title: Influence of canonical structure determining residues on antibody affinity and stability.
abstract: A number of light and heavy chain canonical residue core redesigns were made in a therapeutic antibody (AQC2, anti-VLA1) Fab to explore the consequences to binding affinity and stability. These positions are all loop supporting, primarily CDR1 residues which do not directly contact the antigen. Structure based methods were used with and without consensus sequence information. 30 constructs were made, 24 expressed, and 70% of the designs using consensus sequence information retained binding affinity. Some success maintaining stability with more extreme redesigns suggests a surprising tolerance to mutation, though it often comes at the cost of loss of binding affinity and presumed loop conformation changes. In concordance with the expected need to present an ordered surface for binding, a relationship between decreased affinity and decreased stability was observed. Overpacking the core tends to destabilize the molecule and should be avoided.
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: louie@alumni.northwestern.edu.
authors.forename: Louis A
authors.initials: LA
authors.lastname: Clark
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: kdemarest@me.com.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Demarest
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: john.eldredge@biogenidec.com.
authors.forename: John
authors.initials: J
authors.lastname: Eldredge
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: mjarpe@acetylon.com.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Jarpe
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: tiehan@yahoo.com.
authors.forename: You
authors.initials: Y
authors.lastname: Li
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: kjsimon99@gmail.com.
authors.forename: Ken
authors.initials: K
authors.lastname: Simon
authors.affiliation: Biogen Idec, 14 Cambridge Center, Cambridge, MA 02142, United States. Electronic address: hvvlijme@tibbe.jnj.com.
authors.forename: Herman W T
authors.initials: HW
authors.lastname: van Vlijmen
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D000915:Antibody Affinity; D001665:Binding Sites; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D006860:Hydrogen Bonding; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry* / Q000235:genetics; D007147:Immunoglobulin Light Chains / Q000737:chemistry* / Q000235:genetics; D039222:Integrin alpha1beta1 / Q000737:chemistry / Q000276:immunology; D008958:Models, Molecular; D011485:Protein Binding; D015202:Protein Engineering; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D058767:Protein Unfolding; D051381:Rats; D013816:Thermodynamics
chemical_list: D022801:Complementarity Determining Regions; D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains; D039222:Integrin alpha1beta1
keywords: Antibody structure; Binding affinity; Canonical loop; Canonical residues; Framework residues; Protein design; Protein stability