Stability bounded domain

Figure 17.10 Construction of a two helix truncated Z domain, (a) Diagram of the three-helix bundle Z domain of protein A (blue) bound to the Fc fragment of IgG (green). The third helix stabilizes the two Fc-binding helices, (b) Three phage-display libraries of the truncated Z-domaln peptide were selected for binding to the Fc. First, four residues at the former helix 3 interface ("exoface") were sorted the consensus sequence from this library was used as the template for an "intrafece" library, in which residues between helices 1 and 2 were randomized. The most active sequence from this library was used as a template for five libraries in which residues on the Fc-binding face ("interface") were randomized. Colored residues were randomized blue residues were conserved as the wild-type amino acid while yellow residues reached a nonwild-type consensus, [(b) Adapted from A.C. Braisted and J.A. Wells,...

Molecular insight into the protein conformation states of Src kinase has been revealed in a series of x-ray crystal structures of the Src SH3-SH2-kinase domain that depict Src in its inactive conformation [7]. This form maintains a closed structure, in which the tyrosine-phosphorylated (Tyr527) C-terminal tail is bound to the SH2 domain (Fig. 2). The x-ray data also reveal binding of the SH3 domain to the SH2-kinase linker [adopts a polyproline type II (PP II) helical conformation], providing additional intramolecular interactions to stabilize the inactive conformation. Collectively, these interactions cause structural changes within the catalytic domain of the protein to compromise access of substrates to the catalytic site and its associated activity. Significantly, these x-ray structures provided the first direct evidence that the SH2 domain plays a key role in the self-regulation of Src. 

Li, H., Raman, C. S., Glaser, C. B., Blasko, E., Young,T. A., Parkinson, J. F., Whitlow, M., Poulos. T. L., Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase, ]. Biol.Chem. 

Mg (but not Na" ") results in a structure that is equivalent to the 30-nm compact fiber in the extent of condensation [49]. Finally, the independent and critical function of core histone N-termini in chromatin condensation was demonstrated by showing that nucleosomal filaments reconstituted from core histones lacking their N-terminal domains are unable to condense into folded structures upon an increase of Mg " ", despite the presence of properly bound histone H5 ([50,51], see also Ref. [52] for the discussion of the special role of H3 and H4 tails). Thus, the presence of HI is not a sine-qua-non condition for salt-induced chromatin folding, which can proceed in Hi s absence and is an intrinsic property of filaments consisting of spaced core particles. A key question is how many of the features of the native 30-nm compact fiber are due to the presence of histone HI From the available data it seems that HI may influence the intrinsic folding pathway of the chromatin filament by stabilizing a single ordered conformation. This property can have much to do with the cooperativity of HI interactions within chromatin but also with the way HI is bound to the nucleosome and with the efifect it exerts on the path of linker DNA. 

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