Amino acids FACs

In soluble globular proteins, hydrophilic amino acids tend to be on the exterior of the molecule whereas hydrophobic amino acids are packed in the interior [13]. To quantitatively describe the location of an amino acid in relation to the protein surface, different measures of solvent exposure have been developed. In the present context, the solvent exposure is modeled by the number s of protein atoms that are within a sphere of radius R centered at the position of atom c of amino acid a [5]. If the amino acid is buried in the protein interior, s is large because the surrounding volume is (almost) completely filled by protein atoms. On the other hand, if the amino acid is exposed, part of the volume is occupied by solvent molecules, which results in a smaller s (see Table 11.1 and Figure 11.3). Again, relative frequencies fac(s) and fc(s) are derived from the database and the net potential for solvent exposure is then... 

In this chapter, we provide protocols to determine the ability of a peptide to mediate DNA internalization in cultured human tumor cells. Fluorescence-assisted cell sorting (FACS) analysis is used to obtain quantitative data on the time and temperature dependence of macromolecular delivery. Confocal microscopy is used to study the subcellular localization in both fixed and live cells. Fluorescently labeled transferrin and dextran are used to label the clathrin-dependent (15) and the non-clathrin, non-caveolar (16) endocytic compartments, respectively. Expression of a caveolin-l-YFP fusion protein is used to label cell surface caveolae and intracellular caveosomes (17). Finally a protocol, for the overexpression of dominant-negative dynamin [GTPase deficient dynamin-2 containing the amino acid substitution K44A (18)] is provided to evaluate the dynamin dependence of the uptake mechanism. 

Members of the xanthine oxidase family have MPT coordinated to a fac-MoOY(H20) (Y = O or S) center with no amino acid residue bound. 

The procedure can be modified to prepare the corresponding complexes of other amino acids. For example, if 11.0 g of alanine is substituted for the glycine and if, before addition of the acetic acid, the reaction mixture is heated for an hour after it has become violet, the yields of fac and mer isomere of [Co(H2NCH2CH2COO)3] are 1.5 g (11.6%) and 3.7 g (28.6%), respectively. 

Surprisingly little work has been reported on tris(amino acid) complexes of Rh". Reaction of RhClj-SHjO with sodium bicarbonate causes precipitation of Rh203, which forms [Rh(D-ala)j] if heated immediately with D-alanine. Fractional crystallization allows separation of mer(-) and mer +) isomers, as well as some impure fac isomer. Reaction of the Li salt of DL-methionine (Li MeSCH2CH2CH(NH2)COO ) with anhydrous RhClj in refluxing ethanol leads to the precipitation of [Rh(DL-methionine)3], in which the methionines act as anionic bidentates, bonded through the O and N atoms. The solid state reaction of RhClj with glycine is reported to lead to [Rh(gly)j], characterized thermogravimetrically and by IR, UV and H NMR spectroscopy. Several [Rh(en)2 (amino acid)] " complexes have been prepared and resolved (Section 48.6,2.2.ii). ... 

Rep and Cro are bacteriophage 434 proteins Lam Rep and Cro are bacteriophage proteins CAP, Irp Rep, and Lac Rep are catabolite activator protein, Trp repressor, and fac repressor oiE. coli, respectively. Antpis the homeodomain protein of the Antennapedia gene of the fruit fly Drosophila melanogaster. The numbers in each sequence indicate the location of the HTH within the amino acid sequences of the various polypeptides. 

For the tris(amino acidato)metal(III) complexes four geometrical and chiral isomers are possible, as shown in Scheme 2, where NO is the chelated amino acid anion, mer and fac refer to the meridional and facial geometrical isomers and A and A refer to the configuration at the metal centre. For the glycine complexes A and A are an enantiomeric pair, while for the optically pure forms of the other amino acids they form a diastereomeric pair and hence are easier to separate. For most of the simple bidentate amino acids of the kinetically inert metal ions Cr" , Co " and Rh ", the four isomers have been obtained. The isomers are distinguishable by their UV/visible, CD and NMR spectra. Not all the isomers can be found in certain cases, for example, with L-proline the k-fac isomer could not be prepared, a fact which was predicted on steric grounds." ... 

Several years later, the preparative work on the geometrical isomers was renewed by other workers, who applied the three methods to the preparation of geometrical-optical isomers, or diastereoisomers, of tris-complexes from optically active amino acids. In general, four diastereoisomers are possible for a tris(L- or o-amino-acidato) complex fac ->r), fac —), wer(-t-) and mer —). 

In contrast, the two other amyloid diseases associated with TTR, familial amyloidotic polymeuropathy-l (FAP-1) and familial amyloidotic cardiomyopathy (FAC), are both autosomal dominant disorders (Table 1). The deposits of amyloid fibrils in these disorders form in tissues and organs and are made up of variant TTR, wt protein and TTR fragments. More than 80 TTR variants have been reported, with the majority of these being associated with disease (Hamilton and Benson 2001). These are single amino acid substitutions, with the exception of a Vall22 deletion mutation. It appears that certain amino acid substitutions decrease the stability of the tetramer and favour the formation of amyloidogenic intermediates that can then self-associate to form fibrils. FAR is usually fatal within 7 to 15 years after the appearance of symptoms. 

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