3-O-Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake

Prion-like transcellular spreading of tau in Alzheimer's Disease (AD) is mediated by tau binding to cell surface heparan sulfate (HS). However, the structural determinants for tau–HS interaction are not well understood. Microarray and SPR assays of structurally defined HS oligosaccharides show that a rare 3-O-sulfation (3-O-S) of HS significantly enhances tau binding. In Hs3st1^−/− (HS 3-O-sulfotransferase-1 knockout) cells, reduced 3-O-S levels of HS diminished both cell surface binding and internalization of tau. In a cell culture, the addition of a 3-O-S HS 12-mer reduced both tau cell surface binding and cellular uptake. NMR titrations mapped 3-O-S binding sites to the microtubule binding repeat 2 (R2) and proline-rich region 2 (PRR2) of tau. Tau is only the seventh protein currently known to recognize HS 3-O-sulfation. Our work demonstrates that this rare 3-O-sulfation enhances tau–HS binding and likely the transcellular spread of tau, providing a novel target for disease-modifying treatment of AD and other tauopathies.     

3‐O‐Sulfation of Heparan Sulfate Enhances Tau Interaction and Cellular Uptake

Prion‐like transcellular spreading of tau in Alzheimer's Disease (AD) is mediated by tau binding to cell surface heparan sulfate (HS). However, the structural determinants for tau–HS interaction are not well understood. Microarray and SPR assays of structurally defined HS oligosaccharides show that a rare 3‐O‐sulfation (3‐O‐S) of HS significantly enhances tau binding. In Hs3st1^?/? (HS 3‐O‐sulfotransferase‐1 knockout) cells, reduced 3‐O‐S levels of HS diminished both cell surface binding and internalization of tau. In a cell culture, the addition of a 3‐O‐S HS 12‐mer reduced both tau cell surface binding and cellular uptake. NMR titrations mapped 3‐O‐S binding sites to the microtubule binding repeat 2 (R2) and proline‐rich region 2 (PRR2) of tau. Tau is only the seventh protein currently known to recognize HS 3‐O‐sulfation. Our work demonstrates that this rare 3‐O‐sulfation enhances tau–HS binding and likely the transcellular spread of tau, providing a novel target for disease‐modifying treatment of AD and other tauopathies.     

Hybrid-DFT Study and NBO Analysis of the Stereoelectronic Interaction Effects (Associated with the Anomeric Effects) on the Conformational Properties of 2,3,5,6-Tetrahalo-1,4-dioxanes and Their Analogs Containing S and Se Atoms

NBO analysis and hybrid density functional theory–based method (B3LYP/6-311+G**) was used to study the anomeric effects (AE), dipole–dipole interactions, and steric repulsion effects on the conformational properties of 2,3,5,6-tetrahalo-1,4-dioxane [halo = F (1), Cl (2), Br (3)], 2,3,5,6-tetrahalo-1,4-dithiane [halo = F (4), Cl (5), Br (6)], and 2,3,5,6-etrahalo-1,4-diselenane [halo = F (7), Cl (8), Br (9)]. B3LYP/6-311+G** results revealed a strong axial preference in compounds 1–3. Gibbs free energy difference (G _eq–G _ax) values (e.g., ΔG _eq-ax) between the axial and equatorial conformations of compound 1 to compound 3 are 8.19, 3.86, and 3.13 kcal mol^?1, respectively, as calculated by the B3LYP/6-311+G** level of theory. On the other hand, the NBO analysis of donor–acceptor (bond–antibond) interactions revealed that the AE for compounds 1–3 are ?12.26, ?16.46, and ?18.11 kcal mol^?1, respectively. Contrary to the increase of the AE values from compound 1 to compound 3, the increase of the steric repulsions (e.g., 1,3-syn-axial repulsions) could fairly explain the decrease of the axial conformation stability in compounds 1–3 compared to their equatorial conformations. Further, the correlations between the AE, structural parameters, and conformational behavior of compounds 4–9 have been investigated.     

CH3S与HCS双自由基反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论(DFT)对CH₃S与HCS双自由基单重态反应进行了研究. 在MPW1PW91/ 6-311G(d,p)水平上优化了反应通道上各驻点(反应物、中间体、过渡态和产物)的几何构型, 用内禀反应坐标(IRC)计算和频率分析方法对过渡态进行了验证. 在QCISD(t)/6-311＋＋G(d,p)水平上计算各物种的单点能, 并对总能量进行了零点能校正. 研究结果表明, CH₃S与HCS反应为多通道反应, 有4条可能的反应通道, 反应物首先通过S…S弱相互作用形成具有竞争反应机理的五元环硫-硫偶合中间体a和链状硫-硫偶合中间体c, 再由此经过氢迁移、离解、异构化等不同机理得到主要产物P1 (2CH₂S), 次要产物P2 (CH₃SH＋CS), P3 (CH₄＋CS₂)和P4 [CH₂(SH)CSH]. 根据势能面分析, 所有反应均为放热反应, 生成P1的反应热为－165.55 kJ•mol^－1. 通道R→a→TSa/b→b→P1为标题反应的主通道, 其速控步骤a→TSa/b→b在200～2000 K温度区间内的速率常数可以表示为k₁^CVT/SCT＝1.75×10¹⁰T^0.65exp(－907.6/T) s^－1. P3及P4的生成需要越过很高的活化能垒, 是动力学禁阻步骤, 但在反应体系中加入合适催化剂, 改变其反应机理, 有可能使生成CH₂(SH)CSH, CH₄及CS₂的反应易于进行.     

A positron lifetime and Doppler-broadening study of positron states and free volume in polyethylene

Positron lifetime (LT) and Doppler-broadening (DB) studies of polyethylene have been performed simultaneously in the temperature range between 80 and 300 K. The LT spectra have been analysed assuming four exponential components. Two long-lived components appear, which were attributed too-Ps pick-off annihilation in crystalline regions (₃ = 0.9 to 1.2 ns) and at free-volume holes in the amorphous phase ( to 2.8), The variation in ₄ correponds to an increase of the mean hole size from 0.053 nm³ at 80 K to 0.188 nm³ at 300 K. From the data the glass transition temperature (T _g=195 K), the coefficient of thermal expansion of holes in the glassy and rubbery phase ( _{h, g} = 14.5 · 10^–4 K^–1 and _{h, r} = 189 · 10^–4 K^–1) and the fractional free volume (2.8% to 10.4%) were estimated. The DB curves were fitted by a sum of three Gaussians, the narrowest of which is assumed to represent the self-annihilation ofp-Ps localised at holes. The intensity of the narrow component,I _n, varies between 0 and 7.3% in a similar way as the LT intensityI _4/3 varies. From this it was concluded that other Ps reactions beside pick-off are not important. Further, it was shown that the average positron lifetime is dominated by theo-Ps component,T _{4 g}, while the behaviour of the DB peak height is mainly affected by thep-Ps narrow componentI _n .     

Development of modified force field for cation–amino acid interactions: Ab initio-derived empirical correction terms with comments on cation–π interactions

The modeling of voltage-gated ion-channel proteins is a continuing challenge for force-field calculations because of the diverse range of interactions involved. In particular, current force fields are not parameterized for either ion–amino acid or amino acid–electric field interactions. To address the parameterization of ion–amino acid interactions, we have tested the use of empirical correction terms, derived from ab initio calculations of single amino acids (representing the peptide backbone) interacting with K⁺ ions. Having demonstrated the utility of such an approach, we then extended the application to the amino acid side chains. The calculation of the interaction of K⁺ with serine, cysteine, methionine, lysine, arginine, aspartate, histidine (uncharged), tyrosine, tryptophan, and phenylalanine, both completes the parameterization of the molecular environments contained in the amino acids, and allows specific comment on these ion–functional group interactions. The cation–π interactions were of particular interest, given recent proposals in the literature and the fear that force fields would not be able to treat such interactions. We present a comprehensive comparison of the ab initio (DFT [BLYP], 6-311 G**) and force field (CHARMm22.0) assessments of these interactions. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1515–1525, 1998     

Apolipoprotein E Recognizes Alzheimer's Disease Associated 3-O Sulfation of Heparan Sulfate

Apolipoprotein E (ApoE)’s ϵ4 alle is the most important genetic risk factor for late onset Alzheimer's Disease (AD). Cell-surface heparan sulfate (HS) is a cofactor for ApoE/LRP1 interaction and the prion-like spread of tau pathology between cells. 3-O-sulfo (3-O-S) modification of HS has been linked to AD through its interaction with tau, and enhanced levels of 3-O-sulfated HS and 3-O-sulfotransferases in the AD brain. In this study, we characterized ApoE/HS interactions in wildtype ApoE3, AD-linked ApoE4, and AD-protective ApoE2 and ApoE3-Christchurch. Glycan microarray and SPR assays revealed that all ApoE isoforms recognized 3-O-S. NMR titration localized ApoE/3-O-S binding to the vicinity of the canonical HS binding motif. In cells, the knockout of HS3ST1-a major 3-O sulfotransferase-reduced cell surface binding and uptake of ApoE. 3-O-S is thus recognized by both tau and ApoE, suggesting that the interplay between 3-O-sulfated HS, tau and ApoE isoforms may modulate AD risk.     

Chemical profile and biological activities of Peltigera horizontalis (Hudson) Baumg. thallus and apothecia extracts

Abstract

The aim of this study was to determine, for the first time, the chemical composition of Peltigera horizontalis thallus and apothecia extracts (ether, ethyl acetate, dichloromethane and acetone) by HPLC-UV and GC-MS, and evaluate activity of genotoxic, anticholinesterase, antioxidant and antibacterial potential of acetone extracts. Major constituents of thallus extracts were gyrophoric acid, and methyl gyrophorate while dominant component of apothecia extracts was tenuiorin. The predominant volatile compounds in extracts were methyl orsellinate, dodecyl acrylate, orcinol and orcinol monomethyl ether. The thallus acetone extract at concentration of 2.0 µg mL^?1 gave the greatest decrease in the micronuclei frequency (22.4%) of all tested extracts. Apothecia extract showed stronger antioxidant activity as compared to thallus extract. Tested extracts at concentration of 10?mg mL^?1 exhibited inhibitory effect (16.5% for thallus and 12.8% for apothecia) on pooled human serum cholinesterase. P. horizontalis acetone extracts had no activity against the tested five bacteria strains.     

Investigation of the effects of ionic hydrogen bonds (COH–C and N–HOC) in crystalline dl-proline by ab initio and DFT calculated NQR parameters

In this paper, we have calculated the nuclear quadrupole resonance (NQR) parameters of the quadrupole nuclei involved in the hydrogen bonds (CO⁻H–C and ⁺N–H⁻OC) in the monomer and pentameric cluster of dl-proline by HF and B3LYP methods and basis sets of 6-311+G^* and 6-311++G^**. These computations are performed on the basis of X-ray diffraction structural data of dl-proline. The results indicate that the calculations including hydrogen-bonding (HB) interactions (in pentamer) are in better agreement with the experimental data than those in which these interactions are neglected (in monomer). The quantum chemical calculations show that the intermolecular hydrogen-bonding interactions play an important role in determination of the NQR parameters of ¹⁴N, ²H of group and ¹⁷O.     

Chemical Imaging of RNA-Tau Amyloid Fibrils at the Nanoscale Using Tip-Enhanced Raman Spectroscopy

In the presence of cofactors, tau protein can form amyloid deposits in the brain which are implicated in many neurodegenerative disorders. Heparin, lipids, and RNA are used to recreate tau aggregates in vitro from recombinant protein. However, the mechanism of interaction of these cofactors and the interactions between cofactors and tau are poorly understood. Herein, we use tip-enhanced Raman spectroscopy (TERS) to visualize the spatial distribution of adenine, protein secondary structure, and amino acids (arginine, lysine and histidine) in single polyadenosine (polyA)-induced tau fibrils with nanoscale spatial resolution (<10–20 nm). Based on reference unenhanced and surface-enhanced Raman spectra, we show that the polyA anionic cofactor is incorporated in the fibril structure and seems to be superficial to the β-sheet core, but nonetheless enveloped within the random-coiled fuzzy coat. TERS images also prove the colocalization of positively charged arginine, lysine, and histidine amino acids and negatively charged polyA, which constitutes an important step forward to better comprehend the action of RNA cofactors in the mechanism of formation of toxic tau fibrils. TERS appears as a powerful technique for the identification of cofactors in individual tau fibrils and their mode of interaction.     

Na＋-丙氨酸二肽络合离子结构的密度泛函理论研究

运用密度泛函理论B3LYP方法在6-311＋＋G**基组水平下研究了Na^＋与丙氨酸二肽(AD)分子结合形成的6种Na^＋-AD 络合离子, 其中包括2种双齿结构和4种单齿结构. 考察了6种Na^＋-AD络合离子的相对稳定性, 分析了丙氨酸二肽分子与Na^＋作用过程中分子骨架Ramachandran角f和Ψ以及分子内氢键的变化.     

Engineered Functional Recovery of Microbial Rhodopsin Without Retinal‐Binding Lysine

Definition of rhodopsin is the retinal‐binding membrane protein with the Schiff base linkage at a lysine on the 7^th transmembrane helix. However, ~ 600 microbial rhodopsins lack retinal‐binding lysine at the corresponding position (Rh‐noK) among ~ 5500 known microbial rhodopsins, suggesting that Rh‐noK has each functional role without chromophore. Here, we report successful functional recovery of Rh‐noK. Two Rh‐noKs from bacteria were heterologously expressed in Escherichia coli, which exhibited no color. When retinal‐binding lysine was introduced, one of them gained visible color. Additional mutation of the Schiff base counterion further gained proton‐pumping activity. Successful engineered functional recovery such as visible color and proton‐pump activity suggests that the Rh‐noK protein forms a characteristic structure of microbial rhodopsins.     

The geometry of the nitroguanyl fragment in the simplest nitroguanidine derivatives in the absence of intermolecular interactions: The gas electron diffraction data on 1,1,3,3-tetramethyl-2-nitroguanidine

The structures and force fields of the equilibrium forms of 2-nitroguanidine (1), 1,1,3,3-tetramethyl-2-nitroguanidine (2), and nitroguanyl azide (3) were determined in the MP2(full)/6-311G(3df, 2p) approximation; wagging-inversion motions of the N amine atoms were studied. The internal rotation potential function of the NO₂ group was calculated for 1. Similar functions for 1 and 2 were also obtained in the MP2(full)/6-311G(d, p) approximation. Direct one-dimensional problems for a nonrigid model were solved by the variational method, and the distribution of torsional levels was obtained. In the region of potential minimum, rotation in both molecules had the character of large-amplitude motions. For the first time, electron diffractions data were obtained at 100°C for molecule 2 without noticeable traces of substance decomposition. A structural r _e analysis was performed using the model of large-amplitude motions for characteristic NO₂ group torsional vibrations. Vibrational corrections to internuclear distances and mean amplitudes were calculated taking into account nonlinear kinematic effects using the force fields obtained in this work. The geometry of molecule 2 calculated in the MP2(full)/6-311G(3df, 2p) approximation well corresponds to the gas electron diffraction data. The parameters of molecule 2 in the crystalline phase, however, differ substantially from the parameters of the free molecule. This corresponds with the suggestion of the influence of intermolecular H-bonds involving the imine nitrogen atom and nitro groups oxygen atoms.     

Structural study of a small molecule receptor bound to dimethyllysine in lysozyme

Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx₄) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH₃ ⁺ to Lys-NH(Me₂)⁺. Of the six possible dimethyllysine sites, sclx₄ selected Lys116-Me₂ and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me₂ residues to form cation–π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me₂ in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.     

Quantum chemical and experimental studies on the structure and vibrational spectra of substituted 2-pyranones

A systematic study on the structural characteristics of the 2-pyranone ring containing molecules with bromine, nitrile, and amide substituents at the C-3 position in the ring is conducted in the electronic ground (S ₀) state by DFT calculations using the B3LYP/6-311++G** method. The geometrical structure of the bromine substituted compound, which shows potent hepatoprotective activity, is studied both in the ground (S ₀) and first excited singlet (S ₁) states using RHF/6-311++G** and CIS/6-311++G** methods respectively. The molecules are found to exist in two isomeric forms gauche and trans that have the enthalpy difference of less than 3.32 kcal/mol; the latter is the preferred orientation in the gaseous phase. The S ₁ state is a ¹(π,π*) state that arises π-electron transfer from the region of a double bond in the pyranone ring to the region of the internuclear bond connecting the 2-pyranone and benzene rings. A complete vibrational analysis is conducted for the 3-bromo-6-(4-chlorophenyl)-4-thiomethyl-2H-pyran-2-one molecule based on the experimental infrared spectra in the 50–4000 cm⁻¹ region and DFT/6- 311++G** computations of vibrational frequencies for the gauche and trans isomeric forms. Spectral assignments based on the potential energy distribution along the internal coordinates confirm the nonplanar structure of the molecule.     

An ab initio Investigation of 2-Amino-2-imidazoline: A Key Moiety in Chemical and Biochemical Processes

Abstract

The 2-amino-2-imidazoline moiety is currently used not only in drugs, but also in insecticides, and fungicides. Ab initio calculations are performed to evaluate the molecular properties of the two tautomeric forms and the protonated form with extended basis sets ranging from 6-31G? to 6-311 + +G^?? at Hartree-Fock and density functional (BLYP and B3LYP) levels. Moller-Plesset perturbation is tested at the MP2/6-31G? level only. Optimized geometry structures, energies and thermochemical properties are generated. Basis set and correlation effects on geometries, tautomer equilibrium constant and protonation enthalpy are carefully analysed. Although observed for the isolated molecule, these results may be extrapolated to chemical and biochemical systems of interest.     

Ab Initio Calculations of the Conformational Preferences of 1,3-Oxathiane S-Oxide and its Analogs Containing S and SE Atoms—Evidence for Stereoelectronic Interactions Associated with the Anomeric Effects

Abstract

Stereoelectronic interactions associated with the AE and also the conformational and structural properties of 1,3-oxathiane S-oxide (1), 1,3-dithiane S-oxide (2), 1,3-thiaselenane S-oxide (3), 1,3-oxaselenane Se-oxide (4), 1,3-thiaselenane Se-oxide (5), and 1,3-diselenane Se-oxide (6) were investigated using quantum mechanical methods. These compounds were fully optimized at the B3LYP/6 – 311 + G** and HF/6 – 311 + G** levels of theory. The Gibbs Free Energy, Enthalpy, and Entropy differences (i.e., ΔG, ΔH, and ΔS) between the axial and equatorial conformations were calculated at the B3LYP/6 – 311 + G** and HF/6 – 311 + G** levels of theory. The decrease of the AE is corresponding to the decreases of calculated Δ(G _ax – G _eq) value of the above mentioned compounds. The calculated AE values are more significant for the justification of the conformational dominances of the compounds than steric effects. In this work, the relations between the Anomeric Effects, donor and acceptor orbital energies, occupancies, structural parameters, dipole–dipole interactions, and conformational behavior of the compounds have been studied.     

4,6-二甲氧基-2-[甲氧脲基硫代脲基]嘧啶的合成、晶体结构和理论计算

利用2-氨基-4,6-二甲氧基嘧啶在干燥条件下与硫氰酸钾、氯甲酸甲酯在乙酸乙酯溶液中反应制得4-(4,6-二甲氧基嘧啶-2-基)-3-硫代脲酸甲酯, 在二甲基甲酰胺溶液中培养出单晶, 通过X射线单晶结构分析法测定分子结构和晶体结构, 晶体属单斜晶系, 空间群为C2/m, 晶胞参数为: a＝1.6672(3) nm, b＝0.66383(12) nm, c＝1.1617(2) nm, β＝109.275(2)°, V＝1.2136(4) nm³, D_c＝1.490 g/cm³, μ＝0.281 mm^－1, F(000)＝568, Z＝4, R₁＝0.0341, wR₂＝0.1042. 运用Gaussian 03程序, 在6-311G的基组水平上, 用HF, MP2以及B3LYP三种计算方法对标题化合物进行了几何全优化, 并对其成键情况及自然键轨道(NBO)进行了分析.     

Thermodynamic stability of 2,4,6-tris(nitromethyl)-1,3,5-triazine: an experimental and theoretical study

The molecular geometries and electronic structures of 2,4,6-tris(nitromethyl)-1,3,5-triazine isomers were investigated by the density functional method DFT/B3LYP/6-311++G** to elucidate the structural factors responsible for the stability of these systems. It was shown that a characteristic feature of the nitromethyl tautomer (1) of 2,4,6-tris (nitromethyl)-1,3,5-triazine consists in nonvalence interactions between an oxygen atom of nitro group and a carbon atom of triazine ring, which are probably due to Coulomb attraction between them. The tautomer with the 2,4,6-tris (nitromethylene)-hexahyrdo-1,3,5-triazine structure (2) is stabilized trough direct polar conjugation between the amino and nitro groups at the double bond. Structural strain of the molecule with the 2,4,6-tris(aci-nitromethyl)-1,3,5-triazine structure (3) is the reason for its thermodynamic instability. X-ray data indicate that the compound under study exists in the triazine tautomeric form 1 and the distances between oxygen atoms of nitro group and carbon atom of the triazine ring are shortened. NMR data suggest the existence of triazine in the nitromethyl form 1 in acetonitrile and acetone and a tautomeric equilibrium between the nitromethyl and nitromethylene forms in a more polar solvent (DMSO). The results obtained suggest a Coulomb-type stabilization of the 2,4,6-tris(nitromethyl)-1,3,5-triazine molecule in the gas phase, in the crystal, and in nonpolar solvents.     

Synthesis and crystal structures of two lead(II) complexes of 4,4,4-trifluoro-1-naphthyl-1,3-butanedione ligand,subtle interplay of weak intermolecular interactions

[Pb₂(tfnb)₄ (µ-CH₃OH)] _n (1) and [Pb₂(dmp)₂(tfnb)₄] (2) (tfnb and dmp are the abbreviations for 4,4,4-trifluoro-1-naphthyl-1,3-butanedionate and 2,9-dimethyl-1,10-phenanthroline) have been synthesized and characterized by elemental analysis, IR, ¹H NMR spectroscopy, and thermal analysis. The single-crystal structure of 1 shows that the complex forms two 1-D polymeric networks containing four types of Pb²⁺ with coordination numbers seven for Pb(1) and Pb(3), five for Pb(2), and six for Pb(4). The single-crystal structure of 2 shows that the complex forms a dinuclear complex with eight-coordinate Pb(II). The supramolecular features in this complex are guided by lone-pair activity and the control of weak directional intermolecular interactions and aromatic π–π stacking interactions.