Distributions of the backbone dihedral angles of proteins have been studied for over 40 years. While many statistical analyses have been presented, only a handful of probability densities are publicly available for use in structure validation and structure prediction methods. The available distributions differ in a number of important ways, which determine their usefulness for various purposes. These include: 1) input data size and criteria for structure inclusion (resolution, R-factor, etc.); 2) filtering of suspect conformations and outliers using B-factors or other features; 3) secondary structure of input data (e.g., whether helix and sheet are included; whether beta turns are included); 4) the method used for determining probability densities ranging from simple histograms to modern nonparametric density estimation; and 5) whether they include nearest neighbor effects on the distribution of conformations in different regions of the Ramachandran map. In this work, Ramachandran probability distributions are presented for residues in protein loops from a high-resolution data set with filtering based on calculated electron densities. Distributions for all 20 amino acids (with cis and trans proline treated separately) have been determined, as well as 420 left-neighbor and 420 right-neighbor dependent distributions. The neighbor-independent and neighbor-dependent probability densities have been accurately estimated using Bayesian nonparametric statistical analysis based on the Dirichlet process. In particular, we used hierarchical Dirichlet process priors, which allow sharing of information between densities for a particular residue type and different neighbor residue types. The resulting distributions are tested in a loop modeling benchmark with the program Rosetta, and are shown to improve protein loop conformation prediction significantly. The distributions are available at http://dunbrack.fccc.edu/hdp.
In this paper, for the first time, we report a detailed study of the temperature-dependent solvation dynamics of a probe fluorophore, coumarin-500, in AOT/isooctane reverse micelles (RMs) with varying degrees of hydration (w0) of 5, 10, and 20 at four different temperatures, 293, 313, 328, and 343 K. The average solvation time constant becomes faster with the increase in w0 values at a particular temperature. The solvation dynamics of a RM with a fixed w0 value also becomes faster with the increase in temperature. The observed temperature-induced faster solvation dynamics is associated with a transition of bound- to free-type water molecules, and the corresponding activation energy value for the w0 = 5 system has been found to be 3.4 kcal mol-1, whereas for the latter two systems, it is approximately 5 kcal mol-1. Dynamic light scattering measurements indicate an insignificant change in size with temperature for RMs with w0 = 5 and 10, whereas for a w0 = 20 system, the hydrodynamic diameter increases with temperature. Time-resolved fluorescence anisotropy studies reveal a decrease in the rotational restriction on the probe with increasing temperature for all systems. Wobbling-in-cone analysis of the anisotropy data also supports this finding.
In recent years, the validity of the activation energy barrier crossing model at the micellar surface brings notable controversy (Sen, P.; Mukherjee, S.; Halder, A.; Bhattacharyya, K. Chem. Phys. Lett. 2004, 385, 357-361. Kumbhakar, M.; Pal, H. J. Phys. Chem. B 2004, 108, 19246-19254.) in the literature. In order to check the validity of the model by time-resolved solvation of a probe fluorophore, a wider range of temperature must be considered. At the same time, spatial heterogeneity (solubilization) of the probe and structural perturbation of the host micelle should carefully be avoided, which was not strictly maintained in the earlier studies. We report here the solvation dynamics of 4-(dicyanomethylene)-2-methyl-6(p-dimethylamino-styryl) 4H-pyran (DCM) in the SDS micelle at 298, 323, and 348 K. The probe DCM is completely insoluble in bulk water in this wide range of temperature. The size of the micelle at different temperatures using the dynamic light scattering (DLS) technique is found to have insignificant change. The hydration number of the micelle, determined by sound velocity measurements, decreases with increasing temperature. Time-resolved fluorescence anisotropy reveals the retention of the probe in the micellar interface within the temperature range. The average solvation time decreases with increasing temperature. The result of the solvation study has been analyzed in the light of energetics of bound to free water conversion at a constant size and decreasing hydration number at the micellar surface. The solvation process at the micellar surface has been found to be the activation energy barrier crossing type, in which interfacially bound type water molecules get converted into free type molecules. We have calculated E a to be 3.5 kcal mol -1 , which is in good agreement with that obtained by molecular dynamics simulation studies.
In this contribution we have tried to investigate whether the mechanical properties of the reverse micellar (RM) interface dictate the physical properties of entrapped water molecules in the RM waterpool. We choose AOT/Igepal-520/cyclohexane (Cy) mixed RM as a model system which exhibits synergistic water solubilization behavior as a function of interfacial stoichiometry. Such a phenomenon associates systematic modification of the interface curvature. Dynamic light scattering (DLS) studies reveal linear increase in the droplet size and aggregation number of the RMs with increasing XIgepal (mole fraction of Igepal in the surfactant mixture). FTIR study in the 3000-3800 cm(-1) region identifies that the relative population of the surface-bound water molecules is higher in AOT RM compared to that in Igepal RM, and in mixed systems it also follows a linear trend with XIgepal. Water relaxation dynamics as probed by time-resolved fluorescence spectroscopy using Coumarin-500 also reveals an overall linear trend with no characteristic feature around the solubilization inflation point. Our study clearly identifies that the physical properties of water in RM are mostly governed by the interfacial stoichiometry and water content, and merely bares any dependence on the mechanical properties of the interface.
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