Amino acid sequences and solution structures of manganese stabilizing protein that affect reconstitution of Photosystem II activity

This minireview presents a summary of information available on the secondary and tertiary structure of manganese stabilizing protein (MSP) in solution, and on the identity of amino acid residues that affect binding and functional assembly of this protein into Photosystem II. New data on the secondary structure of C-terminal mutants and 90 °C-heated manganese stabilizing protein, along with earlier data on the secondary structure of N-terminal mutants and the tertiary structure of all modified MSP species, allow for an evaluation of models for spinach MSP secondary and tertiary structure. This summary of previous and new information better documents the natively unfolded behavior of the protein in solution. A two-step mechanism for binding of manganese stabilizing protein to Photosystem II is discussed and possible solution three-dimensional conformations of the wild-type protein and some of its unfolded mutants, are proposed. This revised version was published online in August 2006 with corrections to the Cover Date.     

The tetranuclear manganese complex of Photosystem II

A polynuclear manganese complex functions in Photosystem II both to accumulate oxidizing equivalents and to bind water and catalyze its four-electron oxidation. Recent electron paramagnetic resonance (EPR) spectroscopic studies of the manganese complex show that four manganese ions are required to account for its magnetic properties. The exchange couplings between manganese ions in the S₂ state are characteristic of a Mn₄O₄ cubane-like structure. Based on this structure for the manganese complex in the S₂ state, as well as a consideration of the known properties of the manganese complex in Photosystem II and the coordination chemistry of manganese, structures are proposed for the five intermediate oxidation states of the manganese complex. A molecular mechanism for the formation of an O-O bond and the displacement of O₂ from the S₄ state is suggested.     

Human full-length Securin is a natively unfolded protein

Human Securin, also called PTTG1 (pituitary tumor transforming gene 1 product), is an estrogen-regulated proto-oncogene with multifunctional properties. We characterized human full-length Securin using a variety of biophysical techniques, such as nuclear magnetic resonance, circular dichroism, and size-exclusion chromatography. Under physiological conditions, Securin is devoid of tertiary and secondary structure except for a small amount of poly-(L-proline) type II helix and its hydrodynamic characteristics suggest it behaves as an extended polypeptide. These results suggest that Securin is unstructured in solution and so belongs to the family of natively unfolded proteins. In addition, to gain structural and quantitative insight, we investigated the binding of Securin to p53. Analytical ultracentrifugation and fluorescence anisotropy studies revealed no evidence of any direct interaction between unmodified recombinant Securin and p53 in vitro.     

Prediction of natively unfolded regions in protein chains

Analysis showed that the globular or natively unfolded state of a protein can be inferred not only from a lower hydrophobicity or a higher charge, but also from the average environment density (average number of close residues located within a certain distance of a given one) of its residues. A database of 6626 protein structures was used to construct a statistical scale of the average number of close residues in globular structures for the 20 amino acids. The portion of false predictions in distinguishing between 80 globular and 90 natively unfolded proteins was 11% with the new scale and 17% with a hydrophobicity scale. The new scale proved suitable for predicting the folded or unfolded state for native proteins or the natively unfolded regions for protein chains. In comparisons with the available algorithms, the new method yielded the highest portion of true predictions (87 and 77% with averaging over residues and over proteins, respectively).     

The effect of an ionic detergent on the natively unfolded beta-dystroglycan ectodomain and on its interaction with alpha-dystroglycan

Dystroglycan (DG) is an adhesion complex, expressed in a wide variety of tissues, formed by an extracellular and a transmembrane subunit, alpha-DG and beta-DG, respectively, interacting noncovalently. Recently, we have shown that the recombinant ectodomain of beta-DG, beta-DG(654-750), behaves as a natively unfolded protein, as it is able to bind the C-terminal domain of alpha-DG, while not displaying a defined structural organization. We monitored the effect of a commonly used denaturing agent, the anionic detergent sodium dodecylsulphate (SDS), on beta-DG(654-750) using a number of biophysical techniques. Very low concentrations of SDS (< or =2 mM) affect both tryptophan fluorescence and circular dichroism of beta-DG, and significantly perturb the interaction with the alpha-DG subunit as shown by solid-phase binding assays and fluorescence titrations in solution. This result confirms, as recently proposed for natively unfolded proteins, that beta-DG(654-750) exists in a native state, which is crucial to fulfill its biological function. Two-dimensional NMR analysis shows that SDS does not induce any evident conformational rearrangement within the ectodomain of beta-DG. Its first 70 amino acids, which show a lower degree of mobility, interact with the detergent, but this does not change the amount of secondary structure, whereas the highly flexible and mobile C-terminal region of beta-DG(654-750) remains largely unaffected, even at a very high SDS concentration (up to 50 mM). Our data indicate that SDS can be used as a useful tool for investigating natively unfolded proteins, and confirm that the beta-DG ectodomain is an interesting model system.     

Structural memory of natively unfolded tau protein detected by small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) is a universal low-resolution method to study size and shape of globular proteins in solution but recent developments facilitate the quantitative characterization of the structure and structural transitions of metastable systems like partially or completely unfolded proteins. We present here a study of temperature induced transitions in tau, a natively unfolded protein involved in Alzheimer's disease. Previous studies on full length tau and several disease-related mutants provided information about the residual structure in different domains revealing a specific role and extended conformations of the so-called repeat domains, which are considered to be responsible for the formation of amyloid-like fibrils ("paired helical filaments"). Here, we employ SAXS to investigate the temperature dependent properties of tau. Slow heating/cooling of the full length protein from 10°C to 50°C did not lead to detectable changes in the overall size. Surprisingly, quick heating/cooling caused tau to adopt a significantly more compact conformation, which was stable over up to 3 h and represents a structural "memory" effect. This compaction is not observed for the shorter tau constructs containing largely the repeat domains. The structural and functional implications of the observed unusual behavior of tau under nonequilibrium conditions are discussed.     

The inactivating factor of glutamine synthetase,IF7, is a "natively unfolded" protein

Glutamine synthetase (GS) is the key enzyme responsible for the primary assimilation of ammonium in all living organisms, and it catalyses the synthesis of glutamine from glutamic acid, ATP, and ammonium. One of the recently discovered mechanisms of GS regulation involves protein-protein interactions with a small 65-residue-long protein named IF7. Here, we study the structure and stability of IF7 and its binding properties to GS, by using several biophysical techniques (fluorescence, circular dichroism, Fourier transform infrared and nuclear magnetic resonance spectroscopies, and gel filtration chromatography) which provide complementary structural information. The findings show that IF7 has a small amount of residual secondary structure, but lacks a well defined tertiary structure, and is not compact. Thus, all of the studies indicate that IF7 is a "natively unfolded" protein. The binding of IF7 to GS, its natural binding partner, occurs with an apparent dissociation constant of K(D) = 0.3 +/- 0.1 microM, as measured by fluorescence. We discuss the implications for the GS regulation mechanisms of IF7 being unfolded.     

The structure and function of the 33 kDa extrinsic protein of Photosystem II: A critical assessment

In this review the structure and function of the 33 kDa protein of Photosystem II is examined. Significant controversies exist concerning the solution secondary structure of the protein, the location of its binding site(s) within Photosystem II, the amino acid residues of the 33 kDa protein required for binding and its stoichiometry within the photosystem. The studies which examine these topics are considered from a critical perspective. A hypothetical model of the folding of the 33 kDa extrinsic protein which is supported by site-specific labeling studies and site-directed mutagenesis experiments is presented. Additionally, the function of the protein within the photosystem is unclear. We present a hypothesis that the 33 kDa protein is involved in maintaining the chloride associated with photosynthetic oxygen evolution in close proximity to the oxygen-evolving site.     

The N-terminal half of the peroxisomal cycling receptor Pex5p is a natively unfolded domain

Targeting of most newly synthesised peroxisomal matrix proteins to the organelle requires Pex5p, the so-called PTS1 receptor. According to current models of peroxisomal biogenesis, Pex5p interacts with these proteins in the cytosol, transports them to the peroxisomal membrane and catalyses their translocation across the membrane. Presently, our knowledge on the structural details behind the interaction of Pex5p with the cargo proteins is reasonably complete. In contrast, information regarding the structure of the Pex5p N-terminal half (a region containing its peroxisomal targeting domain) is still limited. We have recently observed that the Stokes radius of this Pex5p domain is anomalously large, suggesting that this portion of the protein is either a structured elongated domain or that it adopts a low compactness conformation. Here, we address this issue using a combination of biophysical and biochemical approaches. Our results indicate that the N-terminal half of Pex5p is best described as a natively unfolded pre-molten globule-like domain. The implications of these findings on the mechanism of protein import into the peroxisome are discussed.     

Effect of the manganese complex on the binding of the extrinsic proteins (17, 23 and 33 kDa) of Photosystem II

Selective extraction-reconstitution experiments with the extrinsic Photosystem II polypeptides (33 kDa, 23 kDa and 17 kDa) have demonstrated that the manganese complex and the 33 kDa polypeptide are both necessary structural elements for the tight binding of the water soluble 17 and 23 kDa species. When the manganese complex is intact the 33 kDa protein interacts strongly with the rest of the photosynthetic complex. Destruction of the Mn-complex has two dramatic effects: i) The binding of the 33 kDa polypeptide is weaker, since it can be removed by exposure of the PS II system to 2 M NaCl, and ii) the 17 and 23 kDa species do not rebind to Mn-depleted Photosystem II membranes that retain the 33 kDa protein.Abbreviations Chl chlorophyll - HQ hydroquinone - MES 2(N-morpholino)ethanesulfonic acid - PS II Photosystem II - Tris 2-amino-2-hydroxymethylpropane-1,3-diol     

Structure and function of the PsbP protein of Photosystem II from higher plants

PsbP is a membrane extrinsic subunit of Photosystem II (PS II), which is involved in retaining Ca²⁺ and Cl⁻, two inorganic cofactors for the water-splitting reaction. In this study, we re-investigated the role of N-terminal region of PsbP on the basis of its three-dimensional structure. In previous paper [Ifuku and Sato (2002) Plant Cell Physiol 43: 1244–1249], a truncated PsbP lacking 19 N-terminal residues (Δ19) was found to bind to NaCl-washed PS II lacking PsbP and PsbQ without activation of oxygen evolution at all. Three-dimensional (3D) structure of PsbP suggests that deletion of 19 N-terminal residues would destabilize its protein structure, as indicated by the high sensitivity of Δ19 to trypsin digestion. Thus, a truncated PsbP lacking 15 N-terminal residues (Δ15), which retained core PsbP structure, was produced. Whereas Δ15 was resistant to trypsin digestion and bound to NaCl-washed PS II membranes, it did not show the activation of oxygen evolution. This result indicated that the interaction of 15-residue N-terminal flexible region of PsbP with PS II was important for Ca²⁺ and Cl⁻ retention in PS II, although the 15 N-terminal residues were not essential for the binding of PsbP to PS II. The possible N-terminal residues of PsbP that would be involved in this interaction are discussed.     

Insights into protein structure and function from disorder-complexity space

Intrinsically disordered proteins have a wide variety of important functional roles. However, the relationship between sequence and function in these proteins is significantly different than that for well-folded proteins. In a previous work, we showed that the propensity to be disordered can be recognized based on sequence composition alone. Here that analysis is furthered by examining the relationship of disorder propensity to sequence complexity, where the metrics for these two properties depend only on composition. The distributions of 40 amino acid peptides from both ordered and disordered proteins are graphed in this disorder-complexity space. An analysis of Swiss-Prot shows that most peptides have high complexity and relatively low disorder. However, there are also an appreciable number of low complexity-high disorder peptides in the database. In contrast, there are no low complexity-low disorder peptides. A similar analysis for peptides in the PDB reveals a much narrower distribution, with few peptides of low complexity and high disorder. In this case, the bounds of the disorder-complexity distribution are well defined and might be used to evaluate the likelihood that a peptide can be crystallized with current methods. The disorder-complexity distributions of individual proteins and sets of proteins grouped by function are also examined. Among individual proteins, there is an enormous variety of distributions that in some cases can be rationalized with regard to function. Groups of functionally related proteins are found to have distributions that are similar within each group but show notable differences between groups. Finally, a pattern matching algorithm is used to search for proteins with particular disorder-complexity distributions. The results suggest that this approach might be used to identify relationships between otherwise dissimilar proteins.     

Dematin exhibits a natively unfolded core domain and an independently folded headpiece domain

Dematin is an actin‐binding protein originally identified in the junctional complex of the erythrocyte plasma membrane, and is present in many nonerythroid cells. Dematin headpiece knockout mice display a spherical red cell phenotype and develop a compensated anemia. Dematin has two domains: a 315‐residue, proline‐rich “core” domain and a 68‐residue carboxyl‐terminal villin‐type “headpiece” domain. Expression of full‐length dematin in E. coli as a GST recombinant protein results in truncation within a proline, glutamic acid, serine, threonine rich region (PEST). Therefore, we designed a mutant construct that replaces the PEST sequence. The modified dematin has high actin binding activity as determined by actin sedimentation assays. Negative stain electron microscopy demonstrates that the modified dematin also exhibits actin bundling activity like that of native dematin. Circular dichroism (CD) and NMR spectral analysis, however, show little secondary structure in the modified dematin. The lack of secondary structure is also observed in native dematin purified from human red blood cells. ¹⁵N‐HSQC NMR spectra of modified dematin indicate that the headpiece domain is fully folded whereas the core region is primarily unfolded. Our finding suggests that the core is natively unfolded and may serve as a scaffold to organize the components of the junctional complex.     

Six specific lysine residues are crucial in maintaining the structure and function of soluble manganese stabilizing protein

When manganese stabilizing protein （MSP） was treated with 0.5 mM N-succinimidyl propionate （NSP）, the rebinding ability and oxygen-releasing capabilities of the modified MSP were not altered, in spite of changes of MSP surface Lys residues. Furthermore, far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed that 0.5 mM NSP-modified MSP retained most of its native secondary and tertiary structure. Mapping of the sites of NSP modification by Staphylococcus V8 protease digestion of the modified protein, as well as analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry, indicated that seven Lys residues were modified. The results suggested that these residues are not absolutely essential to the structure and function of MSP. However, when the NSP concentration was increased to 4 mM, the modified MSP was unable to bind photosystem Ⅱ and completely lost its reactivating capability. Both far-ultraviolet circular dichroism and intrinsic fluorescence spectra analysis revealed a clear conformational change in MSP after 4 mM NSP treatment, suggesting that some Lys residues are involved in maintaining the structure and function of MSP. Analysis by matrix-assisted laser desorption ionization-time of flight mass spectrometry indicated that another six Lys residues, namely Lys20, Lys 101, Lys196, Lys207, Lysl30 （or Lys137） and Lys66 （or Lys76）, were modified by 4 mM NSP. Therefore, these six Lys residues are crucial in maintaining the structure and function of soluble MSP.     

Nitrogen ligation to the manganese cluster of Photosystem II in the absence of the extrinsic proteins and as a function of pH

Three extrinsic proteins (PsbO, PsbP and PsbQ), with apparent molecular weights of 33, 23 and 17 kDa, bind to the lumenal side of Photosystem II (PS II) and stabilize the manganese, calcium and chloride cofactors of the oxygen evolving complex (OEC). The effect of these proteins on the structure of the tetramanganese cluster, especially their possible involvement in manganese ligation, is investigated in this study by measuring the reported histidine-manganese coupling [Tang et al. (1994) Proc Natl Acad Sci USA 91: 704–708] of PS II membranes depleted of none, two or three of these proteins using ESEEM (electron spin echo envelope modulation) spectroscopy. The results show that neither of the three proteins influence the histidine ligation of manganese. From this, the conserved histidine of the 23 kDa protein can be ruled out as a manganese ligand. Whereas the 33 and 17 kDa proteins lack conserved histidines, the existence of a 33 kDa protein-derived carboxylate ligand has been posited; our results show no evidence for a change of the manganese co-ordination upon removal of this protein. Studies of the pH-dependence of the histidine–manganese coupling show that the histidine ligation is present in PS II centers showing the S₂ multiline EPR signal in the pH-range 4.2–9.5. This revised version was published online in June 2006 with corrections to the Cover Date.     

Influence of protein phosphorylation on the electron-transport properties of Photosystem II

Many of the core proteins in Photosystem II (PS II) undergo reversible phosphorylation. It is known that protein phosphorylation controls the repair cycle of Photosystem II. However, it is not known how protein phosphorylation affects the partial electron transport reactions in PS II. Here we have applied variable fluorescence measurements and EPR spectroscopy to probe the status of the quinone acceptors, the Mn cluster and other electron transfer components in PS II with controlled levels of protein phosphorylation. Protein phosphorylation was induced in vivo by varying illumination regimes. The phosphorylation level of the D1 protein varied from 10 to 58% in PS II membranes isolated from pre-illuminated spinach leaves. The oxygen evolution and Q_A ⁻ to Q_B(Q_B ⁻) electron transfer measured by flash-induced fluorescence decay remained similar in all samples studied. Similar measurements in the presence of DCMU, which reports on the status of the donor side in PS II, also indicated that the integrity of the oxygen-evolving complex was preserved in PS II with different levels of D1 protein phosphorylation. With EPR spectroscopy we examined individual redox cofactors in PS II. Both the maximal amplitude of the charge separation reaction (measured as photo-accumulated pheophytin⁻) and the EPR signal from the Q_A ⁻ Fe²⁺ complex were unaffected by the phosphorylation of the D1 protein, indicating that the acceptor side of PS II was not modified. Also the shape of the S₂ state multiline signal was similar, suggesting that the structure of the Mn-cluster in Photosystem II did not change. However, the amplitude of the S₂ multiline signal was reduced by 35% in PS II, where 58% of the D1 protein was phosphorylated, as compared to the S₂ multiline in PS II, where only 10% of the D1 protein was phosphorylated. In addition, the fraction of low potential Cyt b ₅₅₉ was twice as high in phosphorylated PS II. Implications from these findings, were precise quantification of D1 protein phosphorylation is, for the first time, combined with high-resolution biophysical measurements, are discussed. This revised version was published online in June 2006 with corrections to the Cover Date.     

Electron transfer in the water-oxidizing complex of Photosystem II

An overview is presented of secondary electron transfer at the electron donor side of Photosystem II, at which ultimately two water molecules are oxidized to molecular oxygen, and the central role of manganese in catalyzing this process is discussed. A powerful technique for the analysis of manganese redox changes in the water-oxidizing mechanism is the measurement of ultraviolet absorbance changes, induced by single-turnover light flashes on dark-adapted PS II preparations. Various interpretations of these ultraviolet absorbance changes have been proposed. Here it is shown that these changes are due to a single spectral component, which presumably is caused by the oxidation of Mn(III) to Mn(IV), and which oscillates with a sequence +1, +1, +1, –3 during the so-called S₀ S₁ S₂ S₃ S₀ redox transitions of the oxygen-evolving complex. This interpretation seems to be consistent with the results obtained with other techniques, such as those on the multiline EPR signal, the intervalence Mn(III)-Mn(IV) transition in the infrared, and EXAFS studies. The dark distribution of the S states and its modification by high pH and by the addition of low concentrations of certain water analogues are discussed. Finally, the patterns of proton release and of electrochromic absorbance changes, possibly reflecting the change of charge in the oxygen-evolving system, are discussed. It is concluded that nonstoichiometric patterns must be considered, and that the net electrical charge of the system probably is the highest in state S₂ and the lowest in state S₁.     

Stabilization of the water oxidizing polypeptide assembly on Photosystem II membranes by osmolytes and other solutes

The integrity of Photosystem II membranes isolated from chloroplast thylakoids is profoundly affected by the solute environment. Examples are given for stabilizing effects various solutes have on the binding of the 17 and 23 kDa extrinsic polypeptides under conditions conductive to their dissociation. It is concluded that these and many other solute effects on Photosystem II membranes can be accommodated readily in a concept developed by Timasheff and his coworkers according to which the responses of proteins to their solute environment are consequences of interaction preferences among the constituents of the solvent-protein-solute systems.Abbreviations Chl chlorophyll - MES 2-(N-morpholino)ethanesulfonic acid - MOPS (3-[N-morpholino]propanesulfonic acid) - PS II Photosystem II     

Electric-field-induced luminescence emission spectra of Photosystem I and Photosystem II from chloroplasts

The electroluminescence induced by external electric fields in blebs prepared from chloroplasts consists of two kinetically different phases, rapid (R) and slow (S), which were shown to be linked to Photosystem I (PS I) and Photosystem II (PS II) activities, respectively (Symons, M., Korenstein, R. and Malkin, S. (1985) Biochim. Biophys. Acta 806, 305–310). In this report we describe conditions involving heat treatment of broken chloroplasts, which make it possible to observe R phase electroluminescence essentially devoid of any contribution by the S phase. This allowed the precise measurement of the emission spectrum of PS I electroluminescence. The emission spectrum of PS II electroluminescence was obtained using regular broken chloroplasts, which show only S-type emission. The latter emission spectrum is identical to the one obtained for ordinary prompt fluorescence, peaking at 685 nm with a bandwidth of about 25 nm. The PS I emission spectrum is symmetric around 705 nm and is much broader, about 60 nm.