Site-Specific <Emphasis Type="Italic">N</Emphasis>-Glycosylation of Recombinant Pentameric and Hexameric Human IgM

Glycosylation is known to play an important role in IgG antibody structure and function. Polymeric IgM, the largest known antibody in humans, displays five potential N-glycosylation sites on each heavy chain monomer. IgM can exist as a pentamer with a connecting singly N-glycosylated J-chain (with a total of 51 glycosylation sites) or as a hexamer (60 glycosylation sites). In this study, the N-glycosylation of recombinant pentameric and hexameric IgM produced by the same human cell type and culture conditions was site-specifically profiled by RP-LC-CID/ETD-MS/MS using HILIC-enriched tryptic and GluC glycopeptides. The occupancy of all putative N-glycosylation sites on the pentameric and hexameric IgM were able to be determined. Distinct glycosylation differences were observed between each of the five N-linked sites on the IgM heavy chains. While Asn171, Asn332, and Asn395 all had predominantly complex type glycans, differences in glycan branching and sialylation were observed between the sites. Asn563, a high mannose-rich glycosylation site that locates in the center of the IgM polymer, was only approximately 60% occupied in both the pentameric and hexameric IgM forms, with a difference in relative abundance of the glycan structures between the pentamer and hexamer. This study highlights the information obtained by characterization of the site-heterogeneity of a highly glycosylated protein of high molecular mass with quaternary structure, revealing differences that would not be seen by global glycan or deglycosylated peptide profiling.

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Multipole moments for embedding potentials: Exploring different atomic allocation algorithms

Polarizable quantum mechanical (QM)/molecular mechanics (MM)‐embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of large molecular complexes, such as proteins and RNA/DNA, and of molecules in solution. Our aim is to develop a computational methodology for distributed multipole moments and their associated multipole polarizabilities which is accurate, computationally efficient, and with smooth convergence with respect to multipole order. As the first step toward this goal, we herein investigate different ways of obtaining distributed atom‐centered multipole moments that are used in the construction of the electrostatic part of the embedding potential. Our objective is methods that not only are accurate and computationally efficient, but which can be consistently extended with site polarizabilities including internal charge transfer terms. We present a new way of dealing with well‐known problems in relation to the use of basis sets with diffuse functions in conventional atomic allocation algorithms, avoiding numerical integration schemes. Using this approach, we show that the classical embedding potential can be systematically improved, also when using basis sets with diffuse functions, and that very accurate embedding potentials suitable for QM/MM embedding calculations can be acquired. © 2016 Wiley Periodicals, Inc.     

Preparation and structural properties of 7,8-dioxa[6]helicenes and 7a,14c-dihydro-7,8-dioxa[6]helicenes.

The potentially chiral 7,8-dioxa[6]helicenes 1-1c have been prepared by oxidation of their precursors the 7a,14c-dihydro-7,8-dioxa[6]helicenes 3. The crystal structure determination of 3b cis-7a,14c-dihydro-3,12-dibromo-7,8-dioxa[6]helicene unambiguously confirms the cis configuration of the 7a,-14c hydrogens in compounds 3 as previously implied from NMR measurements and also shows that 3b crystallizes in a chiral conformation in the solid state. Selective deuteration of the sterically crowded 1,14 positions of 7,8-dioxa[6]helicene 1 influenced the crystal structure. The deuterium labeled compound D2-1 exhibits a disordered structure, whereas 1 had been found to crystallize in a complex structure which can be described as an analogous partly ordered modulated superstructure. When dehydrogenation of compound 3 to obtain compound 1 was attempted, harsh synthetic conditions gave the unexpected halogenated compounds 5-chloro-7,8-dioxa[6]helicene 1c and cis-7a,14c-dibromo-7,8-dioxa[6]helicene 3c. Compounds 1d and 3b were identified by solving their crystal structure.     

Rational Tuning of Fluorobenzene Probes for Cysteine‐Selective Protein Modification

Fluorobenzene probes for protein profiling through selective cysteine labeling have been developed by rational reactivity tuning. Tuning was achieved by selecting an electron‐withdrawing para substituent in combination with variation of the number of fluorine substituents. Optimized probes chemoselectively arylated cysteine residues in proteins under aqueous conditions. Probes linked to azide, biotin, or a fluorophore were applicable to labeling of eGFP and albumin. Selective inhibition of cysteine proteases was also demonstrated with the probes. Additionally, probes were tuned for site‐selective labeling of cysteine residues and for activity‐based protein profiling in cell lysates.