Ethylene response factor proteins are important for regulating gene expression under different stresses. Different isoforms for ERF have previously isolated from bread wheat (Triticum aestivum L.) and related genera and called from TaERF1 to TaERF5. We isolated, cloned and molecular characterized a novel one based on TdERF1, an isoform in durum wheat (Tri...

To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling o...

BACKGROUND NMR studies of denatured states, both fully unfolded and partially folded, give insight into the conformations and interactions formed during folding. Although the complete structural characterization of partially folded proteins is a very difficult task, the identification of structured subsets, such as hydrophobic clusters, is of value in understanding the structural organization o...

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is th...

HIV proteins contain a multitude of naturally processed cytotoxic T lymphocyte (CTL) epitopes that concentrate in clusters. The molecular basis of epitope clustering is of interest for understanding HIV immunogenicity and for vaccine design. We show that the CTL epitope clusters of HIV proteins predominantly coincide with hydrophobic regions, whereas the noncluster regions are predominantly hyd...

We have identified based on gene cluster analysis that the genes between Rv3799-Rv3807 in M. tuberculosis have orthologs in Corynebacteria, Mycobacteria and Nocardia (CMN) genomes. Therefore, this gene cluster possibly corresponds to the 'Ancient Conserved Region' of CMN mycolyltransferases. The evolutionary trace analysis suggests that twelve amino acid residues; Leu39, Trp51, Pro71, Trp82, Tr...