Browsing by Author "Hayes, Ryan L."

Now showing 1 - 5 of 5
  • Thumbnail Image
    Item
    A magnesium-induced triplex pre-organizes the SAM-II riboswitch
    (Public Library of Science, 2017) Roy, Susmita; Lammert, Heiko; Hayes, Ryan L.; Chen, Bin; LeBlanc, Regan; Dayie, T.Kwaku; Onuchic, José Nelson; Sanbonmatsu, Karissa Y.; Center for Theoretical Biological Physics
    Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function.
  • Thumbnail Image
    Item
    Generalized Manning Condensation Model Captures the RNA Ion Atmosphere
    (American Physical Society, 2015) Hayes, Ryan L.; Noel, Jeffrey K.; Mandic, Ana; Whitford, Paul C.; Sanbonmatsu, Karissa Y.; Mohanty, Udayan; Onuchic, José N.; Center for Theoretical Biological Physics
    RNA is highly sensitive to the ionic environment and typically requires Mg2+ to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg2+ ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg2+ associated with the RNA, Γ2+, because Γ2+ is directly related to the Mg2+-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.
  • Thumbnail Image
    Item
    Intercellular Stress Reconstitution from Traction Force Data
    (Elsevier, 2014) Zimmermann, Juliane; Hayes, Ryan L.; Basan, Markus; Onuchic, José N.; Rappel, Wouter-Jan; Levine, Herbert; Center for Theoretical Biological Physics
    Cells migrate collectively during development, wound healing, and cancer metastasis. Recently, a method has been developed to recover intercellular stress in monolayers from measured traction forces upon the substrate. To calculate stress maps in two dimensions, the cell sheet was assumed to behave like an elastic material, and it remains unclear to what extent this assumption is valid. In this study, we simulate our recently developed model for collective cell migration, and compute intercellular stress maps using the method employed in the experiments. We also compute these maps using a method that does not depend on the traction forces or material properties. The two independently obtained stress patterns agree well for the parameters we have probed and provide a verification of the validity of the experimental method.
  • Thumbnail Image
    Item
    Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch
    (American Chemical Society, 2012) Hayes, Ryan L.; Noel, Jeffrey K.; Mohanty, Udayan; Whitford, Paul C.; Hennelly, Scott P.; Onuchic, José N.; Sanbonmatsu, Karissa Y.; Center for Theoretical Biological Physics
    Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg2+ ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg2+ association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg2+ concentration slows RNA fluctuations. Outer-sphere Mg2+ ions responsible for these effects account for 80% of Mg2+ in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer-sphere Mg2+ are separated from the RNA by a single hydration shell, occupying a thin layer 3–5 Å from the RNA. Distribution functions reveal that outer-sphere Mg2+ are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer-sphere Mg2+ dynamics are glassy. Since outer-sphere Mg2+ ions account for most of the Mg2+ in our simulations, these ions may change the paradigm of Mg2+–RNA interactions. Rather than a few inner-sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer-sphere coordinated Mg2+ that is transiently bound but strongly coupled to the RNA.
  • Thumbnail Image
    Item
    SMOG 2: A Versatile Software Package for Generating Structure-Based Models
    (Public Library of Science, 2016) Noel, Jeffrey K.; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L.; Onuchic, José N.; Whitford, Paul C.; Center for Theoretical Biological Physics
    Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.