Selectivity over coverage in de novo sequencing of IgGs

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab′)₂ part from the conserved Fc part, whereafter the F(ab′)₂ portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab′)₂ or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.     

Qualitative analysis of excess dielectric properties of binary mixtures, ternary mixtures and mixing dynamics measurement using surface plasmon resonance

The analysis of the excess dielectric properties for various binary mixtures and a ternary mixture is demonstrated using a surface plasmon resonance (SPR) sensor. Strong deviations from ideality are seen using SPR to monitor deviations in the dielectric properties following mixing. Binary mixtures with similar refractive index were measured: hexanes/isopropanol, n-heptanes/propanol, 1-acetoxy-2-methoxyethane/2-methoxyethanol, butanol/dipropylamine, hexanes/ethylacetate, and ethylacetate/isopropanol binary mixtures. The ternary mixture was composed of 60 different proportions of hexanes, isopropanol, and ethylacetate. Using SPR, mixing dynamics is easily accessible. The mixing of hexanes and isopropanol in static solution was monitored.     

Near-infrared chiro-optical effects in metallogels

A series of novel metallogelators containing near-IR nickel-bis(dithiolene) absorbers were rationally designed and synthesized. Robust gel networks are formed by right handed helical 1D-nanofibers which generate strong and remarkable chiro-optical effects in the near-infrared region.     

Cluster analysis application identifies muscle characteristics of importance for beef tenderness

Background

Unsaturated fatty acids are susceptible to oxidation and damaged chains are removed from glycerophospholipids by phospholipase A₂. De-acylated lipids are then re-acylated by lysophospholipid acyltransferase enzymes such as LPCAT1 which catalyses the formation of phosphatidylcholine (PC) from lysoPC and long-chain acyl-CoA.

Results

Activity of LPCAT1 is inhibited by Ca²⁺, and a Ca²⁺-binding motif of the EF-hand type, EFh-1, was identified in the carboxyl-terminal domain of the protein. The residues Asp-392 and Glu-403 define the loop of the hairpin structure formed by EFh-1. Substitution of D³⁹² and E⁴⁰³ to alanine rendered an enzyme insensitive to Ca²⁺, which established that Ca²⁺ binding to that region negatively regulates the activity of the acyltransferase amino-terminal domain. Residue Cys-211 of the conserved motif III is not essential for catalysis and not sufficient for sensitivity to treatment by sulfhydryl-modifier agents. Among the several active cysteine-substitution mutants of LPCAT1 generated, we identified one to be resistant to treatment by sulfhydryl-alkylating and sulfhydryl-oxidizer agents.

Conclusion

Mutant forms of LPCAT1 that are not inhibited by Ca²⁺ and sulfhydryl-alkylating and ?Coxidizing agents will provide a better understanding of the physiological function of a mechanism that places the formation of PC, and the disposal of the bioactive species lysoPC, under the control of the redox status and Ca²⁺ concentration of the cell.     

Comparative molecular surface analysis (CoMSA) for virtual combinatorial library screening of styrylquinoline HIV-1 blocking agents

We used comparative molecular surface analysis to design molecules for the synthesis as part of the search for new HIV-1 integrase inhibitors. We analyzed the virtual combinatorial library (VCL) constituted from various moieties of styrylquinoline and styrylquinazoline inhibitors. Since imines can be applied in a strategy of dynamic combinatorial chemistry (DCC), we also tested similar compounds in which the -C=N- or -N=C- linker connected the heteroaromatic and aromatic moieties. We then used principal component analysis (PCA) or self-organizing maps (SOM), namely, the Kohonen neural networks to obtain a clustering plot analyzing the diversity of the VCL formed. Previously synthesized compounds of known activity, used as molecular probes, were projected onto this plot, which provided a set of promising virtual drugs. Moreover, we further modified the above mentioned VCL to include the single bond linker -C-N- or -N-C-. This allowed increasing compound stability but expanded also the diversity between the available molecular probes and virtual targets. The application of the CoMSA with SOM indicated important differences between such compounds and active molecular probes. We synthesized such compounds to verify the computational predictions.     

Capture of Gaseous Iodine in Isoreticular Zirconium-Based UiO-n Metal-Organic Frameworks: Influence of Amino Functionalization,DFT Calculations,Raman and EPR Spectroscopic Investigation

A series of Zr-based UiO-n MOF materials (n=66, 67, 68) have been studied for iodine capture. Gaseous iodine adsorption was collected kinetically from a home-made set-up allowing the continuous measurement of iodine content trapped within UiO-n compounds, with organic functionalities (−H, −CH₃, −Cl, −Br, −(OH)₂, −NO₂, −NH₂, (−NH₂)₂, −CH₂ NH₂) by in-situ UV-Vis spectroscopy. This study emphasizes the role of the amino groups attached to the aromatic rings of the ligands connecting the {Zr₆O₄(OH)₄} brick. In particular, the preferential interaction of iodine with lone-pair groups, such as amino functions, has been experimentally observed and is also based on DFT calculations. Indeed, higher iodine contents were systematically measured for amino-functionalized UiO-66 or UiO-67, compared to the pristine material (up to 1211 mg/g for UiO-67-(NH₂)₂). However, DFT calculations revealed the highest computed interaction energies for alkylamine groups (−CH₂NH₂) in UiO-67 (−128.5 kJ/mol for the octahedral cavity), and pointed out the influence of this specific functionality compared with that of an aromatic amine. The encapsulation of iodine within the pore system of UiO-n materials and their amino-derivatives has been analyzed by UV-Vis and Raman spectroscopy. We showed that a systematic conversion of molecular iodine (I₂) species into anionic I⁻ ones, stabilized as I⁻⋅⋅⋅I₂ or I₃⁻ complexes within the MOF cavities, occurs when I₂@UiO-n samples are left in ambient light.     

Molecular orbitals and photoelectron spectra of some titanium(IV) organometallic compounds

The photoelectron spectra of some titanium(IV) organometallic compounds are reported, and the data and the bonding in the compounds are discussed with the aid of extended CNDO/2 calculations.     

Palladium and nickel-catalyzed reaction of grignard reagents with trichloroethylene. A simple synthesis of 1,1-dichloroalkenes.

The palladium (or nickel) catalyzed reaction of Grignard reagents with trichloroethylene affords 1,1-dichloroalkenes in good yield under mild conditions.     

How to use a very simple microcomputing system for a dynamical conformational analysis of versatile molecules. The case of some anticancer inorganic ring systems

A very simple use of a suitable microcomputing system allows discrimination of a set of X-ray structures of anticancer drugs which (i) are the “natural” preferred conformations and (ii) are the direct relationships logically linking these conformations together. Such an approach appears the main interest for a deep understanding of the relative antitumour activities of drugs, whatever the target may be.     

Synthesis of a new bifunctional chelating agent for samarium complexation

A novel bifunctional chelating agent for samarium complexation has been synthesised in eight steps. A novel synthetic approach involving the introduction of methanephosphonic functions has been developed. The complexing properties of this compound has also been confirmed by labelling with ¹⁵³Sm.