Certain retrovirus and retrotransposons display strong biases in the selection of host DNA sites for integration. To probe the possibility that simple tethering of the retroelement integrase protein to a target DNA site is sufficient to direct integration, the activities of a hybrid composed of human immunodeficiency virus 1 integrase and lambda repressor were analyzed. In in vitro reactions co...

A hybrid protein of ricin and the enzymatically active fragment A of diphtheria toxin (toxin A) has been synthesized and purified. The diphtheria toxin A fragment of the hybrid protein is shown to enter the cytosol compartment of HeLa cells, its presence assayed by the fall of intracellular elongation factor II (EF-2) and the rise of ADP-ribosylated EF-2. Hybrid entrance to HeLa cells is blocke...

The Protein Data Bank contains the description of approximately 27 000 protein-ligand binding sites. Most of the ligands at these sites are biologically active small molecules, affecting the biological function of the protein. The classification of their binding sites may lead to relevant results in drug discovery and design. Clusters of similar binding sites were created here by a hybrid, sequ...

In this paper we develop data mining techniques to predict 3D contact potentials among protein residues (or amino acids) based on the hierarchical nucleation-propagation model of protein folding. We apply a hybrid approach, using a hidden Markov model to extract folding initiation sites, and then apply association mining to discover contact potentials. The new hybrid approach achieves accuracy ...

The structure and shape of the polypeptide chain of proteins are determined by the hybridized states of atomic orbitals in the molecular chain. The calculated s ratio in the sp hybrid orbitals is computed from the fractal dimension D of 81 proteins. The tertiary structures of 8 proteins covering 4 structural classes are analyzed. The proteins in the β-structural class are distinguished quantita...

Nanotechnology offers immense opportunities for regulating and improving biological functions of proteins in vitro. Recent years have witnessed growing efforts to develop protein-incorporated hybrid nanostructured materials with potential applications in functional materials, enzymatic catalysis, drug delivery, and analytical sciences. In this review, recent advances in functional protein-organ...

We have developed a hybrid system to predict the secondary structures (alpha-helix, beta-sheet and coil) of proteins and achieved 66.4% accuracy, with correlation coefficients of C(coil) = 0.429, C alpha = 0.470 and C beta = 0.387. This system contains three subsystems ("experts"): a neural network module, a statistical module and a memory-based reasoning module. First, the three experts indepe...

To the Editor: Class 2 and class 3 porin (PorB) proteins are the major proteins found in the outer membrane of Neisseria meningitidis (1); they function as porins, allowing the passage of small molecules through the outer membrane. PorB outer membrane proteins are transmembrane proteins with 8 predicted surface-exposed loops (IVIII), which vary in length and in amino acid sequences. Several seq...

Speciation often involves the evolution of incompatible gene interactions that cause sterility or lethality in hybrids between populations. These so-called hybrid incompatibilities occur between two or more functionally divergent loci. We show that the nucleoporin 160kDa (Nup160) gene of the fruitfly Drosophila simulans is incompatible with one or more factors on the D. melanogaster X chromosom...

Over the last decade, the yeast two-hybrid system has become the tool to use for the identification of protein-protein interactions and recently, even complete interactomes were elucidated by this method. Nevertheless, it is an artificial system that is sensitive to errors resulting in the identification of false-positive and false-negative interactions. In this study, plant MADS box transcript...