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Topic: Transmembrane helix

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	Computational Methods for Studying Transmembrane -Helices
		Transmembrane alpha-helical sequences are characterized by a largely, if not completely, hydrophobic stretch of around 20 amino acids, however, predictions of which sequences fold into helices may vary slightly depending on which polarity scale is chosen.
		The length of such a helix is determined by the length of the lipid bilayer the helix spans and the angle of the helix with respect to the membrane normal [Engelman et al, 1986].
		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)

	Transmembrane helix - Wikipedia, the free encyclopedia
		Within an integral membrane protein, a transmembrane helix is a segment that is alpha-helical in structure, roughly 20 amino acids in length, and (though it may be presumed to lie within the protein, out of contact with the surrounding lipid bilayer) is said to "span" the membrane.
		An alpha helix of about 20 amino acids long is the minimum required to span the width of the hydrophobic core of a lipid bilayer, although the exact thickness depends on the species of lipids.
		Using hydrophobicity analysis to predict transmembrane helices enables a prediction in turn of the "transmembrane topology" of a protein; i.e.
	en.wikipedia.org /wiki/Transmembrane_helix (263 words)

	Transmembrane Helix 10 (Site not responding. Last check: 2007-10-12)
		It has been found by experiment that tyrosine- and tryptophan-containing peptides representing stretches from the transmembrane domains of different integral membrane proteins (like presenilin and CFTR), are able to prevent oxidative lysis in clonal and primary cells.
		There are 6 positively charged amino acid residues in the transmembrane helices of CFTR (K95 in M1, R134 in M2, R334 and K335 as well as R347 in M6, R1030 in M10) and they seem to be highly conserved between species.
		If amino acids in transmembrane helices line up on the same side of the helix every 3.6 residues, then each amino acid is rotated 100 degrees away from the amino acid residues on either end of it.
	www2.montana.edu /cftr/PointandClick/cftr_point_and_click_helix10.htm (205 words)

	Transmembrane Helix 6
		This helix was the first one suggested (by Anderson, 1991) to be involved in forming pore.
		Lysine (95?) and Lysine (335?) were mutated in this helix to aspartate and glutamate.
		The amino acids from Threonine 351 to Glutamine 353, which form the part of the helix near the cytoplasm, are believed to be part of the pore where it narrows and therefore may be involved in the selectivity filter which selects for anions over cations.
	www2.montana.edu /cftr/PointandClick/cftr_point_and_click_helix6.htm (1278 words)

	Yeagle et al. Mol Vis 2:12, 1996.
		The resulting minimized structure was moved to MacImdad on the same computer, and the carboxyl terminal was docked to the model of the transmembrane domain by superposition of the overlapping portions of the seventh helix.
		Using the overlap between helix 7 of the transmembrane domain and the helix on the N terminus of rhoIVe, the structure of the carboxyl terminal domain was docked with the transmembrane domain.
		This alpha-helix is logically continuous with helix 7 of the transmembrane domain of rhodopsin.
	www.molvis.org /molvis/v2/a12 (2465 words)

	BioMed Central \| Full text \| Prediction of transmembrane helix orientation in polytopic membrane proteins
		Recently, the structures of homo-oligomeric transmembrane (TM) proteins were successfully modeled using the techniques of simulated annealing, molecular dynamics [4-7], Monte-Carlo simulations [8], and an empirical scoring function designed to specifically distinguish tightly packed TM oligomers [9].
		With exception of helix 7, the sequences of computationally predicted and structure-based TM helices have significant overlap throughout the whole length of the helix (Table 2).
		The analogous faces with conserved residues in the PetN TM helix from 1Q90 are buried within a helical bundle and are mainly involved in helix-helix interactions with helix I from subunit IV (Figure 8C).
	www.biomedcentral.com /1472-6807/6/13 (7310 words)

	MODELING THE TRANSMEMBRANE DOMAIN OF A GPCR.
		Proposed interactions of helix 7 with other transmembrane domains are illustrated in Figure 1 on the anticlockwise arrangement corresponding to Baldwin's model and supported by data for rhodopsin.
		If helix 7 is positioned according to the predicted buried face in the transmembrane bundle, the Lys 7.43 residue is appropriately placed in the vicinity of helices 2 and 3.
		The modified helix 7 is shown to fit into the helix bundle packing scheme in a manner that satisfies all the constraints generated from experimental data for the interactions of transmembrane segment 7.
	physiology.med.cornell.edu /faculty/hweinstein/online/KK_poster.html (2494 words)

	Improvement of the Transmembrane Helix Prediction System by Three-Stage Model
		A new method to predict the transmembrane helices from amino acid sequences was developed, in which the effect of the stabilization of helices by interhelix binding was taken into account.
		It was assumed that there are three stages of transmembrane helix conformation: the binding to membrane surface, the formation of transmembrane core region, and the maturation of helix due to the tertiary structure formation in membrane.
		This method was applied to the amino acid sequences of membrane proteins whose number of transmembrane helix are given, and most transmembrane helices were truly predicted.
	www.jsbi.org /journal/GIW96/Poster/GIW96P08.html (112 words)

	Transmembrane helix stability: the effect of helix-helix interactions studied by Fourier transform infrared ...
		Transmembrane helix stability: the effect of helix-helix interactions studied by Fourier transform infrared spectroscopy.
		The slow exchange rates measured for the amide protons of the transmembrane helices of this protein in detergent solution may indicate a destabilization of the helices in detergent solution compared with the membrane.
		We suggest that the observed loss of amide proton protection in the transmembrane helices as they are dissociated might be due to an increase in the helix flexibility and breathing motions as interactions between helices are reduced.
	www.medscape.com /medline/abstract/9533710 (315 words)

	Helix Packing in Polytopic Membrane Proteins: Role of Glycine in Transmembrane Helix Association -- Javadpour et al. 77 ...
		Helix 1(I) of cytochrome c oxidase provides an example of a transmembrane helix having two distinct packing surfaces.
		The number of residues of each amino acid type was determined from the helix-packing curves of the helix pairs in cytochrome c oxidase, bacteriorhodopsin, the photosynthetic reaction center complex, and the bacterial potassium channel.
		The role of helix VIII in the lactose permease of Escherichia coli.
	www.biophysj.org /cgi/content/full/77/3/1609 (5654 words)

	Yeagle, Mol Vis 2000; 6:125-131.
		The sequence of this transmembrane segment overlapped significantly the sequence of a peptide from the carboxyl terminal of rhodopsin, the structure of which was solved previously.
		This amino acid sequence was predicted to form the seventh transmembrane helix of bovine rhodopsin based on hydropathy plots of the primary sequence of rhodopsin [16].
		Studies on three loops [6] and one transmembrane helix (Katragadda et al., unpublished data) of bacteriorhodopsin as peptides in DMSO have shown good fidelity between the structures of the peptides seen in solution and the corresponding region in the crystal structure of the protein.
	www.molvis.org /molvis/v6/a17 (3784 words)

	Faculty Labs: D. Engelman - MB&B - Yale (Site not responding. Last check: 2007-10-12)
		We have shown that the interaction of glycophorin transmembrane helices in the chimeric proteins mimics that of the interactions in glycophorin dimers.
		Subsequent to the modeling and mutagenesis, we determined the structure of the helix dimer in a detergent environment using heteronuclear NMR, and found it to be very similar to the model.
		Fisher, L. E., Engelman, D. M., Sturgis, J. “Effect of detergents on the association of the glycophorin A transmembrane helix” Biophys J. Mitra, K., Ubarretxena-Belandia, I., Taguchi, T., Warren, G., Engelman, D. “Modulation of the bilayer thickness of exocytic pathway membranes by membrane proteins rather than cholesterol” PNAS (2004) 101:4083-4088.
	www.mbb.yale.edu /fl/fl_d_engelman.htm (1406 words)

	SCOP: Fold: Single transmembrane helix
		Photosystem II reaction centre subunit H, transmembrane region [81490] (1)
		Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor [81496] (1)
		Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor [103431] (1)
	scop.mrc-lmb.cam.ac.uk /scop/search.cgi?sunid=81407 (300 words)

	The Escherichia coli aspartate receptor: sequence specificity of a transmembrane helix studied by hydrophobic-biased ...
		The aspartate receptor is a dimer with two transmembrane sequences per subunit, for a total of four transmembrane sequences.
		The second transmembrane sequence connects the periplasmic ligand binding domain to the cytoplasmic signaling domain.
		of the transmembrane helix, the length and the amino acid sequence.
	peds.oxfordjournals.org /cgi/content/full/12/10/863 (5536 words)

	A Model of Inverse Agonist Action at Thyrotropin-Releasing Hormone Receptor Type 1: Role of a Conserved Tryptophan in ...
		Only Asn-110 (transmembrane helix 3), Trp-279 (transmembrane helix 6), midazolam, and the backbone of the receptor (ribbon representation) are shown.
		Transmembrane helix 3 (transmembrane helix 3) is blue, transmembrane helix 5 is cyan, transmembrane helix 6 is yellow, and transmembrane helix 7 is purple.
		Colson AO, Perlman JH, Jinsi-Parimoo A, Nussenzveig DR, Osman R, and Gershengorn MC (1998a) A hydrophobic cluster between transmembrane helices 5 and 6 constrains the thyrotropin-releasing hormone receptor in an inactive conformation.
	molpharm.aspetjournals.org /cgi/content/full/66/5/1192 (5315 words)

	Direct Simulation of Transmembrane Helix Association: Role of Asparagines Biophysical Journal - Find Articles
		The forces contributing to the association of transmembrane helices in folded membrane proteins have received considerable attention recently.
		The interaction between the polar asparagine residues, capable of simultaneously being a hydrogen-bond donor and acceptor, contributes strongly to the stability of associated helices.
		Two Asn mutants (M701N and G708N) of the transmembrane helix [beta]3 of integrin [alpha]IIb[beta]3 have been identified to drive the association by homooligomerization (Li et al., 2003) activating the mutant integrin to constitutively bind fibrinogen.
	www.findarticles.com /p/articles/mi_qa3938/is_200409/ai_n9451588 (893 words)

	A triangle lattice model that predicts transmembrane helix configuration using a polar jigsaw puzzle -- Hirokawa et al. ...
		Polar interaction energy between a transmembrane helix and a probe helix of serine–alanine copolymer is calculated and then used as the polar index of a helix.
		Using two probe helices and rotating a transmembrane helix, 48 polar index values were obtained for simple estimation of helix–helix binding energy (c).
		Helix triangles of CFG clockwise and anticlockwise are highlighted in the helix arrangements.
	peds.oxfordjournals.org /cgi/content/full/13/11/771 (3583 words)

	Membrane proteins
		Considering single span, bitopic transmembrane helices of similar length and hydrophobicity, inorder to explain why some associate, and others do not (at least not with any physiologicalsignificance) one must consider the exact amino acid content of the helices.
		Because the lipid exposed exterior of a transmembrane domain doesnot carry many charged residues or hydrogen bonding groups, the nature of the forcesinvolved with the association of secondary structure elements, and those involved inoligomerisation, are quite different to the analogous aqueous situation.
		The alpha-helical transmembrane domain lends itself particularlywell to such molecular modelling methods, and is a more than worthy subject,given the difficulty of using NMR and crystallography, the normal methods ofprotein structure determination.
	www.bio.cam.ac.uk /~tjs23/mem04.html (3942 words)

	TMpredict documentation
		It should be noted, that errors in the annotation of transmembrane helices are quite frequent since this reflect only the uncertainty of TM-domain prediction and the lacking of experimental data.
		The methodology for grouping the transmembrane proteins into families and for calculating the 'relative degeneracy' is explained in the paragraphs below.
		The helix orientations have been derived from the protein orientation given in tmb_or using the position number of the helix and the assumption of an alternating pattern of i->o and o->i helices.
	www.isrec.isb-sib.ch /tmbase/TMBASE_doc.html (1993 words)

	CLC bio: Transmembrane helix prediction
		Transmembrane segments shown as annotation on the sequence and the topology.
		The Transmembrane Helix Prediction Plug-in can be used to predict transmembrane helices.
		Thus an active Internet connection is required to run the transmembrane helix prediction.
	www.clcbio.com /index.php?id=944&ext=tmhmm (115 words)

	JBSD Online
		Transmembrane Helix Packing of ErbB/Neu Receptor in Membrane Environment: A Molecular Dynamics Study (p.
		MD results indicate that helix-lipid interactions in the bilayer core are extremely similar in the two environments and raise the role of the juxtamembrane residues in helix insertion and helix-helix packing.
		According to the hypothesis of a monomer-dimer equilibrium of the proteins it is likely that the bilayer imposes structural constraints that favor dimerization-competent structure responsible of the proper topology necessary for receptor activation.
	www.jbsdonline.com /index.cfm?CFID=12767896&CFTOKEN=43313114&d=3024&c=4216&p=15334&do=detail (302 words)

	A Transmembrane Helix Dimer: Structure and Implications -- MacKenzie et al. 276 (5309): 131 -- Science (Site not responding. Last check: 2007-10-12)
		Transmembrane glycine zippers: Physiological and pathological roles in membrane proteins.
		Transmembrane S1 Mutations in CNGA3 from Achromatopsia 2 Patients Cause Loss of Function and Impaired Cellular Trafficking of the Cone CNG Channel.
		Conserved transmembrane tyrosine residues of the TCR {beta} chain are required for TCR expression and function in primary T cells and hybridomas.
	www.sciencemag.org /cgi/content/abstract/276/5309/131 (2421 words)

	CLC bio: Transmembrane helix prediction (TMHMM)
		Most membrane proteins have hydrophobic regions which span the hydrophobic core of the membrane bi-layer and hydrophilic regions located on the outside or the inside of the membrane.
		For prediction of transmembrane helices, TMHMM version 2.0 [Krogh et al., 2001] is used.
		To predict transmembrane helixes, simply select the sequences of interest and run the analysis.
	www.clcbio.com /index.php?id=453 (206 words)

	SCOP: Class: Membrane and cell surface proteins and peptides (Site not responding. Last check: 2007-10-12)
		core: up-and-down bundle of seven transmembrane helices tilted 20 degrees with respect to the plane of the membrane
		12 transmembrane helices in an approximate threefold rotational symmetric arrangement
		12 transmembrane helices; duplication: the N- and C-terminal halves of the whole proteins are structurally similar
	scop.berkeley.edu /data/scop.b.g.html (535 words)

	Introduction of a Carboxyl Group in the First Transmembrane Helix of Escherichia coli F1Fo ATPase Subunit c and ...
		Positions equivalent to 28 in helix 1 and position 61 in helix 2 of E.
		Two carboxyl groups in transmembrane helices of subunit c are found in several pathogenic bacteria and in the related vacuolar ATPase.
		helices 3 and 5 that are equivalent to helix 2 in the F-type subunit
	jb.asm.org /cgi/content/full/183/5/1524 (3468 words)

	Transmembrane helix predictions revisited -- Chen et al. 11 (12): 2774 -- Protein Science
		2001) • TMpred, prediction of transmembrane helices (Hofmann and Stoffel 1993) • TopPred2, hydrophobicity-based membrane helix prediction (von Heijne 1992; Cserzö et al.
		Although the two distributions appear rather similar, the higher symmetry in the low-resolution graph hid that the percentages with no difference were quite different: 71% for the high-resolution data and 56% for the low-resolution data.
		of the assignments of transmembrane helices and topology.
	www.proteinscience.org /cgi/content/full/11/12/2774 (7029 words)

	Alanine Insertion Scanning Mutagenesis of Lactose Permease Transmembrane Helices -- Braun et al. 272 (47): 29566 -- ...
		helix that contribute to the dimerization of this protein in vitro
		Previous Cys scanning mutagenesis indicated that none of the residues in helix III is essential with respect to insertion,
		The effect of the insertions on the steady-state amount of lactose permease in the membrane was found to be position-dependent.
	www.jbc.org /cgi/content/full/272/47/29566 (4498 words)

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