Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry

A method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C₂ symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.     

Calculation of two-center overlap integral in molecular coordinate system over Slater type orbital using Löwdin α-radial and Guseinov rotation–angular functions

By use of Löwdin and Guseinov relations for the radial and angular part of two-center overlap integrals, respectively, the computer calculations of overlap integrals over Slater type orbitals (STOs) in molecular coordinate system are performed. The results of calculations are valid for arbitrary principal quantum numbers, screening constants and location of STOs. Excellent agreement with benchmark results and stability of the technique are demonstrated.     

Gene delivery with polycationic fullerene hexakis-adducts

Polyplexes prepared from DNA and globular compact polycationic derivatives constructed around a fullerene hexakis-adduct core have shown remarkable gene delivery capabilities.     

Quantum chemical computations of 1,3-phenylenediacetic acid

Molecular geometry, vibrational wavenumbers and gauge including atomic orbital (GIAO) 13C NMR and 1H NMR chemical shift values of 1,3-phenylenediacetic acid (C10H10O4), in the ground state have been calculated by using ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with 6-311++G(d,p) basis set for the first time. Comparison of the observed fundamental vibrational modes of 1,3-phenylenediacetic acid and calculated results by density functional B3LYP and Hartree-Fock methods indicate that B3LYP is superior to the scaled Hartree-Fock approach for quantum chemical studies. Geometric parameters (bond lengths and bond angles) and vibrational wavenumbers obtained by the HF and DFT/B3LYP methods are in good agreement with the experimental data. Furthermore, this is the first time the results of the calculated JCH and JCC coupling constants of the C10H10O4 molecule are presented in this study.     

Comparison of epithelial and fibroblastic cell behavior on nano/micro-topographic PCL membranes produced by crystallinity control

In this study, the relationship between the cellular morphology and the material surface topography was investigated. Poly(ε-caprolactone) (PCL) membranes were prepared in a wide range of surface wettabilities by means of crystallinity-controlled solvent casting process. Membrane surfaces were characterized by atomic force microscope (AFM), scanning electron microscope (SEM), and static/dynamic water contact angle measurements. It was found that solvent evaporation and non-solvent (methanol) addition to the solvent (THF) are the most decisive parameters to change the surface topography. The non-solvent addition and the decrease in solvent evaporation temperature from room temperature to -20 °C caused increased polymeric chain mobility and crystallization time. Such changes in crystallization parameters led to the formation of micro/nano-sized features on the membrane. Cell culture studies indicated that in contrast to Madin Darby kidney (MDBK) epithelial cells, L929 mouse fibroblast preferred rough and porous surfaces.     

Selective conversion of {Mo132} Keplerate ion into 4-electron reduced crown-capped Keggin derivative [Te5Mo15O57](8-). A key intermediate to single-phase M1 multielement MoVTeO light-alkanes oxidation catalyst

{Mo(132)} Keplerate anion reacts with tellurites to give a soluble precursor to produce in hydrothermal conditions single-phase M1 MoVTeO light-alkanes oxidation catalyst. Characterization of this Te-containing intermediate by single-crystal X-ray diffraction, (125)Te NMR, UV-visible and redox titration reveals a molybdotellurite anion as a crown-capped Keggin derivative.     

NCO quantitative measurement in premixed low pressure flames by combining LIF and CRDS techniques

NCO is a short-lived species involved in NO(x) formation. It has never been quantitatively measured in flame conditions. In the present study, laser-induced fluorescence (LIF) and cavity ring-down spectroscopy (CRDS) were combined to measure NCO radical concentrations in premixed low-pressure flames (p = 5.3 kPa). NCO LIF excitation spectrum and absorption spectrum (using CRDS) measured in a stoichiometric CH(4)/O(2)/N(2)O/N(2) flame were found in good agreement with a simulated spectrum using PGOPHER program that was used to calculate the high-temperature absorption cross section of NCO in the A(2)Σ(+)-X(2)Π transition around 440.479 nm. The relative NCO-LIF profiles were measured in stoichiometric CH(4)/O(2)/N(2)O/N(2) flames where the ratio N(2)O/O(2) was progressively decreased from 0.50 to 0.01 and in rich CH(4)/O(2)/N(2) premixed flames. Then, the LIF profiles were converted into NCO mole fraction profiles from the absorption measurements using CRDS in a N(2)O-doped flame.