title: Secondary structure, a missing component of sequence-based minimotif definitions.
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.
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, Nevada, USA.
authors.forename: David P
authors.initials: DP
authors.lastname: Sargeant
authors.forename: Michael R
authors.initials: MR
authors.lastname: Gryk
authors.forename: Mark W
authors.initials: MW
authors.lastname: Maciejewski
authors.forename: Vishal
authors.initials: V
authors.lastname: Thapar
authors.forename: Vamsi
authors.initials: V
authors.lastname: Kundeti
authors.forename: Sanguthevar
authors.initials: S
authors.lastname: Rajasekaran
authors.forename: Pedro
authors.initials: P
authors.lastname: Romero
authors.forename: Keith
authors.initials: K
authors.lastname: Dunker
authors.forename: Shun-Cheng
authors.initials: SC
authors.lastname: Li
authors.forename: Tomonori
authors.initials: T
authors.lastname: Kaneko
authors.forename: Martin R
authors.initials: MR
authors.lastname: Schiller
mesh_terms: D020816:Amino Acid Motifs; D030562:Databases, Protein; D006801:Humans; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein
chemical_list: D011506:Proteins