Mechanistic insights into type III restriction enzymes

Type III restriction-modification (R-M) enzymes need to interact with two separate unmethylated DNA sequences in indirectly repeated, head-to-head orientations for efficient cleavage to occur at a defined location next to only one of the two sites. However, cleavage of sites that are not in head-to-head orientation have been observed to occur under certain reaction conditions in vitro. ATP hydrolysis is required for the long-distance communication between the sites prior to cleavage. Type III R-M enzymes comprise two subunits, Res and Mod that form a homodimeric Mod(2) and a heterotetrameric Res(2)Mod(2) complex. The Mod subunit in M-2 or R2M2 complex recognizes and methylates DNA while the Res subunit in R2M2 complex is responsible for ATP hydrolysis, DNA translocation and cleavage. A vast majority of biochemical studies on Type III R-M enzymes have been undertaken using two closely related enzymes, EcoP1I and EcoP15I. Divergent opinions about how the long-distance interaction between the recognition sites exist and at least three mechanistic models based on 1D- diffusion and/or 3D-DNA looping have been proposed.

On the two dimensional effective electron mass in quantum wells, inversion layers and NIPI superlattices of Kane type semiconductors in the presence of strong light waves: Simplified theory and relative comparison

An attempt is made to study the two dimensional (2D) effective electron mass (EEM) in quantum wells (Qws), inversion layers (ILs) and NIPI superlattices of Kane type semiconductors in the presence of strong external photoexcitation on the basis of a newly formulated electron dispersion laws within the framework of k.p. formalism. It has been found, taking InAs and InSb as examples, that the EEM in Qws, ILs and superlattices increases with increasing concentration, light intensity and wavelength of the incident light waves, respectively and the numerical magnitudes in each case is band structure dependent. The EEM in ILs is quantum number dependent exhibiting quantum jumps for specified values of the surface electric field and in NIPI superlattices; the same is the function of Fermi energy and the subband index characterizing such 2D structures. The appearance of the humps of the respective curves is due to the redistribution of the electrons among the quantized energy levels when the quantum numbers corresponding to the highest occupied level changes from one fixed value to the others. Although the EEM varies in various manners with all the variables as evident from all the curves, the rates of variations totally depend on the specific dispersion relation of the particular 2D structure. Under certain limiting conditions, all the results as derived in this paper get transformed into well known formulas of the EEM and the electron statistics in the absence of external photo-excitation and thus confirming the compatibility test. The results of this paper find three applications in the field of microstructures. (C) 2011 Elsevier Ltd. All rights reserved.

Structure and Mechanistic Insights into Novel Iron-mediated Moonlighting Functions of Human J-protein Cochaperone, Dph4

J-proteins are obligate cochaperones of Hsp70s and stimulate their ATPase activity via the J-domain. Although the functions of J-proteins have been well understood in the context of Hsp70s, their additional co-evolved ``physiological functions'' are still elusive. We report here the solution structure and mechanism of novel iron-mediated functional roles of human Dph4, a type III J-protein playing a vital role in diphthamide biosynthesis and normal development. The NMR structure of Dph4 reveals two domains: a conserved J-domain and a CSL-domain connected via a flexible linker-helix. The linker-helix modulates the conformational flexibility between the two domains, regulating thereby the protein function. Dph4 exhibits a unique ability to bind iron in tetrahedral coordination geometry through cysteines of its CSL-domain. The oxidized Fe-Dph4 shows characteristic UV-visible and electron paramagnetic resonance spectral properties similar to rubredoxins. Iron-bound Dph4 (Fe-Dph4) also undergoes oligomerization, thus potentially functioning as a transient ``iron storage protein,'' thereby regulating the intracellular iron homeostasis. Remarkably, Fe-Dph4 exhibits vital redox and electron carrier activity, which is critical for important metabolic reactions, including diphthamide biosynthesis. Further, we observed that Fe-Dph4 is conformationally better poised to perform Hsp70-dependent functions, thus underlining the significance of iron binding in Dph4. Yeast Jjj3, a functional ortholog of human Dph4 also shows a similar iron-binding property, indicating the conserved nature of iron sequestration across species. Taken together, our findings provide invaluable evidence in favor of additional co-evolved specialized functions of J-proteins, previously not well appreciated.

Finite Element Method For A Nonlocal Problem Of Kirchhoff Type

The nonlocal term in the nonlinear equations of Kirchhoff type causes difficulties when the equation is solved numerically by using the Newton-Raphson method. This is because the Jacobian of the Newton-Raphson method is full. In this article, the finite element system is replaced by an equivalent system for which the Jacobian is sparse. We derive quasi-optimal error estimates for the finite element method and demonstrate the results with numerical experiments.

Carrier concentration dependence of donor activation energy in n-type GaN epilayers grown on Si (111) by plasma-assisted MBE

The n-type GaN layers were grown by plasma-assisted MBE and either intentionally doped with Si or unintentionally doped. The optical characteristics of a donor level in Si-doped, GaN were studied in terms of photoluminescence (PL) spectroscopy as a function of electron concentration. Temperature dependent PL measurements allowed us to estimate the activation energy of a Si-related donor from temperature-induced decay of PL intensity. PL peak positions, full width at half maximum of PL and activation energies are found to be proportional to the cube root of carrier density. The involvement of donor levels is supported by the temperature-dependent electron concentration measurements. (C) 2012 Elsevier Ltd. All rights reserved.

Sliding wear behavior of plasma nitrided Austenitic Stainless Steel Type AISI 316LN in the temperature range from 25 to 400 degrees C at 10(-4) bar

There is a research knowledge gap for the dry wear data of nitride treated Stainless Steel in high temperature and high vacuum environment. In order to fill this gap, plasma nitriding was done on austenitic Stainless Steel type AISI 316LN (316LN SS) and dry sliding wear tests have been conducted at 25 degrees C, 200 degrees C and 400 degrees C in high vacuum of 1.6 x 10(-4) bar. The two different slider material (316LN SS and Colmonoy) and two different sliding speeds (0.0576 m/s and 0.167 m/s) have been used. The tribological parameters such as friction coefficient, wear mechanism and volume of metal loss have been evaluated. Scanning Electron Microscopy (SEM) was used to study the surface morphology of the worn pins and rings. Electronic balancing machine was used to record the mass of metal loss during wear tests. The 2D optical profilometer was used to measure the depth of the wear track. The Plasma Nitride treated 316LN SS rings (PN rings) exhibit excellent wear resistance against 316LN SS pin and Colmonoy pin at all temperatures. However, PN ring vs. Colmonoy pin Pair shows better wear resistance than PN ring vs. 316LN SS pin Pair at higher temperature. (C) 2012 Elsevier B.V. All rights reserved.

Effect of the Edge Type and Strain on the Structural, Electronic and Magnetic Properties of the BNRs

We present the effect of edge structures on the edge energy and stress of BN nanoribbons. Ab initio density functional calculations show that the armchair edge is lower in energy than the zigzag edge by 0.43 eV/angstrom. Both types of the edges are under the compressive stress. The zigzag edges are mechanically more stable than the armchair edges. Based on the calculated edge energies, the equilibrium shape of the BN flakes are found to be regular hexagonal, and dominated by the armchair edges. The zigzag ribbons are found to be half-metallic, whereas the armchair ribbons are semiconducting.

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis

Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of D-and L-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 angstrom resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with DL-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.