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Topic: Membrane topology

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	Title
		A prominent example for the pharmacological importance of membrane proteins is the large super-family of G protein-coupled receptors (GPCRs), which include receptors for hormone, neurotransmitter, growth factor, light and odour-related ligands [40, 41].
		The lipid membrane bilayer is crossed by the 11 helices in the middle of the structure.
		The topology is defined by the orientation of the helices with respect to the membrane bilayer, here the upper part of the protein is located in the periplasm, the lower part in the cytoplasm.
	cubic.bioc.columbia.edu /papers/2002_rev_htm/paper.html (9744 words)

	PSORT Users' Manual
		Membrane proteins have their spcefic way to integrate into the membrane in respect to the two sides (cytoplasmic or exo-cytoplasmic), which is called as membrane toplogy.
		Many proteins localized at the mitochondrial inner membrane are likely to be peripheral membrane proteins which exist as members of large membrane complexes and their degree of hydrophobicity is relatively low compared with membrane proteins in the vesicular pathway.
		The existence of a GY motif within 17 residues from the membrane boundary in the cytoplasmic tails of type Ia proteins is used as a rule for discrimination.
	psort.nibb.ac.jp /helpwww.html (3551 words)

	Johan Nilsson: Doktorsavhandling från Karolinska Institutet
		When the consensus approach was applied to all putative membrane proteins in a number of completely sequenced genomes, we found that highly reliable topology predictions could be made for nearly half of all membrane proteins in most prokaryotic organisms.
		With the partial consensus topology predictions, the average fraction of prokaryotic membrane proteins for which either a complete or a partial topology of high reliability could be predicted was increased to approximately 70%.
		The optimised method was then applied to all putative membrane proteins in each genome, and the average frequency bias of each amino acid residue type between polar segments on opposite sides of the membrane was estimated.
	diss.kib.ki.se /2004/91-7349-963-3 (581 words)

	Membrane Topology Analysis of Cyclic Glucan Synthase, a Virulence Determinant of Brucella abortus -- Ciocchini et al. ...
		Membrane Topology Analysis of Cyclic Glucan Synthase, a Virulence Determinant of Brucella abortus -- Ciocchini et al.
		Alternative topology models were generated by using the programs SOSUI (36) and HMMTOP (41, 42) (B); TopPred II with the GES hydropathy scale (window size, 21 residues) (12) (C); and TopPred II with the KD hydropathy scale (window size, 21 residues) (12) and TMHMM (24) (D).
		Membrane topology of the DrrB protein of the doxorubicin transporter of Streptomyces peucetius.
	jb.asm.org /cgi/content/full/186/21/7205 (4972 words)

	Dissection of De Novo Membrane Insertion Activities of Internal Transmembrane Segments of ATP-Binding-Cassette ...
		Model I is the predicted topology with all TM segments in the membrane.
		Membranes were pelleted after translation and then treated with PNGase F alone (lanes 2, 6, and 10), proteinase K alone (lanes 3, 7, and 11), or proteinase K followed by PNGase F (lanes 4, 8, and 12).
		Biogenesis of polytopic membrane proteins: membrane segments of P-glycoprotein sequentially translocate to span the ER membrane.
	www.molbiolcell.org /cgi/content/full/9/4/853 (5907 words)

	Membrane Protein Explorer (MPEx)
		A useful adjunct to MPEx is MPtopo, a database of Membrane Protein topology accessible from MPEx.
		MPtopo 3D_helix set of membrane proteins indicate that TM segments can be identified with high accuracy.
		We have constructed a database of membrane proteins of known topology (MPtopo), accessible from MPEx, that is useful for comparing the hydropathy behavior of proteins of unknown topology with the behavior of similar proteins of known topology.
	blanco.biomol.uci.edu /mpex (1809 words)

	Integral membrane protein biosynthesis: why topology is hard to predict -- Ott and Lingappa 115 (10): 2003 -- Journal ...
		topology or its distribution relative to the membrane.
		Shown here are a type I integral membrane protein, a type II integral membrane protein, a C-terminally anchored integral membrane protein, a type II signal-anchored protein and a multi-spanning membrane protein.
		to the translocon, an aqueous pore in the ER membrane responsible
	jcs.biologists.org /cgi/content/full/115/10/2003 (4650 words)

	Determination of the membrane topology of Ost4p and its subunit interactions in the oligosaccharyltransferase complex ...
		Determination of the membrane topology of Ost4p and its subunit interactions in the oligosaccharyltransferase complex in Saccharomyces cerevisiae -- Kim et al.
		in the endoplasmic reticulum (ER) membrane (2, 14, 15).
		Interaction is postulated to occur in the membrane near the mutation-sensitive region of Ost4p located in the cytoplasmic leaflet of the ER membrane.
	www.pnas.org /cgi/content/full/100/13/7460 (3287 words)

	Regulation of the Ribosome-Membrane Junction at Early Stages of Presecretory Protein Translocation in the Mammalian ...
		To determine the membrane topology of the signal sequence at the stages of translocation represented by the TVG60-, 80-, and
		in the absence of membrane, or in the presence of native membranes
		The protein-conducting channel in the membrane of the endoplasmic reticulum is open laterally toward the lipid bilayer.
	www.jcb.org /cgi/content/full/139/7/1697 (7495 words)

	Positive Charges Determine the Topology and Functionality of the Transmembrane Domain in the Chloroplastic Outer ...
		Topology of IEP110, a component of the chloroplastic protein import present in the inner envelope membrane.
		The protein-conducting channel in the membrane of the endoplasmatic reticulum is open laterally toward the lipid bilayer.
		The 2-oxoglutarate/malate translocator of chloroplast envelope membranes: molecular cloning of a transporter containing a 12-helix motif and expression of the functional protein in yeast cells.
	www.jcb.org /cgi/content/full/141/4/895 (6435 words)

	Selected references on membrane topology of P450s
		Black, S.D., Martin, S.T. and Smith, C.A. Membrane topology of liver microsomal cytochrome P450 2B4 determined via monoclonal antibodies directed to the halt-transfer signal.
		Nelson, D.R. and Strobel, H.W. On the membrane topology of vertebrate cytochrome P-450 proteins.
		Szczesna-Skorupa, E. and Kemper, B. An N-terminal glycosylation signal on cytochrome P450 is restricted to the endoplasmic reticulum in a luminal orientation.
	www.icgeb.trieste.it /~p450srv/P450_membrane_topology_reviews.html (899 words)

	Probing Pores with Peptide Plugs: Topology of Membrane-inserted Diphtheria Toxin -- Olsnes and Falnes 115 (4): 417 -- ...
		Glu349 as pivotal for the membrane insertion of the toxin's
		Falnes, P.O., Olsnes, S. Cell-mediated reduction and incomplete membrane translocation of diphtheria toxin mutants with internal disulfides in the A fragment.
		Parker, M.W., Pattus, F. Rendering a membrane protein soluble in water: a common packing motif in bacterial protein toxins.
	www.jgp.org /cgi/content/full/115/4/417 (2844 words)

	Georg Ried, Ralf Koebnik et al.: OmpA membrane topology (Site not responding. Last check: 2007-10-22)
		Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K12
		Thus no experimental evidence had been presented for the turns at the inner leaflet of the membrane and it was not known whether or not the periplasmic part of the polypeptide plays a role in the process of membrane incorporation.
		When ompA genes were constructed coding for proteins ending at residue 228 or 274, the membrane assembly of these proteins was shown to be partially defective with about 20% of the proteins not being assembled.
	www.sfb363.uni-halle.de /koebnik/pub06E.htm (322 words)

	Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase ...
		Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo -- Rojo et al.
		Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo
		In enlarged mitochondria, cristae membranes are swollen and/or difficult to identify.
	jcs.biologists.org /cgi/content/full/115/8/1663 (6371 words)

	The Distribution of Lipid Attached Spin Probes in Bilayers: Application to Membrane Protein Topology -- Vogel et al. 85 ...
		buried in the acyl chain region of the membrane are uninfluenced.
		Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis and (19)F NMR spectroscopy.
		Determining the membrane topology of peptides by fluorescence quenching.
	www.biophysj.org /cgi/content/full/85/3/1691 (5296 words)

	von Heijne lab publications (Site not responding. Last check: 2007-10-22)
		Lundin, M., Monné, M., Widell, A., von Heijne, G., and Persson, M.A.A. (2003) Topology of the membrane associated Hepatitis C virus NS4B protein.
		Kim, H., von Heijne, G., Caputo, G.A., and Lennarz, W.J. (2003) Determination of membrane topology of Ost4p, and its subunit interactions in the oligosaccharyltransferase complex in Saccharomyces cerevisiae.
		Kim, H., von Heijne, G., and Nilsson, I.M. (2005) Membrane topology of the STT3 subunit of the oligosaccharyl transferase complex.
	www.sbc.su.se /gunnar/gvhpub.html (4800 words)

	Eric Beitz: TeXtopo (Site not responding. Last check: 2007-10-22)
		PHD topology predictions are a mighty tool to localize transmembrane domains and the protruding loops.
		Making these data visible in a sophisticated topology plot is an enormous effort when using a standard drawing software.
		Beitz, E. TeXtopo: shaded membrane protein topology plots in LaTeX2e.
	homepages.uni-tuebingen.de /beitz/tte.html (138 words)

	MPtopo Database Search
		We have examined carefully the publications related to the topologies of the proteins before including them in the database.
		While we are reasonably certain of the number of TM segments of each protein included in 1D_Helix, the exact locations and lengths of the segments are less certain.
		The monotopic proteins have no TM segments, and are bound to the membrane surface by hydrophobic alpha-helices running parallel to the membrane plane.
	blanco.biomol.uci.edu /mptopo (659 words)

	TopPred 2 (Site not responding. Last check: 2007-10-22)
		With topology we mean the orientation and location of transmembrane helixes.
		"Membrane Protein Structure Prediction, Hydrophobicity Analysis and the Positive-inside Rule", Gunnar von Heijne, J. Mol.
		"Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method", Miklos Cserzo, Erik Wallin, Istvan Simon, Gunnar von Heijne, and Arne Elofsson, to appear in Protein Engineering, vol.
	www.sbc.su.se /~erikw/toppred2 (98 words)

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