Polyglutamine expansion within the exon1 of huntingtin leads to protein misfolding, aggregation, and cytotoxicity in Huntington's disease. This incurable neurodegenerative disease is the most prevalent member of a family of CAG repeat expansion disorders. Although mature exon1 fibrils are viable candidates for the toxic species, their molecular structure and how they form have remained poorly understood. Using advanced magic angle spinning solid-state NMR, we directly probe the structure of the rigid core that is at the heart of huntingtin exon1 fibrils and other polyglutamine aggregates, via measurements of long-range intramolecular and intermolecular contacts, backbone and side-chain torsion angles, relaxation measurements, and calculations of chemical shifts. These experiments reveal the presence of β-hairpin-containing β-sheets that are connected through interdigitating extended side chains. Despite dramatic differences in aggregation behavior, huntingtin exon1 fibrils and other polyglutamine-based aggregates contain identical β-strand-based cores. Prior structural models, derived from X-ray fiber diffraction and computational analyses, are shown to be inconsistent with the solid-state NMR results. Internally, the polyglutamine amyloid fibrils are coassembled from differently structured monomers, which we describe as a type of "intrinsic" polymorphism. A stochastic polyglutamine-specific aggregation mechanism is introduced to explain this phenomenon. We show that the aggregation of mutant huntingtin exon1 proceeds via an intramolecular collapse of the expanded polyglutamine domain and discuss the implications of this observation for our understanding of its misfolding and aggregation mechanisms.solid-state NMR | Huntington's disease | amyloid disease | protein aggregation | amyloid

Conformer ttc/VIp of glycine and glycine-N,N,O-d(3) has been prepared in low-temperature Ar, Kr, Xe, and N(2) matrices by near-infrared (NIR) laser irradiation of the first OH stretching overtone of conformer ttt/Ip. Glycine (and glycine-N,N,O-d(3)) ttc/VIp was found to convert back to ttt/Ip in the dark by hydrogen-atom tunneling. The observed half-lives of ttc/VIp in Ar, Kr, and Xe matrices at 12 K were 4.4 ± 1 s (50.0 ± 1 h), 4.0 ± 1 s (48.0 ± 1 h), and 2.8 ± 1 s (99.3 ± 2 h), respectively. In correspondence with the observation for the cis-to-trans conversion of formic and acetic acid, the tunneling half-life of glycine ttc/VIp in a N(2) matrix is more than 3 orders of magnitude longer (6.69 × 10(3) and 1.38 × 10(4) s for two different sites) than in noble gas matrices due to complex formation with the host molecules. The present results are important to understand the lack of experimental observation of some computationally predicted conformers of glycine and other amino acids.

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux-based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large-by ab initio standards-molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high-level calculations (DFT, MP2, CI, and Coupled-Cluster) can be performed on systems with up to several thousand basis functions on small (4-32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post-job visualization and display.

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The near- and mid-IR spectra of α-alanine isolated in low-temperature Ar, Kr, and N2 matrixes were measured. Production of the short-lived conformer VI at the expense of the predominant conformer I was observed upon short irradiation with NIR laser light at the first O-H stretching overtone band of conformer I. Conformer VI decays by H-atom tunneling at 12 K with half-lives of 5.7 ± 1 s, 2.8 ± 1 s in Ar (two different sites), 7.0 ± 1 s in Kr, and 2.8 × 10(3) ± 1.2 × 10(3) s in N2. Upon prolonged irradiation, conformer I slowly transformed into conformer IIa. On the basis of these irradiation experiments, the unambiguous vibrational assignments of conformers I, IIa, and VI are given. In contrast to similar experiments for glycine, the irradiation experiments did not lead to the formation of conformer IIIb. This is explained by a very low IIIb → I barrier height computed for alanine, which results in a very fast depletion of conformer IIIb even in low-temperature matrixes.

We present in detail a novel measure that improves the reliability of the assignment procedure for vibrational circular dichroism (VCD) spectra extending the useful robustness concept introduced by Nicu and Baerends. This measure enables spectroscopists to single out bands with unreliable VCD intensities that can be disregarded during analysis and determination of absolute configuration. The previously proposed robustness criterion is shown to be gauge dependent and less reliable than the one proposed here.

This review focuses on the theoretical background of vibrational circular dichroism (VCD) spectroscopy. Besides discussing the first-principle approaches of the theoretical evaluation of VCD spectra, practical computational considerations, such as the available electronic structure computational levels and program packages, are summarized. Illustrative examples are shown for the absolute configuration and conformation determination of mid-sized molecules based on the comparison of calculated end experimental VCD spectra, including the comparison of the performance of different computational levels. The conformational analysis of larger biomolecules, such as carbohydrates, nucleotides, and peptides by VCD spectroscopy, and the theoretical simulation of solvent effects are also discussed. The review is concluded by a short summary of the present stage of the computation of VCD spectra and the expected future direction of theoretical developments.

Several different methods for calculating nuclear magnetic resonance shieldings in density functional theory are compared. All methods were implemented using gauge-including atomic orbitals to eliminate gauge dependence. The calculated shielding tensors are compared to accurate coupled cluster results with perturbative triples correction and to experimental data. We have implemented a simple method based on a uniform shift of virtual orbital energies and determined the optimum level shift in small molecules. Of the methods tested, the uniform level shift and procedure of Wilson, Amos, and Handy show the best performance. Malkin’s correction also gave good results. The optimized exchange functional of Cohen and Handy, in conjunction with the Lee–Yang–Parr (LYP) correlation functional, gives a marked improvement over the Becke exchange plus LYP.