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Topic: Secondary structure

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Primary structure

Tertiary structure

Protein structure

Quaternary structure

Alpha helix

Protein

Beta sheet

Protein folding

MRNA

Circular dichroism

RNA

Proline

Biophysics

Helix

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	SECONDARY STRUCTURE
		Secondary Structure is the local structure which is typically recognized by specific backbone Torsion Angles and specific mainchain Hydrogen Bond pairings.
		The structure of plastocyanin is composed mostly of beta sheets and the Ramachandran plot shows a broad range of values in the -110,+130 region.
		Several definable turns and bends in protein structure have been recognized and classified either by the relationship between the phi,psi angles of the residues in the turn or the hydrogen bonding of their amide N-H and carbonyl-oxygen atoms.
	bmbiris.bmb.uga.edu /wampler/tutorial/prot2.html (904 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).
		The secondary structure of a segment of polypeptide chain is the local spatial arrangement of its main-chain atoms without regard to the conformation of its side chains or to its relationship with other segments (IUPAC-IUB, 1970).
		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.
	www.friedli.com /herbs/phytochem/proteins.html (11287 words)

	Secondary structure of Proteins
		The structure of myoglobin; the ribbon represents the path of the polypeptide chain and is color coded blue at the N-terminus, running through to red at the C-terminus.
		An important factor is that the final secondary structure is the consensus of all amino acids in a region.
		It may not be possible to improve much further, since it is believed that secondary structure adjusts itself due to interactions that arise in the folded form of the protein, which a sequence scan approach can't account for.
	www.chembio.uoguelph.ca /educmat/phy456/456lec01.htm (2216 words)

	CiteULike: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs. (Site not responding. Last check: )
		CiteULike: Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
		Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs.
		We conclude that although a distinct, stable secondary structure is undoubtedly important in most noncoding RNAs, the stability of most noncoding RNA secondary structures is not sufficiently different from the predicted stability of a random sequence to be useful as a general genefinding approach.
	www.citeulike.org /user/dquest/article/118801 (471 words)

	Secondary Structure of the 3' Terminus of Hepatitis C Virus Minus-Strand RNA -- Schuster et al. 76 (16): 8058 -- The ...
		Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs.
		Determination of the secondary structure of and cellular protein binding to the 3'-untranslated region of the hepatitis C virus RNA genome.
		Structure of the 3' terminus of the hepatitis C virus genome.
	jvi.asm.org /cgi/content/full/76/16/8058 (6543 words)

	Secondary structure of prion mRNA
		An algorithm for prediction of conserved secondary structure of single-stranded RNA is presented.
		The secondary structure distributions of the individual fragments were calculated with RNAfold at 50C. With the alignment mentioned above, the consensus base-pair probability matrix was calculated and is presented as dot plot in Figure 6.
		Secondary structure is the major determi-nant for interaction of HIV Rev protein with RNA.
	www.mad-cow.org /prion_mRNA.html (3364 words)

	Secondary structure prediction
		Methods to predict secondary structure have been in development for several decades and consequently the literature is extensive.
		The secondary structure of a particular residue is partly determined by its local sequence environment, but also by its environment with respect to the rest of the folded (or folding) protein which may be separated by tens or hundreds of residues along the chain[
		The structural preferences for the various local sequence environments are learnt by the network during training on sequence alignments with known structures.
	www.sbc.su.se /~maccallr/thesis/node54.html (1181 words)

	BioMed Central \| Full text \| Efficient pairwise RNA structure prediction and alignment using sequence alignment ...
		For example, the predicted secondary structure of ribosomal RNA has been essentially confirmed by recent crystal structures; 97–98% of the predicted base pairs are confirmed by experimental structures [1].
		As there are many RNA structures of biological interest [2,3], it is important to find computational means of accelerating, automating, and improving RNA secondary structure prediction [4].
		The 172 parameters of the pairSCFG were then estimated from the frequencies observed in annotated ribosomal RNA secondary structures from multiple alignments in the European Ribosomal Database [42,43].
	www.biomedcentral.com /1471-2105/7/400 (9134 words)

	Secondary structure predictions
		Further it has been believed that prediction of secondary structures is a step towards the prediction of the three-dimensional structure of a protein, as has been show in some threading methods.
		For a given aminoacid the secondary structure is chosen as the one with the highest probability, summed over all 17 residues.
		Afterwards the predicted secondary structure is feed into the second network.The second networks also predicts the secondary structure for a central residue of a window but using the output from the first net as its input.
	bioinfo.se /~arne/kurser/distanskurs_2002/text/secstr.html (934 words)

	Predicting the Secondary Structure of Your Protein
		Optimisation of parameters and determination of secondary structure.
		DSC (Discrimination of protein Secondary structure Class) is based on dividing secondary structure prediction into the basic concepts and then use of simple and linear statistical methods to combine the concepts for prediction (King and Sternberg, 1996).
		PREDATOR is a secondary structure prediction method based on recognition of potentially hydrogen-bonded residues in a single amino acid sequence (Frishman and Argos, 1996).
	genamics.com /expression/strucpred.htm (894 words)

	Secondary structure
		Consensus structures for IIA and IIB are displayed by the links to the left (adapted from Michel et al., 1989 and Toor et al., 2001).
		More recently, class IIC has been recognized, and is represented by all introns in bacterial class C. We have made consensus RNA structures for all phylogenetic subclasses (the subclasses are based on ORF relationships).
		The mitochondrial class has a standard IIA1 structure; chloroplast-like class 1 has a standard IIB1 structure; chloroplast-like class 2 has a standard IIB2 structure; the remaining bacterial introns have somewhat “hybrid” and novel features.
	www.fp.ucalgary.ca /group2introns/secondarystructure.htm (125 words)

	CiteULike: Pfold: RNA secondary structure prediction using stochastic context-free grammars. (Site not responding. Last check: )
		Pfold: RNA secondary structure prediction using stochastic context-free grammars.
		RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations.
		This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained.
	www.citeulike.org /user/dquest/article/118744 (414 words)

	Secondary Structure Prediction methods and links
		Although they differ in method, the aim of secondary structure prediction is to provide the location of alpha helices, and beta strands within a protein or protein family.
		Secondary structure prediction has been around for almost a quarter of a century.
		An early problem in secondary structure prediction had been the inclusion of structures used to derive parameters in the set of structures used to assess the accuracy of the method.
	www.bmm.icnet.uk /people/rob/CCP11BBS/secstrucpred.html (1890 words)

	Circular Dichroism
		Secondary structure can be determined by CD spectroscopy in the "far-uv" spectral region (190-250 nm).
		The approximate fraction of each secondary structure type that is present in any protein can thus be determined by analyzing its far-uv CD spectrum as a sum of fractional multiples of such reference spectra for each structural type.
		Changes in secondary structure, monitored in the far-UV CD region, can be determined with as little as 50 µg of protein, at concentrations of 0.2 mg/ml.
	www.ap-lab.com /circular_dichroism.htm (1567 words)

	Secondary Structure (Site not responding. Last check: )
		Essentially what is involved in an alpha helix is that the primary structure of the protein twists around upon itself in such a way, somewhat like rolling up this paper model, to form a recurring pattern that is very important.
		A third type of secondary structure involves three strands of protein bonded together between the chains with hydrogen bonds and then twisted into a helix that is referred to as a collagen helix.
		Whatever type of secondary structure is involved in a particular protein, the secondary structure is held in place by hydrogen bonding interactions between the amino group of the amino acid residue and the carbonyl group of another amino acid residue.
	dl.clackamas.cc.or.us /ch106-08/secondar.htm (565 words)

	SWBIC - Secondary Structure Prediction & Assignment (Site not responding. Last check: )
		London] A multiple sequence prediction program that predicts the secondary structures of multiplicatively aligned sequences using physiochemical information, a set of aligned sequences, and secondary structure decision constants.
		Its purpose is to generate hypotheses for structure and function for such hypothetical or putative protein sequences based on fold recognition.
		Predicts three-state description of the secondary structure (alpha-helix, beta-sheet and coil) of non-homologous proteins.
	www.swbic.org /links/1.12.5.php (731 words)

	Secondary Structure of Uracil-DNA Glycosylase Inhibitor Protein -- Balasubramanian et al. 270 (1): 296 -- Journal of ...
		Examination of the spectrum indicated that only one structural form of the protein was present in solution, as there is one cross-peak for the amide of each non-proline residue in the protein.
		The secondary structure has six loop or turn regions in which one half of the 18 acidic amino acid residues of the protein are found.
		The regions 36-40, 49-52, and 61-68 are prime candidates for this activity since these regions are not involved in the secondary structure and contain six of the 18 acidic residues present.
	www.jbc.org /cgi/content/full/270/1/296 (4472 words)

	Heat-Induced Synthesis of sigma 32 in Escherichia coli: Structural and Functional Dissection of rpoH mRNA Secondary ...
		Structure and expression of an rpoH-lacZ gene fusion (TLF247).
		Thermoregulation of a TLF247 gene fusion mediated by an mRNA secondary structure.
		RNA secondary structure among the rpoH homologs (23).
	jb.asm.org /cgi/content/full/181/2/401 (5828 words)

	PredictProtein e-mail Server (Site not responding. Last check: )
		Predict the Secondary Structure of a Protein at EMBL-Heidelberg, Germany.
		PHD is an e-mail service to which you send an amino acid sequence and which sends back by return mail a predicition of the secondary structure.
		The secondary structure prediction method is rated at 72.1% average accuracy for water-soluble globular proteins, in the three states helix, strand, and loop.
	www.public.iastate.edu /~pedro/pprotein_query.html (100 words)

	Consolidating critical binding determinants by noncyclic rearrangement of protein secondary structure -- Tabtiang et ...
		(C) The secondary structure in pArc is a noncyclic permutation of the structure in single-chain Arc-L1-Arc.
		The order of structural elements in Arc-L1-Arc is shown in the upper portion of the panel with the first Arc repeat colored blue and the second repeat colored green.
		This maximizes structural differences between wild type and the remaining portions of pArc, which are most dissimilar in terms of secondary-structure topology.
	www.pnas.org /cgi/content/full/102/7/2305 (2389 words)

	Secondary Structure Prediction (Site not responding. Last check: )
		In between these secondary structure elements there are turns or loops.
		There is a long tradition of attempts to predict local secondary structure based on sequence.
		State-of-the-art secondary structure prediction generally observes the frequencies of occurences of k-tuples in particular secondary structures.
	lectures.molgen.mpg.de /ProteinStructure/SecondaryStructure/index.html (275 words)

	Introduction to Jmol, Part 2 (Site not responding. Last check: )
		Two of the most easily achievable folding patterns of a protein chain correspond to the most common forms of protein secondary structure, the α-helix and the β-pleated sheet.
		A fourth and final type of secondary structure, known as random coil, refers to folds of the protein that do not fit into a classification.
		Secondary structure is stabilized by hydrogen bonds between backbone carbonyl oxygens and the amide hydrogens.
	www3.interscience.wiley.com:8100 /legacy/college/boyer/0471661791/structure/jmol_intro/sec_str.htm (848 words)

	Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA ...
		Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA -- Blight and Rice 71 (10): 7345 -- The Journal of Virology
		Dutkiewicz, M., Ciesiolka, J. Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5' end of the replicative viral strand.
		Cuceanu, N. M., Tuplin, A., Simmonds, P. Evolutionarily conserved RNA secondary structures in coding and non-coding sequences at the 3' end of the hepatitis G virus/GB-virus C genome.
	jvi.asm.org /cgi/content/abstract/71/10/7345 (1400 words)

	Bioluminescence and Secondary Structure Properties of Aequorin Mutants Produced for Site-Specific Conjugation and ...
		To further study the affects of the mutagenesis on the photoprotein structures, circular dichroism (CD) spectra were taken with each individual mutant using mutant 3 as a baseline for comparison of secondary structure.
		CD spectra of these mutants demonstrated that complex changes had occurred within the secondary structure of the proteins as a result of the single amino acid substitutions.
		Since these mutants have different bioluminescence and secondary structure characteristics, it is conceivable that they might demonstrate a change in their luminescence signal upon binding to an appropriate binder.
	pubs.acs.org /cgi-bin/jtextd?bcches/11/i01/html/bc9900800.html (4483 words)

	GeneDoc Secondary Structure Features
		One of the most powerful kinds of integration of structure and sequence information allows the user to visually examine the variation in structure or some structural property that occurs as the sequence varies in a series of homologous proteins.
		Another use for multiple copies of a single sequence in the alignment is to contrast predictions of structure and properties with that observed in an experimentally determined three dimensional structure.
		A wide spread use of the structure shading is to project the structure or properties from a sequence of known structure onto sequences whose structures have not be experimentally determined.
	www.psc.edu /biomed/genedoc/gdsec.htm (658 words)

	Amount of RNA secondary structure required to induce an alternative splice. -- Solnick and Lee 7 (9): 3194 -- Molecular ...
		Amount of RNA secondary structure required to induce an alternative splice.
		RNA secondary structure repression of a muscle-specific exon in HeLa cell nuclear extracts.
		Libri, D, Piseri, A, Fiszman, M. Tissue-specific splicing in vivo of the beta-tropomyosin gene: dependence on an RNA secondary structure.
	mcb.asm.org /cgi/content/abstract/7/9/3194 (421 words)

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