Domain structures, in proteins

As a simple approach the denaturation process can be referred to as a sum of independent two-state transitions [184, 187-189] though this hypothesis can seem unrealistic in view of the complexity of the denaturation process of food macromolecules, the well-established existence of more or less independent domains in protein structures significantly support such an assumption. When this is so, the overall excess heat capacity function is given by ... 

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. 

Jurnak, E, et al. Parallel p domains a new fold in protein structures. Curr. Opin. Struct. Biol. 4 802-806, 1994. 

III PEG MPD Steric exclusion Repulsion from charges To hydrophobic regions Good precipitants stabilizers of native structure at low temp., unfolded structure at high temp. stabilizers and solubilizers of hydrophobic domains in proteins... 

The first major grouping of structures contains domains that are essentially all a-helical. Since there is relatively little other structure besides the helices, the simplest ways of connecting them involve predominantly antiparallel helix interactions, and that is in fact what is observed for these proteins. This category corresponds to Levitt and Chothia s all-a category, but it has more members both because of a number of new structures and because of helical domains in proteins they classified as a + /3 (such as thermolysin). 

The term homology domain or functional domain should be used only for those protein regions that either are known to be domains in the structural sense or that are at least predicted to fulfil that condition. Conserved sequence regions that are too short to fold independently of the rest of the protein should rather be referred to as motifs . A considerable number of those functional motifs have important roles, e.g. by being responsible for specific domain- or protein-recognition events. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

What is meant by a domain of protein structure Give an example of a domain in a real protein. 

Association between elements of the secondary structure form structural domains with properties determined both by the chiral properties of the polypeptide chain and by the packing requirements which effectively minimize the molecule s hydrophobic surface area. Association of domains in proteins results in the formation of the protein s tertiary structure. Furthermore, protein subunits can pack together to form quaternary structure, which can either serve a structural role or provide a structural basis for modification of the protein s functional properties [132]. 

Liebman, M. Quantitative analysis of structural domains in proteins. Biophys. J. 32, 213-215 (1980). 

Janin, J. and Wodak, S. Y. (1983) Structural Domains in Proteins and Their Role in the Dynamics of Protein Function, Prog. Biophys. Mol. Biol. 42, 21-78. 

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