title: Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations.
abstract: A mechanical perturbation method that locally restricts conformational entropy along the protein backbone is used to identify putative allosteric sites in a series of antibody fragments. The method is based on a distance constraint model that integrates mechanical and thermodynamic viewpoints of protein structure wherein mechanical clamps that mimic substrate or cosolute binding are introduced. Across a set of six single chain-Fv fragments of the anti-lymphotoxin-β receptor antibody, statistically significant responses are obtained by averaging over 10 representative structures sampled from a molecular dynamics simulation. As expected, the introduced clamps locally rigidify the protein, but long-ranged increases in both rigidity and flexibility are also frequently observed. Expanding our analysis to every molecular dynamics frame demonstrates that the allosteric responses are modulated by fluctuations within the hydrogen-bond network where the native ensemble is comprised of conformations that both are, and are not, affected by the perturbation in question. Population shifts induced by the mutations alter the allosteric response by adjusting which hydrogen-bond networks are the most probable. These effects are compared using response maps that track changes across each single chain-Fv fragment, thus providing valuable insight into how sensitive allosteric mechanisms are to mutations.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina.
authors.forename: Amit
authors.initials: A
authors.lastname: Srivastava
authors.affiliation: Formulation Sciences, MedImmune Ltd., Cambridge, UK.
authors.forename: Malgorzata B
authors.initials: MB
authors.lastname: Tracka
authors.affiliation: Formulation Sciences, MedImmune Ltd., Cambridge, UK.
authors.forename: Shahid
authors.initials: S
authors.lastname: Uddin
authors.affiliation: Analytical Biochemistry Department, MedImmune LLC, Gaithersburg, Maryland.
authors.forename: Jose
authors.initials: J
authors.lastname: Casas-Finet
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina. Electronic address: drlivesa@uncc.edu.
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Livesay
authors.affiliation: Department of Physics and Optical Science, University of North Carolina at Charlotte, Charlotte, North Carolina. Electronic address: djacobs1@uncc.edu.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Jacobs
mesh_terms: D000494:Allosteric Regulation; D019277:Entropy; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009154:Mutation; D000072417:Protein Domains; D057127:Single-Chain Antibodies / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism
chemical_list: D057127:Single-Chain Antibodies