Protein domain assignment

Marsden, R. L., L. J. McGuffin, and D. T. Jones. 2002. Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Sci 11 2814-24. 

Table 3 Websites for Publicly Available Services or Programs for Protein Domain Assignment ...

To further the assignment of function based on structural relationships, a large-scale structural pro-teomics project has been initiated. The goal is to crystallize and determine the structure of as many proteins and protein domains as possible, in many cases with little or no existing information about protein function. The project has been assisted by the automation of some of the tedious steps of protein crystallization (see Box 4-4). As these structures are revealed, they will be made available in the structural databases described in Chapter 4. The effort should help define the extent of variation in structural motifs. When a newly discovered protein is found to have structural folds that are clearly related to motifs with known functions in the databases, this information can suggest a molecular function for the protein. 

All such cases with novel domain family assignments are characterized by poor sequence identity and therefore may not be interpreted as bona fide members of the protein domain families concerned. They may be interpreted as remotely related to the family concerned, and hence functional similarity between such H. pylori protein sequences with members of the family concerned may or may not exist. 

In some proteins, only a part of the H. pylori protein is assigned a functional domain by Pfam and the rest of the protein is not assigned any function. Remote homology detection methods employed in the current analysis have established relationships between these unassigned regions and Pfam domain families. 

Protein class assignments were based on SCOP database (Murzin et al., 1995), dividing the set of proteins in 31 all-aipha, 31 all-beta, 51 alpha/beta, 21 alpha+beta and 14 irregular or multi-domain. The relative secondary structure composition for each class is given below ... 

Domain assignment domains are basic building blocks of protein 3D structures. Several algorithms have been proposed to identify domains in a protein structure using criteria such as physico-chemical properties of amino acids in certain regions, e.g. hydrophobicity and accessibility, compactness of protein parts and their recurrence in other proteins [116-120]. 

Jones, S., et al., Domain assignment for protein structures using a consensus approach characterization and analysis. Protein Sci, 1998. 7(2) p. 233-42. 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

Fig. 10.10 ESI-FTICR mass spectrum of tryptic digest mixture of multi- phosphorylated human neurofibrillary tau protein. Peak assignments within the m/z detection range, 200—2500, are shown for phosphorylated peptides. The insert shows the peptide fragment of the phosphorylation domain (512-538) the seven phos-...

Domain assignment (i.e. protein structure similarity clustering)... 

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... 

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