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Topic: Structural motif

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	Structural motif - Wikipedia, the free encyclopedia
		Structural alignment is a major method for discovering significant structural motifs.
		Motifs exhibit both tertiary and secondary structure, and may be regarded as a configuration of secondary structures.
		Protein structural motifs often include loops of variable length and unspecified structure, which in effect create the "slack" necessary to bring together in space two elements that are not encoded by immediately adjacent DNA sequences in a gene.
	en.wikipedia.org /wiki/Structural_motif (492 words)

	Sequence motif - Wikipedia, the free encyclopedia
		In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance.
		When a sequence motif appears in the exon of a gene, it may encode the "structural motif" of a protein; that is a stereotypical element of the overall structure of the protein.
		Short coding motifs, which appear to lack secondary structure, include those that label proteins for delivery to particular parts of a cell, or mark them for phosphorylation.
	en.wikipedia.org /wiki/Sequence_motif (1208 words)

	News & Features: Statistical analysis of structural vs. functional motifs in brain networks
		Motifs occur in distinct motif classes that can be distinguished according to the size (M) of the motif, equal to the number of nodes (vertices), and the number and pattern of interconnections.
		In brain networks, a structural motif may consist of a set of brain areas and pathways that can potentially engage in different patterns of interactions depending on their degree of activation, the surrounding neural context or the behavioral state of the organism.
		Given the motif frequency spectrum, one can easily obtain the motif number, defined as the total number of distinct occurrences of any motif of size M, and the motif diversity, defined as the number of classes that are represented within the network by at least one example.
	www.iscid.org /boards/ubb-get_topic-f-1-t-000188.html (2008 words)

	Nick V. Grishin
		None of the numerous methods proposed for a search for structure similarity achieves the most fundamental task—finding structural motifs that satisfy the general definition of a protein fold: globular units with the same secondary structure, topology, and architecture, irrespective of subtle differences in packing between elements.
		While developing a structural motif search algorithm, we were surprised to find that a method providing broad, yet accurate, secondary structure delineation was lacking as well.
		We were able to perform structural annotations of all experimentally characterized kinase families, making this the first large functional class of proteins with a comprehensive structural annotation.
	www.hhmi.org /research/investigators/grishin.html (1139 words)

	[No title]
		Structural Motifs Analogous to sequence motifs, structural motifs provide a description of conserved properties in the three dimensional structure of proteins sharing molecular function.
		By using previous knowledge of the critical residues involved in the catalytic activity, a structural motif representing the conserved relative positions of those residues is constructed.
		In the evaluation of the structural and sequence motifs for calcium binding, we used the presence of calcium ion in the crystal structure as a gold standard.
	helix-web.stanford.edu /psb03/liang.doc (3230 words)

	Structural and Functional Genomics in the Discovery of Novel Antibiotic Drugs
		Motif analysis is another strategy to identify potential antibiotic targets among genes with unknown functions.
		The use of computational methods and expression profiling all point to the need for a nonredundant, complete database of structural and functional annotation of the proteins from known pathogenic bacterial genomes and the human genome, once it is completed.
		Thus, although the use of comparative, functional, and structural genomics speeds up the process drug development, there are many more obstacles toward generating an effective and approved antibiotic.
	bioinfo.mbb.yale.edu /mbb452a/2000/projects/Marlynn-H-Wei.html (1516 words)

	Protein Structure Hierarchy
		Primary structure is the basic level of the hierarchy and is the particular linear sequence of amino acids that comprises one polypeptide chain.
		Secondary structures are usually held together by hydrogen bonds between the carbonyl oxygen and the the amide hydrogen of the peptide bond.
		A structural motif is the arrangement of atoms in 3-D space to produce a particular structural pattern eg.
	wbiomed.curtin.edu.au /biochem/tutorials/prottute/hierarchy.htm (498 words)

	The Brutlag Bioinformatics Group - Projects (Site not responding. Last check: 2007-10-20)
		FoldMiner Performs structural similarity searches and discovers a structural motif common to the query protein and high scoring target structures.
		Motifs are used to improve both the sensitivity and specificity of the search by focusing on conserved portions of the structure.
		Emotif-search -Compares proteins or ORFs of unknown functions against a database of sequence motifs (50,000) of varying specificities to identify functional and structural motifs in the protein.
	motif.stanford.edu /projects.html (543 words)

	[No title] (Site not responding. Last check: 2007-10-20)
		The structure file is completely read into 5 arrays(head, tail, 5side, basepairing and 3side) and then the structure is parsed from those 5 arrays.
		If there are variable regions in the structure motif, then the main loop becomes nested with one nested “for” loop for each variable region.
		Perl was used for the motif generation for “rapid prototyping”, it could be replaced with a C program but there would still be the need to compile the generated struct.c function and link it with the parts that do not change from one motif search to the next.
	mywebpages.comcast.net /mike_ess/searchstruct.doc (1225 words)

	Cell cycle Cyclin guides the way : Nature
		Structural complementarity between substrates and the active sites of enzymes — first proposed more than a hundred years ago by Emil Fischer in his 'lock-and-key' model — is in theory sufficient to account for the ability of the enzymes to discriminate between potential substrates (Fig.
		Whereas the motif to be modified (one or a few amino acids in a protein, for instance) is recognized by the enzyme's active site, discrimination between different substrates bearing that motif is often accomplished through specific interactions between other sites on the enzyme and substrate.
		Whereas responsibility for recognizing the target motif (a serine or threonine followed by a proline) is delegated to a catalytic subunit (the CDK), both genetic and biochemical studies suggest that exchangeable regulatory subunits (the cyclins) have a role in discriminating between distinct protein substrates (Fig.
	www.nature.com /uidfinder/10.1038/434034a (1304 words)

	Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures
		Especially, the tetra-loops in RNA secondary structures are extremely abundant RNA structural elements [2] and are known to function in longrange RNA tertiary interactions, and may provide thermodynamic stability to an adjacent helix.
		For example, two imaginary RNA sequences, A and B, and drawings of corresponding secondary structures are shown in Figure 1 and the loop sequences separated by stems from 5' to 3' in the primary sequence.
		Some of the common structural information generated by the data mining techniques still have inconsistent positions within the rules and the results need to be verified and pruned to be consistent in their positions.
	www.bioinfo.de /isb/gcb01/poster/huang.html (1328 words)

	ISMB 2006: Fortaleza, Brazil, August 6-10
		A significant step towards establishing the structure and function of a protein is the prediction of the local conformation of the polypeptide chain.
		Developing new, informative alphabets of structural motifs, and efficient methods to predict them from the primary sequence is thus of great interest.
		Here we adopted the centroids of these clusters as structural motifs and mapped each tetra-peptide in the S1736 and S435 datasets into the motif corresponding to the cluster i that minimises the same distance metric adopted in [1].
	ismb2006.cbi.cnptia.embrapa.br /poster_abstract.php?id=H-88 (931 words)

	ProfileScan
		Each motif profile is compared to all the sequences in the database using ProfileSearch.
		If the profile does not adequately discriminate between sequences with the motif and those without, and if changing the gap creation and gap extension penalties does not improve the discrimination, the alignments are examined by eye to determine why the sequences without the motif are giving high scores.
		The alignments may represent repeats of a duplicated structure, or they may represent distinct alignments between the motif profile and the same region of the protein sequence.
	www.scs.uiuc.edu /documentation/gcgmanual/profilescan.html (1855 words)

	Tertiary Structure of Proteins
		That is, it is a compact three dimensional structure resulting from the folding of a particular section of the polypeptide chain.
		Hence, the domain is usually seen to be comprised of elements of secondary and supersecondary structure (or motifs) which may or may not be contiguous in the primary structure.
		Indeed the type of secondary structure present in the domain is used as a basis for classification of structural domains.
	wbiomed.curtin.edu.au /biochem/tutorials/prottute/tertiaryindex.htm (715 words)

	InterPro: IPR012921 Spen paralogue and orthologue C-terminal
		Structural links are generated automatically to the CATH and SCOP databases through residue-by-residue mappings with UniProtKB proteins.
		These databases describe the structural architecture of proteins, placing them within hierarchical classification schemes; InterPro entries are mapped to the 'Homologous Superfamily' level of CATH and to the 'Superfamily' level of SCOP.
		Structural links are also provided to the PDB database, via MSD; PDB being the repository for crystallographic and NMR structures.
	www.ebi.ac.uk /interpro/IEntry?ac=IPR012921 (2994 words)

	Motif for Infection - bacteria Science News - Find Articles
		This protein configuration, or structural motif, is called a beta helix.
		When Frances A. Jurnak, now at the University of California, Irvine, and her coworkers first determined the enzyme's three-dimensional structure in 1993, they speculated that its unusual folding pattern might be found in other proteins that incorporate similar sequences of amino acids.
		Because a protein's shape is the key to understanding its biological function and because protein-folding mistakes have been implicated in ailments such as Alzheimer's disease, researchers have been trying to accelerate the structure-determination process.
	www.findarticles.com /p/articles/mi_m1200/is_19_159/ai_75309417 (837 words)

	Gothic Architecture - Earthlore Glossary: Structural Components of Churches And Cathedrals
		Passageways of a church or cathedral, separated from the Nave by rows of pillars; generally running along the north and south sides.
		The turret which serves as the crown to the dome or roof of a structure.
		A structure which does not contain a Clerestory or Triforium, thus the Aisles and Nave will be approximately the same height.
	www.elore.com /Gothic/Glossary/components.htm (623 words)

	Array BioPharma is creating the next generation of orally active drugs
		Recurring fragments or structural motifs are often referred to as “privileged” structures for their affinity to bind to pharmaceutically relevant targets.
		Our approach to identifying these privileged structural motifs was recently validated by experimental evidence that supports the tendency for biphenyl and benzhydryl motifs to bind to proteins of biological interest.1 The Optimer® building block catalog offers numerous additional drug-relevant structural motifs.
		Unsubstituted structural motifs are used in lead generation providing important information that can be used to define SAR studies around a hit.
	www.arraybiopharma.com /OptimerBuildingBlocks/Default.asp (595 words)

	M.R. Bauer Foundation Colloquium Series
		One of the most important and challenging problems in computational biology is that of predicting the threedimensional structure or shape of a protein from its amino acid sequence.
		As a first step to tackling this problem, many researchers have focused on the structural motif recognition problem: given a known local threedimensional structure, or motif, determine whether this motif occurs in a given amino acid sequence.
		The coiled coil motif has many important biological rotes; for example, it is found in some DNA binding proteins and plays a role in the membrane fusion of viruses such as HIV.
	www.bio.brandeis.edu /news/bauer/berger2.html (232 words)

	FoldMiner: Structural motif discovery using an improved superposition algorithm -- Shapiro and Brutlag 13 (1): 278 -- ...
		structures that is the basis for the structural similarity.
		Structural similarity searches were performed by using members of four different SCOP folds as queries and a target database of 2448 SCOP domains of low sequence identity.
		Balaji, S. and Srinivasan, N. Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins.
	protsci.highwire.org /cgi/content/full/13/1/278 (9396 words)

	Mona Singh • Research
		Because of the bewildering complexity of the general protein structure prediction problem, one approach we have taken in our work on protein structure is "bottom up." That is, we have focused on specific local 3D structures, or structural motifs, and have developed fast, sequence-based methods for recognizing them within protein sequences.
		Much of our work has focused on recognizing the coiled coil motif, an important structural motif that is found in proteins that participate in transcription, oncogenesis and cell structure.
		We have been developing a general structural bioinformatics approach for predicting protein interactions that is designed to be applied to specific structural domains.
	www.cs.princeton.edu /~mona/research.html (918 words)

	Evolution mystery: Spider venom and bacteria share same toxin
		Cordes and Binford found a common structural motif at the end of both toxic proteins that is not found in any other proteins.
		"That one structural detail--which resembles a plug or cork at the end of a barrel-shaped enzyme--is evidence that the spider and bacterium share a relatively recent common ancestor," Cordes said.
		If this motif is central to protein function, treatments designed for the spider bites may also work for treating problems caused by the corynebacterial toxin," she added.
	www.eurekalert.org /pub_releases/2006-02/lcc-ems020106.php (508 words)

	A Novel Zinc Snap Motif Conveys Structural Stability to 3-Methyladenine DNA Glycosylase I -- Kwon et al. 278 (21): ...
		A Novel Zinc Snap Motif Conveys Structural Stability to 3-Methyladenine DNA Glycosylase I -- Kwon et al.
		The signature HhH structural motif is highlighted in green, and the remaining elements of the conserved helical domain of the HhH glycosylase fold are colored blue.
		The structure elements that are unique to TAG are shown in orange-red, and the 3-methyladenine binding pocket is indicated with an asterisk.
	www.jbc.org /cgi/content/full/278/21/19442 (2694 words)

	InterPro: IPR001810 Cyclin-like F-box
		The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [ 1, 2 ].
		This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme.
		Craig K.L. Tyers M. The F-box: a new motif for ubiquitin dependent proteolysis in cell cycle regulation and signal transduction.
	www.ebi.ac.uk /interpro/IEntry?ac=IPR001810 (3194 words)

	Light-activated rhodopsin induces structural binding motif in G protein alpha subunit -- Kisselev et al. 95 (8): 4270 ...
		Light-activated rhodopsin induces structural binding motif in G protein alpha subunit -- Kisselev et al.
		structure of Gt, the backbone of the last four residues of Gt was superimposed on the backbone of the first four residues of
		This motif is characterized by an H bond between the amide hydrogen
	www.pnas.org /cgi/content/full/95/8/4270 (4970 words)

	BioMed Central \| Full text \| COMe: the ontology of bioinorganic proteins
		One of the goals of the structural genomics initiative is to provide representative three-dimensional (3-D) structures for as many protein/domain folds as possible to allow successful homology modelling [1].
		Although crystallography is the single most informative method for studying protein structure, it has a number of limitations as far as bioinorganic chemists are concerned [4,5].
		It can be organised as a structured vocabulary in the form of a directed acyclic graph or a network in which each term may be a 'child' of one or more 'parent' [7].
	www.biomedcentral.com /1472-6807/4/3 (3745 words)

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