Automated Antibody De Novo Sequencing and Its Utility in Biopharmaceutical Discovery

Applications of antibody de novo sequencing in the biopharmaceutical industry range from the discovery of new antibody drug candidates to identifying reagents for research and determining the primary structure of innovator products for biosimilar development. When murine, phage display, or patient-derived monoclonal antibodies against a target of interest are available, but the cDNA or the original cell line is not, de novo protein sequencing is required to humanize and recombinantly express these antibodies, followed by in vitro and in vivo testing for functional validation. Availability of fully automated software tools for monoclonal antibody de novo sequencing enables efficient and routine analysis. Here, we present a novel method to automatically de novo sequence antibodies using mass spectrometry and the Supernovo software. The robustness of the algorithm is demonstrated through a series of stress tests.

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Modulation of heme redox potential in the cytochrome c6 family

Cytochrome c6A is a unique dithio-cytochrome of green algae and plants. It has a very similar core structure to that of bacterial and algal cytochromes c6 but is unable to fulfill the same function of transferring electrons from cytochrome f to photosystem I. A key feature is that its heme midpoint potential is more than 200 mV below that of cytochrome c6 despite having His and Met as axial heme-iron ligands. To identify the molecular origins of the difference in potential, the structure of cytochrome c6 from the cyanobacterium Phormidium laminosum has been determined by X-ray crystallography and compared with the known structure of cytochrome c6A. One salient difference of the heme pockets is that a highly conserved Gln (Q51) in cytochrome c6 is replaced by Val (V52) in c6A. Using protein film voltammetry, we found that swapping these residues raised the c6A potential by +109 mV and decreased that of c6 by almost the same extent, -100 mV. X-ray crystallography of the V52Q protein showed that the Gln residue adopts the same configuration relative to the heme as in cytochrome c6 and we propose that this stereochemistry destabilizes the oxidized form of the heme. Consequently, replacement of Gln by Val was probably a key step in the evolution of cytochrome c6A from cytochrome c6, inhibiting reduction by the cytochrome b6f complex and facilitating establishment of a new function.     

History of individuals of the 18th/19th centuries stored in bones,teeth, and hair analyzed by LA–ICP–MS—a step in attempts to confirm the authenticity of Mozart’s skull

A cranium stored in the Stiftung Mozarteum in Salzburg/Austria which is believed to be that of Mozart, and skeletal remains of suspected relatives which have been excavated from the Mozart family grave in the cemetery in Salzburg, have been subjected to scientific investigations to determine whether or not the skull is authentic. A film project by the Austrian television ORF in collaboration with Interspot Film on this issue was broadcast at the beginning of the “Mozart year 2006”. DNA analysis could not clarify relationships among the remains and, therefore, assignment of the samples was not really possible. In our work this skull and excavated skeletal remains have been quantified for Pb, Cr, Hg, As, and Sb content by laser ablation-inductively coupled plasma-mass spectrometry (LA–ICP–MS) to obtain information about the living conditions of these individuals. A small splinter of enamel (less than 1 mm³) from a tooth of the “Mozart cranium” was also available for investigation. Quantification was performed by using spiked hydroxyapatite standards. Single hair samples which are recorded to originate from Mozart have also been investigated by LA–ICP–MS and compared with hair samples of contemporary citizens stored in the Federal Pathologic–Anatomical Museum, Vienna. In general, Pb concentrations up to approximately 16 μg g⁻¹ were found in the bone samples of 18th century individuals (a factor of 7 to 8 higher than in recent samples) reflecting elevated Pb levels in food or beverages. Elevated Pb levels were also found in hair samples. The amount of Sb in the enamel sample of the “Mozart cranium” (approx. 3 μg g⁻¹) was significantly higher than in all the other tooth samples investigated, indicating possible Sb ingestion in early childhood. Elevated concentrations of elements in single hair samples gave additional information about possible exposure of the individuals to heavy metals at a particular point in their life.     

Vibrational Properties of [FeH(N2)(depe)2]+ and [FeCl(N2)(depe)2]+]: Dinitrogen Bonding in the Low Activation Limit

The vibrational properties of the two octahedral Fe^II dinitrogen complexes [FeH(N₂)(depe)₂]⁺ ( 1 ) and [FeCl(N₂)(depe)₂]⁺ ( 2 , depe = 1, 2‐bis(diethylphosphino)ethane) are investigated with the help of infrared and Raman spectroscopies. Vibrational data are evaluated with a Quantum Chemistry Assisted Normal Coordinate Analysis (QCA‐NCA; N. Lehnert, F. Tuczek, Inorg. Chem. 1999 , 38, 1659). In agreement with high values found for ν(NN) and the corresponding force constants f(NN), the N₂ ligands in compounds 1 and 2 are non‐activated which corresponds to the observation that N₂ is not protonable in Fe^II systems. Taking into account the short Fe‐N bond lengths, the values of the Fe‐N stretching force constants (2.55mdyn/Å for 1 and 2.58mdyn/Å for 2 ) are found to be compatible with those of other Fe^II low‐spin compounds coordinated to backbonding N‐coordinating ligands. The force fields obtained for the Fe‐N₂ units of 1 and 2 are almost identical although the thermal stability of 1 and 2 with respect to loss of N₂ is different. This indicates that the zero‐point vibrational levels are unaffected by possible ground‐state level crossing processes occuring at larger Fe‐N bond lengths, as observed for 2 (O. Franke, B. E. Wiesler, N. Lehnert, C. Näther, V. Ksenofontov, J. Neuhausen, F. Tuczek, Inorg. Chem. 2002 , 41, 3491).     

Time resolved valence band photoelectron spectroscopy of liquid palladium and molybdenum

Photoelectron spectroscopy measurements on liquid transition metals are not feasible by conventional steady state experiments because of the elevated vapor pressures of these metals at the melting point. However, dynamic experiments with surface melting induced by pulsed laser irradiation combined with time resolved photoelectron spectroscopy make these experiments possible for the first time. Valence band spectra of Pd and Mo have been obtained by this method in both the high temperature solid phase and the liquid phase under identical experimental conditions. Both the elements reveal distinct changes in the valence band spectra on melting. The shapes of the 4d bands of the two metals in the liquid phase are in good agreement with the calculated spectra based on the ab initio density of states (DOS) calculations.     

Selectivity issues in targeted metabolomics: Separation of phosphorylated carbohydrate isomers by mixed-mode hydrophilic interaction/weak anion exchange chromatography

Phosphorylated carbohydrates are important intracellular metabolites and thus of prime interest in metabolomics research. Complications in their analysis arise from the existence of structural isomers that do have similar fragmentation patterns in MS/MS and are hard to resolve chromatographically. Herein, we present selective methods for the liquid chromatographic separation of sugar phosphates, such as hexose and pentose phosphates, 2‐ and 3‐phosphoglycerate, dihydroxyacetone phosphate and glyceraldehyde 3‐phosphate, as well as glucosamine 1‐ and 6‐phosphate utilizing mixed‐mode chromatography with reversed‐phase/weak anion‐exchangers and a charged aerosol detector. The best results were obtained when the reversed‐phase/weak anion‐exchanger column was operated under hydrophilic interaction liquid chromatography elution conditions. The effects of various chromatographic parameters were examined and are discussed on the basis of a simple stoichiometric displacement model for explaining ion‐exchange processes. Employed acidic conditions have led to the complete separation of α‐ and β‐anomers of glucose 6‐phosphate at low temperature. The anomers coeluted in a single peak at elevated temperatures (>40°C) (peak coalescence), while at intermediate temperatures on‐column interconversion with a plateau in‐between resolved anomer peaks was observed with apparent reaction rate constants between 0.1 and 27.8×10^?4 s^?1. Dynamic HPLC under specified conditions enabled to investigate mutarotation of phosphorylated carbohydrates, their interconversion kinetics, and energy barriers for interconversion. A complex mixture of six hexose phosphate structural isomers could be resolved almost completely.     

Heisenberg’s Uncertainty Relation and Bell Inequalities in High Energy Physics

An effective formalism is developed to handle decaying two-state systems. Herewith, observables of such systems can be described by a single operator in the Heisenberg picture. This allows for using the usual framework in quantum information theory and, hence, to enlighten the quantum features of such systems compared to non-decaying systems. We apply it to systems in high energy physics, i.e. to oscillating meson–antimeson systems. In particular, we discuss the entropic Heisenberg uncertainty relation for observables measured at different times at accelerator facilities including the effect of CP\mathcal{CP} violation, i.e. the imbalance of matter and antimatter. An operator-form of Bell inequalities for systems in high energy physics is presented, i.e. a Bell-witness operator, which allows for simple analysis of unstable systems.     

Monolithic silica-based capillary column with strong chiral cation-exchange type surface modification for enantioselective non-aqueous capillary electrochromatography

A silica-based monolithic stationary phase prepared by the sol-gel process in a 100 microm I.D. fused-silica (FS) capillary has been modified chemically with 3-mercaptopropyl trimethoxysilane followed by immobilization of a strong cation-exchange (SCX) type chiral selector, (S)-N-(4-allyloxy-3,5-dichlorobenzoyl)-2-amino-3,3-dimethylbutane phosphonic acid, by radical addition reaction onto the reactive sulfhydryl surface. After a fine-tuning of the mobile phase composition, the enantioselective capillary column was evaluated for the separation of various chiral basic drugs by enantioselective non-aqueous capillary electrochromatography (CEC), in comparison to capillary column analogs packed with 3.5 microm silica particles having attached the same selector. The performance of the monolithic silica column was further compared to corresponding polymethacrylate-based organic polymer monoliths. The study indicated that strong counter-ions such as 2-aminobutanol or N,N,N',N'-tetramethylethylenediamine are needed, although they reduce the electroosmotic flow velocity and separation factors in comparison to less efficient counter-ions, in order to allow the elution of the oppositely charged solutes in the ion-exchange retention mode within reasonable run time and as sharp zones. In contrast, weak counter-ions such as N,N-diisopropylethylamine (Huenig base) provided stronger electroosmotic flow and much better separation factors, but relatively poor peak efficiencies. Overall, with the chemically functionalized monolithic silica column the high quality separations of packed column analogs could be approximated, with regards to both separation factors and peak performances. On the other hand, the monolithic capillary column certainly outperformed the packed column in terms of system robustness under capillary electrochromatography conditions and showed excellent column longevity. The enantioselective strong cation-exchange-type monolithic silica column performed also well in comparison to the organic polymer monolith.     

New Thioantimonates(III) with Different Sb:S Ratios: Solvothermal Syntheses and Crystal Structures of [(C3H10NO)(C3H10N)][Sb8S13], [(C2H8NO)(C2H8N)(CH5N)][Sb8S13], [(C6H16N2)(C6H14N2)][Sb6S10], and [C8H22N2][Sb4S7]

Four new thioantimonates(III) with compositions [(C₃H₁₀NO)(C₃H₁₀N)][Sb₈S₁₃] ( 1 ) (C₃H₉NO = 1‐amino‐3‐propanol, C₃H₉N = propylamine), [(C₂H₈NO)(C₂H₈N)(CH₅N)][Sb₈S₁₃] ( 2 ) (C₂H₇NO = ethanolamine, C₂H₇N = ethylamine, CH₅N = methylamine), [(C₆H₁₆N₂)(C₆H₁₄N₂)][Sb₆S₁₀] ( 3 ) (C₆H₁₄N₂ = 1,2‐diaminocyclohexane) and [C₈H₂₂N₂][Sb₄S₇] ( 4 ) (C₈H₂₀N₂ = 1,8‐diaminooctane) were synthesized under solvothermal conditions. Compound 1 : triclinic space group P$\bar{1}$ , a = 6.9695(6) Å, b = 13.8095(12) Å, c = 18.0354(17) Å, α = 98.367(11), β = 96.097(11) and γ = 101.281(11)°; compound 2 : monoclinic space group P2₁/m, a = 7.1668(5), b = 25.8986(14), c = 16.0436(11) Å, β = 96.847(8)°; compound 3 : monoclinic space group P2₁/n, a = 11.6194(9), b = 10.2445(5) Å, c = 27.3590(18) Å, β = 91.909(6)°; compound 4 : triclinic space group P$\bar{1}$ , a = 7.0743(6), b = 12.0846(11), c = 13.9933(14) Å, α = 114.723(10), β = 97.595(11), γ = 93.272(11)°. The main structural feature of the two atoms thick layered [Sb₈S₁₃]^2– anion in 1 are large nearly rectangular pores with dimensions 11.2 × 11.7 Å. The layers are stacked perpendicular to [100] to form tunnels being directed along [100]. In contrast to 1 the structure of 2 contains a [Sb₈S₁₃]^2– chain anion with Sb₁₂S₁₂ pores measuring about 8.9 × 11.5 Å. Only if longer Sb–S distances are considered as bonding interactions a layered anion is formed. The chain anion [Sb₆S₁₀]^2– in compound 3 is unique and is constructed by corner‐sharing SbS₃ pyramids. Two symmetry‐related single chains consisting of alternating SbS₃ units and Sb₃S₃ rings are bound to Sb₄S₄ rings in chair conformation. Finally, in the structure of 4 the SbS₃ and SbS₄ moieties are joined corner‐linked to form a chain of alternating SbS₄ units and (SbS₃)₃ blocks. Neighboring chains are connected into sheets that contain relatively large Sb₁₀S₁₀ heterorings. The sheets are further connected by sulfur atoms generating four atoms thick double sheets.     

Sparse graphical models for exploring gene expression data

We discuss the theoretical structure and constructive methodology for large-scale graphical models, motivated by their potential in evaluating and aiding the exploration of patterns of association in gene expression data. The theoretical discussion covers basic ideas and connections between Gaussian graphical models, dependency networks and specific classes of directed acyclic graphs we refer to as compositional networks. We describe a constructive approach to generating interesting graphical models for very high-dimensional distributions that builds on the relationships between these various stylized graphical representations. Issues of consistency of models and priors across dimension are key. The resulting methods are of value in evaluating patterns of association in large-scale gene expression data with a view to generating biological insights about genes related to a known molecular pathway or set of specified genes. Some initial examples relate to the estrogen receptor pathway in breast cancer, and the Rb-E2F cell proliferation control pathway.