Reconstructing the TIR Side of the Myddosome: a Paradigm for TIR-TIR Interactions.

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.

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move.

Exploring the vibrational fingerprint of the electronic excitation energy via molecular dynamics.

A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory.

Analytical characterization of NOTA-modified somatropins.

Chemical modification of biomolecules like the introduction of metal-chelators into proteins can lead to heterogeneous product formation. The nature and extend of the modification is important in interpreting the biological properties of the bioconjugate, given their possible influence on the pharmacokinetics as well as on the binding affinity to the target. The present study describes the synthesis and analytical characterization of somatropin modified on its lysine's ɛ-amino groups with the acylating chelator S-2-(4-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (p-SCN-Bn-NOTA).

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.

Solved? The reductive radiation chemistry of alanine.

The structural changes throughout the entire reductive radiation-induced pathway of l-α-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable" and "stable" alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data.

Structural specificity of alkoxy radical formation in crystalline carbohydrates.

A DFT study of radiation induced alkoxy radical formation in crystalline α-l-rhamnose has been performed to better understand the processes leading to selective radical formation in carbohydrates upon exposure to ionizing radiation at low temperatures. The apparent specificity of radiation damage to carbohydrates is of great interest for understanding radiation damage processes in the ribose backbone of the DNA molecule. Alkoxy radicals are formed by deprotonation from hydroxyl groups in oxidized sugar molecules.

Human IL-34 and CSF-1 establish structurally similar extracellular assemblies with their common hematopoietic receptor.

The discovery that hematopoietic human colony stimulating factor-1 receptor (CSF-1R) can be activated by two distinct cognate cytokines, colony stimulating factor-1 (CSF-1) and interleukin-34 (IL-34), created puzzling scenarios for the two possible signaling complexes. We here employ a hybrid structural approach based on small-angle X-ray scattering (SAXS) and negative-stain EM to reveal that bivalent binding of human IL-34 to CSF-1R leads to an extracellular assembly hallmarked by striking similarities to the CSF-1:CSF-1R complex, including homotypic receptor-receptor interactions. Thus, IL-34 and CSF-1 have evolved to exploit the geometric requirements of CSF-1R activation.

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.

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.

In vitro metabolic stability of iodinated obestatin peptides.

Different iodinated mouse obestatin peptides have been characterized toward their in vitro stability in the main metabolic compartments plasma, liver and kidney. Using HPLC-UV for quantification, significant differences in the degradation kinetics of the iodinated peptides, arising from both enzymatic proteolysis and dehalogenation, were found when compared to the native, unmodified peptide. HPLC-MS/MS analysis demonstrated that the cleavage sites were dependent upon the biological matrix and the location of the amino acid residue incorporating the iodine atom(s).

Cluster or periodic, static or dynamic--the challenge of calculating the g tensor of the solid-state glycine radical.

The calculation of the g tensor of the main (+)NH(3)-˙CH-COO(-) radiation-induced radical in solid-state α-glycine presents a real challenge to computational methods. Density functional calculations of this spectroscopic property struggle with its small anisotropy and the zwitterionic nature of the amino acids in the crystal of this seemingly simple system. Here, several factors influencing the calculated g tensor are examined by comparing with experimental data.

Structures of cyclic dipeptides: an X-ray and computational study of cis- and trans-cyclo(Pip-Phe), cyclo(Pro-Phe) and their N-methyl derivatives.

The crystal structures of eight cyclodipeptides are determined, incorporating pipecolic acid or proline and phenylalanine or N-methyl phenylalanine. This set of structures allows the evaluation of the effects on molecular conformation and crystal packing of imino acid ring-size, relative configuration of the two amino acids, and N-methylation. In the non-methylated compounds, hydrogen-bonding interactions form one-dimensional motifs that dominate the packing arrangement.

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.

Electron magnetic resonance and density functional theory study of room temperature X-irradiated β-D-fructose single crystals.

Stable free radical formation in fructose single crystals X-irradiated at room temperature was investigated using Q-band electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three main crystallographic planes allowed an unambiguous determination of 12 proton HFC tensors. From the EIE studies, these hyperfine interactions were assigned to six different radical species, labeled F1-F6.

On the identity of the radiation-induced stable alanine radical.

Using periodic DFT calculations, it is concluded that the stable radiation-induced alanine radical most probably is the result of reductive deamination and protonation of the detached amino group, yielding an NH(4)(+) ammonium ion and a negatively charged radical.

Conformational sampling of macrocyclic alkenes using a Kennard-Stone-based algorithm.

The properties and functions of (bio)molecules are closely related to their molecular conformations. A variety of methods are available to sample the conformational space at a relatively low level of theory. If a higher level of theory is required, the computational cost can be reduced by selecting a uniformly distributed set of conformations from the ensemble of conformations generated at a low level of theory and by optimizing this selected set at a higher level.

Oxidation and reduction products of X irradiation at 10 K in sucrose single crystals: radical identification by EPR, ENDOR, and DFT.

Electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) measurements on sucrose single crystals at 10 K after in situ X irradiation at this temperature reveal the presence of at least nine different radical species. Nine proton hyperfine coupling tensors were determined from ENDOR angular variations and assigned to six of these species (R1-R6) using EIE. Spectral simulations indicate that four of those (R1-R3 and R6) dominate the EPR absorption.

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.

ENDOR and HYSCORE analysis and DFT-assisted identification of the third major stable radical in sucrose single crystals X-irradiated at room temperature.

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.

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.

Temperature study of a glycine radical in the solid state adopting a DFT periodic approach: vibrational analysis and comparison with EPR experiments.

The major radiation-induced radical in crystalline glycine is examined using DFT calculations, in which both molecular environment and temperature are accounted for. This is achieved by molecular dynamics simulations of the radical embedded in a supercell under periodic boundary conditions. At 100 and 300 K, a vibrational analysis is performed based on Fourier transformation of the atomic velocity autocorrelation functions.

Combined electron magnetic resonance and density functional theory study of 10 K X-irradiated beta-D-fructose single crystals.

Primary free radical formations in fructose single crystals X-irradiated at 10 K were investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three principal crystallographic planes and a fourth skewed plane allowed the unambiguous determination of five proton hyperfine coupling tensors. From the EIE studies, these hyperfine interactions were assigned to three different radicals, labeled T1, T1* and T2.