Domain specificity

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Topic: Domain specificity

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In the News (Fri 25 Dec 09)

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Hugh Jackman

	Marligen Bioscience, Inc. Protein Phosphorylation Products
		SH2 domains have a conserved pocket that recognizes the phosphotyrosine residue and a second variable pocket that binds 3–6 amino acids C-terminal to the phosphotyrosine that confers specificity.
		SH2 domains bind to phosphopeptides with dissociation constants of ~50–500 nM.
		Src-homology 2 (SH2) domains are protein molecules of ~100 amino acids that are found in a large number of proteins involved in signal transduction that bind to specific phospho (pY)-containing peptide motifs.
	www.marligen.com /products/proteinphos.htm (763 words)

	The Carboxyl Terminus of v-Abl Protein Can Augment SH2 Domain Function -- Warren et al. 74 (10): 4495 -- The Journal of Virology
		SH2 domains contribute significantly to the specificity with which tyrosine kinases activate downstream effectors (31, 66),
		SH2 domain specificity and activity modified by a single residue.
		En bloc substitution of the Src homology region 2 domain activates the transforming potential of the c-Abl protein tyrosine kinase.
	jvi.asm.org /cgi/content/full/74/10/4495 (5684 words)

	The role of helix stabilizing residues in GCN4 basic region folding and DNA binding -- Hollenbeck et al. 11 (11): 2740 -- Protein Science
		the Asp-Pro dipeptide at the N-terminus of the bZip domain stabilizes
		GCN4 bZip domain in the absence of DNA.
		Landschulz, W.H., Johnson, P.F., and McKnight, S.L. The DNA binding domain of the rat liver nuclear protein C/EBP is bipartite.
	www.proteinscience.org /cgi/content/full/11/11/2740 (5684 words)

	Chromo Domain
		The chromo domain was originally identified as a protein sequence motif common to the Drosophila chromatin proteins, Polycomb (Pc) and Heterochromatin protein 1 (HP1).
		Due to its relatedness to the chromo domain, and its occurrence in proteins that also have a classical chromo domai n, we call the variant the "chromo shadow domain".
		Chromo domain-containing proteins can therefore be divided into two classes depending on the presence, for example in HP1, or absence, for example in Pc, of the chromo shadow domain.
	www.uib.no /aasland/chromo.html (391 words)

	Bill de hÓra: MetaGraph: Domain knowledge v RDF
		What's very interesting to me at the moment about this is the way they seem to have managed the dissonance between a general labelled graph model and the domain specificity of biology.
		The domain is events: namely arbitrary system and application events from multiple sources supporting a Service Oriented system.
		We, that is, Web, WS, SOA, REST types, spend a lot of time looking at what the likes of Google, Ebay and Amazon are doing to help us peer into the future; innovation in bioinformatics may also be useful in thinking about architectures to meet future demands.
	www.dehora.net /journal/2004/08/metagraph_domain_knowledge_v_rdf.html (391 words)

	Plant Gene Register PGR95-078
		The presence of the two potential leucine zipper domain in 9L implies that it may form heterodimer with other protein factors, such as bZIP and HLH classes of transcriptional factors, and regulate gene expression.
		Acidic domains are present in many transcriptional factors and have activation activities (Ptshne and Gann, 1990).
		The basic domain directly contacts DNA, while the leucine zipper domain is responsible for dimerization.
	www.tarweed.com /pgr/PGR95-078.html (391 words)

	Sudhir Paul, Ph.D.
		Sun, M., Gao, Q.-S., Kirnarskiy, L., Rees, A., and Paul, S. Cleavage specificity of a proteolytic antibody light chain and effects of the heavy chain variable domain.
		Le, A., Dasgupta, S., Planque, S., Paul, S. and Thiagarajan, P. Lupus-derived antiprothrombin autoantibodies from a V gene phage display library are specific for the kringle 2 domain of prothrombin.
		In: Pro-inflammatory and anti-inflammatory peptides, Lung Biology in Health and Disease Series, Sami Said, Ed.
	www.dpalm.med.uth.tmc.edu /faculty/bios/paul/paul.html (391 words)

	Autocrine growth and anchorage independence: two complementing Jun-controlled genetic programs of cellular transformation -- van Dam et al. 12 (8): 1227 -- Genes and Development
		The bZip domains of wild-type or mutant c-Jun were fused to the
		The interaction of mutant c-Jun leucine zipper domains with c-Fos and ATF2-VP16 as measured by mammalian one-hybrid analysis.
		DNA-binding domain (DBD) of the yeast transcription factor Gal4,
	www.genesdev.org /cgi/content/full/12/8/1227 (391 words)

	SH3 domain - Wikipedia, the free encyclopedia
		SH3 domains are often found in functions concerning the cytoskeleton, the ras protein, and the src kinase.
		An SH3 domain is a protein module, a characteristic peptide sequence.
		SH3 domains bind to proline -rich sequences (or polyproline helices).
	en.wikipedia.org /wiki/SH3_domain (391 words)

	2004 Workshop on Generic Object Recognition and Categorization
		Since that time there has been an incredible number of behavioral and, more recently, neuroimaging, studies focusing on questions such as invariance and domain specificity.
		The intensive study of the mechanisms of human object recognition arguably began 20 years ago, sparked, in part, by the publication of David Marr's landmark book, Vision.
		There has been one popular theory, two raucous 'debates,' and at least three generations of new researchers entering the field.
	www.vision.ethz.ch /cvpr04-gorc/abstract-tarr.html (312 words)

	Innateness and Moral Psychology
		Domain specificity has been the focus of much recent discussion of nativism, and while there are different notions of domain specificity, our interests will be in the notion of domain specificity that plays the central role in POS arguments.
		As Cowie puts it in her discussion of POS arguments, nativists invoke domain-specific mechanisms to explain the “gap between the information provided by experience about some domain… and the ideas or beliefs we acquire concerning that domain” (Cowie 1999, 37; see also Laurence and Margolis 2001).
		Nativism does seem a natural answer, and it is at home both with the Chomskian approach and with various evolutionary accounts of morality (e.g., Ruse 1993).
	www.philosophy.utah.edu /faculty/nichols/Papers/innatenessandmoral.htm (8531 words)

	REPRESSION OF SHOOT GROWTH, a bZIP Transcriptional Activator, Regulates Cell Elongation by Controlling the Level of Gibberellins -- Fukazawa et al. 12 (6): 901 -- THE PLANT CELL
		Yeast cells HF7c were simultaneously transformed with a plasmid expressing a GAL4 DNA binding domain fused to the bZIP domain of RSG and with plasmids expressing the GAL4 activation domain fused to the bZIP domains of the indicated RSG, VLP (a RSG-related protein), TGA1a, TAF1, GBF1, HY5, or a control vector.
		The open triangles and circles indicate the amino acid residues at position -10 relative to the first leucine residue in the leucine zipper region, which are important for DNA binding specificity.
		The plasmids pLysGAL1bZIPRSG (encoding the bZIP domain of RSG), pLysGAL1bZIPTGA1a (encoding the bZIP domain of TGA1a), or pLysGAL1 (for a control vector) were transformed with pLeuGADHRSG, which expressed the full-length RSG under the control of an ADH promoter, and selected on a medium without lysine or leucine.
	www.plantcell.org /cgi/content/full/12/6/901 (8531 words)

	[FYN_HUMAN] Basic UniProtKB Entry Viewer - UniProt [the Universal Protein Resource]
		Mulhern T.D. Shaw G.L. Morton C.J. Day A.J. Campbell I.D. "The SH2 domain from the tyrosine kinase Fyn in complex with a phosphotyrosyl peptide reveals insights into domain stability and binding specificity.";
		Noble M.E.M. Musacchio A. Saraste M. Courtneidge S.A. Wierenga R.K. "Crystal structure of the SH3 domain in human Fyn; comparison of the three-dimensional structures of SH3 domains in tyrosine kinases and spectrin.";
		Renzoni D.A. Pugh D.J. Siligardi G. Das P. Morton C.J. Rossi C. Waterfield M.D. Campbell I.D. Ladbury J.E. "Structural and thermodynamic characterization of the interaction of the SH3 domain from Fyn with the proline-rich binding site on the p85 subunit of PI3-kinase.";
	www.ebi.uniprot.org /entry/P06241 (437 words)

	Center for Cancer Research - Staff Pages
		We are currently in the process of evaluating the specificity of trans-splicing using 5' RACE (rapid amplification of cDNA ends) and are also redesigning PTM binding domains as well as other aspects of PTM structure to optimize efficiency and specificity.
		The binding domain controls both target specificity as well as splice site specificity for a target with multiple exons.
		The expression of spliced human papillomavirus E6/E7 pre-mRNAs by the vast majority of cervical cancers provides an absolute difference between cancer cells and normal cells that can be exploited for the specific targeting of these cells.
	ccr.cancer.gov /staff/staff.asp?staffid=359 (437 words)

	Max
		Substituting the ornithine binding domain of OTCase for the aspartate binding domain of ATCase changes the substrate specificity of the reaction so that citrulline is the amine product obtained (rather than carbamoyl aspartate).
		Saccharomyces cerevisiae URA2 gene with the ornithine binding domain of porcine OTCase replacing the aspartate binding domain of ATCase.
		Native OTCase is always monofunctional, but ATCase can be found as part of bi- and trifunctional polypeptide chains that include carbamoyl phosphate synthetase (CPSase) as the first enzymatic activity.
	mark.asci.ncsu.edu /SwineReports/2001/02manjeanne.htm (1653 words)

	Pfam 17.0 : HHH
		The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity MEDLINE:8692686.
		Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix MEDLINE:7664751.
		The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA [2].
	pfam.wustl.edu /cgi-bin/getdesc?name=HHH (1653 words)

	Beyond calcium: new signaling pathways for Tec family kinases -- Takesono et al. 115 (15): 3039 -- Journal of Cell Science
		Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase.
		August, A., Sadra, A., Dupont, B. and Hanafusa, H. Src-induced activation of inducible T cell kinase (ITK) requires phosphatidylinositol 3-kinase activity and the Pleckstrin homology domain of inducible T cell kinase.
		Pursglove, S. E., Mulhern, T. D., Mackay, J. P., Hinds, M. and Booker, G. The solution structure and intramolecular associations of the Tec kinase SRC homology 3 domain.
	jcs.biologists.org /cgi/content/full/115/15/3039 (1653 words)

	Pfam 17.0 : B3
		The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding.
		This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in [1] this domain is found in VP1/AB13 transcription factors [2].
		The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see INTERPRO:IPR001471) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors MEDLINE:9862967.
	pfam.wustl.edu /cgi-bin/getdesc?name=B3 (1653 words)

	Estren Is a Selective Estrogen Receptor Modulator with Transcriptional Activity -- Movérare et al. 64 (6): 1428 -- Molecular Pharmacology
		Metivier R, Petit FG, Valotaire Y, and Pakdel F (2000) Function of N-terminal transactivation domain of the estrogen receptor requires a potential alpha-helical structure and is negatively regulated by the A domain.
		-estradiol and are expressed as a percentage (equal to the percentage of estrogenic activity of estren) and as the relative tissue specificity for the estrogenic activity of estren when the effect on uterus is given as 1 (equal to the relative tissue specificity of estren).
		Estrogens and androgens are of importance for the regulation
	molpharm.aspetjournals.org /cgi/content/full/64/6/1428 (3364 words)

	Tag tertiary-structure
		Here, we report a crystal structure of the 161-nucleotide specificity domain of an A-type ribonuclease P that differs in secondary and tertiary structure from the specificity domain of a B-type molecule.
		Structure of a purine-purine wobble base pair in the decoding center of the ribosome.
		The growing database of RNA structures, coupled with efforts directed at the standardization of nomenclature and classification of motifs, has resulted in the identification and characterization of numerous RNA secondary and tertiary structure motifs.
	130.79.46.225 /tag?tag=tertiary-structure (3364 words)

	HomePage
		West, R. F., and Stanovich, K. The Domain Specificity and Generality of Overconfidence: Individual Differences in Performance Estimation Bias.
		Sá, W. C., West, R. F., and Stanovich, K. The domain specificity and generality of belief bias:Searching for a generalizable critical thinking skill.
		Kokis, J, Macpherson, R., Toplak, M., West, R. F., and Stanovich, K. Heuristic and analytic processing: Age trends and associations with cognitive ability and cognitive styles.
	falcon.jmu.edu /~westrf/shortvita.html (3364 words)

	MEDICAL EXCHANGE INC. Securities Registration: Small Business (SB-2) DESCRIPTION OF PROPERTY
		The single-base specificity of basis-leucine zipper permits the detection of single nucleotide polymorphisms, which are single base pair differences in the DNA of different individuals, and the study of their relationship to disease and drug response, also known as pharmacogenomics.
		The basis-leucine zipper DNA recognition domain is coupled to a functional domain, which causes the basis-leucine zipper transcription factor to control or regulate the gene in a desired manner.
		The single-base specificity of basis-leucine zipper permits the detection of single nucleotide polymorphisms, which we believe are likely to become increasingly important in clinical diagnosis to determine an individual's susceptibility to disease or probable response to drug therapy;
	sec.edgar-online.com /2004/12/02/0001301367-04-000004/section26.asp (2889 words)

	walke90s244.txt
		Measures such as the SDQ (Marsh, 1988) are based on scales representing a compromise between domain specific behaviors and generality, reflecting a level of specificity near the middle of the Shavelson et al (1976) hierarchy.
		Whereas self-efficacy and self-concept researchers agree in recognizing the inadequacy of such global measures and focus on more domain-specific measures, there remains a clear difference in the level of specificity typically assessed in each approach.
		Marsh, Byrne and Shavelson, for example, found that the academic scales from three different instruments had a substantial and logical pattern of relations with academic achievement indicators whereas three general measures of self-concept were unrelated to the achievement indicators.
	www.aare.edu.au /90pap/walke90s244.txt (2889 words)

	Journal of Semantics
		Roger Schwarzschild investigates the possibility that the apparent unique scope-taking abilities of indefinites can be explained in terms of quantifier domain restriction, without departing from the classical view of indefinites as existential quantifiers over individuals whose scope is syntactically constrained in the same way as other quantifiers.
		One paper (Schwarzschild) was invited since it fits very well into this special issue on specificity.
		The key idea is that when the domain of a quantifier is reduced to a singleton set, it becomes effectively scopeless.
	pinguin.philosophie.uni-stuttgart.de /vonHeusinger/publications/editions/jos19.3.html (2889 words)

	French American Colloquia
		On Enc's (1991) account, specificity is defined in terms independent of scope relations as linking NP denotations to previous discourse: an NP is specific iff its referent is a subset of a referent which is already in the domain of discourse, or stands in some recoverable relation to a ``familiar'' object (Heim 1982).
		I suggest that tense is the relevant feature underlying the interpretive effects that are subsumed under the notion of `specificity'.
		She argues that the `free' temporal interpretations of nominals is best captured by an indexical analysis, and provides a characterization of *specificity* in terms of `D(iscourse)-linking'.
	web.mit.edu /linguistics/www/conferences/salt8/lecarme.html (1469 words)

	Content Validity, Face Validity, and Quantitative Face Validity
		The first consideration in deciding to use content validity evidence to support a job-relatedness claim is to apply the "same as" criterion: the test content must be the same as the job domain or, for a knowledge test, the knowledge domain.
		The theme that unifies all of the content validity documentation requirements is that the user is expected to provide the detail and specificity needed to clearly relate the content of the test to the content of the job so that the "inferential leap" is very small.
		The most important implication of the centrality of the sampling process is the truism that whatever is sampled is a member of the domain from which the sample is drawn.
	www.burns.com /wcbcontval.htm (2955 words)

	Multiple Transmembrane Amino Acid Requirements Suggest a Highly Specific Interaction between the Bovine Papillomavirus E5 Oncoprotein and the Platelet-Derived Growth Factor Beta Receptor -- Nappi and Petti 76 (16): 7976 -- The Journal of Virology
		Fully shaded sequences were derived from the EGF receptor transmembrane domain, differentially shaded sequences were derived from the Neu receptor transmembrane domain, and unshaded sequences were derived from the wild-type PDGFßR transmembrane domain.
		Sequence specificity in the dimerization of transmembrane alpha-helices.
		The bovine papillomavirus-1 E5 protein, the 16 kDa membrane pore-forming protein and the PDGF receptor exist in a complex that is dependent on hydrophobic transmembrane interactions.
	jvi.asm.org /cgi/content/full/76/16/7976 (6591 words)

	Resume of Hui Zong
		Zong, H. and Quilliam, L.A. (1997) Determination of the effector-binding domain of the GTPase RhoA.
		Zong, H., and Quilliam, L.A. (1999) Loop 6 of RhoA confers specificity for effector binding, stress fiber formation and cellular transformation.
		Zong, H., Raman N., Mickelson-Young, L.A., Atkinson, S.A., and Quilliam, L.A. (1999) Loop 6 of RhoA confers specificity for effector binding, stress fiber formation and cellular transformation.
	www.stanford.edu /~hzong/career/resume.html (6591 words)

	research theme 1 - project 6
		Current work in the field of cognitive development has seen an increasing number of researchers embracing the notion of domain-specificity as the key to understanding the organisation and acquisition of children's knowledge.
		It is accepted that young children have one domain concerned with naïve physics which encompasses knowledge of mechanics and physical matter.
		Naïve theories; domain specific cognition; naïve biology; naïve physics; theory of mind.
	www.education.ed.ac.uk /research/projects/theme1/proj6.html (244 words)

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In the News (Fri 25 Dec 09)