title: Achieving peptide binding specificity and promiscuity by loops: case of the forkhead-associated domain.
abstract: The regulation of a series of cellular events requires specific protein-protein interactions, which are usually mediated by modular domains to precisely select a particular sequence from diverse partners. However, most signaling domains can bind to more than one peptide sequence. How do proteins create promiscuity from precision? Moreover, these complex interactions typically occur at the interface of a well-defined secondary structure, α helix and β sheet. However, the molecular recognition primarily controlled by loop architecture is not fully understood. To gain a deep understanding of binding selectivity and promiscuity by the conformation of loops, we chose the forkhead-associated (FHA) domain as our model system. The domain can bind to diverse peptides via various loops but only interact with sequences containing phosphothreonine (pThr). We applied molecular dynamics (MD) simulations for multiple free and bound FHA domains to study the changes in conformations and dynamics. Generally, FHA domains share a similar folding structure whereby the backbone holds the overall geometry and the variety of sidechain atoms of multiple loops creates a binding surface to target a specific partner. FHA domains determine the specificity of pThr by well-organized binding loops, which are rigid to define a phospho recognition site. The broad range of peptide recognition can be attributed to different arrangements of the loop interaction network. The moderate flexibility of the loop conformation can help access or exclude binding partners. Our work provides insights into molecular recognition in terms of binding specificity and promiscuity and helpful clues for further peptide design.
authors.affiliation: Department of Chemistry, University of California Riverside, Riverside, California, United States of America.
authors.forename: Yu-Ming M
authors.initials: YM
authors.lastname: Huang
authors.affiliation: Department of Chemistry, University of California Riverside, Riverside, California, United States of America.
authors.forename: Chia-En A
authors.initials: CE
authors.lastname: Chang
mesh_terms: D000595:Amino Acid Sequence; D018797:Cell Cycle Proteins / Q000235:genetics; D064447:Checkpoint Kinase 2 / Q000235:genetics; D019394:Ki-67 Antigen / Q000235:genetics; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding / Q000235:genetics; D054730:Protein Interaction Domains and Motifs / Q000235:genetics*; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D017433:Protein Structure, Secondary / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D013379:Substrate Specificity
chemical_list: D018797:Cell Cycle Proteins; D019394:Ki-67 Antigen; D029701:Saccharomyces cerevisiae Proteins; C104169:DUN1 protein, S cerevisiae; D064447:Checkpoint Kinase 2; C578634:CHEK2 protein, human; D017346:Protein Serine-Threonine Kinases