Gold compound auranofin inhibits IkappaB kinase (IKK) by modifying Cys-179 of IKKbeta subunit

Antirheumatic gold compounds have been shown to inhibit NF-kappaB activation by blocking IkappaB kinase (IKK) activity. To examine the possible inhibitory mechanism of gold compounds, we expressed wild type and mutant forms of IKKalpha and beta subunits in COS-7 cells and determined the effect of gold on the activity of these enzymes both in vivo and in vitro. Substitution of Cys-179 of IKKbeta with alanine (C179A) rendered the enzyme to become resistant to inhibition by a gold compound auranofin, however, similar protective effect was not observed with an equivalent level of IKKalpha (C178A) mutant expressed in the cells. Auranofin inhibited constitutively active IKKalpha and beta and variants; IKKalpha (S176E, S180E) or IKKbeta (S177E, S181E), suggesting that gold directly cause inhibition of activated enzyme. The different inhibitory effect of auranofin on IKKalpha (C178A) and IKKbeta (C179A) mutants indicates that gold could inhibit the two subunits of IKK in a different mode, and the inhibition of NF-kappaB and IKK activation induced by inflammatory signals in gold-treated cells appears through its interaction with Cys-179 of IKKbeta.     

Structural Heterogeneity of Cryotrapped Intermediates in the Bacterial Blue Light Photoreceptor,Photoactive Yellow Protein¶

We investigate by X‐ray crystallographic techniques the cryotrapped states that accumulate on controlled illumination of the blue light photoreceptor, photoactive yellow protein (PYP), at 110 K in both the wild‐type species and its E46Q mutant. These states are related to those that occur during the chromophore isomerization process in the PYP photocycle at room temperature. The structures present in such states were determined at high resolution, 0.95–1.05Å. In both wild type and mutant PYP, the cryotrapped state is not composed of a single, quasitransition state structure but rather of a heterogeneous mixture of three species in addition to the ground state structure. We identify and refine these three photoactivated species under the assumption that the structural changes are limited to simple isomerization events of the chromophore that otherwise retains chemical bonding similar to that in the ground state. The refined chromophore models are essentially identical in the wild type and the E46Q mutant, which implies that the early stages of their photocycle mechanisms are the same.     

Primary Reaction Dynamics of Proteorhodopsin Mutant D97N Observed by Femtosecond Infrared and Visible Spectroscopy†

Femtosecond time‐resolved spectroscopy in the visible and IR range was utilized to study the primary reaction dynamics of the proteorhodopsin (PR) D97N mutant in comparison with wild type PR at different pH values. The analysis of the data obtained in the mid‐IR closely resembles the results for wild type PR. The observation of the first ground state intermediate K is initially obscured by a complex reaction scheme of vibrational relaxation and heating effects, but its spectral signature clearly emerges at long delay times. In the visible range, a biexponential decay of the excited state within 30 ps and the formation of the K photoproduct is observed. The decay time constants derived for the D97N mutant in D₂O are slightly larger than in H₂O due to H/D exchange. This kinetic isotope effect is even less pronounced than for wild type PR at pH 6. These results support the current notion of a pH dependent hydrogen bonding network in the retinal binding pocket of PR and a weaker interaction between the retinal Schiff base and the counter ion complex compared to bacteriorhodopsin.     

Electron Transfer Binding Site of Cytochrome c to Carboxylic Acid-Terminated Alkanethiol Self-assembled Monolayers Immobilized on Gold Electrode

It is proposed that Lys-13 of mammalian cytochrome cfacilitates the most efficient electron transfer (ET) pathway to the carboxylate terminus of alkanethiol self-assembled monolayers (SAM) on gold electrodes. In order to confirm the proposed ET pathway, the ET reaction rate of a rat cytochrome c mutant (RC9K13A), in which lysine-13 is replaced by alanine, is measured at a 3-mercaptopropionate SAM on a gold electrode. The ET rate of K13A is more than six orders of magnitude smaller than that of the native one. In the mutant, Ala-13 can no longer facilitate the ET pathway. Based on the measurements, the potential candidate for the binding site of RC9K13A is Lys-8.     

Real-time scanning tunnelling microscopy imaging of protein motion at electrode surfaces

A mutant (K27C) of the blue copper protein azurin [Eur. J. Biochem. 194 (1990) 109; J. Mol. Biol. 221 (1991) 765] for orientated immobilisation on gold surfaces was analysed by scanning tunnelling microscopy (STM) both in a resting state and following the application of a short potential pulse between the tip and sample.     

Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2 ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.     

Molecular Mechanisms of Aggregation of Canine SOD1 E40K Amyloidogenic Mutant Protein

Canine degenerative myelopathy (DM) is a human amyotrophic lateral sclerosis (ALS)-like neurodegenerative disease. It is a unique, naturally occurring animal model of human ALS. Canine DM is associated with the aggregation of canine superoxide dismutase 1 (cSOD1), which is similar to human ALS. Almost 100% of cases in dogs are familial, and the E40K mutation in cSOD1 is a major causative mutation of DM. Therefore, it is important to understand the molecular mechanisms underlying cSOD1(E40K) aggregation. To address this, we first analyzed the structural model of wild type cSOD1. Interactions were evident between amino acid E40 and K91. Therefore, the mutation at residue E40 causes loss of the interaction and may destabilize the native structure of cSOD1. Differential scanning fluorimetry revealed that the E40K mutant was less stable than the wild type. Moreover, stability could be recovered by the E40K and K91E double mutation. Acceleration of amyloid fibril formation in vitro and aggregate formation in cells of cSOD1(E40K) was also suppressed by the introduction of this double mutation in thioflavin T fluorescence assay results and in transfectant cells, respectively. These results clearly show the importance of the interaction between amino acid residues E40 and K91 in cSOD1 for the stability of the native structure and aggregation.     

Au/Al2O3催化剂的制备及其在CH4/CO2重整反应中的催化活性

采用浸渍法和沉积－沉淀法制备了四种不同的Au/Al2O3催化剂，测定了它们在氢气还原前后及催化反应后的金含量及比表面积，结果表明，制备方法明显影响催化剂的金含量，应用X－光粉末衍射技术研究了这些催化剂经还原处理及反应后的物相变化，金以Au^0物相存在，没有发现氧化态的金物相，考察了该催化剂在CH4／CO2重整反应中的催化活性，发现金催化剂的活性取决于金粒子的大小，浸渍法制备的金催化剂具有较大的金晶粒尺寸，催化活性低，沉积－沉淀法制备的金催化剂金晶粒尺寸较小，催化活性较高，以尿素为沉淀剂制备的催化剂给出1073K时的CH4和CO2转化率分别为8．1％和17．6％，高温反应不仅导致金晶粒的聚集，而且存在明显的金流失现象。     

PHOTOCONTROL OF ANTHOCYANIN SYNTHESIS IN TOMATO SEEDLINGS: A GENETIC APPROACH*

The photocontrol of anthocyanin synthesis in dark-grown seedlings of tomato (Lycopersicon esculentum Mill.) has been studied in an aurea (au) mutant which is deficient in the labile type of phytochrome, a high pigment (hp) mutant which has the wild-type level of phytochrome and the double mutant au/hp , as well as the wild type. The hp mutant demonstrates phytochrome control of anthocyanin synthesis in response to a single red light (RL) pulse, whereas there is no measurable response in the wild type and au mutant. After pretreatment with 12 h blue light (BL) the phytochrome regulation of anthocyanin synthesis is 10-fold higher in the hp mutant than in the wild type, whilst no anthocyanin is detectable in the au mutant, thus suggesting that it is the labile pool of phytochrome which regulates anthocyanin synthesis. The au/hp double mutant exhibits a small (3% of that in the hp mutant) RL/far-red light (FR)-reversible regulation of anthocyanin synthesis following a BL pretreatment. It is proposed that the hp mutant is hypersensitive to the FR-absorbing form of phytochrome (P_fr) and that this (hypersensitivity) establishes response to the low level of P_fl. (below detection limits in phytochrome assays) in the au/hp double mutant.     

SPECTRA OF FLUORESCENCE LIFETIME AND INTENSITY OF Rhodopseudomonas sphaeroides AT ROOM AND LOW TEMPERATURE. COMPARISON BETWEEN THE WILD TYPE, THE C 71 REACTION CENTER-LESS MUTANT AND THE B800–850 PIGMENT-PROTEIN COMPLEX

Abstract— Spectra of the fluorescence lifetime and intensity of chromatophores from the wild type Rhodopseudomonas sphaeroides , from the C 71 reaction center-less mutant and of the B800–850 light harvesting pigment-protein complex have been studied by phase fluorimetry techniques at different light modulation frequencies at room and low temperature.
As already known, closed reaction centers (saturating light) are still quenchers of antenna fluorescence although with a lower efficiency than when they are opened. The fluorescence yields and lifetimes of both the C 71 mutant strain and the B800–850complex are found to increase by about 30% between room and low temperature.
The fluorescence lifetimes obtained for the C 71 strain (0.65 ns at 20C; 0.85 ns at 77 K) and for the B850 complex (1 ns at 20C; 1.3 ns at 77 K) indicate that the non-radiative deactivation pathways, in the antenna, remain important in the absence of the reaction centers even at low temperature. We suggest that these data arise from the presence of special antenna molecules which act as intrinsic quenchers of the B875 antenna fluorescence. Between room and low temperature, the fluorescence yield and lifetime of the wild type are found roughly constant. This result suggests that the energy trapping by the reaction centers is independent of the temperature. The mechanism governing the energy transfer from the antenna to the reaction centers may differ from the mechanism leading to the energy transfer within the antenna. We suggest that a partially irreversible trapping of the excitation energy, on its way to the reaction center, takes place in the vicinity of the reaction center.     

Bacillus anthracis and Bacillus subtilis spore surface properties and transport

Effective decontamination of environments contaminated by Bacillus spores remains a significant challenge since Bacillus spores are highly resistant to killing and could plausibly adhere to many non-biological as well as biological surfaces. Decontamination of Bacillus spores can be significantly improved if the chemical basis of spore adherence is understood. In this research, we investigated the surface adhesive properties of Bacillus subtilis and Bacillus anthracis spores. The spore thermodynamic properties obtained from contact angle measurements indicated that both species were monopolar with a preponderance of electron-donating potential. This was also the case for spores of both species missing their outer layers, due to mutation. Transport of wild type and mutant spores of these two species was further analyzed in silica sand under unsaturated water conditions. A two-region solute transport model was used to simulate the spore transport with the assumption that the spore retention occurred within the immobile region only. Bacillus spore adhesion to the porous media was related to the interactions between the spores and the porous media. Our data indicated that spore surface structures played important roles in spore surface properties, since mutant spores missing outer layers had different surface thermodynamic and transport properties as compared to wild type spores. The changes in surface thermodynamic properties were further evidenced by infrared spectroscopy analysis.     

A scanning tunnelling study of immobilised cytochrome P450cam

A site-specifically engineered surface cysteine residue, located in a region where the haem moiety is closest to the surface, is used to anchor cytochrome P450cam enzyme molecules covalently to a gold electrode. More reproducibly ordered adsorption, at high coverage, occurs with this K344C mutant than with the wild-type enzyme. The subsequently formed close-packed monolayer arrays have been probed by scanning tunnelling microscopy under ambient conditions and under aqueous (buffered) solution at high resolution. Initial indications suggest that the immobilised enzyme is both electrochemically addressable and catalytically active.     

Quantum chemical and molecular mechanics studies on the assessment of interactions between resveratrol and mutant SOD1 (G93A) protein

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that has been associated with mutations in metalloenzyme superoxide dismutase (SOD1) causing protein structural destabilization and aggregation. However, the mechanistic action and the cure for the disease still remain obscure. Herein, we initially studied the conformational preferences of SOD1 protein structures upon substitution of Ala at Gly93 in comparison with that of wild type. Our results corroborated with the previous experimental studies on the aggregation and the destabilizing activity of mutant SOD1 protein G93A. On the therapeutic point of view, we computationally analyzed the influence of resveratrol, a natural polyphenol widely found in red wine on mutant SOD1 relative to wild type, using molecular docking studies. Further, FMO calculations were performed, using GAMESS to study the pair residual interaction on the wild type and mutant complex systems. Consequently, the resveratrol showed greater interaction with mutant than the wild type. Subsequently, we evaluated the conformational preferences of wild type and mutant complex systems, where the protein conformational structures of mutant that were earlier found to lose their conformational stability was regained, upon binding with resveratrol. Similar trend of results were found on the 2-D free energy landscapes of both the wild type and mutant systems. Hence, the combined biophysical and quantum chemical studies in our study supported the results of previous experimental studies, thereby stipulating an action of resveratrol on mutant SOD1 and paving a way for the design of highly potent effective inhibitors against fALS affecting the mankind.     

Accurate long-range distance measurements in a doubly spin-labeled protein by a four-pulse, double electron-electron resonance method

Distance determination in disordered systems by a four-pulse double electron-electron resonance method (DEER or PELDOR) is becoming increasingly popular because long distances (several nanometers) and their distributions can be measured. From the distance distributions eventual heterogeneities and dynamics can be deduced. To make full use of the method, typical distance distributions for structurally well-defined systems are needed. Here, the structurally well-characterized protein azurin is investigated by attaching two (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate spin labels (MTSL) by site-directed mutagenesis. Mutations at the surface sites of the protein Q12, K27, and N42 are combined in the double mutants Q12C/K27C and K27C/N42C. A distance of 4.3 nm is found for Q12C/K27C and 4.6 nm for K27C/N42C. For Q12C/K27C the width of the distribution (0.24 nm) is smaller than for the K27C/N42C mutant (0.36 nm). The shapes of the distributions are close to Gaussian. These distance distributions agree well with those derived from a model to determine the maximally accessible conformational space of the spin-label linker. Additionally, the expected distribution for the shorter distance variant Q12C/N42C was modeled. The width is larger than the calculated one for Q12C/K27C by 21%, revealing the effect of the different orientation and shorter distance. The widths and the shapes of the distributions are suited as a reference for two unperturbed MTSL labels at structurally well-defined sites.     

Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb_5 and Its Mutants by Electrospray Mass Spectrometry

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Effect of phosphatidylglycerol depletion on the surface electric properties and the fluorescence emission of thylakoid membranes

To explore the possible effect of phosphatidylglycerol (PG) on the surface electric properties and chlorophyll fluorescence characteristics we used electric light scattering technique and 77 K chlorophyll fluorescence of thylakoid membranes from a cyanobacterium, Synechocystis PCC6803 (wild type) and its pgsA mutant defective in PG synthesis. We found a strong decrease in the permanent and induced electric dipole moments of the mutant thylakoids, following long-term PG depletion parallel with a decrease of the emission peak from PSI and an increase of the emission peak from PSII. Partial recovery of the electric state of thylakoid membranes was observed at re-addition of PG to the mutant cells depleted of PG for 21days. This change in the electric dipole moments is probably due to a decrease in PG content and progressive structural alterations in the macroorganization of the photosynthetic complexes induced by PG deprivation.

Our results suggest that the depletion of a lipid, which carries a negative charge, despite its small contribution to the overall lipid content, significantly perturbs the surface charge of the membranes. These changes are related with the chlorophyll fluorescence emission ratios of two photosystems and may partly explain our earlier results concerning the PG requirement for the function and assembly of photosystems I and II reaction centers.     

Sequential adsorption of bacteriophage T4 lysozyme stability variants at solid–water interfaces

The sequential adsorption of the wild type T4 lysozyme and one of its structural stability variants was studied, using ellipsometry and ¹²⁵I radioisotope labeling techniques. The mutant lysozyme was produced by substitution of the isoleucine residue at position 3 in the wild type with a tryptophan residue, resulting in a protein with lower structural stability. The mutant protein was more resistant to surfactant-mediated elution, and apparently adsorbed at the interfaces with a greater interfacial area/molecule than the wild typeT4 lysozyme. However, the results of each type of experiment suggested that sequential adsorption and exchange of proteins occurred only in the case of the less stable mutant followed by the wild type. This suggests that, in these exchange reactions, properties of the adsorbing protein (e.g. its ability to adsorb when a relatively small amount of unoccupied area is present) were more important than the apparent binding strength of the adsorbed protein molecules.     

Therapeutic Targeting of Oncogenic K‐Ras by a Covalent Catalytic Site Inhibitor

We report the synthesis of a GDP analogue, SML‐8‐73‐1, and a prodrug derivative, SML‐10‐70‐1, which are selective, direct‐acting covalent inhibitors of the K‐Ras G12C mutant relative to wild‐type Ras. Biochemical and biophysical measurements suggest that modification of K‐Ras with SML‐8‐73‐1 renders the protein in an inactive state. These first‐in‐class covalent K‐Ras inhibitors demonstrate that irreversible targeting of the K‐Ras guanine‐nucleotide binding site is potentially a viable therapeutic strategy for inhibition of Ras signaling.     

Development of a ligase detection reaction/CGE method using a LIF dual‐channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild‐type DNA

We developed an inexpensive LIF dual‐channel detection system and applied it to a ligase detection reaction (LDR)/CGE method to identify the allelic composition of low‐abundance point mutations in a large excess of wild‐type DNA in a single reaction with a high degree of certainty. Ligation was performed in a tube with a nonlabeled common primer and multiplex discriminating primers, each labeled with a different standard fluorophore. The discriminating primers were directed against three mutant variations in codon 12 of the K‐ras oncogene that have a high diagnostic value for colorectal cancer. LDR products generated from a particular K‐ras mutation through successful ligation events were separated from remaining discriminating primers by CGE, followed by LIF detection using the new system, which consists of two photomultiplier tubes, each with a unique optical filter. Each fluorophore label conjugated to the corresponding LDR product produced a distinct fluorescence signal intensity ratio from the two detection channels, allowing spectral discrimination of the three labels. The ability of this system to detect point mutations in a wild‐type sequence‐dominated population, and to disclose their allelic composition, was thus demonstrated successfully.     

Analysis of a Critical Residue Determining Herbicide Efficiency Sensitivity in Carboxyltransferase Domain of Acetyl-CoA Carboxylase from Poaceae by Homology Modeling and Free Energy Simulation

Carboxyltransferase domain(CT) of acetyl-coenzyme A carboxylase(ACCase, EC 6.4.1.2) from a family of Poaceae is an important target of commercial herbicide APPs for controlling grass weed growth. As the abuse of APPs herbicides, the resistant ACCase due to the mutation of a single residue(Ile→Leu), which is lo-cated in CT active site, is emergent in many populations and species of Poaceae. So it is urgent to understand the re-sistant mecha-nism so as to design new effect herbicides. Herein lies the complex of CT dimmer from Lolium rigi-dum and herbicide haloxyfop successfully constructed for wild type enzyme and Ile/Leu mutant, respectively, pro-viding a basis for explaining the resistance from microscopic structure. Moreover, the binding free energy difference between wild type and mutant enzymes was predicted in good agreement with the known observation, and the various contributions to it were analyzed, by Molecular mechanics-Poisson-Boltzmann surface area(MM-PBSA) method. The results indicate the van der Waals interaction difference between the protein and inhibitor, –22.94 kJ/mol of CT wild type lower than that of mutant, is the major reason for resistance. Structure analysis further suggests that van der Waals interaction difference is originated from the steric hindrance between the side chain of mutated residue Leu and the chiral methyl group of haloxyfop. All these findings enhance the understanding of resistant mechanism of ACCase to herbicide by Ile/Leu mutation and provide an important clue for the rational design of high effective herbicides.