Variation in mutation rates caused by RB69pol fidelity mutants can be rationalized on the basis of their kinetic behavior and crystal structures

We have previously observed that stepwise replacement of amino acid residues in the nascent base-pair binding pocket of RB69 DNA polymerase (RB69pol) with Ala or Gly expanded the space in this pocket, resulting in a progressive increase in misincorporation. However, in vivo results with similar RB69pol nascent base-pair binding pocket mutants showed that mutation rates, as determined by the T4 phage rI forward assay and rII reversion assay, were significantly lower for the RB69pol S565G/Y567A double mutant than for the Y567A single mutant, the opposite of what we would have predicted. To investigate the reasons for this unexpected result, we have determined the pre-steady-state kinetic parameters and crystal structures of relevant ternary complexes. We found that the S565G/Y567A mutant generally had greater base selectivity than the Y567A mutant and that the kinetic parameters for dNMP insertion, excision of the 3′-terminal nucleotide residue, and primer extension beyond a mispair differed not only between these two mutants but also between the two highly mutable sequences in the T4 rI complementary strand. Comparison of the crystal structures of these two mutants with correct and incorrect incoming dNTPs provides insight into the unexpected increase in the fidelity of the S565G/Y567A double mutant. Taken together, the kinetic and structural results provide a basis for integrating and interpreting in vivo and in vitro observations.     

NiS2/FeS Holey Film as Freestanding Electrode for High‐Performance Lithium Battery

In this work, a freestanding NiS₂/FeS holey film (HF) is prepared after electrochemical anodic and chemical vapor deposition treatments. With the combination of good electrical conductivity and holey structure, the NiS₂/FeS HF presents superior electrochemical performance, due to the following reasons: (i) Porous structure of HF provides a large surface area and more active sites/channels/pathways to enhance the ion/mass diffusion. Moreover, the porous structure can reduce the damage from the volumetric expansion. (ii) The as‐prepared electrode combines the current collector (residual NiFe alloy) and active materials (sulfides) together, thus reducing the resistance of the electrode. Additionally, the good conductivity of HF can improve electron transport. (iii) Sulfides are more stable as active materials than sulfur, showing only a small capacity decay while retaining high cyclability performance. This work provides a promising way to develop high energy and stable electrode for Li‐S battery.     

A pyridine adduct of bis(di-iso-butyldithiocarbamato-S,S′)cadmium(II): Multinuclear (C, N, Cd) CP/MAS NMR spectroscopy, crystal and molecular structure, and thermal behaviour

Crystalline bis(N,N-di-iso-butyldithiocarbamato-S,S′)(pyridine)cadmium(II) - adduct 1 was prepared and studied by means of multinuclear ¹³C, ¹⁵N, ¹¹³Cd CP/MAS NMR spectroscopy, single-crystal X-ray diffraction and simultaneous thermal analysis (STA). In molecular structure 1, the cadmium atom coordinates with four sulphur atoms and one nitrogen atom of pyridine, forming a coordination polyhedron [CdS₄N], whose geometry is an almost ideal tetragonal pyramidal (C_4v). The coordinated py molecule is in the apical position, while two structurally non-equivalent di-iso-butyldithiocarbamate ligands, playing the same terminal S,S′-chelating function, define the basal plane. To characterise additionally the structural state of the cadmium atom in this fivefold coordination, ¹¹³Cd chemical shift anisotropy (CSA) parameters, δ_aniso and η, were calculated from experimental MAS NMR spectra that revealed an almost axially symmetric ¹¹³Cd chemical shift tensor. From a combination of TG and DSC measurements taken under an argon atmosphere, we found that the mass of adduct 1 is lost in two steps involving initial desorption of coordinated py molecules with subsequent thermal destruction of liberated cadmium(II) di-iso-butyldithiocarbamate, with yellow-orange, fine-powdered solid CdS as the final product.     

Synthesis and performance of 3D-megaporous structures for enzyme immobilization and protein capture

The preparation of megaporous bodies, with potential applications in biotechnology, was attempted by following several strategies. As a first step, naive and robust scaffolds were produced by polymerization of selected monomers in the presence of a highly soluble cross‐linker agent. Ion‐exchange function was incorporated by particle embedding, direct chemical synthesis, or radiation‐induced grafting. The total ionic capacity of such systems was 1.5 mmol H⁺/g, 1.4 mmol H⁺/g, and 17 mmol H⁺/g, respectively. These values were in agreement with the ability to bind model proteins: observed dynamic binding capacity at 50% breakthrough was ?7.2 mg bovine serum albumin/g, ?7.4 hen egg‐white lysozyme (HEWL) mg/g, and ?108 HEWL mg/g. In the later case, total (static) binding capacity reached 220 mg/g. It was observed that the structure and size of the megapores remained unaffected by the grafting procedure which, however, allowed for the highest protein binding capacity. Lysozyme supported on grafted body showed extensive clarification activity against a Micrococcus lysodekticus suspension in the flow‐through mode, i.e., 90% destruction of suspended microbial cells was obtained with a residence time ≈ 18 min. Both protein capture and biocatalysis applications are conceivable with the 3D‐megaporous materials described in this work. © 2011 American Institute of Chemical Engineers Biotechnol. Prog., 2011     

Solvent effects on the conformational transition of a model polyalanine peptide

We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA(14)K-NH(2) molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain's hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: alpha-helix, beta-structures (including beta-hairpin and beta-sheet-like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an alpha-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a beta-hairpin, resulting in an alpha-helical conformation at low temperatures, a beta-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become beta-hairpins and beta-sheet-like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper.     

Energetic approach to the folding of alpha/beta barrels

The folding of a polypeptide into a parallel (alpha/beta)8 barrel (which is also called a circularly permuted beta 8 alpha 8 barrel) has been investigated in terms of energy minimization. According to the arrangement of hydrogen bonds between two neighboring beta-strands of the central barrel therein, such an alpha/beta barrel structure can be folded into six different types: (1) left-tilted, left-handed crossover; (2) left-tilted, right-handed crossover; (3) nontilted, left-handed crossover; (4) nontilted, right-handed crossover; (5) right-tilted, left-handed crossover; and (6) right-tilted, right-handed crossover. Here "tilt" refers to the orientational relation of the beta-strands to the axis of the central beta-barrel, and "crossover" to the beta alpha beta folding connection feature of the parallel beta-barrel. It has been found that the right-tilted, right-handed crossover alpha/beta barrel possesses much lower energy than the other five types of alpha/beta barrels, elucidating why the observed alpha/beta barrels in proteins always assume the form of right tilt and right-handed crossover connection. As observed, the beta-strands in the energy-minimized right-tilted, right-handed crossover (alpha/beta)8-barrel are of strong right-handed twist. The value of root-mean-square fits also indicates that the central barrel contained in the lowest energy (alpha/beta)8 structure thus found coincides very well with the observed 8-stranded parallel beta-barrel in triose phosphate isomerase (TIM). Furthermore, an energetic analysis has been made demonstrating why the right-tilt, right-handed crossover barrel is the most stable structure. Our calculations and analysis support the principle that it is possible to account for the main features of frequently occurring folding patterns in proteins by means of conformational energy calculations even for very complicated structures such as (alpha/beta)8 barrels.     

Chelicerae as male grasping organs in scorpions: sexual dimorphism and associated behaviour

Specialised structures that enable males to grasp females during sexual interactions are highly susceptible to selection and thus diverge relatively rapidly over evolutionary time. These structures are often used to test hypotheses regarding sexual selection such as sexually antagonistic co-evolution and sexual selection by female choice. In the present study, we determine whether there is a relationship between a novel record of scorpion sexual dimorphism, the sexual dimorphism of chelicerae (CSD), and the presence of the mating behaviour termed “cheliceral grip” (CG). The presence of both traits in the order Scorpiones is also reviewed from a phylogenetic perspective. The results confirm a strong relationship between CSD and the presence of CG. The morphological and behavioural patterns associated with “CSD–CG” are opposed to the predictions postulated by the hypothesis of sexually antagonistic co-evolution. However, if the female shows resistance after the deposition of the spermatophore, the possibility that the male exerts pressure as a “cryptic form” of coercion to prevent the interruption of mating cannot be ruled out completely. Female choice by “mechanical fit” could be another explanation for some aspects of the CG's contact zone. The possibility that the “CG–CSD” complex has evolved under natural selection in order to ensure sperm transfer is also considered.     

扁圆封印木（相似种）茎干的解剖特征

贵州省水城矿区晚二叠世煤核中扁圆封印木（相似种Ｓｉｇｉｌｌａｒｉａ ｃｆ．ｂｒａｒｄｉｉＢｒｏｎｇｎ．）茎干的主要解剖特征如下：管状中柱,具多边形薄壁细胞组成的髓。初生木质部成环带状,外缘呈规则的齿槽状,向心式发育。次生木质部显束状特征,横切面管胞为方圆至长方形,纵切面为梯状壁增厚,并具流苏纹。射线１—２列细胞宽,数个至十余个细胞高。叶迹起源于初生木质部外缘的槽中,中始式,但以向心发育为主。     

Copper(II) complexes based on a new chelating 4-(3,5-diphenyl-1H-pyrazol-1-yl)-6-(piperidin-1-yl)pyrimidine ligand: Synthesis and crystal structures. Lone pair-π, C-H···π, π-π and C-H···A (A = N, Cl) non-covalent interactions

A new bidentate chelating pyrazolylpyrimidine ligand bearing a strong electron-donating substituent, i.e. 4-(3,5-diphenyl-1H-pyrazol-1-yl)-6-(piperidin-1-yl)pyrimidine (L) (Scheme 1), has been synthesized and used to obtain the copper(II) complexes by reaction with CuCl₂. The molar ratio Cu:L = 1:2 leads to isolation of a complex having CuL₂Cl₂ empirical formula, while the molar ratio Cu:L = 1:1 gives a complex with CuLCl₂ empirical formula. The crystal structure of L as well as the structures of both complexes were studied by single crystal X-ray diffraction. The crystal structure of CuL₂Cl₂ compound is formed by trans-[CuL₂Cl₂] mononuclear molecules. Surprisingly, in contrast to the previous compound having molecular structure, the crystal structure of CuLCl₂ consists of mononuclear [CuL₂Cl]⁺ complex cations and dinuclear [Cu₂Cl₆]²⁻ anions. Thus, formula of CuLCl₂ complex can be represented as [CuL₂Cl]₂[Cu₂Cl₆]. In both complexes molecules of L adopt bidentate chelating coordination mode through N² atom of pyrazole and N³ atom of pyrimidine rings forming five-membered CuN₃C metallocycles. Owing to C-H···N interactions and π-π-stacking L molecules form 2D network. In the structure of trans-[CuL₂Cl₂] there exist double lone pair(N(piperidine))-π(pyrimidine) interactions and C-H···Cl contacts resulting in the formation of 1D chains. Layered 2D structure of [CuL₂Cl]₂[Cu₂Cl₆] results from C-H···Cl, C-H···π and double lone pair(Cl([CuL₂Cl]⁺ complex cation)-π(pyrimidine) interactions.     

Third-order NLO properties of the DMF solutions of 3-D network and 2-D layered organic-metal polymers with (4, 4) grid units

Reactions of 1,1′-(1,4-butanediyl)bis-1H-benzimidazole (bbbm) with Cd(II), Ni(II), or Co(II) afford three organic-metal polymers: {[Cd(bbbm)(SO₄)(H₂O)₂]CH₃OH}_n (1), {[Ni(bbbm)₂(H₂O)₂](NO₃)₂ · 2CH₃OH · 6H₂O}_n (2) and {[Co(bbbm)₂(H₂O)₂](NO₃)₂ · 2CH₃OH · 6H₂O}_n (3). In 1, bbbm and coordinate to Cd(II) simultaneously leading to a 3-D structure. In 2 and 3, each bridging bbbm ligand links two Ni(II) or Co(II) ions forming the 2-D layered structure with (4, 4) grid units. Each (4, 4) grid unit is a 44-membered ring and constructed by four bbbm ligands acting as four sides and four Ni(II) or Co(II) ions representing four corners. Their third-order nonlinear optical (NLO) properties in DMF solution have been studied by Z-scan technique. The results show that the DMF solution of 2 possesses both the large third-order NLO absorptive and strong refractive behaviors; and 3’s shows large NLO absorptive effect and weak NLO refractive behavior. A reasonably good fit between the experimental data and the theoretical curve suggests that the experimentally obtained NLO effects are effective third-order in nature.