin but is independent of pH from 5.4 to 9.0 in all four cases. That kF is affected by the single mutations but not by pH changes suggests that the residues Asp 42, Glu59, and Glu60 in the wild-type plastocyanin remain deprotonated (i.e., as anions) within the Zncyt/pc(II) complex throughout the pH range examined. This fact agrees with the notion that loss of salt bridges in the initial (redox-inactive) configuration of the complex is compensated by formation of new salt bridges in the rearranged (redox-active) configuration.

Mimicking biological electron transport in sol-gel glass: photoinduced electron transfer from zinc cytochrome C to plastocyanin or cytochrome C mediated by mobile inorganic complexes

Biomimetic studies of electron-transport chains are important for establishing the molecular mechanisms of long-range communications between proteins. We mimic these biological assemblies by encapsulating metalloproteins in sol-gel silica glass and letting mobile inorganic complexes shuttle electrons between the immobilized proteins. We present two examples of such rudimentary electron-transport chains. In both of them the immobilized electron donor is the zinc-substituted cytochrome c, Zncyt; the immobilized electron acceptor is either cupriplastocyanin, pc(II), or ferricytochrome c, cyt(III); and the mobile charge carrier Q/Q(-) is the redox couple FeEDTA(-)(/2)(-) or Ru(NH(3))(6)(3+/2+). The redox processes are photoinduced: Zncyt is excited by the laser pulse and converted to the triplet state, (3)Zncyt, which is a strong reducing agent. Visible absorption, circular dichroism, and electron paramagnetic resonance spectra of the metalloproteins show that encapsulation in sol-gel glass does not affect their intrinsic redox properties. The rigid silica glass spatially separates the proteins from each other. In this matrix, the electron-transfer reactions between (3)Zncyt and pc(II) and between (3)Zncyt and cyt(III), which occur fast in solution, are completely suppressed in the absence of a charge carrier Q/Q(-). The reactivity of FeEDTA(-) and Ru(NH(3))(6)(3+) (as quenchers Q of (3)Zncyt) is minimally affected by the interior of the sol-gel glass. In the glass, the second-order rate constants for the excited-state electron transfer, from (3)Zncyt to Q, are (8.9 +/- 0.6) x 10(6) and (8.0 +/- 2.4) x 10(6) M(-)(1) s(-)(1) for FeEDTA(-) and Ru(NH(3))(6)(3+), respectively. This reaction is followed by the ground-state back electron transfer, from Q(-) to Zncyt(+). In the "monoprotein" glasses Zncyt/Q, the respective second-order rate constants for this back electron-transfer reaction are (4.9 +/- 0.2) x 10(7) and (7.8 +/- 2.7) x 10(7) M(-)(1) s(-)(1). In the "diprotein" glasses Zncyt/Q/pc(II) and Zncyt/Q/cyt(III), containing also the acceptor protein pc(II) or cyt(III), Zncyt(+) decays on two time scales. The faster and major component of this decay is analogous to the only mode of the decay in the Zncyt/Q glasses and is a second-order process. Between 25 and 40% of the initially formed Zncyt(+), however, lives longer (k(slow) =1.1 +/- 0.2 s(-)(1)) and decays by a first-order process. We attribute the lengthening of the Zncyt(+) lifetime to a partial escape of the photogenerated Q(-) into the glass pores, where it reacts with the immobilized pc(II) or cyt(III). Indeed, the visible absorption spectra show the photoinduced reduction of pc(II) and cyt(III). Evidently, the small inorganic complexes, FeEDTA(-)(/2)(-) and Ru(NH(3))(6)(3+/2+), move through the glass pores, react with the encapsulated metalloproteins, and establish the interprotein electron transfer. Each interprotein reaction now occurs in two steps: a mobile charge carrier Q receives an electron from (3)Zncyt, and Q(-) then delivers an electron to pc(II) or cyt(III). Ultimately, the energy of visible light is converted to reducing equivalents for plastocyanin and cytochrome c. The sequential electron transfer described here resembles the events in a rudimentary electron-transport chain. Our findings demonstrate the promise of integrating proteins, with their optimally adjusted redox sites, in photocatalytic materials.

Recombinant equine cytochrome c in Escherichia coli: high-level expression, characterization, and folding and assembly mutants

To promote studies of cytochrome c (Cyt c) ranging from apoptosis to protein folding, a system for facile mutagenesis and high-level expression is desirable. This work used a generally applicable strategy for improving yields of heterologously expressed protein in Escherichia coli. Starting with the yeast Cyt c plus heme lyase construct of Pollock et al. [Pollock, W. B., Rosell, F. I., Twitchett, M. B., Dumont, M. E., and Mauk, A. G. (1998) Biochemistry 37, 6124-6131], an E. coli-based system was designed that consistently produces high yields of recombinant eucaryotic (equine) Cyt c. Systematic changes to the ribosome binding site, plasmid sequence, E. coli strain, growth temperature, and growth duration increased yields from 2 to 3 mg/L to as much as 105 mg/L. Issues related to purification, fidelity of heme insertion, equilibrium stability, and introduction and analysis of mutant forms are described. As an example, variants tailored for folding studies are discussed. These remove known pH-dependent kinetic folding barriers (His26 and His33 and N-terminus), reveal an additional kinetic trap at higher pH due to some undetermined residue(s), and show how a new barrier can be placed at different points in the folding pathway in order to trap and characterize different folding intermediates. In addition, destabilizing glycine mutants in the N-terminal helix are shown to affect the fractional yield of a heme inverted Cyt c isoform.

Effects of pH on protein association: modification of the proton-linkage model and experimental verification of the modified model in the case of cytochrome c and plastocyanin

Effects of pH on protein association are not well understood. To understand them better, we combine kinetic experiments, calculations of electrostatic properties, and a new theoretical treatment of pH effects. The familiar proton-linkage model, when used to analyze the dependence of the association constant K on pH, reveals little about the individual proteins. We modified this model to allow determination not only of the numbers of the H+ ions involved in the association but also of the pK(a) values, in both the separate and the associated proteins, of the side chains that are responsible for the dependence of K on pH. Some of these side chains have very similar pK(a) values, and we treat them as a group having a composite pK(a) value. Use of these composite pK(a) values greatly reduces the number of parameters and allows meaningful interpretation of the experimental results. We experimentally determined the variation of K in the interval 5.4 < or = pH < or = 9.0 for four diprotein complexes, those that the wild-type cytochrome c forms with the wild-type plastocyanin and its mutants Asp42Asn, Glu59Gln, and Glu60Gln. The excellent fittings of the experimental results to the modified model verified this model and revealed some unexpected and important properties of these prototypical redox metalloproteins. Protein association causes a decrease in the pK(a) values of the acidic side chains and an increase in the pK(a) values of the basic side chains. Upon association, three carboxylic side chains in wild-type plastocyanin each release a H+ ion. These side chains in free plastocyanin have an anomalously high composite pK(a) value, approximately 6.3. Upon association, five or six side chains in cytochrome c, likely those of lysine, each take up a H+ ion. Some of these side chains have anomalously low pK(a) values, less than 7.0. The unusual pK(a) values of the residues in the recognition patches of plastocyanin and cytochrome c may be significant for the biological functions of these proteins. Although each mutation in plastocyanin markedly, and differently, changed the dependence of K on pH, the model consistently gave excellent fittings. They showed decreased numbers of H+ ions released or taken up upon protein association and altered composite pK(a) values of the relevant side chains. Comparisons of the fitted composite pK(a) values with the theoretically calculated pK(a) values for plastocyanin indicated that Glu59 and Asp61 in the wild-type plastocyanin each release a H+ ion upon association with cytochrome c. Information of this kind cannot readily be obtained by spectroscopic methods. Our modification of the proton-linkage model is a general one, applicable also to ligands other than H+ ion and to processes other than association.

Redox reactivity and reorganization energy of zinc cytochrome c cation radical

Little is known about transient intermediates in photoinduced electron-transfer reactions of metalloproteins. Oxidative quenching of the triplet state of zinc cytochrome c, 3Zncyt, is done at 20 degrees C, pH 7.00, and ionic strength of 1.00 M, conditions that suppress the thermal back-reaction and prolong the lifetime of the cation radical, Zncyt+. This species is reduced by [Fe(CN)6]4-, [W(CN)8]4-, [Os(CN)6]4-, [Mo(CN)8]4-, and [Ru(CN)6]4- complexes of similar structures and the same charge. The rate constants and thermodynamic driving forces for these five similar electron-transfer reactions were fitted to Marcus theory. The reorganization energy of Zncyt+ is lambda = 0.38(5) eV, lower than that of native cytochrome c, because the redox orbital of the porphyrin cation radical is delocalized and possibly because Met80 is not an axial ligand to the zinc(II) ion in the reconstituted cytochrome c. The rate constant for electron self-exchange between Zncyt+ and Zncyt, k11 = 1.0(5) x 10(7) M(-1) s(-1), is large owing to the extended electron delocalization and relatively low reorganization energy. These results may be relevant to zinc(II) derivatives of other heme proteins, which are often used in studies of photoinduced electron-transfer reactions.

Overexpression in Escherichia coli and characterization of the chloroplast fructose-1,6-bisphosphatase from wheat

An important Calvin cycle enzyme, chloroplast fructose-1, 6-bisphosphatase (FBPase) from wheat, has been cloned and expressed up to 15% of the total cell protein using a pPLc expression vector in Escherichia coli by replacing the codons in the 5'-terminal encoding sequence with optimal and A/T-rich ones. The overexpressed wheat FBPase is soluble, fully active, and heat stable. It can be purified by chromatography in turn on DEAE-Sepharose and Sephacryl S-200, and around 15 mg of purified enzymes (>95%) is obtained from 1 liter of cultured bacteria. Its special activity is 8.8 u/mg, K(cat) is 22.9/S, K(m) is 121 microM, and V(max) is 128 micromol/min. mg. The recombinant FBPase can be activated by DTT, Na(+), or low concentrations of Li(+), Ca(2+), Zn(2+), GuHCl, and urea, while it can be inhibited by K(+) or NH(+)(4).

Improved production and function of llama heavy chain antibody fragments by molecular evolution

The aim of this study was to improve production level of llama heavy chain antibody fragments (V(HH)) in Saccharomyces cerevisiae while retaining functional characteristics. For this purpose, the DNA shuffling technique was used on llama V(HH) fragments specific for the azo-dye reactive red-6. In the DNA shuffling process, three parental llama V(HH) with high amino acid sequence identity with significant differences in production and functional characteristics were used. From these parental sequences, a S. cerevisiae library was created and 16 antigen specific shuffled V(HH) fragments were selected. We found that these shuffled V(HH) fragments were, (i) unique in sequence; (ii) composed of two or three parental sequences; (iii) in three V(HH)s point mutations occurred; and (iv) antigen specificity was not changed. The four highest producers in the yeast S. cerevisiae were selected and production, affinity, and antigen binding at 90 degrees C were compared with parental V(HH)s. One shuffled V(HH) was enhanced both in production (3.4-fold) and affinity (four-fold). A second shuffled V(HH) displayed increased production (1.9-fold), and improved stability (2.4-fold) in antigen binding at 90 degrees C. Structural analysis suggested that improved antigen binding is associated with the A24 --> V24 substitution, which reduces the size of the hydrophobic pit at the llama V(HH) surface. We demonstrate that it is possible to improve desired characteristics of the same V(HH) fragment simultaneously using DNA shuffling. Finally, this is one of the first examples of DNA shuffling improving temperature stability of an antibody fragment.

Side-chain interactions in the plastocyanin-cytochrome f complex

Cytochrome f and plastocyanin are redox partners in the photosynthetic electron-transfer chain. Electron transfer from cytochrome f to plastocyanin occurs in a specific short-lived complex. To obtain detailed information about the binding interface in this transient complex, the effects of binding on the backbone and side-chain protons of plastocyanin have been analyzed by mapping NMR chemical-shift changes. Cytochrome f was added to plastocyanin up to 0.3 M equiv, and the plastocyanin proton chemical shifts were measured. Out of approximately 500 proton resonances, 86% could be observed with this method. Nineteen percent demonstrate significant chemical-shift changes and these protons are located in the hydrophobic patch (including the copper ligands) and the acidic patches of plastocyanin, demonstrating that both areas are part of the interface in the complex. This is consistent with the recently determined structure of the complex [Ubbink, M., Ejdebäck, M., Karlsson, B. G., and Bendall, D. S. (1998) Structure 6, 323-335]. The largest chemical-shift changes are found around His87 in the hydrophobic patch, which indicates tight contacts and possibly water exclusion from this part of the protein interface. These results support the idea that electron transfer occurs via His87 to the copper in plastocyanin and suggest that the hydrophobic patch determines the specificity of the binding. The chemical-shift changes in the acidic patches are significant but small, suggesting that the acidic groups are involved in electrostatic interactions but remain solvent exposed. The existence of small differences between the present data and those used for the structure may imply that the redox state of the metals in both proteins slightly affects the structure of the complex. The chemical-shift mapping is performed on unlabeled proteins, making it an efficient way to analyze effects of mutations on the structure of the complex.

Electron transfer to photosystem 1 from spinach plastocyanin mutated in the small acidic patch: ionic strength dependence of kinetics and comparison of mechanistic models

A set of plastocyanin (Pc) mutants, probing the small acidic patch (Glu59, Glu60, and Asp61) and a nearby residue, Gln88, has been constructed to provide further insight into the electron transfer process between Pc and photosystem 1. The negatively charged residues were changed into their neutral counterparts or to a positive lysine. All mutant proteins exhibited electron transfer kinetics qualitatively similar to those of the wild type protein over a wide range of Pc concentrations. The kinetics were slightly faster for the Gln88Lys mutant, while they were significantly slower for the Glu59Lys mutant. The data were analyzed with two different models: one involving a conformational change of the Pc-photosystem 1 complex that precedes the electron transfer step (assumed to be irreversible) [Bottin, H., and Mathis, P. (1985) Biochemistry 24, 6453-6460] and another where no conformational change occurs, the electron transfer step is reversible, and dissociation of products is explicitly taken into account [Drepper, F., Hippler, M., Nitschke, W., and Haehnel, W. (1996) Biochemistry 35, 1282-1295]. Both models can account for the observed kinetics in the limits of low and high Pc concentrations. To discriminate between the models, the effects of added magnesium ions on the kinetics were investigated. At a high Pc concentration (0.7 mM), the ionic strength dependence was found to be consistent with the model involving a conformational change but not with the model where the electron transfer is reversible. One residue in the small acidic patch, Glu60, seems to be responsible for the major part of the ionic strength dependence of the kinetics.

Plastocyanin binding to photosystem I as a function of the charge state of the metal ion: effect of metal site conformation

The binding of Ag- and Cd-substituted plastocyanin to reduced photosystem 1 of spinach has been studied through the rotational correlation time of plastocyanin measured by the technique of perturbed angular correlation of gamma-rays (PAC). Ag and Cd are used as models for native Cu(I) and Cu(II), respectively. A dissociation constant of 5 microM was found for Ag-plastocyanin, whereas the dissociation constant was at least 24 times higher for Cd-plastocyanin. PAC was further used to characterize the structure of the metal site of Cd- and Ag-plastocyanin. The Cd spectra are characteristic of a planar configuration of one cysteine and two histidines. However, the spectra show an unusual peak broadening and a high degree of internal motion, interpreted as motion of one of the histidines within the plane. (111)Ag decays to (111)Cd, followed by the emission of two gamma-rays used for the PAC experiment. The (111)Ag PAC spectra indicate that one of the coordinating histidines has a different position in the Ag protein than in the Cd protein but that the decay of Ag to Cd causes a relaxation of the position of this histidine to the position in the Cd protein within 20 ns. Binding of Ag-plastocyanin to photosystem I stabilized the Ag metal site structure so that no relaxation was observed on a time scale of 100 ns. This stabilization of the Ag structure upon binding indicates that the metal site structure is involved in regulating how the dissociation constant for plastocyanin depends on the charge of the metal ion.

Comparing the rates and the activation parameters for the forward reaction between the triplet state of zinc cytochrome c and cupriplastocyanin and the back reaction between the zinc cytochrome c cation radical and cuproplastocyanin

This is a comparative study of the photoinduced (so-called forward) electron-transfer reaction 3Zncyt/pc(II) --> Zncyt+/pc(I), between the triplet state of zinc cytochrome c (3Zncyt) and cupriplastocyanin [pc(II)], and the thermal (so-called back) electron-transfer reaction Zncyt+/pc(I) --> Zncyt/pc(II), between the cation (radical) of zinc cytochrome c (Zncyt+) and cuproplastocyanin [pc(I)], which follows it. Both reactions occur between associated (docked) reactants, and the respective unimolecular rate constants are kF and kB. Our previous studies showed that the forward reaction is gated by a rearrangement of the diprotein complex. Now we examine the back reaction and complare the two. We study the effects of temperature (in the range 273.3-302.9 K) and viscosity (in the range 1.00-17.4 cP) on the rate constants and determine enthalpies (DeltaH), entropies (DeltaS), and free energies (DeltaG) of activation. We compare wild-type spinach plastocyanin, the single mutants Tyr83Leu and Glu59Lys, and the double mutant Glu59Lys/Glu60Gln. The rate constant kB for wild-type spinach plastocyanin and its mutants markedly depends on viscosity, an indication that the back reaction is also gated. The activation parameters DeltaH and DeltaS show that the forward and back reactions have similar mechanisms, involving a rearrangement of the diprotein complex from the initial binding configuration to the reactive configuration. The rearrangements of the complexes 3Zncyt/pc(II) and Zncyt+/pc(I) that gate their respective reactions are similar but not identical. Since the back reaction of all plastocyanin variants is faster than the forward reaction, the difference in free energy between the docking and the reactive configuration is smaller for the back reaction than for the forward reaction. This difference is explained by the change in the electrostatic potential on the plastocyanin surface as Cu(II) is reduced to Cu(I). It is the smaller DeltaH that makes DeltaG smaller for the back reaction than for the forward reaction.

Crystal structure of spinach plastocyanin at 1.7 A resolution

The crystal structure of plastocyanin from spinach has been determined using molecular replacement, with the structure of plastocyanin from poplar as a search model. Successful crystallization was facilitated by site-directed mutagenesis in which residue Gly8 was substituted with Asp. The region around residue 8 was believed to be too mobile for the wild-type protein to form crystals despite extensive screening. The current structure represents the oxidized plastocyanin, copper (II), at low pH (approximately 4.4). In contrast to the similarity in the core region as compared to its poplar counterpart, the structure shows some significant differences in loop regions. The most notable is the large shift of the 59-61 loop where the largest shift is 3.0 A for the C(alpha) atom of Glu59. This results in different patterns of electrostatic potential around the acidic patches for the two proteins.

Effects of single and double mutations in plastocyanin on the rate constant and activation parameters for the rearrangement gating the electron-transfer reaction between the triplet state of zinc cytochrome c and cupriplastocyanin

The unimolecular rate constant for the photoinduced electron-transfer reaction 3Zncyt/pc(II) --> Zncyt+/pc(I) within the electrostatic complex of zinc cytochrome c and spinach cupriplastocyanin is kF. We report the effects on kF of the following factors, all at pH 7.0: 12 single mutations on the plastocyanin surface (Leu12Asn, Leu12Glu, Leu12Lys, Asp42Asn, Asp42Lys, Glu43Asn, Glu59Gln, Glu59Lys, Glu60Gln, Glu60Lys, Gln88Glu, and Gln88Lys), the double mutation Glu59Lys/Glu60Gln, temperature (in the range 273.3-302.9 K), and solution viscosity (in the range 1. 00-116.0 cP) at 283.2 and 293.2 K. We also report the effects of the plastocyanin mutations on the association constant (Ka) and the corresponding free energy of association (DeltaGa) with zinc cytochrome c at 298.2 K. Dependence of kF on temperature yielded the activation parameters DeltaH, DeltaS, and DeltaG. Dependence of kF on solution viscosity yielded the protein friction and confirmed the DeltaG values determined from the temperature dependence. The aforementioned intracomplex reaction is not a simple electron-transfer reaction because donor-acceptor electronic coupling (HAB) and reorganizational energy (lambda), obtained by fitting of the temperature dependence of kF to the Marcus equation, deviate from the expectations based on precedents and because kF greatly depends on viscosity. This last dependence and the fact that certain mutations affect Ka but not kF are two lines of evidence against the mechanism in which the electron-transfer step is coupled with the faster, but thermodynamically unfavorable, rearrangement step. The electron-transfer reaction is gated by the slower, and thus rate determining, structural rearrangement of the diprotein complex; the rate constant kF corresponds to this rearrangement. Isokinetic correlation of DeltaH and DeltaS parameters and Coulombic energies of the various configurations of the Zncyt/pc(II) complex consistently show that the rearrangement is a facile configurational fluctuation of the associated proteins, qualitatively the same process regardless of the mutations in plastocyanin. Correlation of kF with the orientation of the cupriplastocyanin dipole moment indicates that the reactive configuration of the diprotein complex involves the area near the residue 59, between the upper acidic cluster and the hydrophobic patch. Kinetic effects and noneffects of plastocyanin mutations show that the rearrangement from the initial (docking) configuration, which involves both acidic clusters, to the reactive configuration does not involve the lower acidic cluster and the hydrophobic patch but involves the upper acidic cluster and the area near the residue 88.

The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics

BACKGROUND

The reduction of plastocyanin by cytochrome f is part of the chain of photosynthetic electron transfer reactions that links photosystems II and I. The reaction is rapid and is influenced by charged residues on both proteins. Previously determined structures show that the plastocyanin copper and cytochrome f haem redox centres are some distance apart from the relevant charged sidechains, and until now it was unclear how a transient electrostatic complex can be formed that brings the redox centres sufficiently close for a rapid reaction.

RESULTS

A new approach was used to determine the structure of the transient complex between cytochrome f and plastocyanin. Diamagnetic chemical shift changes and intermolecular pseudocontact shifts in the NMR spectrum of plastocyanin were used as input in restrained rigid-body molecular dynamics calculations. An ensemble of ten structures was obtained, in which the root mean square deviation of the plastocyanin position relative to cytochrome f is 1.0 A. Electrostatic interaction is maintained at the same time as the hydrophobic side of plastocyanin makes close contact with the haem area, thus providing a short electron transfer pathway (Fe-Cu distance 10.9 A) via residues Tyr1 or Phe4 (cytochrome f) and the copper ligand His87 (plastocyanin).

CONCLUSIONS

The combined use of diamagnetic and paramagnetic chemical shift changes makes it possible to obtain detailed information about the structure of a transient complex of redox proteins. The structure suggests that the electrostatic interactions 'guide' the partners into a position that is optimal for electron transfer, and which may be stabilised by short-range interactions.

The involvement of the two acidic patches of spinach plastocyanin in the reaction with photosystem I

Six different spinach plastocyanin mutants have been constructed by site-directed mutagenesis and expressed in Escherichia coli to probe the importance of the two acidic patches in the interaction with photosystem I. The mutants were: Asp42Lys, Glu43Asn, Glu43Lys, Glu43Gln/Asp44Asn, Glu59Lys/Glu60Gln and Glu43Asn/Glu59Lys/Glu60Gln and they have been characterised by optical absorption and EPR spectroscopy, redox titrations and isoelectric focusing. The electron transfer to photosystem I was investigated by flash-induced time-resolved absorption measurements at 830 nm. The kinetics were interpreted with a model that incorporates a rate-limiting conformational change from inactive to active forms of the plastocyanin-photosystem I complex. All mutations resulted in a displacement of the equilibrium towards the inactive conformation. The strongest impairment of the electron transfer was found for mutations in the larger acidic patch, in particular upon modification of residues 43 or 44. However, mutations of residues 59 and 60 in the smaller acidic patch also resulted in a lower reactivity.