Abstract. The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields, but are also derived from quantum mechanical (QM) computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes (Mulliken, Natural, RESP, Hirshfeld-I, EEM and SQE) applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q 0 , that is suitable to describe biological systems bearing many locally charged functional groups.

Vangl2 was identified as the gene defective in the Looptail mouse model for neural tube defects (NTDs). This gene forms part of the planar cell polarity pathway, also called the non-canonical Frizzled/Dishevelled pathway, which mediates the morphogenetic process of convergent extension essential for proper gastrulation and neural tube formation in vertebrates. Genetic defects in PCP signaling have strongly been associated with NTDs in mouse models. To assess the role of VANGL2 in the complex etiology of NTDs in humans, we resequenced this gene in a large multiethnic cohort of 673 familial and sporadic NTD patients, including 453 open spina bifida and 202 closed spinal NTD cases. Six novel rare missense mutations were identified in 7 patients, five of which were affected with closed spinal NTDs. This suggests that VANGL2 mutations may predispose to NTDs in approximately 2.5% of closed spinal NTDs (5 in 202), at a frequency that is significantly different from that of 0.4% (2 in 453) detected in open spina bifida patients (P=0.027). Our findings strongly implicate VANGL2 in the genetic causation of spinal NTDs in a subset of patients and provide additional evidence for a pathogenic role of PCP signaling in these malformations.

Members of the Toll-like receptor and interleukin-1 (IL-1) receptor families all signal via Toll/IL-1R (TIR) domain-driven assemblies with adaptors such as MyD88. We here combine the mammalian two-hybrid system MAPPIT and saturation mutagenesis to complement and extend crystallographic and nuclear magnetic resonance data, and reveal how TIR domains interact. We fully delineate the interaction sites on the MyD88 TIR domain for homo-oligomerization and for interaction with Mal and TLR4. Interactions between three sites drive MyD88 homo-oligomerization. The BB-loop interacts with the αE-helix, explaining how BB-loop mimetics inhibit MyD88 signaling. The αC'-helix interacts symmetrically. The MyD88 TIR domains thus assemble into a left-handed helix, compatible with the Myddosome death domain crystal structure. This assembly explains activation of MyD88 by Mal and by an oncogenic mutation, and regulation by phosphorylation. These findings provide a paradigm for the interaction of mammalian TIR domains.

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One of the major stable radiation-induced radicals in sucrose single crystals (radical T2) has been identified by means of density functional theory (DFT) calculations of electron magnetic resonance parameters. The radical is formed by a net glycosidic bond cleavage, giving rise to a glucose-centered radical with the major part of the spin density residing at the C 1 carbon atom. A concerted formation of a carbonyl group at the C 2 carbon accounts for the relatively small spin density at C 1 and the enhanced g factor anisotropy of the radical, both well-known properties of this radical from several previous experimental investigations. The experimentally determined and DFT calculated proton hyperfine coupling tensors agree very well on all accounts. The influence of the exact geometrical configuration of the radical and its environment on the tensors is explored in an attempt to explain the occurrence and characteristics of radical T3, another major species that is most likely another conformation of T2. No definitive conclusions with regard to the actual structure of T3 could be arrived at from this study. However, the results indicate that, most likely, T3 is identical in chemical structure to T2 and that changes in the orientation of neighboring hydroxy groups or changes in the configuration of the neighboring fructose ring can probably not account for the type and size of the discrepancies between T2 and T3.

Recently, the chemical structure of two of the three major stable radicals (T2 and T3) produced in sucrose single crystals by X-irradiation at room temperature was identified by comparing Density Functional Theory (DFT) calculations of Electron Magnetic Resonance parameters with experimental results [H. De Cooman, E. Pauwels, H. Vrielinck, E. Sagstuen, F. Callens and M. Waroquier, J. Phys. Chem. B, 2008, 112, 7298-7307]. Ambiguities concerning an unusual proton hyperfine coupling (HFC) tensor prevented the identification of the third major stable radical (T1). In the present work, experimental results of continuous wave Electron Nuclear Double Resonance experiments on sucrose single crystals and Hyperfine Sublevel Correlation Spectroscopy experiments on sucrose powder are presented that lift these remaining ambiguities. Using the final set of experimental HFC tensors and employing advanced DFT calculations, the chemical structure of the T1 radical is established: an allylic-type radical with approximately half of the spin density localised on the C2' carbon of the fructose unit, involving glycosidic bond cleavage at the fructose side and a concerted formation of a carbonyl group at the C1' carbon. The electronic structure of the T1 radical is discussed in more detail by means of additional DFT calculations, yielding a better understanding of the peculiar properties of the unusual proton HFC tensor mentioned above.

Standard normal mode analysis becomes problematic for complex molecular systems, as a result of both the high computational cost and the excessive amount of information when the full Hessian matrix is used. Several partial Hessian methods have been proposed in the literature, yielding approximate normal modes. These methods aim at reducing the computational load and/or calculating only the relevant normal modes of interest in a specific application. Each method has its own (dis)advantages and application field but guidelines for the most suitable choice are lacking. We have investigated several partial Hessian methods, including the Partial Hessian Vibrational Analysis (PHVA), the Mobile Block Hessian (MBH), and the Vibrational Subsystem Analysis (VSA). In this article, we focus on the benefits and drawbacks of these methods, in terms of the reproduction of localized modes, collective modes, and the performance in partially optimized structures. We find that the PHVA is suitable for describing localized modes, that the MBH not only reproduces localized and global modes but also serves as an analysis tool of the spectrum, and that the VSA is mostly useful for the reproduction of the low frequency spectrum. These guidelines are illustrated with the reproduction of the localized amine-stretch, the spectrum of quinine and a bis-cinchona derivative, and the low frequency modes of the LAO binding protein.