Hydrophobic-cluster analysis was used to characterize a conserved domain located near the C-terminal amino acid sequence of wheat (Triticum aestivum) storage proteins. This domain was transformed into a linear template for a global search for similarities in over 5200 protein sequences. In addition to proteins that had already been found to exhibit homology to wheat storage proteins, a previous...

Thermodynamics and kinetics of off-lattice models with side chains for the b-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except refolding time tF) there are no qualitative differences between the full model and the Go# version. The validity of the models is established by comparison of the calculated native structure with the Protein Dat...

Thermodynamics and kinetics of off-lattice models with side chains for the beta-hairpin fragment of immunoglobulin-binding protein and its variants are reported. For all properties (except refolding time tau(F)) there are no qualitative differences between the full model and the Go version. The validity of the models is established by comparison of the calculated native structure with the Prote...

One way of exploring protein unfolding events associated with the development of Amyloid diseases is through the use of multiple Molecular Dynamics Protein Unfolding Simulations. The analysis of the huge amount of data generated in these simulations is not a trivial task. In the present report, we demonstrate the use of Association Rules applied to the analysis of the variation profiles of the ...

Periplasmic binding protein-dependent transport systems are composed of a periplasmic substrate-binding protein, a set of 2 (sometimes 1) very hydrophobic integral membrane proteins, and 1 (sometimes 2) hydrophilic peripheral membrane protein that binds and hydrolyzes ATP. These systems are members of the superfamily of ABC transporters. We performed a molecular phylogenetic analysis of the seq...