Influenza A H5N1 hemagglutinin cleavable signal sequence substitutions.

Eleven influenza A H5N1 hemagglutinin N-terminal cleavable signal sequences, coded by single nucleotide substitutions relative to reference A/Viet Nam/1203/2004, were identified by BLASTN search of GenBank and were characterized by molecular modeling. The signal sequences statistically segregated into two classes of states. Members of one class were uncharged and conformationally compact while members of the second class each carried a 2+ electric charge and were conformationally extended.

HIV-1 GP120 V3 conformational and informational entropies.

In an attempt to analyze structure, function and evolution of HIV-1 GP120 V3, interactions among the Hartree-Fock energy, the conformational entropy and the Shannon entropy were determined for the 1NJ0 set of antibody-bound V3 loop conformers. The Hartree-Fock energy of each conformer was determined at the MINI level with GAMESS. The conformational entropy was determined per conformer and per residue from the mass-weighted covariance matrices.

The HF-SCF energy of HIV-1 MNgp120 V3 hairpin loop conformers.

The purpose of this study is to analyze the structure of the V3 loop of the HIV-1 gp120 molecule at the atomic level. The total energy of each member of the antibody-complexed 16-mer V3 conformer data set of Sharon et al. (PDB 1NJ0) was determined by the Hartree-Fock-self-consistent field (HF-SCF) method and with the GROMOS96 force field.

Histamine as a regulator of allergic and asthmatic inflammation.

The immunologic effects of histamine are exerted via the H1 and H2 histamine receptors (H1R and H2R). The effects of histamine include autoinhibition of histamine release from mast cells and basophils, immunosuppression, and the regulation of the activities of cell-mediated immunity (Th1) and humoral immunity (Th2) cells. The asthma phenotype is associated with relative underexpression of Th1 activities and overexpression of Th2 activities.

Molecular modeling of penicilloate anions: an RHF-SCF analysis.

An ab initio restricted Hartree-Fock self-consistent field (RHF-SCF) analysis of penicilloate anions was performed at the TZV level with GAMESS. Geometry optimization was initialized by the semi-empirical AM1 method followed by optimization at the 6-31++G** level. The total energy obtained was -1116.