Simulating Large-Scale Conformational Changes of Proteins by Accelerating Collective Motions Obtained from Principal Component Analysis

Enhanced sampling methods remain of continuing interest over the past decades because they are able to explore conformational space of proteins much more extensively than conventional molecular dynamics (MD) simulations. In this paper, we report a new sampling method that utilizes a few collective modes obtained from principal component analysis (PCA) to guide the MD simulations. Two multidomain proteins, bacteriophage T4 lysozyme and human vinculin, are studied to test the method. By updating the PCA modes with a proper frequency, our method can sample large-amplitude conformational changes of the proteins much more efficiently than standard MD. Since those PCA modes are calculated from structural ensembles generated by all-atom simulations, the method may overcome an inherent limitation called “tip effect” that would possibly appear in those sampling techniques based on coarse-grained elastic network models. The algorithm proposed here is potentially very useful in developing tools for flexible fitting of protein structures integrating cryo-electron microscope or small-angle X-ray scattering data

Comparing Exploratory Structural Equation Modeling and Existing Approaches for Multiple Regression with Latent Variables

<p>Exploratory structural equation modeling (ESEM) is an approach for analysis of latent variables using exploratory factor analysis to evaluate the measurement model. This study compared ESEM with two dominant approaches for multiple regression with latent variables, structural equation modeling (SEM) and manifest regression analysis (MRA). Main findings included: (1) ESEM in general provided the least biased estimation of the regression coefficients; SEM was more biased than MRA given large cross-factor loadings. (2) MRA produced the most precise estimation, followed by ESEM and then SEM. (3) SEM was the least powerful in the significance tests; statistical power was lower for ESEM than MRA with relatively small target-factor loadings, but higher for ESEM than MRA with relatively large target-factor loadings. (4) ESEM showed difficulties in convergence and occasionally created an inflated type I error rate under some conditions. ESEM is recommended when non-ignorable cross-factor loadings exist.</p

Dynamic Mechanisms for Ammonia Borane Thermolysis in Solvent: Deviation from Gas-Phase Minimum-Energy Pathways

The dynamic mechanisms involved in the dehydrogenation of ammonia borane are investigated using quasi-classical trajectory simulations. The effects of solvent and nuclear motion yield qualitatively different results compared to simulations where these considerations are neglected. Not only are rate-limiting barriers substantially different from the gas to solvent phase, trajectories leading from transition states branch to different products depending on the presence or lack of solvent. In addition, the formation of the diammoniate of diborane is shown to be noncompetitive in the gas phase due to the presence of a lower-barrier dehydrogenation pathway. The first comparative analysis of the pathways leading to the thermolysis of ammonia−borane is presented herein

The shearing process for 3D DDF-SECSY data of butyl methacrylate in DMSO: (A) original 3D spectrum before shearing and (B) processed 3D spectrum after shearing.

<p>The given F1–F2 plane where a singlet signal at 3.1 ppm lies is selected to show the rotation of signal streaks by shearing process. Before shearing, the signal streaks are parallel to the F2–F3 plane and perpendicular to the F1 dimension. After shearing process, the signal streaks only stretch along F2 dimension and are perpendicular to the F1–F3 plane, resulting in high-resolution SECSY information on the F1–F3 plane.</p

SECSY spectra of an aqueous solution of brain metabolites.

<p>(A) Conventional spectrum in an inhomogeneous field with a line-width of 200 Hz; (B) DDF-SECSY spectrum using ultrafast acquisition scheme. The marked regions are expanded for comparison.</p

SECSY spectra of a solution of butyl methacrylate in DMSO.

<p>(A, B) Conventional spectrum with 1D projection along the F2 axis in a well-shimmed field (A) and in an inhomogeneous field with a line-width of 150 Hz (B); (C, D) spectra with 1D projection along the F3 axis in the same inhomogeneous field acquired from DDF-SECSY (C) and DDF-SECSY with ultrafast acquisition scheme (D). The regions of component peak of <i>a</i> and both component and cross peaks of <i>e</i> are expanded for comparison. The structure of butyl methacrylate with proton marked is shown on the top of the frame.</p

<i>S</i>. <i>aureus</i> bacteria were efficiently cleared from ocular surface of WT mice compared to SP-D KO mice.

<p>The CFUs recovered from the tear fluid of infected WT mice were examined at 3, 6, 12 or 24 h post-inoculation with <i>S</i>. <i>aureus</i> (10⁷ CFU/eye). Rapid clearance of the bacteria was in time-dependent manner. The CFUs of <i>S</i>. <i>aureus</i> from the ocular surface in infected WT and SP-D KO mice were compared at 3, 6, 12, and 24 h after inoculation of 10⁷ CFU/eye. A significant difference of the recovered bacteria in the tear fluid exists between infected WT and SP-D KO mice after infection. The results were from three independent experiments (n = 8 to 10 mice per group). Data are shown as the median (central black bar in boxes) with upper and lower quartiles (boxed area), and range of the data (error bars).* p<0.05 in Mann-Whitney U test.</p

Complexation of Curium(III) with DTPA at 10–70 °C: Comparison with Eu(III)–DTPA in Thermodynamics, Luminescence, and Coordination Modes

Separation of trivalent actinides (An­(III)) from trivalent lanthanides (Ln­(III)) is a challenging task because of the nearly identical chemical properties of these groups. Diethylenetriaminepentaacetate (DTPA), a key reagent used in the TALSPEAK process that effectively separates An­(III) from Ln­(III), is believed to play a critical role in the An­(III)/Ln­(III) separation. However, the underlying principles for the separation based on the difference in the complexation of DTPA with An­(III) and Ln­(III) remain unclear. In this work, the complexation of DTPA with Cm­(III) at 10–70 °C was investigated by spectrophotometry, luminescence spectroscopy, and microcalorimetry, in conjunction with computational methods. The binding strength, the enthalpy of complexation, the coordination modes, and the luminescence properties are compared between the Cm­(III)–DTPA and Eu­(III)–DTPA systems. The experimental and computational data demonstrated that the difference between Cm­(III) and Eu­(III) in the binding strength with DTPA can be attributed to the stronger covalence bonding between Cm­(III) and the nitrogen donors of DTPA

Comparison of eye injury of WT and SP-D KO mice after <i>S</i>. <i>aureus</i> infection in the presence or absence of E₆₄.

<p>Mouse corneal integrity (eye injury) was examined using fluorescein staining method after inoculation of <i>S</i>. <i>aureus</i> for 24 h. The results show increased fluorescein staining (arrows) in the cornea of SP-D KO mice compared to WT mice. E₆₄ treatment could reduce fluorescein staining in WT mice but not in SP-D KO mice. Corneal fluorescein staining scores in SP-D KO mice were higher than that in WT mice (B). WT, WT mice. KO, SP-D KO mice. The figures shown are from three independent experiments (n = 8 to 10 mice per group). Data are shown as the median (central black bar in boxes) with upper and lower quartiles (boxed area), and range of the data (error bars).* p<0.05 in Mann-Whitney U test.</p

Western blotting analysis of SP-D level in mouse tear fluid.

<p>SP-D levels in the mouse tear fluid were examined by Western blot analysis. Mouse tear fluid was collected and pooled from five WT mice. The tear fluid was incubated with <i>S</i>. <i>aureus</i> conditioned medium in the presence or absence of 10 nM E₆₄ for 1 h. After Western blot analysis with SP-D antibody, a band of SP-D (about 43 KDa) was detected in mouse tear fluid (Lane 2), but the level of SP-D in the tear fluid with <i>S</i>. <i>aureus</i> conditioned medium was reduced (Lane 3) compared to the tear fluid without <i>S</i>. <i>aureus</i> conditioned medium (lane 2). In the presence of inhibitor E₆₄, SP-D level of the sample (Lane 4) has similar to the tear fluid sample (Lane 2), suggesting that decreasing of SP-D level was inhibited by E₆₄. Mouse lung BAL fluid was used as SP-D positive control (Lane 1). As expected, the tear fluid from SP-D KO mice did not show an SP-D band (Lane 5). WT,WT mice. KO, SP-D KO mice.BAL, lung bronchoalveolar lavage. Three independent experiments were performed.</p