Stark fluorescence spectroscopy on peridinin–chlorophyll–protein complex of dinoflagellate,Amphidinium carterae

Photosynthesis Research - Because of their peculiar but intriguing photophysical properties, peridinin–chlorophyll–protein complexes (PCPs), the peripheral light-harvesting antenna...     

Reconstitution of the Peridinin–chlorophyll a Protein (PCP): Evidence for Functional Flexibility in Chlorophyll Binding

The coding regions for the N-domain, and full length peridinin–chlorophyll a apoprotein (full length PCP), were expressed in Escherichia coli. The apoproteins formed inclusion bodies from which the peptides could be released by hot buffer. Both the above constructs were reconstituted by addition of a total pigment extract from native PCP. After purification by ion exchange chromatography, the absorbance, fluorescence excitation and CD spectra resembled those of the native PCP. Energy transfer from peridinin to Chl a was restored and a specific fluorescence activity calculated which was ~86% of that of native PCP. Size exclusion analysis and CD spectra showed that the N-domain PCP dimerized on reconstitution. Chl a could be replaced by Chl b, 3-acetyl Chl a, Chl d and Bchl using the N-domain apo protein. The specific fluorescence activity was the same for constructs with Chl a, 3-acetyl Chl a, and Chl d but significantly reduced for those made with Chl b. Reconstitutions with mixtures of chlorophylls were also made with eg Chl b and Chl d and energy transfer from the higher energy Qy band to the lower was demonstrated.     

Characterization of chlorophyll–protein complexes isolated from a Siphonous green alga, Bryopsis corticulans

Six chlorophyll–protein complexes are isolated from thylakoid membranes of Bryopsis corticulans by dodecyl-β-d-maltoside polyacrylamide gel electrophoresis. Unlike that of higher plants, the 77 K fluorescence emission spectrum of the CP1 band, the PSI core complexes of B. corticulans, presents two peaks, one at 675 nm and the other at 715–717 nm. The emission peak at 715–717 nm is slightly higher than that at 675 nm in the CP1 band when excited at 438 or 540 nm. However, the peak at 715 nm is obviously lower than that at 675 nm when excited at 480 nm. The excitation spectra of CP1 demonstrate that the peak at 675 nm is mainly attributed to energy from Chl b while it is the energy from Chl a that plays an important role in exciting the peak at 715–717 nm. Siphonaxanthin is found to contribute to both the 675 nm and 715–717 nm peaks. We propose from the above results that chlorophyll a and siphonaxanthin are mainly responsible for the transfer of energy to the far-red region of PSI while it is Chl b that contributes most of the transfer of energy to the red region of PSI. The analysis of chlorophyll composition and spectral characteristics of LHCP¹ and LHCP³ also indicate that higher content of Chl b and siphonaxanthin, mainly presented in LHCP¹, the trimeric form of LHCII, are evolved by B. corticulans to absorb an appropriate amount of light energy so as to adapt to their natural habitats.     

Validation of a new restraint docking method for solution structure determinations of protein–ligand complexes

A new method is proposed for docking ligands into proteins in cases where an NMR-determined solution structure of a related complex is available. The method uses a set of experimentally determined values for protein–ligand, ligand–ligand, and protein–protein restraints for residues in or near to the binding site, combined with a set of protein–protein restraints involving all the other residues which is taken from the list of restraints previously used to generate the reference structure of a related complex. This approach differs from ordinary docking methods where the calculation uses fixed atomic coordinates from the reference structure rather than the restraints used to determine the reference structure. The binding site residues influenced by replacing the reference ligand by the new ligand were determined by monitoring differences in ¹H chemical shifts. The method has been validated by showing the excellent agreement between structures of L. casei dihydrofolate reductase.trimetrexate calculated by conventional methods using a full experimentally determined set of restraints and those using this new restraint docking method based on an L. casei dihydrofolate reductase.methotrexate reference structure.     

UV–Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 2: selected applications

In Part 2 we discuss application of several different types of UV–Vis spectroscopy, such as normal, difference, and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, of the side-chain of tyrosine residues in different molecular environments. We review the ways these spectroscopies can be used to probe complex protein structures.     

The "prismane" protein resolved: X-ray structure at 1.7 Å and multiple spectroscopy of two novel 4Fe clusters

The three-dimensional structure of the native "putative prismane" protein from Desulfovibrio vulgaris (Hildenborough) has been solved by X-ray crystallography to a resolution of 1.72?Å. The molecule does not contain a [6Fe-6S] prismane cluster, but rather two 4Fe clusters some 12?Å apart and situated close to the interfaces formed by the three domains of the protein. Cluster 1 is a conventional [4Fe-4S] cubane bound, however, near the N-terminus by an unusual, sequential arrangement of four cysteine residues (Cys 3, 6, 15, 21). Cluster 2 is a novel 4Fe structure with two μ₂-sulfido bridges, two μ₂-oxo bridges, and a partially occupied, unidentified μ₂ bridge X. The protein ligands of cluster 2 are widely scattered through the second half of the sequence and include three cysteine residues (Cys 312, 434, 459), one persulfido-cysteine (Cys 406), two glutamates (Glu 268, 494), and one histidine (His 244). With this unusual mixture of bridging and external type of ligands, cluster 2 is named the "hybrid" cluster, and its asymmetric, open structure suggests that it could be the site of a catalytic activity. X-ray absorption spectroscopy at the Fe K-edge is readily interpretable in terms of the crystallographic model when allowance is made for volume contraction at 10?K; no Fe··Fe distances beyond 3.1?Å could be identified. EPR, Mössbauer and MCD spectroscopy have been used to define the oxidation states and the magnetism of the clusters in relation to the crystallographic structure. Reduced cluster 1 is a [4Fe-4S]¹⁺ cubane with S?=?3/2; it is the first biological example of a "spin-admixed" iron-sulfur cluster. The hybrid cluster 2 has four oxidation states from (formally) all Fe^III to three Fe^II plus one Fe^III. The four iron ions are exchange coupled resulting in the system spins S?=?0, 9/2, 0 (and 4), 1/2, respectively, for the four redox states. Resonance Raman spectroscopy suggests that the bridging ligand X which could not be identified unambiguously in the crystal structure is a solvent-exchangeable oxygen.     

X-ray absorption spectroscopic analysis of Fe(II) and Cu(II) forms of a herbicide-degrading α-ketoglutarate dioxygenase

 The first step in the degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) by Ralstonia eutropha JMP134 is catalyzed by the α-ketoglutarate (α-KG)-dependent dioxygenase TfdA. Previously, EPR and ESEEM studies on inactive Cu(II)-substituted TfdA suggested a mixture of nitrogen/oxygen coordination with two imidazole-like ligands. Differences between the spectra for Cu TfdA and α-KG- and 2,4-D-treated samples were interpreted as a rearrangement of the g–tensor principal axis system. Herein, we report the use of X-ray absorption spectroscopy (XAS) to further characterize the metal coordination environment of Cu TfdA as well as that in the active, wild-type Fe(II) enzyme. The EXAFS data are interpreted in terms of four N/O ligands (two imidazole-like) in the Cu TfdA sample and six N/O ligands (one or two imidazole-like) in the Fe TfdA sample. Addition of α-KG results in no significant structural change in coordination for Cu or Fe TfdA. However, addition of 2,4-D results in a decrease in the number of imidazole ligands in both Cu and Fe TfdA. Since this change is seen both in the Fe and Cu EXAFS, loss of one histidine ligand upon 2,4-D addition best describes the phenomenon. These XAS data clearly demonstrate that changes occur in the atomic environment of the metallocenter upon substrate binding. Received: 3 July 1998 / Accepted: 13 October 1998     

A new insulin-mimetic bis(allixinato)zinc(II) complex: structure–activity relationship of zinc(II) complexes

During the investigation of the development of insulin-mimetic zinc(II) complexes with a blood glucose-lowering effect in experimental diabetic animals, we found a potent bis(maltolato)zinc(II) complex, Zn(ma)₂, exhibiting significant insulin-mimetic effects in a type 2 diabetic animal model. By using this Zn(ma)₂ as the leading compound, we examined the in vitro and in vivo structure–activity relationships of Zn(ma)₂ and its related complexes. The in vitro insulin-mimetic activity of these complexes was determined by the inhibition of free fatty acid release and the enhancement of glucose uptake in isolated rat adipocytes treated with epinephrine. A new Zn(II) complex with allixin isolated from garlic, Zn(alx)₂, exhibited the highest insulin-mimetic activity among the complexes analyzed. The insulin-mimetic activity of the Zn(II) complexes examined strongly correlated (correlation coefficient=0.96) with the partition coefficient (logP) of the ligand, indicating that the activity of Zn(ma)₂-related complexes depends on the lipophilicity of the ligand. The blood glucose-lowering effects of Zn(alx)₂ and Zn(ma)₂ were then compared, and both complexes were found to normalize hyperglycemia in KK-A^y mice after a 14-day course of daily intraperitoneal injections. However, Zn(alx)₂ improved glucose tolerance in KK-A^y mice much more than did Zn(ma)₂, indicating that Zn(alx)₂ possesses greater in vivo anti-diabetic activity than Zn(ma)₂. In addition, Zn(alx)₂ improved leptin resistance and suppressed the progress of obesity in type 2 diabetic KK-A^y mice. On the basis of these observations, we conclude that the Zn(alx)₂ complex is a novel potent candidate for the treatment of type 2 diabetes mellitus.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00775-004-0590-8     

The formation and reactivity of sulfito complexes of tetraethylenepentamine-cobalt(III): X-ray structure of αα-[co(tetren)SO3]ClO4

The synthesis of complexes of the type Co(tetren)-OH₂³⁺ (tetren = tetraethylenepentamine) and their reactions with sulfite to produce O- and S-bonded isomers were studied in detail. The linkage isomerization reaction of αβS-Co(tetren)OSO₂⁺ to αβS-Co(tetren)SO₃⁺ is accompanied by a geometrical isomerization to αα-Co(tetren)SO₃⁺. The latter species was isolated as pure crystals and an X-ray structure was determined. The structure data clearly show the strong trans effect of the sulfito ligand, which may account for the geometrical isomerization process.     

The influence of quaternary structure on the stability of Fenna–Matthews–Olson (FMO) antenna complexes

Photosynthesis Research - The trimeric nature of the Fenna–Matthews–Olson (FMO) protein antenna complex from green sulfur phototrophic bacteria was investigated. Mutations were...     

PRICE (PRotein Interface Conservation and Energetics): a server for the analysis of protein–protein interfaces

Residues in a protein–protein interface that are important for forming and stabilizing the interaction can usually be identified by looking at patterns of evolutionary conservation in groups of homologous proteins and also by the computational identification of binding hotspots. The PRICE (PRotein Interface Conservation and Energetics) server takes the coordinates of a protein–protein complex, dissects the interface into core and rim regions, and calculates (1) the degree of conservation (measured as the sequence entropy), as well as (2) the change in free energy of binding (∆∆G, due to alanine scanning mutagenesis) of interface residues. Results are displayed as color-coded plots and also made available for download. This enables the computational identification of binding hot spots, based on which further experiments can be designed. The method will aid in protein functional prediction by correct assignment of hot regions involved in binding. Consideration of sequence entropies for residues with large ∆∆G values may provide an indication of the biological relevance of the interface. Finally, the results obtained on a test set of alanine mutants has been compared to those obtained using other servers/methods. The PRICE server is a web application available at .     

Force spectroscopy and fluorescence microscopy of dsDNA–YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region

When individual dsDNA molecules are stretched beyond their B-form contour length, they reveal a structural transition in which the molecule extends 1.7 times its contour length. The nature of this transition is still a subject of debate. In the first model, the DNA helix unwinds and combined with the tilting of the base pairs (which remain intact), results in a stretched form of DNA (also known as S-DNA). In the second model the base pairs break resulting effectively in two single-strands, which is referred to as force-induced melting. Here a combination of optical tweezers force spectroscopy with fluorescence microscopy was used to study the structure of dsDNA in the overstretching regime. When dsDNA was stretched in the presence of 10 nM YOYO-1 an initial increase in total fluorescence intensity of the dye–DNA complex was observed and at an extension where the dsDNA started to overstretch the fluorescence intensity leveled off and ultimately decreased when stretched further into the overstretching region. Simultaneous force spectroscopy and fluorescence polarization microscopy revealed that the orientation of dye molecules did not change significantly in the overstretching region (78.0°± 3.2°). These results presented here clearly suggest that, the structure of overstretched dsDNA can be explained accurately by force induced melting.     

UV–Vis spectroscopy of tyrosine side-groups in studies of protein structure. Part 1: basic principles and properties of tyrosine chromophore

Spectroscopic properties of tyrosine residues may be employed in structural studies of proteins. Here we discuss several different types of UV–Vis spectroscopy, like normal, difference and second-derivative UV absorption spectroscopy, fluorescence spectroscopy, linear and circular dichroism spectroscopy, and Raman spectroscopy, and corresponding optical properties of the tyrosine chromophore, phenol, which are used to study protein structure.     

Interaction of zinc ions with d(CGCAATTGCG) in a 2.9 Å resolution X-ray structure

We have synthesized and crystallized in the presence of Zn(2+) ions the peptidyl-oligonucleotide adduct CH(3)CO-(Arg)(4)-NH-(CH(2))(6)-NH-p-d(CGCAATTGCG). This is the first structure obtained from a deoxyoligonucleotide crystallized in the presence of zinc ions. Zn ions are clearly visible in the 2.9 A resolution map. On the other hand, the peptide tail is not visible in the crystal structure as determined by X-ray diffraction. The terminal bases C1 and G10 are found in extra-helical positions. Their phosphates are ligands of a Zn(2+) ion, located in a special position of the unit cell. This ion plays an important role in the packing arrangement, since it binds four different DNA molecules. Two other Zn(2+) ions are also important for DNA packing. They interact specifically with the N7 atoms of the terminal G2 and G10 bases, but not with the internal G8. This result supports the hypothesis that transition metals do not interact with the bases of duplex DNA in the B form.     

Synthesis,X-ray structures,and magnetic properties of heterometal dinuclear Cr(III)–M(II) complexes

New 3,5-bis(2-pyridyl)pyrazolato (bpypz) bridged heterometal dinuclear complexes [(nta)Cr(μ-bpypz)M^II(picen)]⁺ (M = Mn(II), Ni(II)) and [(acac)₂Cr(μ-bpypz)Ni^II(picen)]²⁺ (nta = nitrilotriacetate, picen = N,N′-bis(2-pyridylmethyl)ethylenediamine, acac = acetylacetate) were synthesized and characterized by the X-ray analysis, ESI-MS and the magnetic measurements, and/or ²H NMR spectra. The molecular structures were compared from a viewpoint of the conformation of the picen depending on M^II ionic radii or different modes of hydrogen bonds. The picen in [(nta)Cr(μ-bpypz)Mn^II(picen)]BF₄ takes an abnormal conformation with intramolecular bifurcated three-center hydrogen bonds between two carboxylate oxygens of nta and an amine proton of the picen as found for the previously reported corresponding Fe(II) complex [K. Ni-iya, A. Fuyuhiro, T. Yagi, S. Nasu, K. Kuzushita, S. Morimoto, S. Kaizaki, Bull. Chem. Soc. Jpn. 74 (2001) 1891]. On the other hand, for both Ni(II)-nta and Ni(II)-acac complexes, the picen takes a normal conformation with only a two-center hydrogen bond between non-bridging ligands. The magneto-structural relation is discussed for the Cr(III)–Ni(II) complexes in connection with the orthogonality or orbital overlap arising from the difference in distortion around Cr(III) moiety.