Docking glycosaminoglycans to proteins: analysis of solvent inclusion

Glycosaminoglycans (GAGs) are anionic polysaccharides, which participate in key processes in the extracellular matrix by interactions with protein targets. Due to their charged nature, accurate consideration of electrostatic and water-mediated interactions is indispensable for understanding GAGs binding properties. However, solvent is often overlooked in molecular recognition studies. Here we analyze the abundance of solvent in GAG-protein interfaces and investigate the challenges of adding explicit solvent in GAG-protein docking experiments. We observe PDB GAG-protein interfaces being significantly more hydrated than protein–protein interfaces. Furthermore, by applying molecular dynamics approaches we estimate that about half of GAG-protein interactions are water-mediated. With a dataset of eleven GAG-protein complexes we analyze how solvent inclusion affects Autodock 3, eHiTs, MOE and FlexX docking. We develop an approach to de novo place explicit solvent into the binding site prior to docking, which uses the GRID program to predict positions of waters and to locate possible areas of solvent displacement upon ligand binding. To investigate how solvent placement affects docking performance, we compare these results with those obtained by taking into account information about the solvent position in the crystal structure. In general, we observe that inclusion of solvent improves the results obtained with these methods. Our data show that Autodock 3 performs best, though it experiences difficulties to quantitatively reproduce experimental data on specificity of heparin/heparan sulfate disaccharides binding to IL-8. Our work highlights the current challenges of introducing solvent in protein-GAGs recognition studies, which is crucial for exploiting the full potential of these molecules for rational engineering.     

Two step, hydrolytic-solvothermal synthesis of redispersible titania nanocrystals and their gas-sensing properties

A titanium chloromethoxide solution was prepared by reacting TiCl₄ with methanol, followed by water addition. The starting solutions were characterized by Fourier Transform Infrared (FTIR) spectroscopy, evidencing that the in situ generated water results in early hydrolysis of the chloroalkoxide. The solution was reacted with molten dodecylamine at room temperature, obtaining a white slurry of amorphous titania nanoparticles. Stable, redispersible TiO₂ nanocrystals could be prepared by subsequent solvothermal treatment in oleic acid at 250???C. The use of oleic acid was essential for obtaining crystalline structures, while other surfactants prevented crystallization. The nanocrystals were characterized by X-ray Diffraction and Transmission Electron Microscopy, confirming the formation of anatase TiO₂ nanocrystals with a mean size of 3.3?nm. The TiO₂ nanocrystals were used for fabricating gas-sensing devices, which were tested towards ethanol vapors. The initial small size of the nanocrystals, and the limited size growth during the high-temperature sensor operation, result in remarkable sensing performances if compared with bulk titania sensors.     

Synthesis, crystal structures and magnetic properties of M(II)Cu(II) chains (M = Mn and Co) with sterically hindered alkyl-substituted phenyloxamate bridging ligands

A series of neutral oxamato‐bridged heterobimetallic chains of general formula [MCu(L^x)₂(S)₂] ? p S ? q H₂O [p=0–1, q=0–2.5; L¹=N‐2,6‐dimethylphenyloxamate, S=DMF with M=Mn ( 1 a ) and Co ( 1 b ); L²=N‐2,6‐diethylphenyloxamate, S=DMF with M=Mn ( 2 a ) and Co ( 2 b ) or S=DMSO with M=Mn ( 2 c ) and Co ( 2 d ); L³=N‐2,6‐diisopropylphenyloxamate, S=DMF with M=Mn ( 3 a ) and Co ( 3 b ) or S=DMSO with M=Mn ( 3 c ) and Co ( 3 d )] were prepared by treating the corresponding anionic oxamatocopper(II) complexes [Cu(L^x)₂]^2? (x=1–3) with M²⁺ cations (M=Mn and Co) in DMF or DMSO as the solvent. The single‐crystal X‐ray structures of 2 a and 3 a reveal the occurrence of well‐isolated, zigzag, oxamato‐bridged manganese(II)–copper(II) chains. The intrachain Cu ??? Mn distances across the oxamato bridge are 5.3761(7) and 5.4002(17) Å for 2 a and 3 a , respectively, whereas the shortest interchain Mn ??? Mn distances are 9.4475(16) and 8.1649(14) Å for 2 a and 3 a , respectively. All of these M^IICu^II chains (M=Mn and Co) exhibit 1D ferrimagnetic behaviour with moderately strong intrachain antiferromagnetic coupling between the square‐planar Cu^II and octahedral high‐spin M^II ions across the oxamato bridge [?J=31.4–35.2 and 33.4–44.8 cm^?1, respectively; H =∑_i?J S _M,i( S _Cu,i+ S _Cu,i?1)]. Only the Co^IICu^II chains show slow magnetic relaxation effects characteristic of single‐chain magnets (SCMs). Analysis of the magnetic relaxation dynamics of 3 d shows a thermally activated mechanism (Arrhenius law dependence) with values of the pre‐exponential factor (τ₀=2.6×10^?9 s) and activation energy (E_a=7.7 cm^?1) that are typical of SCMs. In contrast, two relaxation regimes are observed for 2 d in different temperature regions (τ₀=3.2×10^?10 s and E_a=24.7 cm^?1 for T<4.5 K and τ₀=3.2×10^?14 s and E_a=37.5 cm^?1 for T>4.5 K).     

A valveless microfluidic device for integrated solid phase extraction and polymerase chain reaction for short tandem repeat (STR) analysis

A valveless microdevice has been developed for the integration of solid phase extraction (SPE) and polymerase chain reaction (PCR) on a single chip for the short tandem repeat (STR) analysis of DNA from a biological sample. The device consists of two domains--a SPE domain filled with silica beads as a solid phase and a PCR domain with an ~500 nL reaction chamber. DNA from buccal swabs was purified and amplified using the integrated device and a full STR profile (16 loci) resulted. The 16 loci Identifiler? multiplex amplification was performed using a non-contact infrared (IR)-mediated PCR system built in-house, after syringe-driven SPE, providing an ~80-fold and 2.2-fold reduction in sample and reagent volumes consumed, respectively, as well as an ~5-fold reduction in the overall analysis time in comparison to conventional analysis. Results indicate that the SPE-PCR system can be used for many applications requiring genetic analysis, and the future addition of microchip electrophoresis (ME) to the system would allow for the complete processing of biological samples for forensic STR analysis on a single microdevice.     

S K-edge XAS and DFT calculations on SAM dependent pyruvate formate-lyase activating enzyme: nature of interaction between the Fe4S4 cluster and SAM and its role in reactivity

S K-edge X-ray absorption spectroscopy on the resting oxidized and the S-adenosyl-l-methionine (SAM) bound forms of pyruvate formate-lyase activating enzyme are reported. The data show an increase in pre-edge intensity, which is due to additional contributions from sulfide and thiolate of the Fe(4)S(4) cluster into the C-S σ* orbital. This experimentally demonstrates that there is a backbonding interaction between the Fe(4)S(4) cluster and C-S σ* orbitals of SAM in this inner sphere complex. DFT calculations that reproduce the data indicate that this backbonding is enhanced in the reduced form and that this configurational interaction between the donor and acceptor orbitals facilitates the electron transfer from the cluster to the SAM, which otherwise has a large outer sphere electron transfer barrier. The energy of the reductive cleavage of the C-S bond is sensitive to the dielectric of the protein in the immediate vicinity of the site as a high dielectric stabilizes the more charge separated reactant increasing the reaction barrier. This may provide a mechanism for generation of the 5'-deoxyadenosyl radical upon substrate binding.     

Particle-particle particle-mesh method for dipolar interactions: on error estimates and efficiency of schemes with analytical differentiation and mesh interlacing

The interlaced and non-interlaced versions of the dipolar particle-particle particle-mesh (P(3)M) method implemented using the analytic differentiation scheme (AD-P(3)M) are presented together with their respective error estimates for the calculation of the forces, torques, and energies. Expressions for the optimized lattice Green functions, and for the Madelung self-forces, self-torques and self-energies are given. The applicability of the theoretical error estimates are thoroughly tested and confirmed in several numerical examples. Our results show that the accuracy of the calculations can be improved substantially when the approximate (mesh computed) Madelung self-interactions are subtracted. Furthermore, we show that the interlaced dipolar AD-P(3)M method delivers a significantly higher accuracy (which corresponds approximately to using a twice finer mesh) than the conventional method, allowing thereby to reduce the mesh size with respect to the non-interlaced version for a given accuracy. In addition, we present similar expressions for the dipolar ik-differentiation interlaced scheme, and we perform a comparison with the AD interlaced scheme. Rough tests for the relative speed of the dipolar P(3)M method using ik-differentiation and the interlaced/non-interlaced AD schemes show that when FFT computing time is the bottleneck, usually when working at high precisions, the interlaced AD-scheme can be several times faster than the other two schemes. For calculations with a low accuracy requirement, the interlaced version can perform worse than the ik and the non-interlaced AD schemes.     

Highly stereoselective double (R)-phenylglycinol-induced cyclocondensation reactions of symmetric aryl bis(oxoacids)

The double cyclocondensation of symmetric pyridyl bis(oxoacids) 2b and 3b with (R)-phenylglycinol stereoselectively gave access to bis-phenylglycinol-derived oxazolopyrrolidine 9 and oxazolopiperidone 10, respectively. Application of the stereocontrolled cyclocondensation reaction to phenyl bis-γ-oxoacid 4b provided 11, which was converted to the corresponding enantiopure di(pyrrolidinyl)benzene 22. The absolute configuration of the new stereogenic centers generated in the key cyclocondenstion step was unambiguously established by X-ray crystallographic analysis.     

Large-scale asymmetric synthesis of the bioprotective agent JP4-039 and analogs

JP4-039 is a novel nitroxide conjugate capable of crossing lipid bilayer membranes and scavenging reactive oxygen species (ROS). An efficient and scalable one-pot hydrozirconation-transmetalation-imine addition methodology has been developed for its asymmetric preparation. Furthermore, this versatile methodology allows for the synthesis of cyclopropyl and fluorinated analogs of the parent lead structure.     

A new bacterial biosensor for trichloroethylene detection based on a three-dimensional carbon nanotubes bioarchitecture

Trichloroethylene (TCE), a suspected human carcinogen, is one of the most common volatile groundwater contaminants. Many different methodologies have already been developed for the determination of TCE and its degradation products in water, but most of them are costly, time-consuming and require well-trained operators. In this work, a fast, sensitive and miniaturised whole cell conductometric biosensor was developed for the determination of trichloroethylene. The biosensor assembly was prepared by immobilising Pseudomonas putida F1 bacteria (PpF1) at the surface of gold interdigitated microelectrodes through a three-dimensional alkanethiol self-assembly monolayer/carbon nanotube architecture functionalised with Pseudomonas antibodies. The biosensor response was linear from 0.07 to 100 μM of TCE (9–13,100 μg L⁻¹). No significant loss of the enzymatic activity was observed after 5 weeks of storage at 4 °C in the M457 pH 7 defined medium (two or three measurements per week). Ninety-two per cent of the initial signal still remained after 7 weeks. The biosensor response to TCE was not significantly affected by cis-1,2-dichloroethylene and vinyl chloride and, in a limited way, by phenol. Toluene was the major interference found. The bacterial biosensor was successfully applied to the determination of TCE in spiked groundwater samples and in six water samples collected in an urban industrial site contaminated with TCE. Gas chromatography–mass spectrometric analysis of these samples confirmed the biosensor measurements.     

Very long-distance magnetic coupling in a dicopper(II) metallacyclophane with extended π-conjugated diphenylethyne bridges

Self-assembly of the rigid rodlike ligand N,N'-4,4'-diphenylethynebis(oxamate) (dpeba) and Cu(2+) ions affords a novel dinuclear copper(II) metallacyclophane (nBu(4)N)(4)[Cu(2)(dpeba)(2)]·4MeOH·2Et(2)O (1) featuring a very long intermetallic distance (r = 15.0 ?). Magnetic susceptibility measurements for 1 reveal a moderately weak but nonnegligible intramolecular antiferromagnetic coupling between the two metal centers across the double para-substituted diphenylethynediamidate bridge (J = -3.9 cm(-1); H = -JS(1)S(2), where S(1) = S(2) = S(Cu) = (1)/(2)). Density functional electronic structure calculations on 1 support the occurrence of a spin polarization mechanism.