title: Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design.
abstract: Noncanonical amino acids (NCAAs) can be used in a variety of protein design contexts. For example, they can be used in place of the canonical amino acids (CAAs) to improve the biophysical properties of peptides that target protein interfaces. We describe the incorporation of 114 NCAAs into the protein-modeling suite Rosetta. We describe our methods for building backbone dependent rotamer libraries and the parameterization and construction of a scoring function that can be used to score NCAA containing peptides and proteins. We validate these additions to Rosetta and our NCAA-rotamer libraries by showing that we can improve the binding of a calpastatin derived peptides to calpain-1 by substituting NCAAs for native amino acids using Rosetta. Rosetta (executables and source), auxiliary scripts and code, and documentation can be found at (http://www.rosettacommons.org/).
authors.affiliation: Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America.
authors.forename: P Douglas
authors.initials: PD
authors.lastname: Renfrew
authors.forename: Eun Jung
authors.initials: EJ
authors.lastname: Choi
authors.forename: Richard
authors.initials: R
authors.lastname: Bonneau
authors.forename: Brian
authors.initials: B
authors.lastname: Kuhlman
mesh_terms: D000596:Amino Acids / Q000378:metabolism*; D002135:Calcium-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D002154:Calpain / Q000737:chemistry / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D005454:Fluorescence Polarization; D008958:Models, Molecular; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012984:Software; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D002135:Calcium-Binding Proteins; D019151:Peptide Library; D010455:Peptides; D011506:Proteins; C033668:calpastatin; D002154:Calpain