title: A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA.
abstract: Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. Such advances also suggest the possibility of using chemical shifts to characterize the conformational fluctuations of these molecules. Here we describe a method of using methyl chemical shifts as restraints in replica-averaged molecular dynamics (MD) simulations, which enables us to determine the conformational ensemble of the HU dimer and characterize the range of motions accessible to its flexible β-arms. Our analysis suggests that the bending action of HU on DNA is mediated by a mechanical clamping mechanism, in which metastable structural intermediates sampled during the hinge motions of the β-arms in the free state are presculpted to bind DNA. These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms.
authors: Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.
authors: Arvind
authors: A
authors: Kannan
authors: Carlo
authors: C
authors: Camilloni
authors: Aleksandr B
authors: AB
authors: Sahakyan
authors: Andrea
authors: A
authors: Cavalli
authors: Michele
authors: M
authors: Vendruscolo
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D019281:Dimerization; D009682:Magnetic Resonance Spectroscopy; D008697:Methane / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C040330:histone-like protein HU, bacteria; D004247:DNA; D008697:Methane