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Topic: Hydrophobicity analysis

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	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.
		Because the interior of the bilayer and the interiors of most proteins of known structure are hydrophobic, it is presumed to be a requirement of the amino acids that span a membrane that they be hydrophobic as well.
		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 (245 words)

	Clusters of proteins in archaeal and bacterial proteomes using compositional analysis
		Although the usual approach followed for sequence analysis and classification of proteins is based on sequence alignment [15], several approaches have been developed using amino acid composition.
		In a comparative analysis of the proteomes of enteric pathogens, sequence complexity analysis showed that species patterns exist in a limited set of low complexity proteins that parallels taxonomic classification [26, 27].
		The ribosomal proteins of each species serve as a good reference point for comparative analysis of the 'atypical' proteins since they are universal, appear as typical proteins in all proteomes, are part of core biological functions of the cell and are also highly expressed [1].
	www.bioinfo.de /isb/2004/04/0048/main.html (6579 words)

	Title
		This hydrophobic moment differed between transmembrane and globular helices and could thus be explored to predict transmembrane regions [77].
		In contrast, Jahnig suggested that a generalisation of hydrophobicity analysis was sufficient to predict membrane-spanning amphiphilic a-helices and b-strands [118].
		This hydrophobicity gradient may facilitate the penetration of a membrane and may thus destabilise the packing of the lipids in the membrane bilayer and/or of the protein/water interface.
	cubic.bioc.columbia.edu /papers/2002_rev_htm/paper.html (9744 words)

	A to H
		Comparative molecular field analysis (CoMFA) is a 3D-QSAR method that uses statistical correlation techniques for the analysis of the quantitative relationship between the biological activity of a set of compounds with a specified alignment, and their three-dimensional electronic and steric properties.
		Hansch analysis is the investigation of the quantitative relationship between the biological activity of a series of compounds and their physicochemical substituent or global parameters representing hydrophobic, electronic, steric and other effects using multiple regression correlation methodology.
		Hydrophobicity is the association of non-polar groups or molecules in an aqueous environment which arises from the tendency of water to exclude non polar molecules.
	www.chem.qmul.ac.uk /iupac/medchem/ah.html (2005 words)

	JYI: A Computational the Analysis of Sunflower (Helianthus annuus L.) Glyoxysomal 3-oxoacyl-CoA Thiolase (Site not responding. Last check: 2007-10-29)
		The hydrophobicity profiles of the eight thiolase sequences are obtained using ProtScale (http://www.expasy.ch/cgi-bin/protscale.pl).
		The hydrophobicity plot of sunflower thiolase II is compared to the seven plant thiolase sequences; a linear regression analysis of the profiles is then done to find trends (Figure 3).
		Kyte and Doolittle hydrophobicity analysis of sunflower thiolase II, soybean thiolase, and Japanese rice thiolase.
	www.jyi.org /volumes/volume11/issue3/articles/umer.html (4137 words)

	Transmembrane helix predictions revisited
		In contrast, most simple hydrophobicity scale-based methods were significantly less accurate than any advanced method as they over-predicted membrane helices and confused membrane helices with hydrophobic regions outside of membranes.
		Overall, the most successful hydrophobicity scale appeared the Ben-Tal scale which is based on the free energy of transferring an amino acid from water into the centre of the hydrocarbon region of a lipid bilayer [2].
		It embeds a number of statistical preferences and rules into a Hidden Markov model to optimise the prediction of the localisation of membrane helices and their orientation (note: similar concepts are used for HMMTOP [16]).
	cubic.bioc.columbia.edu /papers/2002_htm_eval/paper.html (10714 words)

	Hydrophobicity Analysis of Amino Acids (Site not responding. Last check: 2007-10-29)
		Based on a principal component analysis of 47 published attempts to quantify hydrophobicity in terms of a single scale, we define a representation of the 20 amino acids as points in a 3-dimensional hydrophobicity space and display it by means of a minimal spanning tree.
		The assignment of the amino acids to a quantitative hydrophobicity scale is a controversial problem.
		A minimal spanning tree analysis (see also here) reveals that the appropriate nearest neighbor relation between amino acids is not fully linear.
	archivumphysicum.physicsarchives.com /HydrophobicityAnalysisofAminoAcids.htm (970 words)

	doc 63 (Site not responding. Last check: 2007-10-29)
		Hydrophobicity analysis suggested that the cleavage-activation domain became more hydrophobic and could be less accessible for host-specific protease(s); dibasic residues next to the F1 N-terminus were shown to be important for keeping the cleavage-activation site in exposed positioning, suitable for F protein activation.
		Comparative sequence analysis of the NDV F proteins revealed a striking homology between lentogenic La Sota and mesogenic Beaudette C strains.
		Furthermore, 58 variable positions were recorded in the NDV F protein, excluding signal sequence; some of these mutations, in the cysteine-clustered region, were surmised to alter virulence.
	www.fsagx.ac.be /bp/abstracts/a63.htm (188 words)

	Wolfram syndrome: a clinical and molecular genetic analysis -- Eller et al. 38 (11): 37 -- Journal of Medical Genetics
		The prevalence of Wolfram syndrome was estimated at 1/100 000 in a North American population and 1/770 000 in the United Kingdom.
		Sequence analysis of the WFS1 gene of patient 1.1.
		Analysis of the family showed (A) that patient 2.1 and her father were heterozygous for the 2315ins(T) mutation, and (B) that patient 2.1 and her mother were heterozygous for the 2638-2643del(GACTTC) mutation.
	jmg.bmjjournals.com /cgi/content/full/38/11/e37 (3067 words)

	Nucleotide sequence and genetic complementation analysis of lep from Azotobacter vinelandii. (Site not responding. Last check: 2007-10-29)
		Nucleotide sequence and genetic complementation analysis of lep from Azotobacter vinelandii.
		Southern blotting analysis of the A. vinelandii chromosome by probing with lep specific DNA revealed that lep is present as a single copy per the chromosome.
		The putative membrane topology of the protein seems similar to that of E. coli leader peptidase I based on the hydrophobicity analysis of the predicted amino acid sequence.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/1207225.html (178 words)

	[No title] (Site not responding. Last check: 2007-10-29)
		The structural analysis routines are designed to help the user in determining important aspects of structure and function in those cases where very little is known about the protein of interest.
		Hydrophobicity plots may additionally be used to locate membrane spanning regions in some types of proteins (hydrophobic regions of 20 or more residues).
		Hydrophobicity charts may be used to approximate the positions of coil regions, exposed loops or B-cell antigenic determinants in many proteins (hydrophilic regions).
	www.pence.ca /software/seqsee/latest/doc.seqman (12800 words)

	Molecular cloning, sequence analysis, and expression of the yeast alcohol acetyltransferase gene. (Site not responding. Last check: 2007-10-29)
		Molecular cloning, sequence analysis, and expression of the yeast alcohol acetyltransferase gene.
		Molecular cloning, sequence analysis, and expression of the yeast alcohol acetyltransferase gene.The nucleotide sequence of the ATF1 gene isolated from S. cerevisiae was determined.
		A Southern analysis of the yeast genomes in which the ATF1 gene was used as a probe revealed that S. cerevisiae has one ATF1 gene, while brewery lager yeast has one ATF1 gene and another, homologous gene (Lg-ATF1).
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/131722.html (174 words)

	[No title]
		From this analysis, it appears that myosin is composed primarily of amino acids arranged in a helical formation.
		This segment is predicted in the 2d structure analysis by the long blue helix containing a green turn in the middle of the diagram.
		This figure is a Kyte-Doolittle hydrophobicity analysis of the mouse protein myosin.
	www.bio.davidson.edu /Courses/Molbio/MolStudents/01jeklotz/analysis.html (804 words)

	Scales of Amino Acid Attributes (Site not responding. Last check: 2007-10-29)
		Hydrophobicity scale (H) for proteins of aa class, Ponnuswamy's 1980 procedure was used.
		Hydrophobic Potential Derived from X-ray Structures of Globular Proteins is able to Identify Native Folds".
		Statistical scale of hydrophobicity based on information theory of the observed solvent accessibility of residues in proteins of known structure.
	garlic.mefos.hr /split/scales.html (2728 words)

	Analysis of the Membrane Topology of the Acid-sensing Ion Channel 2a -- Saugstad et al. 279 (53): 55514 -- Journal of ...
		Analysis of the Membrane Topology of the Acid-sensing Ion Channel 2a -- Saugstad et al.
		analysis, and the predicted amino acid sequences were determined
		to hydrophobicity analysis and homology with ENaC channels (3).
	www.jbc.org /cgi/content/full/279/53/55514 (3385 words)

	Intracellular gene transfer: Reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochrome c oxidase -- ...
		The mature Cox2 is denoted M.) Western blot analysis of mitochondria and mitoplasts used in D, with antisera raised to porin (outer mitochondrial membrane), cyt c (intermembrane space), Ucp (inner mitochondrial membrane), and Hsp70 (matrix).
		Hydrophobicity was calculated by using the scale of KD (19).
		hydrophobicity preclude the transfer of a gene to the nucleus.
	www.pnas.org /cgi/content/full/99/16/10510 (4365 words)

	On Hydrophobicity Correlations in Protein Chains -- Irbäck and Sandelin 79 (5): 2252 -- Biophysical Journal
		Our statistical analysis of hydrophobicity strings can be divided into two parts.
		Hydrophobicity plays a key role in the formation of protein structures, which makes it of utmost interest to understand the
		Statistical distribution of hydrophobic residues along the length of protein chains: implications for protein folding and evolution.
	www.biophysj.org /cgi/content/full/79/5/2252 (2819 words)

	Genomic and Proteomic Analysis of Mitochondrial Carrier Proteins in Arabidopsis -- Millar and Heazlewood 131 (2): 443 ...
		Hydrophobic proteins are rarely identified in proteomic analysis.
		The hydrophobicity of each transmembrane domain in each carrier protein was calculated using the augmented Wimley-White (aWW) scale at http://blanco.biomol.uci.edu/mpex.
		Liu Q, Dunlap J (1996) Isolation and analysis of the arg-13 gene of Neurospora crassa.
	www.plantphysiol.org /cgi/content/full/131/2/443 (5554 words)

	Molecular dynamics simulations of individual alpha-helices of bacteriorhodopsin in dimyristoylphosphatidylcholine. II. ...
		Table 4 continues this analysis by presenting data from the 2BRD structure for the 10 lipids that were resolved.
		Hydrophobic moments have been used for the prediction of membrane protein tertiary structure (e.g., Taylor et al., 1994
		Analysis of membrane and surface protein sequences with the hydrophobic moment plot.
	www.biophysj.org /cgi/content/full/74/1/115 (5545 words)

	Interaction between the User and Heijne's membrane topology prediction algorithm TOPPRED (Site not responding. Last check: 2007-10-29)
		In the top spreadsheet (spreadsheetalig2), I ran a Toppred analysis without User Data and in the bottom one (spreadsheetalig3), I ran a Toppred analysis with user information (user segment labelled in red).
		Indeed, the output result of a first Toppred analysis can be fed with user data and be re-used as the input data for a second Toppred run.
		Hydrophobicity analysis and the positive-inside rule J. Mol.
	www.pasteur.fr /~letondal/biok/usermixin.html (1437 words)

	Isolation and Characterization of the Gene Encoding a Novel Factor Xa-directed Anticoagulant from the Yellow Fever ...
		A biochemical analysis of the anticoagulant in the yellow fever mosquito, Aedes aegypti, a culicine, showed that it was a
		SDS-PAGE Analysis and Electrophoretic Transfer-- SDS-PAGE was performed in 10 or 12.5% polyacrylamide slab gels according to Laemmli (11) and stained with Coomassie Brilliant
		The serpin sequences were chosen based on their similarities after a blast analysis of the AFXa cDNA that identified conservation within three domains near the carboxyl termini.
	www.jbc.org /cgi/content/full/273/33/20802 (5810 words)

	Human-derived bradeion proteins, DNA coding for the proteins, and uses thereof - US Patent 6423504 (Site not responding. Last check: 2007-10-29)
		This analysis is one method for predicting a high-order structure of a protein based on its amino acid sequence, whereby the distributions of hydrophobic and hydrophilic portions of the protein can be determined.
		This analysis therefore allows to study the presence of a three-dimensional structure or a transmembranous domain.
		As a result, the bradeion proteins of the invention were found to be membrane proteins with a structure characteristic of an interleukin receptor even in the structure of a transmembranous portion in the amino acid sequences.
	www.patentstorm.us /patents/6423504.html (7034 words)

	Mechanisms of quinolone resistance in clinical isolates: accumulation of sparfloxacin and of fluoroquinolones of ...
		Mechanisms of quinolone resistance in clinical isolates: accumulation of sparfloxacin and of fluoroquinolones of various hydrophobicity, and analysis of membrane composition -- Denis and Moreau 32 (3): 379 -- Journal of Antimicrobial Chemotherapy
		Mechanisms of quinolone resistance in clinical isolates: accumulation of sparfloxacin and of fluoroquinolones of various hydrophobicity, and analysis of membrane composition
		hydrophobicity emphasized the importance of this property in the uptake of
	jac.oupjournals.org /cgi/content/abstract/32/3/379 (358 words)

	New structure and function in plant K+ channels: KCO1, an outward rectifier with a steep Ca2+ dependency (Site not responding. Last check: 2007-10-29)
		Hydrophobicity values were calculated according to the Kyte and Doolittle method (window size 11 amino acids) (Kyte and Doolittle, 1982) and were plotted against the amino acid position.
		Amino acid positions of the EF-hands within the respective proteins, as well as accession numbers (#) are given.
		The basic amino acid stretch (KR) at the N−terminus and the two EF-hands present at the C-terminus are shown as boxes.
	www.nature.com /emboj/journal/v16/n10/fig_tab/7590242f1.html (328 words)

	{alpha}-Helical Structural Elements within the Voltage-sensing Domains of a K+ Channel -- Li-Smerin et al. 115 (1): 33 ...
		Open bars mark the approximate limits of the four transmembrane segments defined by hydrophobicity analysis.
		cross the hydrophobic core of the lipid membrane.
		-PI are observed at minima in the hydrophobicity analysis (Figure 9).
	www.jgp.org /cgi/content/full/115/1/33 (7120 words)

	Cell Wall Mannan and Cell Surface Hydrophobicity in Candida albicans Serotype A and B Strains -- Masuoka and Hazen 72 ...
		Cell Wall Mannan and Cell Surface Hydrophobicity in Candida albicans Serotype A and B Strains -- Masuoka and Hazen 72 (11): 6230 -- Infection and Immunity
		Cell Wall Mannan and Cell Surface Hydrophobicity in Candida albicans Serotype A and B Strains
		hydrophobicity of the two serotypes is qualitatively different,
	iai.asm.org /cgi/content/abstract/72/11/6230 (283 words)

	Ion channel structure and function
		So called hydropathy plots indicate the grouping of hydrophobic stretches in the sequence that are identified as spanning the membrane, usually in the form of
		Because of the size of the cavity, this central ion is proposed to be hydrated.
		Furthermore, the structure shows that, with the exception of the selectivity filter (12Å long), the pore lining is mainly hydrophobic (cytoplasmic side of channel lumen, corresponds to lower half of pore in above figure), a general property of K-channels.
	www.whatislife.com /reader/channels/channels.html (2080 words)

	Cell Wall Mannan and Cell Surface Hydrophobicity in Candida albicans Serotype A and B Strains -- Masuoka and Hazen 72 ...
		Analysis of mono- and oligosaccharide isomers derivatized with 9-aminopyrene-1,4,6-trisulfonate by capillary electrophoresis with laser-induced fluorescence.
		Relationship of cell surface hydrophobicity to morphology of monomorphic and dimorphic fungi.
		Structural analysis of phospho-D-mannan-protein complexes isolated from yeast and mold form cells of Candida albicans NIH A-207 serotype A strain.
	iai.asm.org /cgi/content/full/72/11/6230 (4228 words)

	Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by ...
		Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by Nonlinear Signal Analysis of Acylphosphatase and A{beta}(1-40) -- Zbilut et al.
		Protein Aggregation/Folding: The Role of Deterministic Singularities of Sequence Hydrophobicity as Determined by Nonlinear Signal Analysis of Acylphosphatase and Aß(1–40)
		by means of nonlinear signal analysis of their chain hydrophobicity.
	www.biophysj.org /cgi/content/abstract/85/6/3544 (207 words)

	Analysis of F Factor TraD Membrane Topology by Use of Gene Fusions and Trypsin-Sensitive Insertions -- Lee et al. 181 ...
		Analysis of F Factor TraD Membrane Topology by Use of Gene Fusions and Trypsin-Sensitive Insertions -- Lee et al.
		Analysis of F Factor TraD Membrane Topology by Use of Gene Fusions and Trypsin-Sensitive Insertions
		Analysis of the sequence and gene products of the transfer region of the F sex factor.
	jb.asm.org /cgi/content/full/181/19/6108 (4145 words)

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