title: NMR and Computation Reveal a Pressure-Sensitive Folded Conformation of Trp-Cage.
abstract: Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b. Pressure effects on protein conformation are based on volume differences between states, providing a subtle continuous variable for perturbing conformations. 2D proton TOCSY spectra of Tc5b were acquired as a function of pressure at different temperature, pH, and urea concentration. In contrast to urea and pH which lead to unfolding of Tc5b, pressure resulted in modulation of the structures that are populated within the folded state basin. The results of molecular dynamics simulations on Tc5b displayed remarkable agreement with the NMR data. Principal component analysis identified two structural subensembles in the folded state basin, one of which was strongly destabilized by pressure. The pressure-dependent structural perturbations observed by NMR coincided precisely with the changes in secondary structure associated with the shifting populations in the folded state basin observed in the simulations. These results highlight the deep structural insight afforded by pressure perturbation in conjunction with high resolution experimental and advanced computational tools.
authors.affiliation: Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York.
authors.forename: Soichiro
authors.initials: S
authors.lastname: Kitazawa
authors.affiliation: Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York.|Laboratoire Charles Coulomb UMR 5221 CNRS-UM, Montpellier, France.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Fossat
authors.affiliation: Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York.
authors.forename: Scott A
authors.initials: SA
authors.lastname: McCallum
authors.affiliation: Department of Physics, Rensselaer Polytechnic Institute , Troy, New York.
authors.forename: Angel E
authors.identifier: 0000-0002-0912-0960
authors.initials: AE
authors.lastname: Garcia
authors.affiliation: Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York.
authors.forename: Catherine A
authors.identifier: 0000-0002-2670-3391
authors.initials: CA
authors.lastname: Royer
mesh_terms: D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011312:Pressure; D011487:Protein Conformation; D017510:Protein Folding; D011994:Recombinant Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011994:Recombinant Proteins; C476389:TC5b protein, synthetic