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Topic: Supersecondary structure

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	PPS 96' - Tertiary Structure: Overview of Terminology
		Secondary structure is defined by the phi and psi angles of the backbone atoms of the amino acid residues, and the hydrogen bonds between main chain atoms.
		Classic units of supersecondary structure include the alpha-alpha unit (two antiparallel alpha-helices joined by a 'hairpin' bend changing the chain direction by 180°); the beta-beta unit (two antiparallel strands connected by a hairpin); and the beta-alpha-beta unit (two parallel strands, separated by an alpha-helix antiparallel to them, with 2 hairpins separating the three secondary structures).
		Quaternary structure is the subject of a later chapter of the course.
	www.cryst.bbk.ac.uk /PPS2/course/section9/9_term.html (1257 words)

	Electronic dissertations library
		The secondary structure of a protein is the 3D arrangement of amino acid residues that are relatively near one another in the linear sequence (Stryer (1988)).
		Secondary structure is created by hydrogen bonding between the alpha-amide groups and alpha-carbonyl groups of the backbone, to enable globular proteins to retain a minimum energy conformation (Chothia (1984)), and common patterns occur in the majority of proteins, despite vastly dissimilar overall structures.
		Protein structure is often divided into four classes: ‘all-alpha‘ have only alpha-helical structures, ‘all-ß‘ have only ß-sheet structures, ‘alpha+ß‘ have both alpha-helices and ß-sheets but the two types of structure are in different sections of the linear sequence, and ‘alpha/ß‘ have both structures mixed along the protein chain (Levitt and Chothia (1976)).
	panizzi.shef.ac.uk /elecdiss/edl0002/proteina.html (2930 words)

	Proteins
		The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom).
		An intermediate compact structure known as the molten globule which is different from the native structure and whose formation is determined mainly by non-specific interactions of amino acid residues with their environment was presented.
		The degree to which the three-dimensional structure of a protein may differ from the native state may vary from a change in a single noncovalent bond or side-chain orientation to the case where almost no atom exist in the same spatial relationship to others except for the constraints of the primary structure.
	www.friedli.com /herbs/phytochem/proteins.html (11287 words)

	Protein Structure (Site not responding. Last check: 2007-10-15)
		Primary Structure - Sequence of amino acids from the N-terminus of the protein to the C-terminus.
		Although we ignore them in visualizing the structure, secondary structures are stabilized by hydrogen bonds between elements of the peptide bonds of different amino acid residues.
		The structure is stabilized by hydrogen bonds between amino acids in neighboring turns of the helix.
	www.park.edu /bhoffman/courses/bi350/recap/protstructure.htm (1190 words)

	Protein Supersecondary Structure (Site not responding. Last check: 2007-10-15)
		Supersecondary structures (also called motifs) involves the association of secondary structures in a particular geometric arrangement.
		If we use this definition then a beta sheet could also be considered a supersecondary structure, but for our puposes we have discussed this as a secondary structure.
		Some of these supersecondary structures are known to have a specific biological, or structural, role but for others their role is unknown.
	wbiomed.curtin.edu.au /biochem/tutorials/prottute/supersecondindex.htm (129 words)

	SUPERSECONDARY STRUCTURE (Site not responding. Last check: 2007-10-15)
		Secondary structure elements are observed to combine in specific geometric arrrangements known as motifs or supersecondary structures.
		Beta-hairpins are one of the simplest supersecondary structures and are widespread in globular proteins.
		The structures of reverse turns are outlined in the section on peptide geometry.
	www.rpi.edu /dept/chem-eng/Biotech-Environ/Ryan/super1.html (496 words)

	SUPERSECONDARY STRUCTURE (Site not responding. Last check: 2007-10-15)
		Secondary structure elements are observed to combine in specific geometric arrrangements known as motifs or supersecondary structures.
		Beta-hairpins are one of the simplest supersecondary structures and are widespread in globular proteins.
		The structures of reverse turns are outlined in the section on peptide geometry.
	www.cryst.bbk.ac.uk /PPS95/course/6_super_sec/super1.html (496 words)

	References: The Anatomy & Taxonomy of Protein Structure
		Structure of a bacteriochlorophyll a-protein from the green photosynthetic bacterium Prosthecochloris aestuarii.
		Structure determination at 2.5 A resolution and a comparison of the conformation and sequence of its two domains.
		Structure of the haemagglutinin membrane glycoprotein of influenza virus at 3 Å resolution.
	suna.biochem.duke.edu /teaching/anatax/html/anatax.ref.html (4782 words)

	Lecture 6. Global Folding - Supersecondary Structure and Protein Morphology
		This structure therefore is often referred to as the "pleated sheet structure".
		The structure of the DNA binding and dimerization region of several representatives of this family have been determined (the yeast protein GCN4 - Ellenberger et al., Cell 71,1223-1237, 1993; MyoD, Ma et al., Cell 77, 451-459, 1994).
		The vertebrate visual pigment rhodopsin has a very similar structure, and the same holds for a large number of receptors for hormones and neurotransmitters, which consequently have been referred to as the opsin family (opsin is the apoprotein of rhodopsin), and are now often called seven-pass receptors.
	www.sunysb.edu /biochem/courses/lectures/5bmo520.html (2105 words)

	SUPERSECONDARY STRUCTURE (Site not responding. Last check: 2007-10-15)
		Hence, the second helix of the helix-turn-helix motif has an important role in recognising the DNA while the remainder of the structure serves to keep the two helices in the correct relative position for fitting in the major groove of DNA.
		The helix axis is roughly parallel with the beta-strands and all three elements of secondary structure interact forming a hydrophobic core.
		A novel super-secondary structure of proteins and the relation between the structure and amino acid sequence, A.F.Efimov, FEBS Lett.
	www.rpi.edu /dept/chem-eng/Biotech-Environ/Ryan/super5.html (504 words)

	The pattern of common supersecondary structure (motifs) in protein database (Site not responding. Last check: 2007-10-15)
		The pattern of common supersecondary structure (motifs) in protein database
		Supersecondary motifs have been analysed in 240 proteins defined at resolutions of 0.25 nm or better.
		Using five classes of residue conformation (a,b,e,l,t) in the non-regular structure regions, we have identified 50 classes that occur at least five times, and eleven classes that occur more than twenty-five times.
	csdl2.computer.org /persagen/DLAbsToc.jsp?resourcePath=/dl/proceedings/&toc=comp/proceedings/hicss/1995/6921/00/6921toc.xml&DOI=10.1109/HICSS.1995.375325 (186 words)

	EMBL - Research - Research Units - EMBL Hamburg - Lamzin Group - Publications (Site not responding. Last check: 2007-10-15)
		Crystal structure of the family 7 endoglucanase I (Cel7B) from Humicola insolens at 2.2 A resolution and identification of the catalytic nucleophile by trapping of the covalent glycosyl-enzyme intermediate.
		The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
		The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism.
	www.db.embl-heidelberg.de /jss/EmblGroupsOrg/g_93?sP=3 (2027 words)

	Journal Club 1998-05-18
		A long standing goal in pro-tein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experi-mental constraints as well as for theoretical protein folding and inverse folding computer experiments.
		According to SCOP, the classifica-tion of structural classes for protein domains is based on the evolutionary relationship and on the principles that govern the 3D structure of proteins, and hence is more natural and reliable.
		The native 3-D structure is predicted correctly for 3 of 12 proteins com-posed mainly from the a-helices.
	www.sbc.su.se /~arne/jclub/jclub_19980518.html (1655 words)

	ULB - SCMBB: Research Activities (Site not responding. Last check: 2007-10-15)
		The classification yielded 15 structural families of alpha-beta and 15 with beta-alpha turns.
		In a second study, the classification approach was modified and extended to super-secondary structure units consisting of two hydrogen bonded beta-strands preceded or followed by an alpha-helix (Boutonnet et al., 1998
		The latter arrangements seem to be fostered by a set of favourable side-by-side packing interactions between the secondary structure elements, by local interactions in the alpha-beta connection or by the stabilising environment of the parent protein.
	www.ucmb.ulb.ac.be /SCMBB/P04.html (346 words)

	No Title
		Biomolecular complexes for which crystal structures of both the complexed and uncomplexed proteins are available were used for eight of the ten test systems.
		Predictions are made for the known structures of protomers from 28 homo-dimers, large protomers from 11 hetero-complexes, small protomers from 14 hetero-complexes, and antigens from six antibody-antigen complexes.
		The stability and structural flexibility of seven of the redesigned proteins were determined experimentally and showed that core variants containing as many as 6 of 10 possible mutations retain native-like properties.
	www.sbc.su.se /~arne/jclub/jclub_19971020.html (1263 words)

	Citations: Identification of structural motifs from protein coordinate data: Secondary structure and first-level ... (Site not responding. Last check: 2007-10-15)
		Richards, F.M. and Kundrot, C.E., Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure, Proteins, 3:71--84, 1988.
		F.M. Richards and C.E. Kundrot, Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure, Protein Structures, 3 (1988), 71--84.
		F.M. Richards and C.E. Kundrot, Identification of structural motifs from protein coordinate data: Secondary structure and firstlevel supersecondary structure, Protein Structures, 3 (1988), 71--84.
	citeseer.ist.psu.edu /context/351319/0 (1009 words)

	structure of keratin
		Structure of fibrous proteins : feather keratin / Robert Schor.
		Keratin is a protein used by numerous groups of animals as a structural element, and is a classic example of a fibrous protein.
		The structure of myoglobin; the ribbon represents the path of the polypeptide chain and is color...
	www.hairstyles-7.com /hairinfo/structure+of+keratin.html (592 words)

	The Protein Structure Database (PSdb)
		The classification of protein structural information, especially using the overall structure of the protein (the fold) as the basis for the classification [1], is an exciting area of research in structural biology.
		Two of the most important and difficult problems in molecular biology, the protein folding problem and the structure-function relationship in proteins, are directly concerned with relating the three-dimensional structure of a protein to the primary sequence.
		Indeed, one of the driving forces in the development of the PSdb is to understand the role of metal ions in the stabilization of specific tertiary structures and the propensities of the various side-chains to interact with specific metal ions [56].
	www.psc.edu /~deerfiel/PSdb/PSdbPaper/PSdb.html (3563 words)

	Molecular Tools
		This supersecondary structure is a common motif found in many DNA-binding proteins.
		It is either found as a flat planar structure or as a slightly curved planar structure.
		The software allows you to manipulate the colors, size, and structural view of the molecule in a matter of seconds depending on the size of the file and the speed of the computer.
	home.san.rr.com /dna/darryl/predicting3rdstructure.html (653 words)

	ISMB 2005: Michigan, June 25-29
		Abstract: Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrates that the properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and tethered oligonucleotide probe in a microarray experiment.
		Abstract: One approach to prediction of protein structure from sequence is to predict a contact map and structural features, and then reconstruct the protein from its predicted contact map.
		A ``motif'' for 3D structure is characterized by the number of persistent components and holes, and their relative sizes.
	www.iscb.org /ismb2005/posters_list.html (13873 words)

	Session 4: Protein structure (Site not responding. Last check: 2007-10-15)
		Homology-based approaches attempt to determine the tertiary structure of a protein by comparing its primary sequence to that of a related proteins whose structure is known.
		One of them is homology modeling, which predicts the structure of a protein by comparing its sequence to the (homologous) sequence of a protein of known structure ("template").
		Given the alignment, the backbone structure of the unknown protein is derived from the template.
	www.itb.uni-stuttgart.de /training/bioinformatics99/session_5.html (4393 words)

	Liwei Peng's Publications
		Database of protein supersecondary motifs is set up, and artificial neural network method is applied to the predictions of those supersecondary motifs from protein sequences.
		These results are useful for the further study of the relationship between the structure and the function of proteins.
		This work provides insight into the problem of predicting a protein's local structure accurately, and is of particular value in protein modeling, prediction, and molecule design.
	ncmi.bcm.tmc.edu /homes/lpeng/doc/publications.html (714 words)

	Scanning Tunneling Microscopy of a Wheat Seed Storage Protein Reveals Details of an Unusual Supersecondary Structure -- ...
		Scanning tunneling microscopy has been used to demonstrate that a spiral structure based on ß-reverse turns is adopted by the repeat sequences present in a group of wheat gluten proteins.
		This structure is similar to the ß-spiral formed by a synthetic polypentapeptide based on a repeat sequence present in elastin.
		Wheat gluten and elastin are both elastomeric and it is possible that the spiral structure contributes to this property.
	www.pnas.org /cgi/content/abstract/88/1/68 (299 words)

	Berkeley Scientists Create First 3-D Map Of Protein Universe
		Milestone In Mitochondrial Structure Revealed (August 20, 1998) -- In the short-term, the announcement is of consequence only to those cell biologists whose focus is on "mitochondria," the subcellular structures which generate energy for living cells.
		An internationally recognized authority on protein structures, he expressed surprise at how closely the map, which is based solely on empirical data and a mathematical formula, mirrored the widely used Structural Classification System of Proteins (SCOP), which is based on the visual observations of scientists who have been solving protein structures.
		These structures essentially stay the same for proteins from all three kingdoms of life -- bacteria, archaea, and eukarya - even though the DNA sequences encoding for a specific type of protein can wildly vary from the genome of one organism to another, and sometimes even within the same organism.
	www.sciencedaily.com /releases/2003/02/030220081053.htm (1189 words)

	hicss,28th Hawaii International Conference on System Sciences (HICSS'95) (Site not responding. Last check: 2007-10-15)
		The pattern of common supersecondary structure (motifs) in protein database
		Supersecondary motifs have been analysed in 240 proteins defined at resolutions of 0.25 nm or better.
		Using five classes of residue conformation (a,b,e,l,t) in the non-regular structure regions, we have identified 50 classes that occur at least five times, and eleven classes that occur more than twenty-five times.
	csdl.computer.org /comp/proceedings/hicss/1995/6921/00/69210312abs.htm (192 words)

	Define_s Document
		This program produces a list of the secondary structure of a protein and some relations between the secondary elements based solely on the coordinates of the alpha carbon atoms.
		The principal procedure uses difference distance matrices for evaluating the match of interatomic distances in the protein to those from idealized secondary structures.
		Once the secondary elements have been established, the axes of helices and strands are calculated by reference to the original input coordinates.
	www.csb.yale.edu /userguides/datamanip/define_s/define_s_doc.html (2184 words)

	Protein Structure and Function Course Page
		Lecture 1 (Aug 31): Taxonomy I: Primary & Secondary Structure [PDF]
		Lecture 4 (Sep 12): Folding I: Forces that Determine Protein Structure [PDF]
		Lecture 20 (Nov 9): NMR V: Protein Structure Determination [PDF]
	dasher.wustl.edu /bio5325 (499 words)

	Abstract 12 de l'année 2001 (Site not responding. Last check: 2007-10-15)
		It is well established that protein structures are more conserved than protein sequences.
		One-third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of alpha-helical hairpin, beta hairpin and betaalphabeta supersecondary structural elements.
		In this study, we explore the ability of a recent Monte Carlo-based procedure to generate the 3D structures of eight polypeptides which correspond to units of supersecondary structure and three-stranded antiparallel beta sheet.
	igs-server.cnrs-mrs.fr /igs/abstract/an2001/abstract12.html (186 words)

	Biochem: Protein
		– The native conformation is the three-dimensional structure of a protein that is functional.
		• Tertiary structure is 3D folding due to all atoms including side chains and prosthetic groups (groups other than amino acids).
		• The amino acid sequence is the basis for structure and function of the protein.
	departments.ozarks.edu /msc/Biology/Biochem/bcprotein.htm (2224 words)

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