title: Benchmarking all-atom simulations using hydrogen exchange.
abstract: Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.
authors.affiliation: Departments of Biochemistry and Molecular Biology and.
authors.forename: John J
authors.initials: JJ
authors.lastname: Skinner
authors.affiliation: Departments of Biochemistry and Molecular Biology and Center for Proteome Biophysics, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Korea.
authors.forename: Wookyung
authors.initials: W
authors.lastname: Yu
authors.affiliation: Departments of Biochemistry and Molecular Biology and.
authors.forename: Elizabeth K
authors.initials: EK
authors.lastname: Gichana
authors.affiliation: Departments of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637; and.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Baxa
authors.affiliation: Chemistry.
authors.forename: James R
authors.initials: JR
authors.lastname: Hinshaw
authors.affiliation: Chemistry, James Franck Institute, Computation Institute, and freed@uchicago.edu trsosnic@uchicago.edu.
authors.forename: Karl F
authors.initials: KF
authors.lastname: Freed
authors.affiliation: Departments of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637; and Computation Institute, and freed@uchicago.edu trsosnic@uchicago.edu.
authors.forename: Tobin R
authors.initials: TR
authors.lastname: Sosnick
mesh_terms: D041961:Deuterium Exchange Measurement; D019204:GTP-Binding Proteins / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D017434:Protein Structure, Tertiary; D058767:Protein Unfolding; D011994:Recombinant Proteins / Q000737:chemistry
chemical_list: D011994:Recombinant Proteins; D006859:Hydrogen; D019204:GTP-Binding Proteins
keywords: HX; denatured states; molecular dynamics; protein folding; unfolded state