Cells require distinct adhesion complexes to form contacts with their neighbors or the extracellular matrix, and vinculin links these complexes to the actin cytoskeleton. Metavinculin, an isoform of vinculin that harbors a unique 68-residue insert in its tail domain, has distinct actin bundling and oligomerization properties and plays essential roles in muscle development and homeostasis. Moreo...

The a-helix, first characterized by Linus Pauling in 1951 (Pauling et al., 1951), has been extensively studied due to its prevalence in structural biology (Brandon, 1991). a-Helices are the most common secondary conformation in natural proteins ( 40% of amino acids adopt helical conformations) (Ruan et al., 1990). A typical a-helix completes one rotation with 3.6 amino acid residues, each with ...

Human papillomaviruses (HPVs) are small DNA tumor viruses that are the causative agent of warts and are associated with many anogenital cancers. The viral gene encoding the E6 protein has been found to be involved in HPV oncogenesis. E6 is known to inactivate the cellular tumor suppressor, p53. In addition, E6 has been shown to bind to a variety of other cellular proteins. The focus of this stu...

Antimicrobial alpha-helical alpha-peptides are part of the host-defense mechanism of multicellular organisms and could find therapeutic use against bacteria that are resistant to conventional antibiotics. Recent work from Hamuro et al. has shown that oligomers of beta-amino acids ("beta-peptides") that can adopt an amphiphilic helix defined by 14-membered ring hydrogen bonds ("14-helix") are ac...

The amphipathic alpha helix is an often-encountered secondary structural motif in biologically active peptides and proteins. An amphipathic helix is defined as an alpha helix with opposing polar and nonpolar faces oriented along the long axis of the helix. In a recent review article we grouped amphipathic helixes into seven distinct classes (A, H, L, G, K, C, and M) based upon a detailed analys...

We have determined the sequences of the ssb gene and protein of Escherichia coli. The coding region of ssb is 534 base pairs and is preceeded and followed by dyad symmetries of 39 base pairs and 27 base pairs, respectively. The promoter for ssb is close to that for uvrA and these two genes are transcribed in opposite directions: ssb clockwise and uvrA counterclockwise on the standard E. coli ge...

The GrpE heat shock protein from Escherichia coli has a homodimeric structure. The dimer interface encompasses two long alpha-helices at the NH(2)-terminal end from each monomer (forming a "tail"), which lead into a small four-helix bundle from which each monomer contributes two short sequential alpha-helices in an antiparallel topological arrangement. We have created a number of different dele...

A male zebra finch learns a song by listening to a tutor, but song learning is normally restricted to a critical period in juvenile development. Here we identify an RNA whose expression in the song control circuit is altered during this critical period. The RNA encodes a soluble presynaptic protein that forms a predicted amphipathic alpha helix typical of the lipid-binding domain in apolipoprot...

Multiple approaches have been developed in order to predict the protein secondary structure. In this paper, we propose an approach to such a problem based on evolutionary computation. The proposed approach considers various amino acids properties in order to predict the secondary structure of a protein. In particular, we will consider the hydrophobicity, the polarity and the charge of amino aci...