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Topic: Structural domain

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	[No title]
		The main idea of the method is to detect structural domains as regions of the protein structure where most of the interactions between atoms or residues occur within the regions and least without.
		For the extraction of domain definitions it is necessary that this stage in the evaluation is detected and the iteration terminated, allowing the assignment of residues with common label as a domain.
		Domain boundaries may be marked by a shift in general character, the beginning and end of periodic region or internal duplication, or cluster basic residues.
	www.cs.rutgers.edu /pub/seredin/DomainRewievEng.doc (2365 words)

	Untitled Document
		That is, nothing occurs in the molecular domain through an external cause, and all that happens occurs as determined by the structural coherences inherent in the circumstances in which it occurs.
		The structural changes triggered in the interactions of a structure determined system arise moment after moment determined by its structure also, but they follow a course that is generated moment after moment by the succession of encounters with the medium in which the system participates.
		That is, we human beings exist in structural coupling with all the other living and not living entities that compose the biosphere, and we operate in language as our manner of being in the present in the flow of our interactions in structural coupling as integral components of the biosphere.
	www.isss.org /maturana.htm (8548 words)

	Articles - Structural domain (Site not responding. Last check: 2007-11-04)
		Within a protein, a structural domain ("domain") is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain.
		Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the "calcium-binding domain of calmodulin.
		Given the fact that phosphoinositides are sequestered to the cell membrane due to their long lipophilic tail, the PH domain usually causes localization of the protein in question to the cell membrane, which is useful for expediting activation of the protein and continuation of a signaling pathway.
	www.greensky.biz /articles/Structural_domain (455 words)

	Berkeley Structural Genomics Center: Job Opportunities
		Structural genomics is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins.
		In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: A significant fraction (about 30-40% of the proteins and 40-60% of the residues) of each proteome is classified in small families, which may have little overlap with other species of interest.
		The high-resolution structure of a receptor cytoplasmic domain has recently been determined by crystallographic methods and is largely consistent with a structural model independently generated by chemical studies of the domain in the full-length, membrane-bound receptor.
	www.strgen.org /pubs/abstracts.html (11844 words)

	Review hypertext
		Each domain was shown to retain characteristic catalytic and spectral properties, whereas the rate of electron transfer between the isolated domains is considerably slower than for the native enzyme.
		as N-terminus and the FAD domain of spinach assimilatory NADH:nitrate reductase as C-terminus.
		Correll, C.C., Ludwig, M.L., Bruns, C.M. and Karplus, P.A. Structural prototypes for an extended family of flavoprotein reductases: comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin.
	www.icgeb.trieste.it /~p450srv/PE_8_8_1995_text.html (8400 words)

	Protein Science 5(2):296-309. Structural coupling of Ets-1 auto-inhibitory regions
		A: Schematic representation of the secondary structure of Ets-1DeltaN280.
		The HTH and beta-sheet structures of the ETS domain are represented as a globular DNA-binding domain.
		In this study, we have determined the secondary structure of Ets-1DeltaN280, a low-affinity deletion mutant of Ets-1 and demonstrated that the helices in the amino- and carboxy-terminal inhibitory regions are coupled to one another and to the intervening ETS domain.
	otter.biochem.ubc.ca /publications/Ets16_Prot_Sci_5_296 (8949 words)

	Structural Characterization of the Human Proteome -- Müller et al. 12 (11): 1625 -- Genome Research
		Structural annotation is a homology to a known structure.
		The expansion of a superfamily relative to the human proteome is plotted as the number of domains in superfamily X in proteome Y divided by the number of domains in superfamily X in human (times 100), so that all superfamilies are 100% in human.
		The number of domains in a superfamily that are found in proteins that have at least one transmembrane helix are shown for the different proteomes.
	www.genome.org /cgi/content/full/12/11/1625 (9137 words)

	What are the central issues in the definition of structural domains (Site not responding. Last check: 2007-11-04)
		Agreeing on a “unified” definition of a structural domain is critical for the improvement of automatic methods of domain assignment.
		In summary, further improvement of automatic domain assignments will require new working definitions of structural domains based on existing data, which encompasses evolutionary, structural and functional approaches.
		In the absence of such comprehensive and robust domain definitions, the community of structural biologists should at least be aware of the discord and understand the conceptual underpinnings of structural domains as determined by each assignment method.
	pdomains.sdsc.edu /unresloved_issues.htm (721 words)

	Annotation Transfer for Genomics: Measuring Functional Divergence in Multi-Domain Proteins -- Hegyi and Gerstein 11 ...
		Figure 3 Distribution of proteins amongst broad structural and functional classes; the distribution of the matches among the seven structural and two functional classes in single- and multi-domain proteins.
		Chothia, C. and Lesk, A. The relation between the divergence of sequence and structure in proteins.
		Gerstein, M. A structural census of genomes: comparing bacterial, eukaryotic, and archaeal genomes in terms of protein structure.
	www.genome.org /cgi/content/full/11/10/1632 (4074 words)

	Protein domain database: DOMO (Site not responding. Last check: 2007-11-04)
		A major issue related to protein classification is the decomposition of biomolecules into their constituent structural domains typically defined as independent and globular folding units within a three-dimensional protein structure (1).
		The domain boundaries and alignments have been inferred by a fully automated analysis process involving the detection and subsequent clustering of amino acid sequence similarities, followed by delineation of the domain boundaries, and then multiple sequence alignment of the related protein segments(9,10).
		The domain boundaries were not inferred from three-dimensional data but exclusively from the relative positions of homologous segment pairs within the same protein (repeats) or within homologous proteins at different distances from their respective N- or C-termini.
	www.infobiogen.fr /services/domo (1722 words)

	3Dee - Database of Protein Domain Definitions (Site not responding. Last check: 2007-11-04)
		3Dee contains structural domain definitions for all protein chains in the Protein Databank (PDB), currated by the EBI and the RCSB, that have 20 or more residues and are not theoretical models.
		These domains have been clustered by both sequence and structural similarity.
		In order to be able to view the structural superpositions you must install some software on your Unix workstation.
	www.compbio.dundee.ac.uk /3Dee (235 words)

	Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif -- Terasawa et al. ... (Site not responding. Last check: 2007-11-04)
		Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif -- Terasawa et al.
		Secondary structural elememts of Cdc24p PCCR are shown above the sequences together with the locations and the notations of the loops.
		Nassar,N., Horn,G., Herrmann,C., Scherer,A., McCormick,F. and Wittinghofer,A. (1995) The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue.
	embojournal.npgjournals.com /cgi/content/full/20/15/3947 (5764 words)

	X ray crystallization of recombinant membrane proximal structural domain of human GABAA receptor α1 subunit ... (Site not responding. Last check: 2007-11-04)
		X ray crystallization of recombinant membrane proximal structural domain of human GABAA receptor α1 subunit overexpressed in Escherichia coli Hong Xue1,2,ManKit Tse1, DaoWei Zhu3, Hui Zheng1 and ShengXiang Lin3 1Department of Biochemistry, and 2Cooperative Research Center for Soluble Receptor Biology, Hong Kong University of Science and Technology, Clear Water Bay,Hong Kong, China.
		Previously, we identified two adjacent -rich independent structural domains in human GABAA receptor 1 subunit, Q28-E165 and C166-L296, by means of bioinformatics tools and successfully overexpressed in Escherichia coli..
		Our result support the existence of a stable structural domain in the C166-L296 fragment and provides a chance to obtain X ray diffraction data for three dimensional structural investigations on the LGICS superfamily.
	www.iscb.org /ismb2004/posters/hxueATust.hk_960.html (297 words)

	Structural Protein Domain Classifications (Site not responding. Last check: 2007-11-04)
		Classification of DNA-binding domains with ( Table 1) and without ( Table 2) structural neighbors.
		Protein Domain Parser (PDP) and the Combinatorial Extension (CE) algorithm for structural alignment.
		The approach involves the analysis of 3D-interaction patterns in DNA-protein interfaces, assignment of structural domains interacting with DNA, clustering of domains based on structural similarity and DNA-interacting patterns.
	spdc.sdsc.edu /DNA_prot_page.html (131 words)

	DOMPLOT (Site not responding. Last check: 2007-11-04)
		These diagrams are based on three-dimensional structural information and incorporate annotations derived from the co-ordinates.
		The diagrams illustrate the pattern of interactions between the domain and any metal ions, ligands and/or nucleic acids which it binds, allowing a fast analysis of the location of specific intermolecular interactions with respect to the domain sequence.
		Homologous domains are found to share a similar pattern of ligand contacts, and so DOMPLOT is a useful tool to aid identification of protein homologues.
	www.biochem.ucl.ac.uk /bsm/domplot (215 words)

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