Structure and domains

Src Homology-2 Domains and Structure-Based, Small-Molecule Library Approaches to Drug Discovery... 

As a result from computational model 1 a hybrid grid for a laboratory size OK flotation cell with unstructured cells in the rotor domain and structured cells in the stator and tank domain was generated. The tank was a cylindrical, unbaffled tank with Outokumpu s rotor-stator mixing device. Computational geometry is shown in figure 8. Geometrical details of the tank are given in table 2. 

The SMD simulations were based on an NMR structure of the Ig domain 127 of the cardiac titin I-band (Improta et ah, 1996). The Ig domains consist of two /9-sheets packed against each other, with each sheet containing four strands, as shown in Fig. 8b. After 127 was solvated and equilibrated, SMD simulations were carried out by fixing one terminus of the domain and applying a force to the other in the direction from the fixed terminus to the other terminus. Simulations were performed as described by Eq. (1) with V = 0.5 A/ps and if = 10 ksT/A 414 pN/A. The force-extension profile from the SMD trajectory showed a single force peak as presented in Fig. 8a. This feature agrees well with the sawtooth-shaped force profile exhibited in AFM experiments. 

This is the domain of structure elucidation, which, for most part, utilizes information from a battery of spectra (infrared, NMR, and mass spectra). 

Polymers are difficult to model due to the large size of microcrystalline domains and the difficulties of simulating nonequilibrium systems. One approach to handling such systems is the use of mesoscale techniques as described in Chapter 35. This has been a successful approach to predicting the formation and structure of microscopic crystalline and amorphous regions. 

On the basis of simple considerations of connected motifs, Michael Leviff and Cyrus Chothia of the MRC Laboratory of Molecular Biology derived a taxonomy of protein structures and have classified domain structures into three main groups a domains, p domains, and a/p domains. In ct structures the core is built up exclusively from a helices (see Figure 2.9) in p structures the core comprises antiparallel p sheets and are usually two P sheets packed... 

Janin, J., Chothia, C. Domains in proteins definitions, location and structural principles. Methods Enzymol. 115 420-430, 1985. 

Tom Blundell has answered these questions by superposing the Ca atoms of the two motifs within a domain with each other and by superposing the Ca atoms of the two domains with each other. As a rule of thumb, when two structures superpose with a mean deviation of less than 2 A they are considered structurally equivalent. For each pair of motifs Blundell found that 40 Ca atoms superpose with a mean distance of 1.4 A. These 40 Ca atoms within each motif are therefore structurally equivalent. Since each motif comprises only 43 or 44 amino acid residues in total, these comparisons show that the structures of the complete motifs are very similar. Not only are the individual motifs similar in stmcture, but they are also pairwise arranged into the two domains in a similar way since superposition of the two domains showed that about 80 Ca atoms of each domain were structurally equivalent. 

Figure 6.6 Schematic diagram of the structure of the enzyme lysozyme which folds into two domains. One domain is essentially a-helical whereas the second domain comprises a three stranded antiparallel p sheet and two a helices. There are three disulfide bonds (green), two in the a-helical domain and one in the second domain.

By comparing the crystal structures of these complexes with a further complex of the 434 repressor DNA-binding domain and a synthetic DNA containing the operator region OR3, Harrison has been able to resolve at least in part the structural basis for the differential binding affinity of 434 Cro and repressor to the different 434 operator regions. 

Figure 13.16 Schematic diagram of the phosducin molecule. Helices are blue, p strands are red and loop regions are orange. The structure folds into two separate domains, a N-terminal helical domain and a C-terminal domain that has the thioredoxin fold. Some of the loop regions in the helical domain are not well defined. (Adapted from R. Gaudet et al.. Cell 87 577-588, 1996.)...

Figure 13.30 Ribbon diagram of the structure of Src tyrosine kinase. The structure is divided in three units starting from the N-terminus an SH3 domain (green), an SH2 domain (blue), and a tyrosine kinase (orange) that is divided into two domains and has the same fold as the cyclin dependent kinase described in Chapter 6 (see Figure 6.16a). The linker region (red) between SH2 and the kinase is bound to SH3 in a polyproline helical conformation. A tyrosine residue in the carboxy tail of the kinase is phosphorylated and bound to SH2 in its phosphotyrosine-binding site. A disordered part of the activation segment in the kinase is dashed. (Adapted from W. Xu et al.. Nature 385 595-602, 1997.)...

Src tyrosine kinase contains both an SH2 and an SH3 domain linked to a tyrosine kinase unit with a structure similar to other protein kinases. The phosphorylated form of the kinase is inactivated by binding of a phosphoty-rosine in the C-terminal tail to its own SH2 domain. In addition the linker region between the SH2 domain and the kinase is bound in a polyproline II conformation to the SH3 domain. These interactions lock regions of the active site into a nonproductive conformation. Dephosphorylation or mutation of the C-terminal tyrosine abolishes this autoinactivation. 

Waksman, G., et al. Binding of a high affinity phosphoty-rosyl peptide to the Src SH2 domain crystal structures of the complexed and peptide-free forms. Cell 72 779-790, 1993. 

In this chapter we will discuss immunoglobulins of the IgG class, which is the major type of immunoglobulin in normal human serum, and which has the simplest structure. Each chain of an IgG molecule is divided into domains of about 110 amino acid residues. The light chains have two such domains, and the heavy chains have four. 

T-cell receptors (TCR) are heterodimeric transmembrane glycoproteins found exclusively in T cells, with extracellular domains that closely resemble antibody Fab structures. Each of the TCR a and p chains forms half of an extracellular antigen-binding domain, and in addition has one transmembrane... 

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