Structure of Fab

The four individual domains are paired in two types of close trans-interaction (Fig. 4) [103,17], The VH and VL domains are paired by extensive contact between the 

Vh GhI and VL-CL m-interactions are very limited allowing flexibility about the V-C switch region or elbow bending [11,12]. In the crystallographic analyses of Fab structures this is reflected in an elbow angle, i.e. angle between the VH-VL and CH1-CL pseudo two-fold axes, varying between about 137° and 180° [8]. 

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Lascombe, M.-B., et al. Three-dimensional structure of Fab R 19.9, a monoclonal murine antibody specific for the p-azobenzenearsonate group. Proc. Natl. Acad. Sci. USA 86 607-611, 1989. 

Fig. 3.4. A. Reconibinant synthesis of Fab fragment in bacteria by secretion. B. Structures of Fab, Fv and single-chain antibodies.

Tris(pentafluorophenyl)borane, known as "FAB" (structure below), is the most common arylborane used as cocatalyst for single site catalysts. FAB is a strongly Lewis acidic, air-sensitive solid (T 126-131 °C) that is only slightly soluble in hydrocarbon solvents. The structure of FAB is given below. 

The FAB source operates near room temperature, and ions of the substance of interest are lifted out from the matrix by a momentum-transfer process that deposits little excess of vibrational and rotational energy in the resulting quasi-molecular ion. Thus, a further advantage of FAB/LSIMS over many other methods of ionization lies in its gentle or mild treatment of thermally labile substances such as peptides, proteins, nucleosides, sugars, and so on, which can be ionized without degrading their. structures. 

The techniques described thus far cope well with samples up to 10 kDa. Molecular mass determinations on peptides can be used to identify modifications occurring after the protein has been assembled according to its DNA code (post-translation), to map a protein structure, or simply to confirm the composition of a peptide. For samples with molecular masses in excess of 10 kDa, the sensitivity of FAB is quite low, and such analyses are far from routine. Two new developments have extended the scope of mass spectrometry even further to the analysis of peptides and proteins of high mass. 

Figure 15.17 The three-dimensional structure of an intact IgG. Hinge regions connecting the Fab arms with the Fc stem are relatively flexible, despite the presence of disulfide bonds in this region linking the heavy and light chains. Carbohydrate residues that bridge the two Ch2 domains are not shown. (Courtesy of A. McPherson and L. Harris, Nature 360 369-372, 1992, by copyright permission of Macmillan Magazines Limited.)...

Wang, J., et al. Atomic structure of an ap T-cell receptor (TCR) heterodimer in complex with an anti-TCR Fab fragment derived from a mitogenic antibody. EMBO J. 17 10-26, 1988. 

Structure of Oxy-F Compound F is extremely unstable and is difficult to obtain at a level of purity suitable for NMR studies. However, an oxidation product, Oxy-F, formed when F is left standing at — 20° C, is considerably more stable than F and can be purified to a sufficiently high level of purity. Oxy-F is nonfluorescent and shows absorption maxima at 237 nm and 275 nm (shoulder). The high-resolution FAB mass spectrum indicated the molecular formula of Oxy-F to be C33H3809N4Na2 [m/z 703.2363 (M + Na)+ and 681.2483 (M + H)"1"]. The H and 13C NMR data allowed the assignment of structure 7 to oxy-F (Fig. 3.2.6 Nakamura et al., 1988). 

Structure ofF Although F has never been obtained in a completely pure state, the FAB mass spectral data of F [m/z 687 (M + Na)+ and 665 (M+H)+], and the comparison of the H and 13C NMR spectra of F with those of Oxy-F, suggested structure 6 for this compound. To confirm this structure, F was subjected to ozonolysis, followed by diazomethane treatment. The expected diester 5 was successfully isolated, indicating that 6 is indeed the structure of compound F (Nakamura et al., 1988). The structure of the luminescence reaction product of F is considered to be 8 on the basis of comparison with the dinoflagellate luminescence system (see Chapter 8). 

The luciferin produces a blue oxidation product during its purification process. In the DEAE chromatography of luciferin, this blue compound is eluted before the fractions of luciferin. The fractions of the blue compound were combined and purified by HPLC on a column of Hamilton PRP-1 (7 x 300 mm) using methanol-water (8 2) containing 0.1% ammonium acetate. The purified blue compound showed absorption peaks at 234, 254, 315, 370, 410, 590 (shoulder) and 633 nm. High-resolution FAB mass spectrometry of this compound indicated a molecular formula of C l C Nai m/z 609.2672 (M - Na + 2H)+, and mlz 631.2524 (M + H)+]. These data, together with the HNMR spectral data, indicated the structure of the blue compound to be 8. 

Using PTLC six major fractions of lipids (phospholipids, free sterols, free fatty acids, triacylglycerols, methyl esters, and sterol esters) were separated from the skin lipids of chicken to smdy the penetration responses of Schistosoma cercaria and Austrobilharzia variglandis [79a]. To determine the structure of nontoxic lipids in lipopolysaccharides of Salmonella typhimurium, monophosphoryl lipids were separated from these lipids using PTLC. The separated fractions were used in FAB-MS to determine [3-hydroxymyristic acid, lauric acid, and 3-hydroxymyristic acids [79b]. 

Preparation of Reagent and Labelling Procedures. The structure of F-D [2-(2,4-diazobicyclo-2,2,2-octyl)-4-(5-aminofluoresceinyl)-6-morpholinyl 1,3,5-triazine] has been confirmed by its FAB-MS, IR, and H-NMR spectra (9). Briefly, F-D was synthesized by the treatment of fluorescamine isomer I with cyanuric chloride, then reaction with morpholine and DABCO (l,4-diazobicyclo-2,2,2-octane), as illustrated... 

Garcia, K.C., Ronco, P.M., Verroust, P.J., Briinger, AT. and Mazel, L.M. (1992) Three-dimensional structure of an angiotensin II-Fab complex at 3 A hormone recognition by an anti-idiotypic antibody, Science, 257, 502-507. 

Similarly, other cycloadducts of nitrile oxides with C6o were synthesized. The cycloadducts were characterized by 13C NMR spectroscopy and high-resolution fast atom bombardment (FAB) mass spectrometry. It should be mentioned that X-ray structure determination of the 3-(9-anthryl)-4,5-dihydroisoxazole derivative of C6o, with CS2 included in the crystals, was achieved at 173 K (255). Cycloaddition of fullerene C60 with the stable 2-(phenylsulfonyl)benzonitrile oxide was also studied (256). Fullerene formed with 2-PhSC>2C6H4CNO 1 1 and 1 2 adducts. The IR, NMR, and mass spectra of the adducts were examined. Di(isopropoxy)phosphorylformonitrile oxide gives mono- and diadducts with C60 (257). Structures of the adducts were studied using a combination of high performance liquid chromatography (HPLC), semiempirical PM3 calculations, and the dipole moments. 

Compound [25] was thus shown to have an unusual affinity for Ag+ cations. X-ray crystallographic determination of the structures of the free ligand, sodium and silver complexes were carried out and are shown in Fig. 17. The Ag-Fe distance in the silver complex of [25] is only 3.37 A, whereas the Na-Fe distance in the sodium complex is 4.39 A. This evidence together with the FAB MS data and UV spectroscopic data suggests that there may be an interaction between the silver cation and the iron present in the ferrocene moiety. 

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