Topography of the free-energy landscape probed via mechanical unfolding of proteins

Single-molecule experiments in which proteins are unfolded by applying mechanical stretching forces generally force unfolding to proceed along a reaction coordinate that is different from that in chemical or thermal denaturation. Here we simulate the mechanical unfolding and refolding of a minimalist off-lattice model of the protein ubiquitin to explore in detail the slice of the multidimensional free-energy landscape that is accessible via mechanical pulling experiments. We find that while the free-energy profile along typical "chemical" reaction coordinates may exhibit two minima, corresponding to the native and denatured states, the free energy G(z) is typically a monotonic function of the mechanical coordinate z equal to the protein extension. Application of a stretching force along z tilts the free-energy landscape resulting in a bistable (or multistable) free energy G(z)-fz probed in mechanical unfolding experiments. We construct a two-dimensional free-energy surface as a function of both chemical and mechanical reaction coordinates and examine the coupling between the two. We further study the refolding trajectories after the protein has been prestretched by a large force, as well as the mechanical unfolding trajectories in the presence of a large stretching force. We demonstrate that the stretching forces required to destabilize the native state thermodynamically are larger than those expected on the basis of previous experimental estimates of G(z). This finding is consistent with the recent experimental studies, indicating that proteins may refold even in the presence of a substantial stretching force. Finally, we show that for certain temperatures the free energy of a polyprotein chain consisting of multiple domains is a linear function of the chain extension. We propose that the recently observed "slow phase" in the refolding of proteins under mechanical tension may be viewed as downhill diffusion in such a linear potential.     

Kinetics of zinc and cadmium dissociation of metallothionein in the presence of chelating agents

The dissociation kinetics of metal ions from native metallothionein (Cd₅Zn₂-MT) of rat liver has been studied in the presence of external ligands including amino acids, peptide and polyamino polycarboxylic acids at 25°C. The study shows that the solution pH affects the metal dissociation process. Different ligands present different multiphasic kinetics. The possible mechanism of metal dissociation from metallothionein has been proposed.     

The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233: characterisation of an aminotransferase involved in the formation of 2-deoxystreptamine

The biosynthetic gene cluster of the 2-deoxystreptamine (DOS)-containing aminoglycoside antibiotic neomycin has been cloned for the first time by screening of a cosmid library of Streptomyces fradiae NCIMB 8233. Sequence analysis has identified 21 putative open reading frames (ORFs) in the neomycin gene cluster (neo) with significant protein sequence similarity to gene products involved in the biosynthesis of other DOS-containing aminoglycosides, namely butirosin (btr), gentamycin (gnt), tobramycin (tbm) and kanamycin (kan). Located at the 5'-end of the neo gene cluster is the previously-characterised neomycin phosphotransferase gene (apH). Three genes unique to the neo and btr clusters have been revealed by comparison of the neo cluster to btr, gnt, tbm and kan clusters. This suggests that these three genes may be involved in the transfer of a ribose moiety to the DOS ring during the antibiotic biosynthesis. The product of the neo-6 gene is characterised here as the L-glutamine : 2-deoxy-scyllo-inosose aminotransferase responsible for the first transamination in DOS biosynthesis, which supports the assignment of the gene cluster.     

Development of a bioreactor based on trypsin immobilized on monolithic support for the on-line digestion and identification of proteins

The preparation and characterization of a new trypsin-based bioreactor is here described for on-line protein digestion and peptide analysis. Trypsin was immobilized on an epoxy-modified silica monolithic support with a single reaction step and the amount of immobilized enzyme was found to be 66.07 mg (+/-11.75 S.D.)/column (n = 6). The bioreactor was coupled through a switching valve to an analytical column for the on-line digestion, peptide separation and identification of test proteins by ESI-MS-MS. The influence of various parameters (flow rate, temperature, buffer pH and molarity, etc.) on enzymatic activity was investigated by an experimental design and the mostly significant factor was found to be the flow rate. The efficacy of the reported on-line bioreactor for tryptic mapping is reported for somatostatin and myoglobin, selected as model compounds. Tryptic peptide maps obtained by on-line digestion of myoglobin were compared to those obtained by traditional off-line digestion. Sequence coverage obtained with the on-line protocol (21 peptides, 75.16% coverage of myoglobin sequence) was found to be comparable to the one obtained with the off-line protocol (18 peptides, 76.47% coverage). Sensitivity for myoglobin digestion and identification was 0.1 mg/ml. The reproducibily of the peptide maps in terms of retention time was from 1.53 to 4.31%, R.S.D.     

Force acting on the microparticles in electrorheological solids under the application of a nonuniform ac electric field

Under the application of electric fields, the structure of electrorheological (ER) solids can be changed from the body-centered tetragonal lattice to other lattices. We have derived the dipole factor for the lattice by taking into account the local-field effect through the Ewald–Kornfeld formulation, and expressed it in the spectral representation exactly. It is found that when the ER solid is subject to a nonuniform ac electric field, the force acting on the microparticle can be affected by the structure transformation, and local-field effect as well as field frequency. Our results are very well understood in the spectral representation theory.     

SYNTHESIS AND CHARACTERIZATION OF PHTHALAZINONE POLY(ARYL ETHER SULFONE KETONE)WITH CARBONYL GROUP*

A kind of novel heat-resistant, high performance engineering thermoplastic phthalazinone poly(aryl ether sulfoneketone) (PPESK) containing a carboxyl group in its side chain was prepared by the nucleophilic displacement reaction of 4-(4-hydroxylphenyl)-1(2H)-phthalazinone with di(4-chlorophenyl) sulfone, 4,4'-difluoro-benzophenone and phenolphthalin insulfolane in the presence of K_2CO_3 to produce high molecular weight polymers which can be dissolved in some polarsolvents such as chloroform and nitrobenzene at room temperature and can be easily can into flexible, yellowish andtransparent films. PPESK is an amorphous polymer having a decomposition temperature above 400℃, which indicates that ithas high thermal stability. At the same time, the thermal properties of PPESKs with dicyandiamide (DICY) as curing agentindicated that the heat-resistance properties of the PPESKs are improved after curing. The apparent activation energy (ΔE) ofthe cross-linking reaction and the reaction order (n) of PPESK/DICY were found to be 52.2 kJ/mol and ca. 1.0, respectively.Therefore, the cross-linking reaction is approximately a first order reaction.     

Theoretical study on structures and stability of C4P isomers

The structures, energetics, spectroscopies, and stabilities of doublet C(4)P isomeric species are explored at the DFT/B3LYP, QCISD, and CCSD(T) (singlet-point) levels. A total of 12 minimum isomers and 27 interconversion transition states are located. At the CCSD(T)/6-311G(2df)//QCISD/6-311G(d)+ZPVE level, the lowest-lying isomer is a floppy CCCCP 1 (0.0 kcal/mol) mainly featuring a cumulenic structure |C=C=C=C=P*|, which differs much from the analogous C4N radical (|*C-C[triple bond]C-C[triple bond]N|). The quasi-linearity and the low bending mode of 1 are in contrast to the previous prediction. The second energetically followed isomer PC-cCCC 3 (14.9 kcal/mol) possesses a CCC ring-bonded to CP. The two low-lying isomers are separated by a high-energy ring-closure/open transition state (26.5 kcal/mol) and thus are very promising candidates for future laboratory and astrophysical detection. Furthermore, four high-energy isomers, that is, two bent isomers CCPCC 2 (68.4 kcal/mol) and CCPCC 2' (68.5 kcal/mol) and two cagelike species 10 (56.0 kcal/mol) and 11 (67.9 kcal/mol), are also stabilized by considerable barriers. The present work is the first detailed potential energy survey of CnP clusters and can provide useful information for the investigation of larger CnP radicals and for understanding the isomerism of P-doped C vaporization processes.     

Studies on the properties of ionic liquid EMIInCl4

This paper reports that an ionic liquid (IL) has been prepared by directly mixing InCl₃ and 1-methyl-3-ethylimidazolium chloride (EMIC) with molar ratio 1/1 under dry argon atmosphere. The densities, and surface tension of the pure IL were determined at temperature range of 293.15 to 343.15 ± 0.1 K. The volumetric properties and the properties of surface for ionic liquid based on group III were discussed by Glasser's theory and Yang's interstice model.     

Validation of the extended simultaneous kinetics and ringdown model by measurements of the reaction NH2 + NO

The determination of rate constants for fast chemical reactions from nonexponential cavity ringdown profiles requires a consideration of the interfering laser bandwidth effect that arises if the line width of the ringdown probe laser exceeds the absorption line width of the detected species. The deconvolution of the kinetics and the bandwidth effect can be accomplished with the extended simultaneous kinetics and ringdown (eSKaR) model presented by Guo et al. (Guo, et al. Phys. Chem. Chem. Phys. 2003, 5, 4622). We present a detailed validation of this eSKaR model by a corresponding investigation of the well-known rate constant for the reaction NH2 + NO. Line profiles of the pulsed ringdown probe laser and the NH2 absorption line were determined from forward modeling of experimental ringdown profiles and verified by narrow-bandwidth laser absorption measurements. In addition, the rate constant for the title reaction was evaluated using the eSKaR model and also by means of a conventional pump-probe approach with variable time delays between the photolysis (pump) and ringdown (probe) laser pulses. The resulting room temperature rate constant for the NH2 + NO reaction, k1= (8.5 +/- 1.0) x 10(12) cm(3) mol(-1) s(-1), and the room temperature pressure broadening coefficient of NH2, = 2.27 GHz/bar, measured on the A2A1<-- X2B1 transition at wavelengths around lambda = 597 nm, were found to be in excellent agreement with the available literature data.     

Fe(II) in different macrocycles: electronic structures and properties

A theoretical comparative study of complexes of porphyrin (P), porphyrazine (Pz), phthalocyanine (Pc), porphycene (Pn), dibenzoporphycene (DBPn), and hemiporphyrazine (HPz) with iron (Fe) has been carried out using a density functional theory (DFT) method. The difference in the core size and shape of the macrocycle has a substantial effect on the electronic structure and properties of the overall system. The ground states of FeP and FePc were identified to be the 3A2g [(d(xy))2(d(z)2)2(d(pi))2] state, followed by 3E(g) [(d(xy))2(d(z)2)1(d(pi))3]. For FePz, however, the 3E(g)-3A2g energy gap of 0.02 eV may be too small to distinguish between the ground and excited states. When the symmetry of the macrocycle is reduced from D4h to D2h, the degeneracy of the d(pi) (d(xz), d(yz)) orbitals is removed, and the ground state becomes 3B2g [(d(xy))2(d(z)2)1(d(yz))2(d(xz))1] or 3B3g [...(d(yz))1(d(xz))2] for FePn, FeDBPn, and FeHPz. The calculations also show how the change of the macrocycle can influence the axial ligand coordination of pyridine (Py) and CO to the Fe(II) complexes. Finally, the electronic structures of the mono- and dipositive and -negative ions for all the unligated and ligated iron macrocycles were elucidated, which is important for understanding the redox properties of these compounds. The differences in the observed electrochemical (oxidation and reduction) properties between metal porphycenes (MPn) and metal porphyrins (MP) can be accounted for by the calculated results (orbital energy level diagrams, ionization potentials, and electron affinities).