Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions

David P. Sargeant, Michael R. Gryk, Mark W. Maciejewski, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun Cheng Li, Tomonori Kaneko, Martin R. Schiller

Research output: Contribution to journalReview article

6 Scopus citations

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.

Original languageEnglish (US)
Article numbere49957
JournalPloS one
Volume7
Issue number12
DOIs
StatePublished - Dec 7 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Sargeant, D. P., Gryk, M. R., Maciejewski, M. W., Thapar, V., Kundeti, V., Rajasekaran, S., Romero, P., Dunker, K., Li, S. C., Kaneko, T., & Schiller, M. R. (2012). Secondary Structure, a Missing Component of Sequence-Based Minimotif Definitions. PloS one, 7(12), [e49957]. https://doi.org/10.1371/journal.pone.0049957