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Topic: Helices

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	Method for producing a sieve belt of thermosettable synthetic resin helices for a papermaking machine - Patent 4392902
		The invention relates to a sieve belt composed of a multiplicity of helices of thermosettable synthetic resin monofilament in which adjacent helices are interlocked such that the windings of one helix enter between the windings of the adjacent helix, and having a pintle passed through the channel formed by adjacent helices.
		For this reason the helices must be oval to begin with, and in cross section of the helices the inner clearance between the nearly parallel portions or legs of the ovals must be greater than the diameter of the inserted pintle-filament.
		Helices of oval cross section are produced from polyester monofilamentary material of 0.7 mm thickness, the maximum and minimum diameters of the oval being 6.8 mm and 3.8 mm, respectively.
	www.freepatentsonline.com /4392902.html (3745 words)

	Helix article - Helix screw spiral biology proteins alpha helices chirality mathematics - What-Means.com (Site not responding. Last check: 2007-10-21)
		A helix (plural: helices) is a twisted shape like a spring, screw or a spiral staircase.
		Helices are important in biology, as DNA is helical and many proteins have helical substructures, known as alpha helices.
		In music pitch space is often modeled with helixes or double helixes, most often extending out of a circle such as the circle of fifths, so as to represent octave equivalency.
	www.what-means.com /encyclopedia/Helix (300 words)

	Lect. 4 (Site not responding. Last check: 2007-10-21)
		A very important feature of helices is their dipole moment, due to the vector sum of the individual dipoles from the peptide bonds aligned along the axis of the helix.
		One reason for the sidedness of helices is that they are often on the surface of a protein, and their non-polar side is packed against the non-polar interior.
		The helices are connected by short loops and form a box in which the heme resides.
	www.chemistry.ucsc.edu /teaching/Winter02/Chem200A/Outline-4.htm (1649 words)

	Long membrane helices and short loops predicted less accurately
		Helices from 17-27 residues accounted for less than half of the high-resolution and for 93% of the low-resolution data.
		The lengths of the membrane helices were assigned using DSSP for the high-resolution data (36 unique chains; 131 helices), and using the annotation in SWISS-PROT for the low-resolution data (165 unique proteins; 339 helices).
		At first sight, the drop in prediction accuracy for helices longer than 32 residues may appear irrelevant in context of predicting membrane helical proteins for entire proteomes [31, 18, 32, 33, 34, 35, 36, 19, 29].
	cubic.bioc.columbia.edu /papers/2002_htm_length/paper.html (4205 words)

	Anatax: Helices
		Helices had frequently been proposed before as the α structure, but none of them could adequately match the diffraction pattern because they had been limited by the implicit assumption that a regular helix would necessarily have an integral number of amino acid residues per turn.
		It was shown that the myoglobin helices matched Pauling's calculated structure quite closely, and also that they were all right-handed (for L-amino acids, the left-handed α-helix has a close approach between the carbonyl oxygen and the β-carbon).
		Such interrupted helices (broken on one side of the double helix) are apparently a fundamental feature of nucleic acid structure as illustrated by tRNA, but are exceedingly rare in protein structure.
	kinemage.biochem.duke.edu /~jsr/html/anatax.2a.html (2741 words)

	Computational Methods for Studying Transmembrane -Helices
		Helical constraints and interhelical constraints are applied during the relaxation to maintain helical structure and to keep the two helices together.
		Although the helices are predicted to pack closer with each other than with the lipids, the details of environment may effect the tertiary structure of the protein.
		This information is useful for determining where transmembrane helices may start and stop in a given sequence of amino acids, as is the average length of a transmembrane helix, which is around 26 amino acids [Bowie, 1997a].
	bioinfo.mbb.yale.edu /course/projects/final-3 (3338 words)

	Daniel McFarland Cook's Electro-Magnetic Battery
		In the use of the simple helices for convenience, and to favor the insulation in the resistance to obtain a sufficient tension and quantity of current for action, it is desirable to use a long iron core, A, Fig.
		In the use of the compound helices it is preferable, in some cases, to use a small wire, say No.30, or even less, for a primary helix, and No.16, or even larger, for a secondary helix.
		The poles of the two helices being connected the action is the same as in the compound helices, there being but four currents developed, two initial and two terminal currents, the latter flowing constantly in the same direction – in effect there being but one current in the same direction.
	my.voyager.net /~jrrandall/CookCoil.htm (1018 words)

	Structural Model for 12-Helix Transporters Belonging to the Major Facilitator Superfamily -- Hirai et al. 185 (5): 1712 ...
		The helices are grouped into three sets: those colored green are nearly perpendicular to the plane of the membrane, those colored yellow contain bends in the transmembrane region, and those colored magenta contain both a bend and curve in the transmembrane region (from Hirai et al.
		The average lengths of the loop regions connecting helices 2 and 3 in various MFS proteins are likely to be even shorter (perhaps as few as six) than the span of conserved residues (shaded in green) since there is a marked prevalence of nonpolar amino acids on the N-terminal side of these conserved residues.
		Once we had made the assumption (see text) that helices 1 and 7 are at the center on the periplasmic side, there were four possible ways in which these helices could be placed into the density map, of which one arrangement is shown in A as viewed from the cytoplasmic side.
	jb.asm.org /cgi/content/full/185/5/1712 (3611 words)

	3.1 Helices
		In a helical conformation, the relationship of one peptide unit to the next is the same for all alpha-carbons.
		Helices are classified as repetitive secondary structure since their backbone phi and psi angles repeat (for the geometrically ideal, right-handed, alpha helix, these values are phi = -57.8 and psi = -47.0).
		Helices are the most abundant form of secondary structure containing approximately 32-38% of the residues in globular proteins (Kabsch and Sander, 1983).
	www.cryst.bbk.ac.uk /PPS2/course/section8/ss-960531_5.html (601 words)

	Helices (Site not responding. Last check: 2007-10-21)
		Information about the geometry of the helix is given as follows: length and unit rise (both in Angstroms), the number of residues per turn (ideaally 3.6) for alpha helices), the helix pitch in Angstroms and a measure of the deviation of the helix geometry from an ideal helix (in degrees).
		The interaction type describes where in each of the helices the distance of closest approach occurs (C: beyond the C terminus of the helix, N: beyond the N terminus of the helix, I: internal to the helix).
		The number of interacting pairs of residues and the number of residues in each of the two helices involved in the interaction are also given.
	www.biochem.ucl.ac.uk /bsm/promotif/helices.html (317 words)

	[No title]
		Helices A and ab show strong mutabilty moments, and several of the membrane helices show strong moments for both hydrophobicity and mutability at their ends.
		For six of the transmembrane helices, A - F, choice among alternative arrangements for packing the structure around the liganding helices B and D is strongly dependent on the weight attached to the suggested role of the conserved glycines ([15] and item 7 above).
		At the QR-site, a conserved span showing helical amphipathy (helix a) is found to the N-terminal side of a residue associated with diuron resistance in yeast.
	www.life.uiuc.edu /crofts/ahab/japan92.html (2934 words)

	COILED COIL
		First, the overall secondary structure is alpha helical and secondly, the hydrophobic residues are arranged on one side of the helices.
		A common way of illustrating the amphipathic nature of helices is to use a helical wheel represention, in which the helices are viewed from the end.
		The former is common when the helices belong to different polypeptides and the latter prevails in coiled coils made up from a single polypeptide chain.
	www.rpi.edu /dept/chem-eng/Biotech-Environ/Ryan/cc.html (1470 words)

	volume 6 article 2 (Site not responding. Last check: 2007-10-21)
		To evaluate the effectiveness of this approach the transmembrane helices of bacteriorhodopsin (BR) were chosen as the model system since both its helix - helix and lipid - helix interfaces have been structurally defined by crystallography.
		The ideal alpha-helix geometry of the TM helices of the BR, mimicking the transmembrane helices, were used to study the interaction with the lipophilic probe and hence to map the surface as a test case.
		The calculated lipid facing surfaces of three TM helices substantially agreed with lipid observed interacting surfaces of TM helices in the crystal structure.
	www.ijc.com /abstracts/abstract6n2.html (277 words)

	Biophysical Journal: Uniformity, ideality, and hydrogen bonds in transmembrane (alpha)-helices
		Transmembrane helices exist in the relatively uniform low dielectric interstices of the lipid bilayer, largely devoid of water and with a very hydrophobic distribution of amino acid residues.
		Helices are the most common secondary structure found in globular proteins, and many analyses have been performed on a-helical structural geometry, packing, and regularity (Chothia et al., 1977; Richmond and Richards, 1978; Barlow and Thornton, 1988).
		Helices from water-soluble proteins display a considerable spread of (A, qi torsion angles as a result of numerous interactions between the helix and its heterogeneous environment, potentially including the aqueous surroundings, the hydrophobic protein interior, and hydrophilic regions.
	www.findarticles.com /p/articles/mi_qa3938/is_200210/ai_n9109167 (1001 words)

	left23 (Site not responding. Last check: 2007-10-21)
		The circles represent the helices, the squares represent strands, and the lines are the loops and coils.
		The secondary and tertiary structures of the protein are stabilized by an intricate meshwork of hydrogen bonds and hydrophobic interactions.
		Hydrophobic interactions are the stabilizing factor between the helices and the strands.
	www.bimcore.emory.edu /home/molmod/Ohern/left.html (1042 words)

	C5a Receptor Activation. GENETIC IDENTIFICATION OF CRITICAL RESIDUES IN FOUR TRANSMEMBRANE HELICES -- Baranski et al. ...
		Helical wheel representations are based on the Baldwin model (16).
		Helices are presented as viewed from the cytoplasm and in positions that correspond to their relative positions at the middle of the bilayer (16).
		In panels A and B, the yellow grids (lines separated by 10 Å) indicate the proposed extracellular and cytoplasmic borders, respectively, of the lipid core of the membrane (16); the ribbon coloring scheme is the same as in Fig.
	www.jbc.org /cgi/content/full/274/22/15757 (6041 words)

	Motifs of protein structure.
		helices are what you would get if you pulled an -helix and stretched it out.
		There are two main types of all- protein topologies; the 4-helix bundle and the so-called globin fold, or Greek key helix bundle.
		It was observed some time ago, from examination of crystallographically determined structures, that helices tended to pack against each other at characteristic angles, namely either 20o or 50o.
	www.chemistry.ucsc.edu /~fink/200lecture/9-97.htm (1885 words)

	Parallel-stranded helices (Site not responding. Last check: 2007-10-21)
		Helices with both strands having the same orientation (different from standard double helical nucleic acids) have been identified as non-standard nucleic acid structures..
		Such helices have electrophoretic mobilities, hypochromic effects and other properties of anti-parallel helices, but are resistant to the action of T4 DNA ligase (ref).
		When these strands from a known triple helical DNA were mixed without the anti-parallel strand, a duplex formed at acidic pH that had properties suggesting it was the double-stranded parallel DNA (ref).
	opbs.okstate.edu /~melcher/N1/N1342.html (292 words)

	CH..O Analysis
		Backbone dihedral angles were calculated for all the proteins and 296 helices were identified in the dataset.
		Of these, four helices were at the termini of the protein and hence did not posses T+1 residue.
		The length of the helices were calculated using Helidata, and the length distribution of the helices was obtained.
	www.mrc-lmb.cam.ac.uk /genomes/madanm/articles/cho.htm (931 words)

	TMpred output for lmpb1 (Site not responding. Last check: 2007-10-21)
		The number of putative transmembrane proteins, 8, is exactly the same; however, the locations of the start and end sites of a few of the helices differ slightly, with either equal or slightly higher scores allotted to the predictions below.
		Here is shown, which of the inside->outside helices correspond to which of the outside->inside helices.
		These suggestions are purely speculative and should be used with extreme caution since they are based on the assumption that all transmembrane helices have been found.
	smi-web.stanford.edu /people/waugh/TMPREDResultHigh.html (282 words)

	Relative positions of C. elegans transmembrane helices (Site not responding. Last check: 2007-10-21)
		Each sequence was divided into 20 sections, and the beginning location of the predicted TM helices was assigned one of these 20 "bins".
		Proteins with 2 TMH's (inset) usually have a relatively short loop between the two helices; it is rare to have a large domain between two transmembrane segments.
		Proteins that have large number of TMH's tend to have short loops between each TMH and any large globular domains are present at the N- or C-terminus (see 4 TMH plot in lower right corner).
	www.fccc.edu /research/labs/dunbrack/genomes/CE_TM.html (220 words)

	MEDLINE Database, 1987 to date Document Reader (Site not responding. Last check: 2007-10-21)
		The program gives information on the total number of base paired helices that are conserved between related sequences and provides detailed information about common helices that have a minimum of one or more compensating base changes.
		The results of the analyses with random sequences were compared with the number and type of helices found in the phylogenetic model of the secondary structure of 16S ribosomal RNA.
		In addition, conserved helices in the 16S rRNAs are, on the average, longer than the complementary segments that are found in comparable random sequences.
	www.bioinfo.rpi.edu /~zukerm/ref/CHAL91.html (335 words)

	Polyproline helices - Description (Site not responding. Last check: 2007-10-21)
		There were no PPI helical segments identified (yet?) in proteins, but poly-L-proline in apolar solvents (alcohols with long carbon-chain) was found to adopt this conformation in some circumstances.
		PPII helices seem to be stabilized by main chain-water hydrogen bonds (in the absence of main chain- main chain H-bonds), and tend to have a regular pattern of hydrogen bonds with water.
		After this, it is not surprising, that PPII helices are found mostly on the protein surface, and has a preference, to hydrophilic residues (and proline).
	www.cryst.bbk.ac.uk /pps97/assignments/projects/szabo/PPHELIX.HTM (580 words)

	Biophysical Journal: Influence of the environment in the conformation of (alpha)-helices studied by protein database ...
		Thus, the helical bundle motif frequently builds the three-dimensional structure of membrane proteins along with the beta-barrel motif also observed in membrane-spanning proteins (White and Wimley, 1999).
		The influence of the environment in the conformation of a-helices has been studied by surveying crystal structures of both soluble and membrane proteins and by molecular dynamics simulations of poly-Ala alpha-helices in water and methane.
		Thus, membrane proteins incorporate in the sequence of their transmembrane helices specific residues like Pro, Gly, Ser, and Thr (Series et al., 2000), which add flexibility and assist in the conformational change (Ballesteros et al., 2000; Gether et al., 1997; Govaerts et al., 2001 a; Palczewski et al., 2000; Ri et al., 1999).
	www.findarticles.com /p/articles/mi_qa3938/is_200206/ai_n9092736 (1299 words)

	Structure and Dynamics of K Channel Pore-Lining Helices: A Comparative Simulation Study -- Shrivastava et al. 78 (1): ...
		The helices are shown as ribbons and the P atoms of the lipid headgroups as van der Waals spheres.
		helices: the termini and (to a lesser extent) the center of the
		helicity was due to the attempt to bury a cluster of hydrophilic
	www.biophysj.org /cgi/content/full/78/1/79 (5942 words)

	Rhodopsin activation blocked by metal-ion-binding sites linking transmembrane helices C and F
		In rhodopsin, the photoreceptor of retinal rod cells, we substituted histidine residues for natural amino acids at the cytoplasmic ends of the TM helices C and F. The resulting mutant proteins were able to activate the visual G protein transducin in the absence but not in the presence of metal ions.
		These results indicate that the TM helices C and F are in close proximity and suggest that movements of these helices relative to one another are required for transducin activation.
		Thus a change in the orientations of TM helices C and F is likely to be a key element in the mechanism for coupling binding of ligands (or isomerization of retinal) to the activation of G-protein-coupled receptors.
	www.nature.com /cgi-taf/DynaPage.taf?file=/nature/journal/v383/n6598/abs/383347a0.html (526 words)

	Long membrane helices and short loops predicted less accurately -- Chen and Rost 11 (12): 2766 -- Protein Science
		About half the high-resolution helices (47%) are 17–27 residues long, whereas 93% of the low-resolution helices fall into this interval (gray line).
		Half of the low-resolution helices (50%) are 20–24 residues long, whereas 25% of the high-resolution helices fall into this interval (dashed line).
		Turns in transmembrane helices: Determination of the minimal length of a "helical hairpin" and derivation of a fine-grained turn propensity scale.
	www.proteinscience.org /cgi/content/full/11/12/2766 (3620 words)

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