Proteins domain structures determination

Petoukhov, M. V., and Svergun, D. I. (2003). New methods for domain structure determination of proteins from solution scattering data.J. Appl. Crystallogr. 36, 540-544. 

CATH includes four classes (C) alpha, beta, alpha and beta, and few secondary structure (ESS). The alpha-beta class includes both alternating alpha/beta structures and alpha -I- beta structures, originally defined by Levitt and Chothia. The class of a protein domain is determined according to its secondary structure composition and packing. Ninety percent of the protein domains were automatically assigned to their class in CATH 2.5.1, using the method developed by Michie et The remaining 10% of domains... 

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Figure 9.19 shows the sequence of the DNA that was used for the structure determination of the p53-DNA complex the bases involved in sequence-specific binding to the protein are shaded. One molecule of the DNA-bind-ing domain of p53 binds to the minor and the major grooves of the DNA making sequence-specific interactions with both strands (Figure 9.20). 

The immunoglobulin structure in Figure 6.45 represents the confluence of all the details of protein structure that have been thus far discussed. As for all proteins, the primary structure determines other aspects of structure. There are numerous elements of secondary structure, including /3-sheets and tight turns. The tertiary structure consists of 12 distinct domains, and the protein adopts a heterotetrameric quaternary structure. To make matters more interesting, both intrasubunit and intersubunit disulfide linkages act to stabilize the discrete domains and to stabilize the tetramer itself. 

In order to make as much data on the structure and its determination available in the databases, approaches for automated data harvesting are being developed. Structure classification schemes, as implemented for example in the SCOP, CATH, andFSSP databases, elucidate the relationship between protein folds and function and shed light on the evolution of protein domains. 

Due to the ready accessibility of SH2 domains by molecular biology techniques, numerous experimentally determined 3D structures of SH2 domains derived by X-ray crystallography as well as heteronuclear multidimensional NMR spectroscopy are known today. The current version of the protein structure database, accessible to the scientific community by, e.g., the Internet (http //www.rcsb.org/pdb/) contains around 80 entries of SH2 domain structures and complexes thereof. Today, the SH2 domain structures of Hck [62], Src [63-66], Abl [67], Grb2 [68-71], Syp [72], PLCy [73], Fyn [74], SAP [75], Lck [76,77], the C- and N-terminal SH2 domain ofp85a [78-80], and of the tandem SH2 domains Syk [81,82], ZAP70 [83,84], and SHP-2 [85] are determined. All SH2 domains display a conserved 3D structure as can be expected from multiple sequence alignments (Fig. 4). The common structural fold consists of a central three-stranded antiparallel ft sheet that is occasionally extended by one to three additional short strands (Fig. 5). This central ft sheet forms the spine of the domain which is flanked on both sides by regular a helices [49, 50,60]. 

The dependence of the residual dipolar coupling on the angle that the vector forms with a reference axis explains why the use of dipolar couplings makes possible the determination of the relative orientation of different domains in a multidomain protein and facilitates nucleic acid structure determination. Dipolar couplings can constitute up to 50% of the total structural data available for nucleic acids, while this number drops to 10-15% in proteins. Thus, the impact of the use of dipolar couplings on the structure determination of nucleic acids is generally more substantial than in the case of proteins. Furthermore, the presence or absence of tertiary structure in a protein or nucleic acid does not have a major influence on the number of dipolar couplings that can be measured, in contrast to the case of the NOE. 

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