Domains SMART

This class of smart materials is the mechanical equivalent of electrostrictive and magnetostrictive materials. Elastorestrictive materials exhibit high hysteresis between strain and stress (14,15). This hysteresis can be caused by motion of ferroelastic domain walls. This behavior is more compHcated and complex near a martensitic phase transformation. At this transformation, both crystal stmctural changes iaduced by mechanical stress and by domain wall motion occur. Martensitic shape memory alloys have broad, diffuse phase transformations and coexisting high and low temperature phases. The domain wall movements disappear with fully transformation to the high temperature austentic (paraelastic) phase. 

Similar residues in the cores of protein structures especially hydrophobic residues at the same positions, are responsible for common folds of homologous proteins. Certain sequence profiles of conserved residue successions have been identified which give rise to a common fold of protein domains. They are organized in the smart database (simple modular architecture research tool) http //smait.embl-heidelberg.de. 

Ponting CP, Schultz J, Milpetz F, Bork P. SMART identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 1999 27[l] 229-232. 

Fig. 1. Schematic representation of the modular architecture of selected pharmaceutically relevant SH2 domain-containing targets involved in signal transduction. For further details refer to http //smart.embl-heidelberg.de [9,10]...

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

To facilitate cross referencing between the names of domain families used in this article and structural, functional, and evolution information available from the literature, the domain names used by the WWW-based resource SMART (http //smart.embl-heidelberg) are shown in bold and in a proportional font. 

Sequence motifs are detected by SMART in a similar manner to domains. In situations where motifs are identified within detected domains, both the motif and the domain are shown. 

Newly Identified Domain Homologs from Recent SMART Database Update... 

A variety of domain or motif families occur only as extensions to other domains. The Bruton s tyrosine kinase motif (BTK), for example, is found only at the C terminus of PH domains. Similarly, a C-terminal extension (the S TK X domain) to some subfamilies of serine/threonine kinases (S TK) is not found in isolation. Cases where only the extension, and not the preceding domain, is found are strong evidence that the proteins are wrongly assembled from genomic sequence or else represent partial cDNA sequences (Fig. 9, see Color insert). Indeed, all five proteins annotated in SMART as containing a S TK X domain with no catalytic domain are noted to be fragments in their corresponding sequence database entries. 

Schultz, J., et al., SMART, a simple modular architecture research tool identification of signaling domains. Proc Natl Acad Sci USA, 1998, 95(11), 5857-64. 

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

This class of smart materials is the mechanical equivalent of electrostrictive and magnetostrictive materials. Elastorestrictive materials exhibit high hysteresis between strain and stress. This hysteresis can be caused by motion of fenoelastic domain walls. Tins behavioi is mote complicated and complex near a martensitic phase transformation. 

A variety of databases and online tools exist to facilitate searches for protein motifs (Table 6). The most comprehensive resource for the detection of large protein motifs is the Conserved Domain Database (CDD) provided by NCBI. The CDD includes all data present in the SMART and PFAM databases, along with some manually curated entries. All protein-protein BLAST... 

Le Botlan, D., Ouguerram, L., Smart, L., Pugh, L. 1999. Characterization of a semisolid state in milk fat through T2 resolved T1 distributions by time domain nuclear magnetic resonance. 1. Am. Oil Chem. Soc. 76, 255-261. 

Ponting, C. P., Bork, P. (2002). Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242-244. 

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