title: Distinct Roles for Conformational Dynamics in Protein-Ligand Interactions.
abstract: Conformational dynamics has an established role in enzyme catalysis, but its contribution to ligand binding and specificity is largely unexplored. Here we used the Tiam1 PDZ domain and an engineered variant (QM PDZ) with broadened specificity to investigate the role of structure and conformational dynamics in molecular recognition. Crystal structures of the QM PDZ domain both free and bound to ligands showed structural features central to binding (enthalpy), while nuclear-magnetic-resonance-based methyl relaxation experiments and isothermal titration calorimetry revealed that conformational entropy contributes to affinity. In addition to motions relevant to thermodynamics, slower microsecond to millisecond switching was prevalent in the QM PDZ ligand-binding site consistent with a role in ligand specificity. Our data indicate that conformational dynamics plays distinct and fundamental roles in tuning the affinity (conformational entropy) and specificity (excited-state conformations) of molecular interactions. More broadly, our results have important implications for the evolution, regulation, and design of protein-ligand interactions.
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Xu
authors.initials: X
authors.lastname: Liu
authors.affiliation: Department of Chemistry, Loras College, Dubuque, IA 52004-0178, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Speckhard
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Tyson R
authors.initials: TR
authors.lastname: Shepherd
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Young Joo
authors.initials: YJ
authors.lastname: Sun
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Hengel
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Carver College of Medicine Medical Nuclear Magnetic Resonance Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Liping
authors.initials: L
authors.lastname: Yu
authors.affiliation: Carver College of Medicine Medical Nuclear Magnetic Resonance Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: C Andrew
authors.initials: CA
authors.lastname: Fowler
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Protein Crystallography Facility, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA.
authors.forename: Lokesh
authors.initials: L
authors.lastname: Gakhar
authors.affiliation: Department of Biochemistry, University of Iowa, Iowa City, IA 52242-1109, USA; Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242-1109, USA; Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109, USA. Electronic address: ernesto-fuentes@uiowa.edu.
authors.forename: Ernesto J
authors.initials: EJ
authors.lastname: Fuentes
mesh_terms: D000818:Animals; D001665:Binding Sites; D020662:Guanine Nucleotide Exchange Factors / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D051379:Mice; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D054731:PDZ Domains; D011485:Protein Binding; D011487:Protein Conformation; D000075684:T-Lymphoma Invasion and Metastasis-inducing Protein 1; D013816:Thermodynamics
chemical_list: D020662:Guanine Nucleotide Exchange Factors; D008024:Ligands; D000075684:T-Lymphoma Invasion and Metastasis-inducing Protein 1; C087334:TIAM1 protein, human; C447620:Tiam2 protein, mouse
keywords: PDZ domain; Tiam1; X-ray crystallography; conformational dynamics; nuclear magnetic resonance; protein design; protein-ligand interaction; thermodynamics