title: Consensus design of a NOD receptor leucine rich repeat domain with binding affinity for a muramyl dipeptide, a bacterial cell wall fragment.
abstract: Repeat proteins have recently emerged as especially well-suited alternative binding scaffolds due to their modular architecture and biophysical properties. Here we present the design of a scaffold based on the consensus sequence of the leucine rich repeat (LRR) domain of the NOD family of cytoplasmic innate immune system receptors. Consensus sequence design has emerged as a protein design tool to create de novo proteins that capture sequence-structure relationships and interactions present in nature. The multiple sequence alignment of 311 individual LRRs, which are the putative ligand-recognition domain in NOD proteins, resulted in a consensus sequence protein containing two internal and N- and C-capping repeats named CLRR2. CLRR2 protein is a stable, monomeric, and cysteine free scaffold that without any affinity maturation displays micromolar binding to muramyl dipeptide, a bacterial cell wall fragment. To our knowledge, this is the first report of direct interaction of a NOD LRR with a physiologically relevant ligand.
authors.affiliation: Department of Chemistry, Virginia Tech, Blacksburg, Virginia, 24060.
authors.forename: Rachael
authors.initials: R
authors.lastname: Parker
authors.forename: Ana
authors.initials: A
authors.lastname: Mercedes-Camacho
authors.forename: Tijana Z
authors.initials: TZ
authors.lastname: Grove
mesh_terms: D000119:Acetylmuramyl-Alanyl-Isoglutamine / Q000737:chemistry* / Q000378:metabolism*; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D002473:Cell Wall / Q000737:chemistry*; D007930:Leucine / Q000737:chemistry*; D010457:Peptidoglycan; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D002352:Carrier Proteins; D010457:Peptidoglycan; D011506:Proteins; D000119:Acetylmuramyl-Alanyl-Isoglutamine; D007930:Leucine
keywords: MDP; NOD; binding scaffold; consensus design; leucine rich repeat; repeat protein