Ewald Pauwels

Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides.

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 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, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (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.

Comparative Study of Various Normal Mode Analysis Techniques Based on Partial Hessians

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.

Investigating the Halochromic Properties of Azo Dyes in an Aqueous Environment by Using a Combined Experimental and Theoretical Approach

The halochromism in solution of a prototypical example of an azo dye, ethyl orange, was investigated by using a combined theoretical and experimental approach. Experimental UV/Vis and Raman spectroscopy pointed towards a structural change of the azo dye with changing pH value (in the range pH 5-3). The pH-sensitive behavior was modeled through a series of ab initio computations on the neutral and various singly and doubly protonated structures. For this purpose, contemporary DFT functionals (B3LYP, CAM-B3LYP, and M06) were used in combination with implicit modeling of the water solvent environment. Static calculations were successful in assigning the most-probable protonation site. However, to fully understand the origin of the main absorption peaks, a molecular dynamics simulation study in a water molecular environment was used in combination with time-dependent DFT (TD-DFT) calculations to deduce average UV/Vis spectra that take into account the flexibility of the dye and the explicit interactions with the surrounding water molecules. This procedure allowed us to achieve a remarkable agreement between the theoretical and experimental UV/Vis spectrum and enabled us to fully unravel the pH-sensitive behavior of ethyl orange in aqueous environment.

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules.

In an earlier work, the authors developed a new method, the mobile block Hessian (MBH) approach, to accurately calculate vibrational modes for partially optimized molecular structures [ J. Chem. Phys. 2007 , 126 ( 22 ), 224102. ]. It is based on the introduction of blocks, consisting of groups of atoms, that can move as rigid bodies. The internal geometry of the blocks need not correspond to an overall optimization state of the total molecular structure. The standard MBH approach considers free blocks with six degrees of freedom. In the extended MBH approach introduced herein, the blocks can be connected by one or two adjoining atoms, which further reduces the number of degrees of freedom. The new approach paves the way for the normal-mode analysis of biomolecules such as proteins. It rests on the hypothesis that low-frequency modes of proteins can be described as pure rigid-body motions of blocks of consecutive amino acid residues. The method is validated for a series of small molecules and further applied to alanine dipeptide as a prototype to describe vibrational interactions between two peptide units; to crambin, a small protein with 46 amino acid residues; and to ICE/caspase-1, which contains 518 amino acid residues.

Identification and conformational study of stable radiation-induced defects in sucrose single crystals using density functional theory calculations of electron magnetic resonance parameters.

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.

Structural basis of the proinflammatory signaling complex mediated by TSLP

Thymic stromal lymphopoietin (TSLP), a cytokine produced by epithelial cells at barrier surfaces, is pivotal for the development of widespread chronic inflammatory disorders such as asthma and atopic dermatitis. The structure of the mouse TSLP-mediated signaling complex reveals how TSLP establishes extensive interfaces with its cognate receptor (TSLPR) and the shared interleukin 7 receptor α-chain (IL-7Rα) to evoke membrane-proximal receptor-receptor contacts poised for intracellular signaling. Binding of TSLP to TSLPR is a mechanistic prerequisite for recruitment of IL-7Rα to the high-affinity ternary complex, which we propose is coupled to a structural switch in TSLP at the crossroads of the cytokine-receptor interfaces. Functional interrogation of TSLP-receptor interfaces points to putative interaction hotspots that could be exploited for antagonist design. Finally, we derive the structural rationale for the functional duality of IL-7Rα and establish a consensus for the geometry of ternary complexes mediated by interleukin 2 (IL-2)–family cytokines.

Radiation-induced radicals in glucose-1-phosphate. II. DFT analysis of structures and possible formation mechanisms.

Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1-R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.

Influence of protein environment on the electron paramagnetic resonance properties of flavoprotein radicals: a QM/MM study.

The neutral and anionic semiquinone radicals of the flavin adenine dinucleotide (FAD) cofactor noncovalently bound in glucose oxidase from A. niger are examined with the aid of QM/MM molecular modeling methods, enabling complete inclusion of the protein environment. Recently, the electron paramagnetic resonance (EPR) characteristics, the anisotropic g tensor and all the significant hyperfine couplings, of these flavoprotein radicals were determined at high resolution (J. Phys. Chem. B 2008, 112, 3568). A striking difference between the neutral and anionic radical forms was found to be a shift in the g(y) principal value. Within the QM/MM framework, geometry optimization and molecular dynamics simulations are combined with EPR property calculations, employing a recent implementation by some of the authors in the CP2K software package. In this way, spectroscopic characteristics are computed on the fly during the MD simulations of the solvated protein structure, mimicking as best as possible the experimental conditions. The general agreement between calculated and experimental EPR properties is satisfactory and on par with those calculated with other codes (Gaussian 03, ORCA). The protonation state of two histidines (His559 and His516) at the catalytic site of this flavoprotein is found to have a remarkable influence on the isotropic hyperfine coupling of one of the methyl groups on the neutral FAD radical, which is consistent with experimental findings in other flavoproteins (J. Biol. Chem. 2007, 282, 4738). Furthermore, the shift in the g(y) principal values between the neutral and anionic radicals is well reproduced by QM/MM simulations. Incorporation of at least the nearest protein environment of the cofactor radicals proves to be vital for a correct reproduction, indicating that this shift is a global feature of the protein rather than a local one. In addition, QM/MM techniques are used to make a prediction of relative angles between important spectroscopic principal directions, which are not readily determined by conventional EPR experiments. Significantly, the directions of the g(x) and the g(y) components of the g-tensor that lie in the plane of the isoalloxazine moiety are rotated by approximately 59° between the neutral and the anionic radicals.

Evidence for a Grotthuss-like mechanism in the formation of the rhamnose alkoxy radical based on periodic DFT calculations.

Abstract Pauwels, E., Declerck, R., Van Speybroeck, V. and Waroquier, M. Evidence for a Grotthuss-Like Mechanism in the Formation of the Rhamnose Alkoxy Radical Based on Periodic DFT Calculations. Radiat. Res. 169, 8–18 (2008). Molecular modeling adopting a periodic approach based on density functional theory (DFT) indicates that a Grotthuss-like mechanism is active in the formation of the radiation-induced alkoxy radical in α-l-rhamnose. Starting from an oxidized crystal structure, a hydroxyl proton is transferred along an infinite hydrogen bond chain pervading the entire crystal. The result of this proton shuttling mechanism is a stable radical species dubbed RHop. Only after several reorientations of crystal waters and hydroxyl groups, the more stable radical form RO4 is obtained, which differs in structure from the former by the absence of only one hydrogen bond. Calculations of the energetics associated with the mechanism as well as simulated spectroscopic properties reveal that different variants of the rhamnose alkoxy radical can be observed depending on the temperature of irradiation and consecutive EPR measurement. Cluster calculations on both radical variants provide hyperfine coupling and g tensors that are in good agreement with two independent experimental measurements at different temperatures.

Radiation-Induced Radicals in Glucose-1-phosphate. I. Electron Paramagnetic Resonance and Electron Nuclear Double Resonance Analysis of in situ X-Irradiated Single Crystals at 77 K

Electron magnetic resonance analysis of radiation-induced defects in dipotassium glucose-1-phosphate dihydrate single crystals in situ X-irradiated and measured at 77 K shows that at least seven different carbon-centered radical species are trapped. Four of these (R1-R4) can be fully or partly characterized in terms of proton hyperfine coupling tensors. The dominant radical (R2) is identified as a C1-centered species, assumedly formed by a scission of the sugar-phosphate junction and the concerted formation of a carbonyl group at the neighboring C2 carbon. This structure is chemically identical to a radical recently identified in irradiated sucrose single crystals. Radical species R1 and R4 most likely are C3- and C6-centered species, respectively, both formed by a net hydrogen abstraction. R3 is suggested to be chemically similar to but geometrically different from R4. Knowledge of the identity of the sugar radicals present at 77 K provides a first step in elucidating the formation mechanism of the phosphoryl radicals previously detected after X-irradiation at 280 K. In paper II, the chemical identity, precise conformation, and possible formation mechanisms of these radical species are investigated by means of DFT calculations and elementary insight into the radiation chemistry of sugar and sugar derivatives is obtained.