title: Energy landscapes associated with macromolecular conformational changes from endpoint structures.
abstract: Conformational changes modulate macromolecular function by promoting the specific binding of ligands (such as in antigen recognition) or the stabilization of transition states in enzymatic reactions. However, quantitative characterization of the energetics underlying dynamic structural interconversions is still challenging and lacks a unified method. Here, we introduce a novel in silico approach based on the combined use of essential dynamics sampling and nonequilibrium free-energy calculations to obtain quantitative data on conformational energy landscapes. This technique allows the unbiased investigation of highly complex rearrangements, and does not require the crucial definition of user-defined collective variables. We show that free-energy values derived from profiles connecting the unliganded and ligand-bound X-ray structures of a bacterial nucleoside hydrolase match the experimental binding constant. This approach also provides first evidence for a rate-limiting character of the conformational transition in this enzyme, and an unexpected role of the protonation state of a single residue in regulating substrate binding and product release.
authors.affiliation: Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, Scientific Institute San Raffaele, Via Olgettina 58, 20132 Milan, Italy. arianna.fornili@kcl.ac.uk
authors.forename: Arianna
authors.initials: A
authors.lastname: Fornili
authors.forename: Barbara
authors.initials: B
authors.lastname: Giabbai
authors.forename: Gianpiero
authors.initials: G
authors.lastname: Garau
authors.forename: Massimo
authors.initials: M
authors.lastname: Degano
mesh_terms: D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism*; D050113:Imino Furanoses / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D056004:Molecular Dynamics Simulation; D009699:N-Glycosyl Hydrolases / Q000737:chemistry* / Q000378:metabolism*; D010655:Phenylenediamines / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: C552727:3,4-diaminophenyliminoribitol; D029968:Escherichia coli Proteins; D050113:Imino Furanoses; D008024:Ligands; D010655:Phenylenediamines; D009699:N-Glycosyl Hydrolases; C422988:RihB protein, E coli