Chemotaxonomy of the Rubiaceae family based on leaf fatty acid composition

With 10,700 species distributed in 637 genera, the Rubiaceae family is one of the largest of the angiosperms. Since it was previously evidenced that the fatty acid composition of photosynthetic tissues can be a tool for chemotaxonomic studies, the fatty acid composition of leaves from 107 Rubiaceae species highly representative of the diversity of the family was determined. Principal component analysis allowed a clear-cut separation of Coffeae, Psychotrieae and Rubieae. The occurrence of C16:3 fatty acid, a marker of the prokaryotic plastidial lipid biosynthetic pathway, concerned at least two branches: Theligoneae/Rubieae and Anthospermeae-Anthosperminae which appeared to be in close relationship. Additional experiments were carried out to ensure the correlation between the presence of C16:3 fatty acid and the prokaryotic biosynthetic pathway.     

Ribosome inactivating proteins and apoptosis

Ribosome inactivating proteins (RIPs) are protein toxins that are of plant or microbial origin that inhibit protein synthesis by inactivating ribosomes. Recent studies suggest that RIPs are also capable of inducing cell death by apoptosis. Though many reports are available on cell death induced by RIPs, the mechanism involved is not well studied. Comparison of pathways of apoptosis and cellular events induced by various RIPs suggests a central role played by mitochondria, probably acting as an integrator of cellular stress and cell death. The purpose of this review is to compare the various apoptotic pathways that may be involved and propose a general pathway in RIP-induced cell death.     

The stability of transmembrane helix interactions measured in a biological membrane

Despite some promising progress in the understanding of membrane protein folding and assembly, there is little experimental information regarding the thermodynamic stability of transmembrane helix interactions and even less on the stability of transmembrane helix-helix interactions in a biological membrane. Here we describe an approach that allows quantitative measurement of transmembrane helix interactions in a biological membrane, and calculation of changes in the interaction free energy resulting from substitution of single amino acids. Dimerization of several variants of the glycophorin A transmembrane domain are characterized and compared to the wild-type (wt) glycophorin A transmembrane helix dimerization. The calculated DeltaDeltaG(app) values are further compared with values found in the literature. In addition, we compare interactions between the wt glycophorin A transmembrane domain and helices in which critical glycine residues are replaced by alanine or serine, respectively. The data demonstrate that replacement of the glycine residues by serine is less destabilizing than replacement by alanine with a DeltaDeltaG(app) value of about 0.4 kcal/mol. Our study comprises the first measurement of a transmembrane helix interaction in a biological membrane, and we are optimistic that it can be further developed and applied.     

Concepts on charge transfer through naturally vibrating DNA molecule

Delocalization of charges thorough DNA occurs due to the natural and continuous movements of molecule which stimulates the charge transfer through the molecule. A model is presented showing that the mechanism of electrical conduction occurs mainly by thermally-activated drift motion of holes under control of the localized carriers; where electrons are localized in the conduction band. These localized (stationary-trapped) electrons control the movements of the positive charges and do not play an effective role in the electrical conduction itself. It is found that the localized charge-carriers in the bands have characteristic relaxation times at 5×10(^-2)s, 1.94×10(^-4)s, 5×10(^-7)s, and 2×10(^-11)s respectively which are corresponding to four intrinsic thermal activation energies 0.56eV, 0.33eV, 0.24eV, and 0.05eV respectively. The ac-conductivity of some published data are well fitted with the presented model and the total charge density in DNA molecule is calculated to be n=1.88×10(^19)cm(^-3) at 300K which is corresponding to a linear electron density n=8.66×10(^3)cm(^-1) at 300K. The model shed light on the role of transfer and/or localization of charges through DNA which has multiple applications in medical, nano-technical, bio-sensing and different domains. So, repair DNA by adjusting the charge transport through the molecule is future challenges to new medical applications.     

The foldon substructure of staphylococcal nuclease

To search for submolecular foldon units, the spontaneous reversible unfolding and refolding of staphylococcal nuclease under native conditions was studied by a kinetic native-state hydrogen exchange (HX) method. As for other proteins, it appears that staphylococcal nuclease is designed as an assembly of well-integrated foldon units that may define steps in its folding pathway and may regulate some other functional properties. The HX results identify 34 amide hydrogens that exchange with solvent hydrogens under native conditions by way of large transient unfolding reactions. The HX data for each hydrogen measure the equilibrium stability (ΔG_HX) and the kinetic unfolding and refolding rates (k_op and k_cl) of the unfolding reaction that exposes it to exchange. These parameters separate the 34 identified residues into three distinct HX groupings. Two correspond to clearly defined structural units in the native protein, termed the blue and red foldons. The remaining HX grouping contains residues, not well separated by their HX parameters alone, that represent two other distinct structural units in the native protein, termed the green and yellow foldons. Among these four sets, a last unfolding foldon (blue) unfolds with a rate constant of 6 × 10^− 6 s^− 1 and free energy equal to the protein's global stability (10.0 kcal/mol). It represents part of the β-barrel, including mutually H-bonding residues in the β4 and β5 strands, a part of the β3 strand that H-bonds to β5, and residues at the N-terminus of the α2 helix that is capped by β5. A second foldon (green), which unfolds and refolds more rapidly and at slightly lower free energy, includes residues that define the rest of the native α2 helix and its C-terminal cap. A third foldon (yellow) defines the mutually H-bonded β1-β2-β3 meander, completing the native β-barrel, plus an adjacent part of the α1 helix. A final foldon (red) includes residues on remaining segments that are distant in sequence but nearly adjacent in the native protein. Although the structure of the partially unfolded forms closely mimics the native organization, four residues indicate the presence of some nonnative misfolding interactions. Because the unfolding parameters of many other residues are not determined, it seems likely that the concerted foldon units are more extensive than is shown by the 34 residues actually observed.