The effects of cleavage of the inter-chain disulphide bonds of rabbit IgG on its ability to bind C1q

Immune complexes prepared from rabbit anti-ovalbumin IgG in which the interchain disulphide bonds had been reduced and then blocked with N-( iodoacetylaminoethyl )-8-naphthylamine-1-sulphonic acid retained the ability to bind 125I-labelled C1q. This ability was lost when a small alkylating agent (iodoacetamide) was used to block the cleaved disulphide bonds. The ability of the IgG to form insoluble immune complexes was partially compromised when iodoacetamide was used to block the disulphide bonds, but was unimpaired when N-( iodoacetylaminoethyl )-8-naphthylamine-1-sulphonic acid was used. These data are consistent with the suggestion that access to the C1q binding site in IgG in immune complexes is modulated by movement of the Fab arms, which may block access to the site.     

Nucleotide conformations in codon-anticodon interactions

The amount of distortion required of the sugar-phosphate backbone in RNA double-helices to accommodate various non-standard base pairs was examined by means of a linked-atom least-squares computer program. Compressive pyrimidine-pyrimidine pairs were found to entail more strain than the extensive adenine-hypoxanthine pair, as predicted by the wobble hypothesis. Purine-pyrimidine pairs involving guanine and uracil also require little torsional strain, indicating the acceptability of such pairings in hairpin stems as well as in codon-anticodon bindings.     

Heme-linked ionizations in horseradish peroxidase detected by Raman difference spectroscopy

Heme-linked ionizations of the acidic and basic isoenzymes of ferrous horseradish peroxidase influence both the Fe-histidine stretching mode and the oxidation-state marker line. First, Raman difference spectroscopy of horseradish peroxidase confirms earlier work showing that v(Fe-His) undergoes a transition in frequency with a pK that is characteristic of the enzyme's functional properties. The Fe-histidine mode shifts by about 2.5-3.0 cm-1 for horseradish peroxidase C and by about 6 cm-1 for the acidic isoenzyme. Further, we find that the oxidation-state marker line v4 also exhibits a transition with the same pK. For horseradish peroxidase C the shift in v4 is 0.4 cm-1 and the pK is 7.1 +/- .5, in good agreement with the pK found by other techniques. Shifts in these two Raman lines are correlated for the pK 7.1 transition and attain their highest frequency at low pH. The correlation is in marked contrast with R/T shifts in hemoglobins for which delta v(Fe-His) and delta v4 are also linearly related but shift in opposite directions. The shift in v4 suggests a mechanism for pH control of catalytic function based on ring pi-charge density effects on the energy of charge-depleted high oxidation-state intermediates. A second transition in v4 (delta v4 = 2.6 cm-1) with a pK of 10.0 is interpreted in terms of a change in ligation and spin state.     

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/.