A conformational change associated with the phototransformation of Pisum phytochrome A as probed by fluorescence quenching

An exploration of the interaction mechanism of Direct Red 80 with α-Amylase at the molecular level

The use and production of Direct Red 80 (DR80) dye are growing rapidly, and a large amount of dye wastewater is discharged into the soil without treatment. DR80 accumulated in soil or sludge can lead to enzyme poisoning, inhibit microbial activity, and affect the transformation of substances in the soil. In this research, the interaction mechanism between DR80 and α-Amylase (a typical enzyme in soil and sludge) was investigated by multi-spectra, molecular docking, thermodynamics analysis and enzyme activity experiment. The results of UV-visible and resonance light scattering (RLS) spectra showed that the skeleton of α-Amylase became loosened and unfolded under the exposure of Direct Red. The size of α-Amylase was smaller and α-Amylase became dispersed under high concentration of DR80. Molecular docking and thermodynamic analysis showed that DR80 bound to the surface of domain A rather than the active site of α-Amylase in the form of hydrogen bonds, and the binding process was an exothermic reaction. In addition, the inhibition of α-Amylase activity by DR80 was verified by enzyme activity experiment. These results indicate that DR80 has an effect on the structure and function of α-Amylase at molecular level, which means that the toxicity of DR80 should receive more attention.

Copper complexes containing thiosemicarbazones derived from 6-nitropiperonal: Antimicrobial and biophysical properties

A series of four thiosemicarbazones from 6-nitropiperonal along with the corresponding copper complexes were synthesized. The biophysical characteristics of the complexes were investigated by the binding to DNA and human serum albumin. The binding to DNA is moderate; the binding constants run from (0.49-7.50)×10⁴M^-1. In relation to HSA, the complexes interact strongly with binding constants on the order of 10⁵M^-1. The complexes also display antioxidant behavior as determined by the ability to scavenge diphenylpicrylhydrazyl (dpph) and nitric oxide radicals. The antimicrobial profiles of the compounds, tested against a panel of microbes including five of the ESKAPE pathogens (Staphylococcus aureus, MRSA, Escherichia coli, Klebsiella pneumoniae, MDR, Acinetobacter baumannii, Pseudomonas aeruginosa) and two yeasts (Candida albicans and Cryptococcus neoformans var. grubii), are also described. The compounds contain a core moiety that is similar to oxolinic acid, a quinolone antibiotic that targets DNA gyrase and topoisomerase (IV). The binding interaction between the complexes and these important antibacterial targets were studied by computational methods, chiefly docking studies. The calculated dissociation constants for the interaction with DNA gyrase B (from Staphylococcus aureus) range from 4.32 to 24.65μM; the binding was much stronger to topoisomerase IV, with dissociation constants ranging from 0.37 to 1.27μM.

Acridone in a biological nanocavity: detailed spectroscopic and docking analyses of probing both the tryptophan residues of bovine serum albumin

AD initially gets hooked to Trp 212 housed in domain IIA, inducing conformational changes in the protein and paving the way for the ligand to reach Trp 134 located in domain IB.

Molecular mechanism on cadmium-induced activity changes of catalase and superoxide dismutase

Cadmium contributes to adverse effects of organisms probably because of its ability to induce oxidative stress via alterations in activities of antioxidant enzymes catalase (CAT) and superoxide dismutase (SOD), but their molecular mechanisms remain unclear. We investigated the molecular mechanism of CAT and SOD response under Cd-induced oxidative stress in the liver of zebrafish. The enzyme activity changes observed in vitro were consistent with those seen in vivo, indicating the direct interaction of CAT and SOD with Cd contributes to their activity change in vivo. Further experiments utilizing multiple spectroscopic methods, isothermal titration calorimetry and a molecular docking study were performed to explore the mechanism of molecular interaction of CAT and SOD with Cd. Different interaction patterns were found that resulted in misfolding and changed the enzyme activities. Taken together, we suggest the misfolding of CAT and SOD contributes to their activity change under Cd-induced oxidative stress in vivo.

A novel interaction mode between acrylamide and its specific antibody

Since the discovery of high-level acrylamide (Acr) contamination in food, extensive international studies have focused on its toxicity and detection. By using a novel antigen synthetic strategy, we have successfully obtained a specific antibody towards acrylamide (Acr-Ab). Herein, the Acr-Ab and its interactions with Acr were characterized. Enzyme-linked immunosorbent assay (ELISA) and dynamic light scattering (DLS) investigations revealed that the conformational structure of Acr-Ab was sensitive to buffers. It showed a satisfied immunoreactivity in phosphate buffered saline (PBS), but denatured in water. In natural state, Acr-Ab had a trend of getting aggregation through their complementarity determining regions (CDRs). Adding Acr leaded to their disassembling. While mixed with Acr, Acr-Ab exhibits not only a fast, high-specific, and reversible non covalent binding (by surface plasmon resonance, SPR), but also a covalent alkylation with Acr through cysteine and histidine residues on its surface, as demonstrated by high-performance liquid chromatography (HPLC). Neither of the two reactions involves conformational change in secondary or tertiary structures as shown in circular dichroism spectra (CD). These special properties of Acr-Ab and the entirely new interaction mode with Acr will extend our knowledge of Acr related biosystem and facilitate the development of new detection strategies for Acr.

Albumin antioxidant response to stress in diabetic nephropathy progression

Background

A new component of the protein antioxidant capacity, designated Response Surplus (RS), was recently described. A major feature of this component is the close relationship between protein antioxidant capacity and molecular structure. Oxidative stress is associated with renal dysfunction in patients with renal failure, and plasma albumin is the target of massive oxidation in nephrotic syndrome and diabetic nephropathy. The aim of the present study was to explore the albumin redox state and the RS component of human albumin isolated from diabetic patients with progressive renal damage.

Methods/Principal Findings

Serum aliquots were collected and albumin isolated from 125 diabetic patients divided into 5 groups according to their estimated glomerular filtration rate (GFR). In addition to clinical and biochemical variables, the albumin redox state, including antioxidant capacity, thiol group content, and RS component, were evaluated. The albumin antioxidant capacity and thiol group content were reciprocally related to the RS component in association with GFR reduction. The GFR decline and RS component were significantly negatively correlated (R = –0.83, p<0.0001). Age, creatinine, thiol groups, and antioxidant capacity were also significantly related to the GFR decline (R = –0.47, p<0.001; R = –0.68, p<0.0001; R = 0.44, p<0.001; and R = 0.72, p<0.0001).

Conclusion/Significance

The response of human albumin to stress in relation to the progression of diabetic renal disease was evaluated. The findings confirm that the albumin molecular structure is closely related to its redox state, and is a key factor in the progression of diabetes nephropathy.

Novel short-chain analogues of somatostatin as ligands for Cu(II) ions. Role of the metal ion binding on the spatial structure of the ligand

In this paper we present the studies on coordination abilities of two short-chain analogues of somatostatin with free N-terminal and protected amino group towards copper (II) ions. The octreotide is the most popular analogue of the somatostatin (peptide hormone) used in medicine. Somatostatin analogues are used in diagnosis and treatment of the neuroendocrine tumors. Both analyzed analogues are characterized by the presence of two His instead of Cys residues in characteristic fragment of native peptide. We characterize coordination abilities of the ligands using potentiometric and spectroscopic methods. His-analogues of somatostatin are effective ligands for copper (II) ions. Both peptides are able to form the complexes with the cyclic structure.

The tricks plants use to reach appropriate light

The perception of ambient light signals that produce a relevant response to ensure exposure to appropriate levels of light energy is vital for plants. In response to this, intricate molecular mechanisms to mediate light signaling have evolved in plants. Among the responses induced by light, seedling extension is a determining event for plant survival in darkness, especially in the initial stage of plant growth. Here we review previous studies and recent progress towards an understanding of light signaling that regulates seedling elongation. We focus on the three regions of the sunlight spectrum that primarily control seedling elongation, namely red/far-red light, blue/UV-A light and UV-B light, and summarize the four signaling pathways that correspond to the three effective spectra.

Decoding of light signals by plant phytochromes and their interacting proteins

Phytochromes are red/far-red light photoreceptors that convert the information contained in external light into biological signals. The decoding process starts with the perception of red light, which occurs through photoisomerization of a chromophore located within the phytochrome, leading to structural changes that include the disruption of intramolecular interactions between the N- and C-terminal domains of the phytochrome. This disruption exposes surfaces required for interactions with other proteins. In contrast, the perception of far-red light reverses the photoisomerization, restores the intramolecular interaction, and closes the interacting surfaces. Light information represented by the concentration of opened interacting surfaces is converted into biological signals through the modulating activity of interacting proteins. This review summarizes plant phytochromes, phytochrome-interacting proteins, and signal transmission from phytochromes to their interacting proteins.

A rice phytochrome A in Arabidopsis: The Role of the N-terminus under red and far-red light

The phytochrome (phy)A and phyB photoreceptors mediate three photobiological response modes in plants; whereas phyA can mediate the very-low-fluence response (VLFR), the high-irradiance response (HIR) and, to some extent, the low fluence response (LFR), phyB and other type II phytochromes only mediate the LFR. To investigate to what level a rice phyA can complement for Arabidopsis phyA or phyB function and to evaluate the role of the serine residues in the first 20 amino acids of the N-terminus of phyA, we examined VLFR, LFR, and HIR responses in phyB and phyAphyB mutant plants transformed with rice PHYA cDNA or a mutant rice PHYA cDNA in which the first 10 serine residues were mutated to alanines (phyA SA). Utilizing mutants without endogenous phyB allowed the evaluation of red-light-derived responses sensed by the rice phyA. In summary, the WT rice phyA could complement VLFR and LFR responses such as inhibition of hypocotyl elongation under pulses of FR or continuous R light, induction of flowering and leaf expansion, whereas the phyA SA was more specific for HIR responses (e.g. inhibition of hypocotyl elongation and anthocyanin accumulation under continuous far-red light). As the N-terminal serines can no longer be phosphorylated in the phyA SA mutant, this suggests a role for phosphorylation discriminating between the different phyA-dependent responses. The efficacy of the rice phyA expressed in Arabidopsis was dependent upon the developmental age of the plants analyzed and on the physiological response, suggesting a stage-dependent downstream modulation of phytochrome signaling.

Differential interactions of phytochrome A (Pr vs. Pfr) with monoclonal antibodies probed by a surface plasmon resonance technique

Phytochromes are red- and far-red light-reversible photoreceptors for photomorphogenesis in plants. Phytochrome A is a dimeric chromopeptide that mediates very low fluence and high irradiance responses. To analyze the surface properties of phytochrome A (phyA), the epitopes of 21 anti-phyA monoclonal antibodies were determined by variously engineered recombinant phyA proteins and the dissociation constants of seven anti-phyA monoclonal antibodies with phyA were measured using a surface plasmon resonance (SPR)-based resonant mirror biosensor (IAsys). Purified oat phyA was immobilized on the sensor surface using a carboxymethyl dextran cuvette in advance, and the interactions of each chosen monoclonal antibody against phyA in either red light absorbing form (Pr) or far-red light absorbing form (Pfr) at different concentrations were monitored. The binding profiles were analyzed using the FAST Fit program of IAsys. The resultant values of dissociation constants clearly demonstrated the differential affinities between the phyA epitopes and the monoclonal antibodies dependent upon Pr vs. Pfr conformations. Monoclonal antibody mAP20 preferentially recognized the epitope at amino acids 653-731 in the Pr form, whereas mAA02, mAP21 and mAR07/mAR08 displayed preferential affinities for the Pfr's surfaces at epitopes 494-601 (the hinge region between the N- and C-terminal domains), 601-653 (hinge in PASI domain), and 772-1128 (C-terminal domain), respectively. The N-terminal extension (1-74) was not recognized by mAP09 and mAP15, suggesting that the N-terminal extreme is not exposed in the native conformation of phyA. On the other hand, the C-terminal domain becomes apparently exposed on Pr-to-Pfr phototransformation, suggesting an inter-domain cross-talk. The use of surface plasmon resonance spectroscopy offers a new approach to study the surface properties of phytochromes associated with the photoreversible structural changes, as well as for the study of protein-protein interactions of phytochromes with their interacting proteins involved in light signaling events in plants.

Structural analysis of Arabidopsis thaliana nucleoside diphosphate kinase-2 for phytochrome-mediated light signaling

In plants, nucleoside diphosphate kinases (NDPKs) play a key role in the signaling of both stress and light. However, little is known about the structural elements involved in their function. Of the three NDPKs (NDPK1-NDPK3) expressed in Arabidopsis thaliana, NDPK2 is involved in phytochrome-mediated signal transduction. In this study, we found that the binding of dNDP or NTP to NDPK2 strengthens the interaction significantly between activated phytochrome and NDPK2. To better understand the structural basis of the phytochrome-NDPK2 interaction, we determined the X-ray structures of NDPK1, NDPK2, and dGTP-bound NDPK2 from A.thaliana at 1.8A, 2.6A, and 2.4A, respectively. The structures showed that nucleotide binding caused a slight conformational change in NDPK2 that was confined to helices alphaA and alpha2. This suggests that the presence of nucleotide in the active site and/or the evoked conformational change contributes to the recognition of NDPK2 by activated phytochrome. In vitro binding assays showed that only NDPK2 interacted specifically with the phytochrome and the C-terminal regulatory domain of phytochrome is involved in the interaction. A domain swap experiment between NDPK1 and NDPK2 showed that the variable C-terminal region of NDPK2 is important for the activation by phytochrome. The structure of Arabidopsis NDPK1 and NDPK2 showed that the isoforms share common electrostatic surfaces at the nucleotide-binding site, but the variable C-terminal regions have distinct electrostatic charge distributions. These findings suggest that the binding of nucleotide to NDPK2 plays a regulatory role in phytochrome signaling and that the C-terminal extension of NDPK2 provides a potential binding surface for the specific interaction with phytochromes.

Phytochrome phosphorylation modulates light signaling by influencing the protein-protein interaction

Plant photoreceptor phytochromes are phosphoproteins, but the question as to the functional role of phytochrome phosphorylation has remained to be elucidated. We investigated the functional role of phytochrome phosphorylation in plant light signaling using a Pfr-specific phosphorylation site mutant, Ser598Ala of oat (Avena sativa) phytochrome A (phyA). The transgenic Arabidopsis thaliana (phyA-201 background) plants with this mutant phyA showed hypersensitivity to light, suggesting that phytochrome phosphorylation at Serine-598 (Ser598) in the hinge region is involved in an inhibitory mechanism. The phosphorylation at Ser598 prevented its interaction with putative signal transducers, Nucleoside Diphosphate Kinase-2 and Phytochrome-Interacting Factor-3. These results suggest that phosphorylation in the hinge region of phytochromes serves as a signal-modulating site through the protein-protein interaction between phytochrome and its putative signal transducer proteins.

Reaction mechanism of plant 2-Cys peroxiredoxin. Role of the C terminus and the quaternary structure

Barley 2-cysteine peroxiredoxin (2-Cys Prx) was analyzed for peroxide reduction, quaternary structure, thylakoid attachment, and function as well as in vivo occurrence of the inactivated form, with emphasis on the role of specific amino acid residues. Data presented show the following. 1) 2-Cys Prx has a broad substrate specificity and reduces even complex lipid peroxides such as phosphatidylcholine dilineoyl hydroperoxide, although at low rates. 2) 2-Cys Prx partly becomes irreversibly oxidized by peroxide substrates during the catalytic cycle in a concentration-dependent manner, particularly by bulky hydroperoxides. 3) Using dithiothreitol and thioredoxin (Trx) as reductants, amino acids were identified that are important for peroxide reduction (Cys64, Arg140, and Arg163), regeneration by Trx (Cys185), and conformation changes from dimer to oligomer (Thr66, Trp99, and Trp189). 4) Oligomerization decreased the rate of Trx-dependent peroxide detoxification. 5) Comparison of PrxWT, W99L, and W189L using static and time-resolved LIF techniques demonstrated the contributions of the tryptophan residues and yielded information about their local environment. Data indicated protein dynamics in the catalytic site and the carboxyl terminus during the reduction-oxidation cycle. 6) Reduced and inactivated barley 2-Cys Prx oligomerized and attached to the thylakoid membrane in isolated chloroplasts. The in vivo relevance of inactivation was shown in leaves subjected to cold and wilting stress and during senescence. Based on these results, it is hypothesized that in addition to its function in peroxide detoxification, 2-Cys Prx may play a role as a structural redox sensor in chloroplasts.

Interaction of the 18.5-kD isoform of myelin basic protein with Ca2+ -calmodulin: effects of deimination assessed by intrinsic Trp fluorescence spectroscopy, dynamic light scattering, and circular dichroism

The effects of deimination (conversion of arginyl to citrullinyl residues) of myelin basic protein (MBP) on its binding to calmodulin (CaM) have been examined. Four species of MBP were investigated: unmodified recombinant murine MBP (rmMBP-Cit(0)), an engineered protein with six quasi-citrullinyl (i.e., glutaminyl) residues per molecule (rmMBP-qCit(6)), human component C1 (hMBP-Cit(0)), and human component C8 (hMBP-Cit(6)), both obtained from a patient with multiple sclerosis (MS). Both rmMBP-Cit(0) and hMBP-Cit(0) bound CaM in a Ca(2+)-dependent manner and primarily in a 1:1 stoichiometry, which was verified by dynamic light scattering. Circular dichroic spectroscopy was unable to detect any changes in secondary structure in MBP upon CaM-binding. Inherent Trp fluorescence spectroscopy and a single-site binding model were used to determine the dissociation constants: K(d) = 144 +/- 76 nM for rmMBP-Cit(0), and K(d) = 42 +/- 15 nM for hMBP-Cit(0). For rmMBP-qCit(6) and hMBP-Cit(6), the changes in fluorescence were suggestive of a two-site interaction, although the dissociation constants could not be accurately determined. These results can be explained by a local conformational change induced in MBP by deimination, exposing a second binding site with a weaker association with CaM, or by the existence of several conformers of deiminated MBP. Titration with the collisional quencher acrylamide, and steady-state and lifetime measurements of the fluorescence at 340 nm, showed both dynamic and static components to the quenching, and differences between the unmodified and deiminated proteins that were also consistent with a local conformational change due to deimination.

Influence of a stationary magnetic field on water relations in lettuce seeds. Part II: experimental results

An experimental study on water absorption by lettuce seeds previously treated in a stationary magnetic field of 0-10 mT is presented. A significant increase in the rate with which the seeds absorb water is observed in the interval 0-10 mT of magnetic treatment. An increment in the total mass of absorbed water in this interval is also observed. These results are consistent with the reports on the increase of germination rate of the seeds, and the theoretical calculation of the variations induced by magnetic fields in the ionic currents across the cellular membrane. The fields originate in changes in the ionic concentration and thus in the osmotic pressure which regulates the entrance of water to the seeds. The good correlation between the theoretical approach and experimental results provides strong evidence that the magnetic field alters the water relations in seeds, and this effect may be the explanation of the reported alterations in germination rate of seeds by the magnetic field.

Inter-domain crosstalk in the phytochrome molecules

Phytochromes are bifunctional photoreceptors with a two-domain structure, consisting of the N-terminal photosensory domain and the C-terminal regulatory domain. The photo-induced Pr <--> Pfr phototransformation accompanies subtle conformational changes, primarily triggered by the apoprotein-chromophore interactions in the N-terminal domain. The conformational signals are subsequently transmitted to the C-terminal domain through various inter-domain crosstalks, resulting in the interaction of the activated C-terminal domain with phytochrome interacting factors. Thus the inter-domain crosstalks play critical roles in the photoactivation of the phytochromes. Protein phosphorylation, such as that of Ser-598, is implicated in this process by inducing conformational changes and by modulating inter-domain signaling.

Surface topography of phytochrome A deduced from specific chemical modification with iodoacetamide

Phytochromes are a photoreversible photochromic light switch for photomorphogenesis in plants. The molecular structure and functional mechanism of phytochromes are not fully understood. On the basis of complete mapping of total tryptic digest of the iodoacetamide-modified oat phytochrome A (phyA), the molecular surface topography of phyA was probed by specific chemical modification of cysteine residues with [14C]iodoacetamide. Under native conditions, only two cysteines (Cys-158 and Cys-311) of eleven half-cystines of the N-terminal chromophore binding domain were modified to a significant extent. In the C-terminal domain, six cysteine residues (Cys-715, Cys-774, Cys-809, Cys-869, Cys-961, Cys-995) were readily accessible to iodoacetamide. Among the reactive cysteine residues, only cysteine-311 displayed reactivity that was dependent on the photochromic form (Pr left arrow over right arrow Pfr) of the photoreceptor. Surprisingly, the modification of Cys-311 in the vicinity of the chromophore attachment site (Cys-321) did not have any detectable effect on spectral properties of phyA. Most of the cysteines of the N-terminal domain (Cys-83, Cys-175, Cys-291, Cys-370, Cys-386, Cys-445, Cys-506) are deeply buried in the core of the chromophore binding domain, as they can be modified only after denaturation of the chromoprotein. In the C-terminal domain, modification of only one cysteine residue (Cys-939) required protein denaturation. Since all 22 half-cystines can be modified with iodoacetamide without reduction of the chromoprotein, it follows that oat phyA does not have any disulfide bonds. We found that Cys-311, Cys-774, Cys-961, and Cys-995 could be easily partially oxidized under the conditions used for phytochrome isolation. The surface topography/conformation of oat phyA and its role in protein-protein recognition in phytochrome-mediated signal transduction are discussed in terms of the relative reactivity of cysteine residues.

The structure and function of phytochrome A: the roles of the entire molecule and of its various parts

Phytochrome A is readily cleavable by proteolytic agents to yield an amino-terminal fragment of 66 kilodalton (kDa), which consists of residues 1 to approximately 600, and a dimer of the carboxy-terminal 55-kDa fragment, from residue 600 or so to the carboxyl terminus. The former domain, carrying the tetrapyrrole chromophore, has been studied extensively because of its photoactivity, while less attention has been paid to the non-chromophoric portion until quite recently. However, the evidence gathered to date suggests that this domain is also of great improtance. We present here a review of the structure and the biochemical and physiological functions of the two domains, of parts of these domains, and of the cooperation between them.

Fourier-transform infrared spectroscopy of phytochrome: difference spectra of the intermediates of the photoreactions

The photocycle of 124 kDa phytochrome A from Avena sativa was studied by Fourier-transform infrared spectroscopy at low temperatures. Difference spectra between the parent state Pr and the intermediates of the Pr-->Pfr pathway, i.e. lumi-R, meta-Ra, and meta-Rc, and between Pfr and the intermediates of the Pfr-->Pr pathway, lumi-F and meta-F, were obtained in 1H2O and 2H2O for the first time. Each spectrum shows characteristic spectral features which allow a clear distinction between the different intermediates. A general feature is that greater changes occur with increasing temperature, i.e. at the later steps of the photoreactions. Nevertheless, the changes in the spectral regions of the protein (amide I and amide II) were found to be surprisingly small, excluding larger conformational changes of the protein. All spectra of the intermediates are characterized by a strong negative band around 1700 cm-1. This band is tentatively assigned to the C = O stretch of ring D of the chromophore. Since it is not observed in the difference spectra between the parent states, it is concluded that ring D is located in a similar molecular environment in Pr and Pfr. In the photoproducts lumi-R and lumi-F, this band undergoes an upshift to 1720 cm-1. The high frequencies suggest that the chromophore is protonated in these intermediates as well as in Pr and Pfr.

Protein folding thermodynamics applied to the photocycle of the photoactive yellow protein

Two complementary aspects of the thermodynamics of the photoactive yellow protein (PYP), a new type of photoreceptor that has been isolated from Ectothiorhodospira halophila, have been investigated. First, the thermal denaturation of PYP at pH 3.4 has been examined by global analysis of the temperature-induced changes in the UV-VIS absorbance spectrum of this chromophoric protein. Subsequently, a thermodynamic model for protein (un)folding processes, incorporating heat capacity changes, has been applied to these data. The second aspect of PYP that has been studied is the temperature dependence of its photocycle kinetics, which have been reported to display an unexplained deviation from normal Arrhenius behavior. We have extended these measurements in two solvents with different hydrophobicities and have analyzed the number of rate constants needed to describe these data. Here we show that the resulting temperature dependence of the rate constants can be quantitatively explained by the application of a thermodynamic model which assumes that heat capacity changes are associated with the two transitions in the photocycle of PYP. This result is the first example of an enzyme catalytic cycle being described by a thermodynamic model including heat capacity changes. It is proposed that a strong link exists between the processes occurring during the photocycle of PYP and protein (un)folding processes. This permits a thermodynamic analysis of the light-induced, physiologically relevant, conformational changes occurring in this photoreceptor protein.