title: Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.
abstract: The effects of somatic mutations that transform polyspecific germline (GL) antibodies to affinity mature (AM) antibodies with monospecificity are compared among three GL-AM Fab pairs. In particular, changes in conformational flexibility are assessed using a Distance Constraint Model (DCM). We have previously established that the DCM can be robustly applied across a series of antibody fragments (VL to Fab), and subsequently, the DCM was combined with molecular dynamics (MD) simulations to similarly characterize five thermostabilizing scFv mutants. The DCM is an ensemble based statistical mechanical approach that accounts for enthalpy/entropy compensation due to network rigidity, which has been quite successful in elucidating conformational flexibility and Quantitative Stability/Flexibility Relationships (QSFR) in proteins. Applied to three disparate antibody systems changes in QSFR quantities indicate that the VH domain is typically rigidified, whereas the VL domain and CDR L2 loop become more flexible during affinity maturation. The increase in CDR H3 loop rigidity is consistent with other studies in the literature. The redistribution of conformational flexibility is largely controlled by nonspecific changes in the H-bond network, although certain Arg to Asp salt bridges create highly localized rigidity increases. Taken together, these results reveal an intricate flexibility/rigidity response that accompanies affinity maturation.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
authors.forename: Tong
authors.initials: T
authors.lastname: Li
authors.affiliation: Department of Formulation Sciences, MedImmune Ltd., Cambridge, United Kingdom.
authors.forename: Malgorzata B
authors.initials: MB
authors.lastname: Tracka
authors.affiliation: Department of Formulation Sciences, MedImmune Ltd., Cambridge, United Kingdom.
authors.forename: Shahid
authors.initials: S
authors.lastname: Uddin
authors.affiliation: Analytical Biochemistry Department, MedImmune LLC, Gaithersburg, Maryland, United States of America.
authors.forename: Jose
authors.initials: J
authors.lastname: Casas-Finet
authors.affiliation: Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Jacobs
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America.
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Livesay
mesh_terms: D000906:Antibodies / Q000737:chemistry* / Q000235:genetics* / Q000648:ultrastructure; D003198:Computer Simulation; D019143:Evolution, Molecular; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000235:genetics* / Q000648:ultrastructure; D008956:Models, Chemical; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship
chemical_list: D000906:Antibodies; D007140:Immunoglobulin Fab Fragments