Intrinsic Determinants of Aβ12–24 pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies

The propensity of amyloid- (A) peptide to self-assemble into highly ordered amyloid structures lies at the core of their accumulation in the brain during Alzheimer's disease. By using all-atom explicit solvent replica exchange molecular dynamics simulations, we elucidated at the atomic level the intrinsic determinants of the pH-dependent dimerization of the central hydrophobic segment A and related these with the propensity to form amyloid fibrils measured by experimental tools such as atomic force microscopy and fluorescence. The process of A dimerization was evaluated in terms of free energy landscape, side-chain two-dimensional contact probability maps, -sheet registries, potential mean force as a function of inter-chain distances, secondary structure development and radial solvation distributions. We showed that dimerization is a key event in A amyloid formation; it is highly prompted in the order of pH 5.02.98.4 and determines further amyloid growth. The dimerization is governed by a dynamic interplay of hydrophobic, electrostatic and solvation interactions permitting some variability of -sheets at each pH. These results provide atomistic insight into the complex process of molecular recognition detrimental for amyloid growth and pave the way for better understanding of the molecular basis of amyloid diseases

Structural characterization of Al\u3csub\u3e10\u3c/sub\u3eO\u3csub\u3e6\u3c/sub\u3e\u3csup\u3ei\u3c/sup\u3eBu\u3csub\u3e16\u3c/sub\u3e(μ-H)\u3csub\u3e2\u3c/sub\u3e, a high aluminum content cluster: Further studies of methylaluminoxane (MAO) and related aluminum complexes

The first structurally characterized isobutyl-containing aluminoxane compound is presented. The Al10O6iBu 16(μ-H)2 (I) cluster is produced from neat octakis-isobutyltetraluminoxane (Al4O2iBu 8) at 80°C in 6-8 h followed by slow crystallization. The crystal is triclinic (space group P1) with the molecule lying on an inversion center. This aluminoxane contains both nearly linear, 154(2)°, aluminum-bridging hydrides and three-coordinate aluminum sites. Solid-state 27Al magic-angle spinning (MAS) NMR experiments were done at 19.6 and 40 T (833 MHz and 1.703 GHz, 1H) and at 30-35 kHz spinning speeds, leading to the determination of the Cq and η values for the two four-coordinate Al sites and a lower limit of Cq for the three-coordinate Al site. Geometry-optimized restricted Hartree-Fock calculations at the double-ζ level of an idealized structure (methyl substituted, D2h geometry) yielded Cq and η in close agreement with experiment; C q agrees within 3 MHz. © 2007 American Chemical Society

Structural Characterization of Al₁₀O₆<i>ⁱ</i>Bu₁₆(μ-H)₂, a High Aluminum Content Cluster: Further Studies of Methylaluminoxane (MAO) and Related Aluminum Complexes

The first structurally characterized isobutyl-containing aluminoxane compound is presented. The Al10O6iBu16(μ-H)2 (I) cluster is produced from neat octakis-isobutyltetraluminoxane (Al4O2iBu8) at 80 °C in 6−8 h followed by slow crystallization. The crystal is triclinic (space group P1̄) with the molecule lying on an inversion center. This aluminoxane contains both nearly linear, 154(2)°, aluminum-bridging hydrides and three-coordinate aluminum sites. Solid-state 27Al magic-angle spinning (MAS) NMR experiments were done at 19.6 and 40 T (833 MHz and 1.703 GHz, 1H) and at 30−35 kHz spinning speeds, leading to the determination of the Cq and η values for the two four-coordinate Al sites and a lower limit of Cq for the three-coordinate Al site. Geometry-optimized restricted Hartree−Fock calculations at the double-ζ level of an idealized structure (methyl substituted, D2h geometry) yielded Cq and η in close agreement with experiment; Cq agrees within 3 MHz

Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors

TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5′ end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism