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Topic: Coiled coil

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Structural motif

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	Coiled-Coil Protein (Site not responding. Last check: 2007-10-14)
		The amino acids in a coiled-coil structure reside on seven different structural positions on the coil, forming a heptad repeat, as illustrated in Figure-2.
		Each strand of a coiled-coil protein may be viewed as a repeated consensus substrings of the form (a-b-c-d-e-f-g)n, where a, b, c,...,g are the seven different structural positions on the coil.
		When the two strands coil around each other positions a and d are internalized, stabilizing the structure, while positions b, c, e, f, g are exposed on the surface of the protein.
	cis.poly.edu /~jps/coilcoil.html (160 words)

	Genome Biology \| Full text \| Predicting specificity in bZIP coiled-coil protein interactions
		Coiled coils are found in proteins that participate in many diverse processes, including transcription, oncogenesis and membrane fusion; predicting protein-protein interactions mediated by this motif will have important biological ramifications.
		Coiled-coil sequences are taken from a database of non-redundant interacting coiled coils containing approximately 29,000 residues from one of two classes: homodimeric coiled coils in myosin, tropomyosin, cortexillin and types III and V intermediate filament proteins; and heterodimeric coiled coils in keratin proteins [8,24].
		Each of these studies [14,16,19,38,39,44-47] provides an ordering of the stabilities of the coiled coils considered, and thus constraints of the type in equation 2 are introduced.
	www.genomebiology.com /2004/5/2/R11 (5898 words)

	packard (Site not responding. Last check: 2007-10-14)
		Coiled coils have already shown their usefulness in constructing biomaterials, for example, in the design of hydrogels.
		The chemical forces that govern the stability of coiled coils, and proteins in general, are well-understood and include hydrophobic, electrostatic, and amino acid side-chain packing interactions.
		However, since coiled coils are among the most constrained and regular of protein structures, they offer an ideal venue for continuum methods.
	www.haverford.edu /biology/nanoscience_program/nanoscience.htm (1942 words)

	Coiled Garden Hose Coil Anaconda 2
		From calculating tubing diameters, coil ratios and tail lengths, to wall thickness, burst pressure and tensile strength, Coil Solution understands it all.
		All the Garden Coil indoor hoses come with a sink adapter and a professional-grade watering wand capable of producing ultra-fine mists, perfectly controlled sprays or a soft gentle stream of water.
		The Anaconda is made from a premium polyether base polyurethane whereas other cheap coiled hoses are made from an inferior grade plastic that will degrade from water and weather exposure.
	www.naturestapestry.com /gardencoil.html (389 words)

	Protein Design Group at Sussex: Coiled coils
		The coiled coil is a ubiquitous protein motif that is often used to control oligomerisation.
		Very long coiled coils are found in proteins such as tropomyosin, intermediate filaments and spindle-pole-body components.
		Coiled coils are ideal candidates for protein folding and design studies, as they represent probably the simplest tertiary structure.
	www.biols.susx.ac.uk /Biochem/Woolfson/html/coils.html (594 words)

	X-ray of coiled coils and PLP-dependent enzymes (P. Burkhard)
		While this segment might yield a coiled coil within an isolated dimer, monomeric 1A helices are likely to play a role in specific dimer-dimer interactions during IF assembly.
		The X-ray crystal structure of the 18-heptad repeat alpha-helical coiled coil domain of the actin bundling protein cortexillin I from Dictyostelium discoideum is a tightly packed parallel two-stranded alpha-helical coiled coil.
		-helical coiled coils for applications such as two-stage drug targeting and delivery systems, coiled coils as templates for combinatorial helical libraries for drug discovery and as synthetic carrier molecules.
	www.biozentrum.unibas.ch /personal/burkhard/coiled-coil.html (765 words)

	JPred - Hints and Tips (Site not responding. Last check: 2007-10-14)
		Coiled coils are another special type of secondary structure element.
		If the coiled coil prediction methods predict a coiled coil you will need to re-examine your sequence.
		If there are coiled coil or TM regions within your protein, the predictions at the boundaries of coiled coil or transmembrane regions and the rest of the sequence are likely to be incorrect.
	www.compbio.dundee.ac.uk /~www-jpred/tips.html (354 words)

	Membrane Fusion Mediated by Coiled Coils: A Hypothesis -- Bentz 78 (2): 886 -- Biophysical Journal
		N-terminus of the native coiled coil and a helix-turn occurring
		Here, the results of this kinetic analysis are coupled to the proposal that the formation of the extended coiled coil of HA is the defect forming conformational change.
		2 is the hypothesis for fusion mediated by coiled coils.
	www.biophysj.org /cgi/content/full/78/2/886 (9266 words)

	Open-and-shut cases in coiled-coil assembly: {{alpha}}-sheets and {{alpha}}-cylinders -- Walshaw and Woolfson 10 (3): ...
		The coiled coil is a ubiquitous protein-folding motif.
		of the coiled coil is the seven-residue heptad repeat.
		O'Shea, E.K., Rutkowski, R., and Kim, P.S. Evidence that the leucine zipper is a coiled coil.
	www.proteinscience.org /cgi/content/full/10/3/668?ck=nck (2859 words)

	A Procedure for Refining a Coiled Coil Protein Structure Using X-Ray Fiber Diffraction and Modeling -- Briki et al. 83 ...
		Coiled coil structures are widespread motifs involved in a large number of oligomerization domains in various proteins.
		Until recently, the atomic structure of coiled coils was only known for short pieces involved in protein domains.
		FIGURE 4 Calculated pattern from the experimental structure of the cortexillin coiled coil protein (pdb entry: 1D7M) (A), calculated patterns on the same backbone structure as in (A) but with the side chains configured using the different procedures (B) SMD, (C) Confmat, (D) SCWRL.
	www.biophysj.org /cgi/content/full/83/4/1774 (4748 words)

	Coiled Coils
		This was the first useful algorithm for predicting coiled coils in protein sequences.
		Hard-boiled coiled coils Coiled Coils at Sussex University School of Biological Sciences.
		Algorithm for Matching Coiled-coil Proteins Resources for identifying coiled coils and predicting conserved epitopes between two coiled-coil proteins.
	www.york.ac.uk /depts/biol/units/coils/coilcoil.html (553 words)

	Instructions for using MULTICOIL on the web (Site not responding. Last check: 2007-10-14)
		The MultiCoil program for locating and distinguishing parallel dimeric and trimeric coiled coils is based upon the PairCoil program for locating dimeric coiled coils.
		Two are graphs of the probability that each residue lies in a coiled coil.
		The "Absolute Register" is an integer representation of the register of the coiled coil, and remains constant over the length of the coiled coil.
	theory.lcs.mit.edu /~elwolf/webcoil.html (912 words)

	EMBOSS: pepcoil (Site not responding. Last check: 2007-10-14)
		Coiled coils are formed by two or three alpha helices in parallel and in register that cross at an angle of approximately 20 degrees, are strongly amphipathic and display a pattern of hydrophilic and hydrophobic residues that is repeated every seven residues.
		The seven positions of the heptad repeat are designated a through g, a and d being generally hydrophobic, while the others are hydrophilic.
		The parallel two-stranded alpha-helical coiled coil is the most frequently encountered subunit-oligomerization motif in proteins.
	www.agri.huji.ac.il /embossdocs/pepcoil.html (320 words)

	Classification of Human B-ZIP Proteins Based on Dimerization Properties -- Vinson et al. 22 (18): 6321 -- Molecular and ...
		End view of a coiled coil with the seven unique positions of the heptad presented as ellipses, looking from the N terminus to the C terminus.
		Leucine is the most stabilizing aliphatic amino acid in the d position of a dimeric leucine zipper coiled coil.
		The role of position a in determining the stability and oligomerization state of alpha-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.
	mcb.asm.org /cgi/content/full/22/18/6321 (7710 words)

	Stabilization of a pH-sensitive apoptosis-linked coiled coil through single point mutations -- Dutta et al. 12 (2): 257 ... (Site not responding. Last check: 2007-10-14)
		coiled coil similar in nature to that formed by the WT peptide.
		Dutta, K., Alexandrov, A., Huang, H., and Pascal, S.M. pH-induced folding of an apoptotic coiled coil.
		Krylov, D., Barchi, J., and Vinson, C. Inter-helical interactions in the leucine zipper coiled coil dimer: pH and salt dependence of coupling energy between charged amino acids.
	intl.proteinscience.org /cgi/content/full/12/2/257 (3782 words)

	pH-induced folding of an apoptotic coiled coil -- Dutta et al. 10 (12): 2531 -- Protein Science
		Jelesarov, I. and Bosshard, H.R. Thermodynamic characterization of the coupled folding and association of heterodimeric coiled coils (leucine zippers).
		Jelesarov, I., Durr, E., Thomas, R.M., and Bosshard, H.R. Salt effects on hydrophobic interaction and charge screening in the folding of a negatively charged peptide to a coiled coil (leucine zipper).
		Marti, D.N., Jelesarov, I., and Bosshard, H.R. Interhelical ion pairing in coiled coils: Solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains.
	www.proteinscience.org /cgi/content/full/10/12/2531?ck=nck (5619 words)

	Coiled Coil Inspector: A description for the coiled coil inspector job
		Coiled Coil Inspector - Examines tungsten filament coils of electric light bulbs for concentricity and burrs by rolling coils under fingers on workbench, using tweezers to separate coils.
		The fl coil slowly was unwound from a giant spool as it was fed through the various stages of the coating process, all before being coiled again.
		An Oneonta man said his brother found a rattler coiled up in a garage at the Knapp family property on the corner of Hemlock and West Davenport roads on Tuesday.
	www.job-descriptions.org /coiled-coil-inspector.html (1190 words)

	INFO MARCOIL ON THE NET VERSION C1
		These matrices are MTIDK, derived from 5 and MTK derived from three "families" of proteins.
		The scale is roughly comparable to that of the COILS program (but not to that of the PAIRCOIL program).
		COILS is more specific for parallel dimeric coiled-coils and has a scale that generally attributes lower probabilities to false as well as to true coiled-coils.
	www.isrec.isb-sib.ch /webmarcoil/webmarcoilINFOC1.html (734 words)

	Paircoil Scoring Form
		Two are graphs of the residue-by-residue probability of that residue lying in a coiled coil.
		This document contains the sequence name, the probability cutoff, whether any domain in the sequence did meet this cutoff, and where the most likely coiled coil domain of the sequence was located, as well as how well this maximal point did score.
		The data generated by using this program is not saved from session to session and the user is advised to save all relevant data after analyzing the sequence and before leaving the page.
	searchlauncher.bcm.tmc.edu /seq-search/Help/paircoils.html (383 words)

	coiled-coil proteins (Site not responding. Last check: 2007-10-14)
		The alpha-helical coiled coil is one of the principal subunit oligomerization motifs in proteins.
		Its most characteristic feature is a heptad repeat pattern of primarily apolar residues that constitute the oligomer interface.
		Coiled coils: a highly versatile protein folding motif.
	www.humpath.com /article-printable.php3?id_article=2147 (100 words)

	Coiled coil Parameterization (Site not responding. Last check: 2007-10-14)
		Parallel vs. antiparallel coiled coils: The orientation of each helix is automatically determined, so there is no difference between saying a chain consists of residues C3-24 instead of C24-3.
		Global vs. Piecewise parameters: It is generally quite enlightening to look at how the superhelical parameters vary throughout the length of the coiled coil.
		This is implemented by repeating the same fit-analysis on each overlapping subsegment of, say, 7 residues in the coiled coil.
	ucxray.berkeley.edu /~mark/fitcc_doc.html (356 words)

	Golgins: coiled-coil-rich proteins associated with the Golgi Complex
		Given that the sera used for the cloning of both golgin-245 and golgin-97 came from patients with SS and the existence of other reports of anti-Golgi antibodies detected in patients with SS, it is intriguing to consider that these autoantibody-autoantigen systems play a significant role in the secretory defects in Sjögren's exocrine glands (Table 1).
		The golgins are related as they have similar overall secondary structures as predicted by analysis programs such as COILS (Lupas et al., 1991) and PAIRCOIL (Berger et al., 1995).
		It is interesting that the golgins also show significant sequence similarity to several cytoskeleton-related proteins including kinesin (Bloom and Brashear, 1989), the 150 kD dynein-associated protein (Holzbaur et al., 1991), the myosin family proteins (heavy chain myosin, tropomyosin), and desmin.
	www.ejbiotechnology.info /content/vol1/issue2/full/1/index.html (5138 words)

	PEP: Predictions for Entire Proteomes
		The Euclid system is based on a simple learning procedure from examples provided by human experts (Tamames, J., Ouzounis, C., Casari, G., Sander, C. & Valencia, A. EUCLID: automatic classification of proteins in functional classes by their database annotations.
		COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score.
		By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation.
	cubic.bioc.columbia.edu /PEP/methods.html (736 words)

	An engineered leucine zipper a position mutant with an unusual three-state unfolding pathway -- Zhu et al. 10 (1): 24 ...
		Gloss, L.M. and Matthews, C.R. Urea and thermal Equilibrium denaturation studies on the dimerization domain of Escherichia coil Trp Repressor.
		Lumb, K.J., Carr, C.M., and Kim, P.S. Subdomain folding of the coiled coil leucine zipper from the bZIP transcriptional activator GCN4.
		Su, J.Y., Hodges, R.S., and Kay, C.M. Effect of chain length on the formation and stability of synthetic alpha-helical coiled coils.
	protsci.highwire.org /cgi/content/full/10/1/24 (4226 words)

	Research and Reviews: Meat, Special Circular 172-99, Filament Assembly Properties of the Sarcomeric Myosin Heavy Chain
		The rod consists of two right hand a-helical coils that intertwine around one another forming a left-handed coiled-coil characteristics of the side-chain residues of the amino acids in the primary sequence are repeated every 28 amino acids.
		Connected ovals at the bottom of the diagram represent the fact that these residues are in a random coil motif.
		The observation of this pattern has prompted some investigators to suggest that the reduction in the free energy by the neutralization of opposite charges between myosin rods could provide the energy necessary for myosin assembly if the molecules were staggered by odd multiples of 14 residues (Matsuda et al.
	ohioline.osu.edu /sc172/sc172_4.html (3508 words)

	ABC News: Scientists Unlock Herpes Virus' Defenses (Site not responding. Last check: 2007-10-14)
		B5, the first fusion receptor ever identified, appears to be the means by which herpes simplex slips into the cell, she said.
		The researchers also discovered that the B5 molecule is shaped like a "coiled coil," which might allow it to fit into the structure of some viral fusion proteins.
		Coincidentally, these findings were published at the same time that a team of Italian researchers reported finding a likely "key" on the surface of the herpes virus — one that appears to match the B5 lock identified by Fuller and her team.
	abcnews.go.com /Health/Healthology/story?id=980172 (793 words)

	Unique stabilizing interactions identified in the two-stranded {alpha}-helical coiled-coil: Crystal structure of a ...
		Campbell, K.M., Sholders, A.J., and Lumb, K.J. Contribution of buried lysine residues to the oligomerization specificity and stability of the fos coiled coil.
		-helical coiled coils: 20 amino acid stability coefficients in the hydrophobic core of proteins.
		Zhu, H., Celinski, S.A., Scholtz, J.M., and Hu, J.C. The contribution of buried polar groups to the conformational stability of the GCN4 coiled coil.
	www.proteinscience.org /cgi/content/full/12/7/1395 (5832 words)

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