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Graphical abstract Highlights • Three mutations decreasing pKa values of catalytic residues of Amy7C were designed. • Three single and two double mutants were constructed and characterized. • All mutants shifted pH optima and pH-activity profiles toward more acidic values. • N271H decreased pH optimum by 2 units without comprising the catalytic efficiency. • A270 K/N271H increased catalytic efficiency by 3.94-fold at optimum pH of 4.5. Abstract The aim of this study was to rationally engineer the acidic adaptation of B. subtilis Ca-independent alpha-amylase (Amy7C) by decreasing the pKa values of catalytic residues through mutations at active site. Within 4.5 Å of three catalytic residues of Amy7C, three mutations R172 K, A270 K and N271H were identified by computational homology modeling and pKa prediction analyses. Five single and double mutants consisting of these three mutations were constructed and characterized. Compared to the wild-type, all mutants shifted the pH optima and pH-activity profiles toward lower pH values without comprising the thermostablity. Double mutants showed simultaneous accumulation of advantageous mutations. The best mutant, A270 K/N271H showed 2 units decrease in optimum pH and about 3.94-fold increase of catalytic efficiency. Structural analysis suggested that the improved acidic adaptation could be attributed to the decreased pKa values of catalytic nucleophile and proton donor residues. Protein engineering of α-amylase for acidic adaptation here provides a successful example of the extent to which mutations near active site and computational models can be used for industrial enzyme improvements. [ABSTRACT FROM AUTHOR]

Abstract: Muconic acid (MA), a high value-added bio-product with reactive dicarboxylic groups and conjugated double bonds, has garnered increasing interest owing to its potential applications in the manufacture of new functional resins, bio-plastics, food additives, agrochemicals, and pharmaceuticals. At the very least, MA can be used to produce commercially important bulk chemicals such as adipic acid, terephthalic acid and trimellitic acid. Recently, great progress has been made in the development of biotechnological routes for MA production. This present review provides a comprehensive and systematic overview of recent advances and challenges in biotechnological production of MA. Various biological methods are summarized and compared, and their constraints and possible solutions are also described. Finally, the future prospects are discussed with respect to the current state, challenges, and trends in this field, and the guidelines to develop high-performance microbial cell factories are also proposed for the MA production by systems metabolic engineering. [Copyright &y& Elsevier]

Abstract: The neuraminidase (NA) and M2 proton channel of influenza virus are the drug-targeting proteins, based on which several drugs were developed. However these once powerful drugs encountered drug-resistant problem to the H5N1 and H1N1 flu. To address this problem, the computational 3D structures of NA and M2 proteins of 2009-H1N1 influenza virus were built using the molecular modeling technique and computational chemistry method. Based on the models the structure features of NA and M2 proteins were analyzed, the docking structures of drug–protein complexes were computed, and the residue mutations were annotated. The results may help to solve the drug-resistant problem and stimulate designing more effective drugs against 2009-H1N1 influenza pandemic. [Copyright &y& Elsevier]

Abstract: In this study the excess chemical potential of the integral equation theory, 3D-RISM-HNC [Q. Du, Q. Wei, J. Phys. Chem. B 107 (2003) 13463–13470], is visualized in three-dimensional form and localized at interaction sites of solute molecule. Taking the advantage of reference interaction site model (RISM), the calculation equations of chemical excess potential are reformulized according to the solute interaction sites s in molecular space. Consequently the solvation free energy is localized at every interaction site of solute molecule. For visualization of the 3D-RISM-HNC calculation results, the excess chemical potentials are described using radial and three-dimensional diagrams. It is found that the radial diagrams of the excess chemical potentials are more sensitive to the bridge functions than the radial diagrams of solvent site density distributions. The diagrams of average excess chemical potential provide useful information of solute–solvent electrostatic and van der Waals interactions. The local description of solvation free energy at active sites of solute in 3D-RISM-HNC may broaden the application scope of statistical mechanical integral equation theory in solution chemistry and life science. [Copyright &y& Elsevier]

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O 2 –2H 2 interaction structure is smaller than the dimension of CO 2 –2H 2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O 2 + 2H 2 ) cluster in clathrate hydrate. [ABSTRACT FROM AUTHOR]

Abstract: The cation–π interactions occur frequently within or between proteins due to six (Phe, Tyr, Trp, Arg, Lys, and His) of the twenty natural amino acids potentially interacting with metallic cations via these interactions. In this study, quantum chemical calculations and molecular orbital (MO) theory are used to study the energies and properties of cation–π interactions in biological structures. The cation–π interactions of H+ and Li+ are similar to hydrogen bonds and lithium bonds, respectively, in which the small, naked cations H+ and Li+ are buried deep within the π-electron density of aromatic molecules, forming stable cation–π bonds that are much stronger than the cation–π interactions of other alkali metal cations. The cation–π interactions of metallic cations with atomic masses greater than that of Li+ arise mainly from the coordinate bond comprising empty valence atomic orbitals (AOs) of metallic cations and π-MOs of aromatic molecules, though electrostatic interactions may also contribute to the cation–π interaction. The binding strength of cation–π interactions is determined by the charge and types of AOs in the metallic cations. Cation–π interaction energies are distance- and orientation-dependent; energies decrease with the distance (r) and the orientation angle (θ). In solution, the cation–π energies decrease with the increase of the dielectric constant (ɛ) of the solvent; however, solvation has less influence on the H+–π and H3O+–π interactions than on interactions with other cations. The conclusions from this study provide useful theoretical insights into the nature of cation–π interactions and may contribute to the development of better force field parameters for describing the molecular dynamics of cation–π interactions within and between proteins. [Copyright &y& Elsevier]

Abstract: The interaction potential energies of water–water and water–methane in structure-I unit cell of methane hydrate are calculated from 2.1 to 8.0Å using density functional theory (DFT) B3LYP/TZVP. The curves of potential energies are corrected for basis set superposition error (BSSE) and dispersion interaction using a 4-term L–J (4,6–8,12) correction equation, which is derived from CCSD(T)/cc-pVTZ calculations of water–water and water–methane molecular pairs, using least squares curve-fitting. The methane hydrate unit cell is a regular water dodecahedron cell consisting of 20 water molecules with a methane molecule in the center. The geometries of water and methane are optimized at CCSD(T)/cc-pVTZ level. The BSSE-corrections are calculated for water–water and water–methane interaction energies as functions of the side length, l, of the dodecahedron cell at B3LYP/TZVP level in the range from 2.1 to 8.0Å. The BSSE CP-corrected and dispersion-corrected potential energy surfaces (PES) of water–water and water–methane are useful for molecular dynamics simulation of gas clathrate–hydrates. [Copyright &y& Elsevier]

In this study, a sugarcane bagasse cellulose bundle crystal is converted to a cellulose few-layer two-dimensional (2D) crystal by a specially designed technique scheme, which consists of (1 → 4)-β-D-glucan chains bound to each other by hydrogen bonds in a plane. A graphene few-layer 2D crystal is fabricated from the cellulose 2D crystal by pyrolysis reaction. The fabricated graphene 2D crystal is further analysed and characterised using scanning electron microscopy, high-resolution transmission electron microscopy (HRTEM), atomic force microscopy, and Raman, X-ray diffraction and X-ray photoelectric spectroscopies. A very clear 2D crystal pattern of graphene is observed in the HRTEM image of the carbon product prepared from the cellulose 2D crystal. As a control, in a parallel experiment, multi-layer graphene (or graphite) is obtained from the cellulose bundle crystal. The following possible mechanism is proposed. During carbonization of the cellulose 2D crystal, the glucose units (C 6 H 10 O 5) n lose oxygen and hydrogen atoms in the form of water, and the six carbon units (C 6) n reorganise, forming the graphene 2D crystal at the structural basis of the 2D crystal of cellulose. The findings from this study provide an economical and environmentally friendly approach to the fabrication of graphene and extend the applications of sustainable biomass cellulose. Image 1044 • The cellulose bundle crystal was hydrolysed to the few-layer 2D crystal of cellulose. • The graphene 2D crystal was successfully fabricated from the cellulose 2D crystal. • A clear 2D crystalline pattern was observed in the TEM image of the graphene sample. • The most important techniques, from 2D cellulose to 2D graphene, were illustrated. • A mechanism from the 2D cellulose crystal to the 2D graphene crystal was proposed. [ABSTRACT FROM AUTHOR]