Domain interface

Phosphoryl transfer to asp351 allows dissociation of ADP, and then the N and P domain interface opens. The A domain rotates so that the TGES loop closes into the gap left by the loss of ADP. The A domain rotation, in turn, causes marked rearrangement in transmembrane hehces, opening the lumenal gate and releasing Ca " ions into the lumen. 

The two domains in each P. aeruginosa CCP monomer are connected by three strands of chain and an antiparallel p-sheet (Fig. 7). The domain interface is hydrophobic and provides a Ca + ion site with unusual ligation (Fig. 9). A detailed biochemical study of P. denitrificans CCP has suggested am essential role for Ca + ions in catalysis. This enzyme appears to bind two Ca + ions, the first with high affinity in... 

Note 3 Morphology coarsening can be substantially stopped by, for example, vitrification, crosslinking, and pinning, the slowing down of molecular diffusion across domain interfaces. 

Note A representation of the domain interface as a two-dimensional surface oversimplifies the actual structure. All interfaces have a third dimension, namely, the interphase or... 

Figure 31-5 The extensive conserved hydrogen-bonding pattern in an immunoglobulin variable domain provided by polar residues buried inside the VL and VH domains. (A) To facilitate orientation, prominent side chains are displayed here and identified by names and numbers in the same orientation as in (B). (B) Polypeptide chain backbones of both domains are denoted by heavy lines and hydrogen bonds by light lines. In addition to the regular interbackbone hydrogen-bonding network characteristic of antiparallel (3-sheets, there are hydrogen bonds provided by side-chain atoms. Note the two hydrogen bonds of Gln-38 (VL) and Gin-39 (VH) that span the domain—domain interface. From Novotny and Haber.75...

Lodowski, D. T., Barnhill, J. F., Pyskadlo, R. M., Ghirlando, R., Sterne-Marr, R., and Tesmer, J. J. (2005). The role of Gfly and domain interfaces in the activation of G protein-coupled receptor kinase 2. Biochemistry 44, 6958-6970. 

Grishina, G., and Berlot, C. H. (1998). Mutations at the domain interface of GOT impair receptor-mediated activation by altering receptor and guanine nucleotide binding. / Biol. Chem. 273, 15053-15060. 

Protein design by site-directed mutagenesis on pyruvate decarboxylase became possible after the 3D-structure of the enzyme from Saccharomyces uvarum had become available [35], Based on sequence comparison and secondary structure prediction, the 3D-structure of the yeast enzyme served as a model for PDCZ.m. [163], The point mutations which have been introduced into the two enzymes (Tables 4 and 5) concern catalytically important residues as well as significant side-chain interactions at the domain interface of the dimer. Besides, site-directed mutagenesis offered a powerful tool to improve the car-boligase reaction of PDCZ.m. with respect to the synthesis of (P)-PAC [163,164,170]. 

Fig. 4. Computer graphics of the domain interface building the channel to the active center in PDC. The thiazolium ring of ThDP is visible at the bottom of the channel. A tryptophane residue (blue) has been engineered into the crystal structure of PDCS.u. by means of computer graphics. The picture was generated by J. Grotzinger using the program GRASP [181]...

Fig. 12. C2HR domain orientations. Each C2HR is labeled with its characteristic tilt (e), roll (r), and swivel (tr), parameters (Deivanayagam et at, 2000) along with the amount of amino acid surface area buried in its domain interface (bs). The C2HRs adopt three distinct D1/D2 orientations. Similar orientations are observed for IL-lORl and 1FNAR2 (group 1), IFN-7RI and TF (group 2), and GHR (group 3). The difference between each group is most obvious if shovm by superimposing the D1 domains of the receptors. (See Color Insert.)...

Using the program GRASP (Nicholls ei al.. 1991). accessible surface area calculations based on the Shrake Rupley (1973) Hydrogen bonds in domain interfaces, with water-mediated hydrogen bonds in parentheses. 

Survey and classification of structural domain-domain interfaces... 

Kim, W.K. and Ison, J.C. (2005) Survey of the geometric association of domain-domain interfaces. Proteins 61, 1075-1088. 

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