The analysis of network motifs, patterns of local interconnections with potential functional properties, has applications in many fields of science. Network motif analysis is particularly important for the exploration of biological networks. The distribution and multiple occurrences of motifs in a network, complicated by different concepts for the determination of motif frequency, create variou...

PURPOSE Previous studies indicate that the CCCTC binding transcription factor (CTCF) regulates homeobox PAX6 gene transcription in corneal epithelial cells. In the present study, the effect was investigated of CTCF activity on PAX6 transcription through interaction with five essential motifs located in an 80-bp region upstream from the PAX6 P0 promoter. METHODS An electrophoretic mobility shi...

To identify functional structural motifs from protein structures of unknown function becomes increasingly important in recent years due to the progress of the structural genomics initiatives. Although certain structural patterns such as the Asp-His-Ser catalytic triad are easy to detect because of their conserved residues and stringently constrained geometry, it is usually more challenging to d...

Self-assembly of amyloid proteins and peptides into fibrils is usually associated with many humane diseases such as Alzheimer's, Parkinson's type 2 diabetes. Functional amyloids bacterial amyloids, on the other hand, also have vital functions including strengthening attachment to surfaces enhancing stability stiffness biofilms. FapC precursor protein a functional expressed in Pseudomonas. seque...

Traditionally, proteins are represented as amino acid sequences. There are, though, other (potentially more exciting) representations; e.g. each protein can be viewed as (maybe partially) containing some conserved domains/motifs. Using this “functional representation” of proteins we are suggesting a method for exploring similarities of conserved domains/motifs.

Network motifs are overrepresented interconnection patterns found in real-world networks. What functional advantages may they offer for building complex systems? We show that most network motifs emerge from interconnections patterns that best exploit the intrinsic stability characteristics of individual nodes. This feature is observed at different scales in a network, from nodes to modules, sug...

Background: Cytotoxin-associated gene A (CagA)-positive strains of Helicobacter pylori are associated with gastroduodenal diseases. Evidences have suggested that the type of H pylori CagA EPIYA motifs may be associated with specific disorders (i.e., gastritis, peptic ulcer, or gastric cancer).  We investigated the prevalence of different EPIYA motifs (A, B, C, or D) in H. pylori strains is...

The discovery of motifs underlying gene expression is a challenging one. Some of these motifs are known transcription factors, but sequence inspection often provides valuable clues, even discovery of novel motifs with uncharacterized function in gene expression. Coupled with the complexity underlying tissuespecific gene expression, there are several motifs that are putatively responsible for ex...

Computational grafting of functional motifs onto scaffold proteins is a promising way to engineer novel proteins with pre-specified functionalities. Typically, protein grafting involves the transplantation of protein side chains from a functional motif onto structurally homologous regions of scaffold proteins. Using this approach, we previously transplanted the human immunodeficiency virus 2F5 ...