for non-equilibrium backbone dynamics; as the thiyl radicals separate under the influence of backbone motion, their recombination rate decreases, so that ob- servation of the transient thiyl absorbance provides access to backbone dynam- ics. Unlike fluorescence or triplet quenching experiments, which often are used for the study of polypeptide dynamics, this method observes processes far from equilibrium, and has no intrinsic limitation of the accessible time scale. The encounter probability of the thiyl radicals was found to decay with time following a power law t -0.94 which is incompatible with simple diffusion. Thus, the relative motion of the radicals is affected by the dynamics of the con- necting backbone, resulting in an unusual power law for the re-encounter prob- ability which could be described as (fractal) diffusion in a reduced non-integer dimensional space. The scaling law was found to extend over the full experi- mentaltime window, covering nine orders of magnitude in time (1 ps to 1 ms), although very different processes govern backbone motion on these dif- ferent time scales. Furthermore, the same scaling law was observed in a folding protein having secondary and tertiary structure, in simple model peptides forming only secondary structure, and in a protein under unfolding conditions, indicating an intrinsic behaviour of the polypeptide backbone itself. 1650-Pos Board B494 Mobility of a Loop of a B. subtilis Carboxylesterase and its Effect on Substrate Conversion Xiaozhen Yu 1 , Monika Wierdl 2 , Philip M. Potter 2 , Randy M. Wadkins 1 . 1 Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA, 2 Dept. of Mol. Pharmacol., St. Jude Children’s Res. Hospital, Memphis, TN, USA. Carboxylesterases (CEs) are ubiquitous enzymes responsible for the detoxifi- cation of xenobiotics. CEs can metabolize and hydrolyze a variety of esterified drugs, including the anticancer agent CPT-11. The specificity of CEs for a par- ticular substrate or inhibitor depends on the enzyme’s molecular structure and the dynamics of conformational substructures when a substrate is bound. We have used a series of biophysical techniques to understand differences in sub- strate selectivity of CEs. First, we used molecular dynamics simulations (MD) and normal mode analysis (NMA) to identify the loop region of high fluctua- tion in a CE from B. subtilis. Second, we calculated the root-mean-square de- viation (RMSD) from both MD and NMA trajectory data. Then we used these RMSD data along with its secondary structure to make correlations with en- zyme activity. Meanwhile, we generated a series of mutations at specific amino acid residues that are located near this flexible loop region in order to restrictits mobility.Then we measured enzyme activity of these mutant CEs and compared them with the wild type. Our hypothesis is that the molec- ular dynamics of this enzyme is correlated with substrate conversion efficiency for selected CEs. These experiments provide the first data toward testing this hypothesis. These studies were supported by NSF grant EPS-0556308 and ALSAC. 1651-Pos Board B495 Reality’s A Drag: Accounting For Friction In Simple Protein Models Timothy R. Lezon, Ivet Bahar. University of Pittsburgh, Pittsburgh, PA, USA. Elastic network models (ENMs) are widely used for studying the global equi- librium dynamics of proteins because they predict motions on timescales that are generally inaccessible to molecular dynamics (MD) simulations. Although the slowest motions predicted by in vacuo ENMs have repeatedly shown to cor- relate well with experiment, the timescales of these motions do not. Here we develop a simple algorithm for scaling the characteristic timescales of slow mo- tions predicted by an ENM to reflect the true timescales of the molecular mo- tions. Using MD trajectories on the order of tens of nanoseconds, we calculate ideal friction constants for Langevin models of three proteins. We then demon- strate that the difference between the slowest vibrational frequencies predicted by the Langevin model and those predicted by an in vacuo ENM can be ex- plained through simple physical arguments. We provide an expression for scal- ing the normal mode frequencies of an in vacuo ENM to realistic values and discuss the utility of our results in combining ENMs with MD simulations to predict large-scale protein dynamics. 1652-Pos Board B496 Coupling Of Solvent And Protein Dynamics: Mossbauer And Incoherent Neutron Scattering From Dielectric Relaxation Data Paul W. Fenimore 1 , Guo Chen 1 , Hans Frauenfelder 1 , Benjamin H. McMahon 1 , Jan Swenson 2 , Helen Jansson 3 , Izabela Stroe 4 , Robert D. Young 5 , Joel Berendzen 1 . 1 Los Alamos National Laboratory, Los Alamos, NM, USA, 2 Chalmers University of Technology, Goteborg, Sweden, 3 Goteborg University, Goteborg, Sweden, 4 Worcester Polytechnic Institute, Worcester, MA, USA, 5 Northern Arizona State University, Flagstaff, AZ, USA. A wide variety of protein dynamics are accounted for by two classes of s processes: the bulk-solvent viscosity and hydration-shell dynamics. In glass- forming solvents the bulk viscosity arises from the well-characterized mi scopic alpha relaxation; in liquid solvents that freeze the alpha process is essentially molecular reorientation. In past work we showed that the solvent alpha relaxation determines the activation enthalpy of alpha-slaved protein motions. We have now measured the dielectric spectrum of the hydration-shell dy in myoglobin solutions as a function of hydration, temperature and frequ These hydration-shell data and a minimal model of protein-solvent coupling predicthe temperature- and hydration-dependence of the Mossbauer eff Furthermore, we show agreement between incoherent neutron scatterin and our measurements of hydration dynamics. These improvements in understanding protein-solvent dynamical couplin be discussed in terms of earlier work describing the slaving of many pro functional motions to the solvent alpha-process and the slaving of protei ing. We demonstrate that many enthalpy barriers to protein motion arise entirely from solvent dynamical processes. 1653-Pos Board B497 A Detailed Comparison Between The NMR Ensemble, Two X-ray Models And ComputationalPredictionsOf Motions For A Designed Sugar Binding Protein Lin Liu, Leonardus M.I. Koharudin, Angela M. Gronenborn, Ivet Bahar. University of Pittsburgh, Pittsburgh, PA, USA. Coarse-grained elastic network models with single point representation of amino acids are becoming increasingly popular for describing conformat flexibility and equilibrium dynamics of proteins. In particular, the Gaussian network model (GNM) predictions have been fairly successful in interpre the residue-level root-mean-square variations in residue positions inferred from NMR ensembles of structural models for a given protein and the flu tions in residue positions indicated by crystallographic B-factors. Here, w ried out a detailed analysis for a designed sugar binding protein whose s was solved in two crystal formsby X-ray crystallography and by NMR. Comparison with experimental data and results from molecular dynamic ulations confirm that the GNM predicts well the equilibrium dynamics of protein and correlates better with the NMR derived data than crystallogr B-factors. The results further stipulate the importance of examining multip structures determined by different methods as well as performing both a ical and numerical studies, toward gaining an accurate understanding of the type and range of conformational motions accessible to a given protein u native state conditions. 1654-Pos Board B498 Molecular Dynamics Simulations of Phosphorylation-induced Conforma- tional Transitions in the Mycobacterium tuberculosis Response Regulator PrrA Guo Chen, Benjamin H. McMahon, Chang-Shung Tung. Los Alamos National Laboratory, Los Alamos, NM, USA. Phosphorylation-mediated activation of response regulators (RRs) is pred inantly used by microorganisms as a central strategy in the regulatory a ities of their two-component systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted mo- lecular dynamics simulations of the phosphorylation-induced conformati transitions in the Mycobacterium tuberculosis RR, PrrA, to obtain the dy- namical details that are relevant to the RR activation. From the full-length structure of unphosphorylated PrrA we generated a computational model for the phosphorylated PrrA state by changing the phospho-accepting as partic acid Asp-58 in the regulatory domain to the phosphoaspartate pho Asp-58.The resultant structural relaxations were simulated through a rapid sampling ofprotein motions using a conformation-biased all heavy-atom potential energy function without explicitsolvent.Marked structural rear- rangements have been observed across the interdomain interface of the phorylated PrrA, manifesting the global effectof the localphosphorylation upon a single residue of aspartate. Such changes have also been found to in- volve the domain-crossing motions that disruptthe hydrophilic and hydro- phobic interactions within the interdomain space and thus transform Prr from a compact structure to a more extended conformation featuring a w domain-domain separation and a more exposed transactivation loop. These simulated motions reflect the essential early-stage activation dynamics for the relief of the inhibitory role of the regulatory domain in PrrA. In effect, each moreextended PrrA becomes moresuited to interact with DNA and RNA polymerase;the activationof manyproteinsalso shifts the population-equilibrium of PrrA towards more active states, therefore leading to a phosphorylation-enhanced allostericregulationfor the controlof transcription. Monday, March 2, 2009 323a