1. Secondary structure, a missing component of sequence-based minimotif definitions
- Author
-
Sargeant, David P., Gryk, Michael R., Maciejewski, Mark W., Thapar, Vishal, Kundeti, Vamsi, Rajasekaran, Sanguthevar, Romero, Pedro, Dunker, Keith, MacDonald, Shun Cheng, Rogers, J., Bucci, L., Mousmanis, P., Lang, E., Halperin, S. A., Bowles, S., Halpert, C., Ipp, M., Asmundson, G. J.G., Rieder, M., Robson, K., Uleryk, E., Antony, M. M., Dubey, V., Hanrahan, A., Lockett, D., and Scott, J.
- Subjects
Protein Structure ,Protein Folding ,Amino Acid Motifs ,Biophysics ,lcsh:Medicine ,Computational biology ,Biology ,Biochemistry ,Protein Structure, Secondary ,Biophysics Theory ,03 medical and health sciences ,Sequence Analysis, Protein ,Component (UML) ,Macromolecular Structure Analysis ,Humans ,Biomacromolecule-Ligand Interactions ,Databases, Protein ,Protein Interactions ,lcsh:Science ,Protein secondary structure ,030304 developmental biology ,Sequence (medicine) ,Structure (mathematical logic) ,Genetics ,0303 health sciences ,Multidisciplinary ,030302 biochemistry & molecular biology ,lcsh:R ,Proteins ,Computational Biology ,Protein structure prediction ,Computing Methods ,Cellular signal transduction ,Computer Science ,Posttranslational modification ,lcsh:Q ,Sequence Analysis ,Research Article ,Computer Modeling - Abstract
Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis of occurrences of minimotifs in structured and disordered regions of proteins, and review of the literature support a new model for minimotif definitions that includes sequence, structure, and function. © 2012 Sargeant et al.
- Published
- 2012