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Hydrophobic Amino Acids (hydrophobic + amino_acids)
Selected AbstractsSingle amino acid repeats in signal peptidesFEBS JOURNAL, Issue 15 2010abaj There has been an increasing interest in single amino acid repeats ever since it was shown that these are the cause of a variety of diseases. Although a systematic study of single amino acid repeats is challenging, they have subsequently been implicated in a number of functional roles. In general surveys, leucine runs were among the most frequent. In the present study, we present a detailed investigation of repeats in signal peptides of secreted and type I membrane proteins in comparison with their mature parts. We focus on eukaryotic species because single amino acid repeats are generally rather rare in archaea and bacteria. Our analysis of over 100 species shows that repeats of leucine (but not of other hydrophobic amino acids) are over-represented in signal peptides. This trend is most pronounced in higher eukaryotes, particularly in mammals. In the human proteome, although less than one-fifth of all proteins have a signal peptide, approximately two-thirds of all leucine repeats are located in these transient regions. Signal peptides are cleaved early from the growing polypeptide chain and then degraded rapidly. This may explain why leucine repeats, which can be toxic, are tolerated at such high frequencies. The substantial fraction of proteins affected by the strong enrichment of repeats in these transient segments highlights the bias that they can introduce for systematic analyses of protein sequences. In contrast to a general lack of conservation of single amino acid repeats, leucine repeats were found to be more conserved than the remaining signal peptide regions, indicating that they may have an as yet unknown functional role. [source] PC1/3, PC2 and PC5/6A are targeted to dense core secretory granules by a common mechanismFEBS JOURNAL, Issue 16 2007Jimmy D. Dikeakos There are seven members of the proprotein convertase (PC) family of secreted serine proteases that cleave their substrates at basic amino acids, thereby activating a variety of hormones, growth factors, and viruses. PC1/3, PC2 and PC5/6A are the only members of the PC family that are targeted to dense core secretory granules, where they carry out the processing of proteins that are secreted from the cell in a regulated manner. Previous studies have identified ,-helices in the C-termini of the PC1/3 and PC2 proteases that are required for this subcellular targeting. In the current study, we demonstrate that a predicted ,-helix in the C-terminus of PC5/6A is also critical for the ability of this domain to target a heterologous protein to the regulated secretory pathway of mouse endocrine AtT-20 cells. Analysis of the subcellular distribution of fusion proteins containing the C-terminal domains of PC1/3, PC2 and PC5/6A confirmed that all three domains have the capacity to redirect a constitutively secreted protein to the granule-containing cytoplasmic extensions. Analysis of the predicted structures formed by these three granule-sorting helices shows a correlation between their granule-sorting efficiency and the clustering of hydrophobic amino acids in their granule-targeting helices. [source] Increasing the thermal stability of euphauseraseFEBS JOURNAL, Issue 1 2001A cold-active, multifunctional serine protease from Antarctic krill A molecular model of Antarctic krill euphauserase based on the known crystal structure of its fiddler crab analog, collagenase I, indicates that the core structure of these enzymes is almost identical. Euphauserase is a cold-active and thermally sensitive enzyme with a high affinity for Lys, Arg and large hydrophobic amino acids. Residue Phe137 in euphauserase, localized in loop D (autolysis loop), is highly exposed on the surface of the molecule. Therefore, it appeared to be an easy target for autolysis. The broadly specific euphauserase has a low affinity for negatively charged residues. In order to increase the stability of the enzyme, two mutants were created in which residue Phe137 was replaced by a Glu and an Asp residue. Both mutations resulted in increased stability of the recombinant euphauserase towards thermal inactivation. [source] Molecular characterization of two novel milk proteins in the tsetse fly (Glossina morsitans morsitans)INSECT MOLECULAR BIOLOGY, Issue 2 2010G. Yang Abstract Purpose: Milk proteins are an essential component of viviparous reproduction in the tsetse fly. Milk proteins are synthesized in and secreted from the milk gland tissue and constitute 50% of the secretions from which the intrauterine larva derives its nourishment. To understand milk protein function and regulation during viviparous reproduction, milk proteins need to be identified and characterized. Methods: Two putative unknown secretory proteins (GmmMGP2 and GmmMGP3) were selected by bioinformatic analysis of tissue specific tsetse cDNA libraries. RT-PCR analysis was performed to verify their milk gland/fat body specific expression profile. Detailed characterization of developmental and tissue specific expression of these proteins was performed by northern blot analysis and fluorescent in situ hybridization. Functional analysis of the milk gland proteins during the tsetse gonotrophic cycle was performed using RNA interference (RNAi). Results: The predicted proteins from gmmmgp2 and gmmmgp3 are small ,22 kD and contain a high proportion of hydrophobic amino acids and potential phosphorylation sites. Expression of both genes is tissue specific to the secretory cells of the milk gland. Transcript abundance for both genes increases over the course of intrauterine larval development and parallels that of gmmmgp, a well characterized milk protein gene considered to be the major milk protein. Phenotypic analysis of flies after RNA interference treatment revealed a significant effect upon fecundity in the gmmmgp2 knockdown flies, but not the gmmmgp3 flies. Knockdown of gmmmgp2 resulted in disruption of ovulation and consequent oocyte accumulation and degradation. Gmmmgp2 knockdown also had a significant impact on fly mortality. Conclusions: This work identifies two novel genes, the proteins of which appear to function in response to intrauterine larvigenesis in tsetse. These proteins may be nutritional components of the milk secretions provided to the larva from the mother. Phenotypic data from knockdown of gmmmgp2 suggests that this protein may also have a regulatory function given the defect in ovulation observed in knockdown flies. Further analysis of these genes will be important (in conjunction with other milk proteins) for identification of transcriptional regulation mechanisms that direct milk gland/pregnancy specific gene expression. [source] Preparation and Characterization of Hydrolyzed Proteins from Defibrinated Bovine PlasmaJOURNAL OF FOOD SCIENCE, Issue 2 2002P.K.J.P.D. Wanasundara ABSTRACT: Proteins from defibrinated bovine blood plasma were enzymatically hydrolyzed with food-grade microbial proteases Alcalase 2.4 L® and Flavourzyme L&TM;, and a substrate consisting of small peptides and free amino acids was obtained. Hydrolysis of the plasma proteins with Flavourzyme resulted in a maximum degree of hydrolysis of 43% at an enzyme concentration of 110 LAPU/g protein after 15.5 h of hydrolysis. Among the free amino acids in the hydrolysate, hydrophobic amino acids were predominant. The major plasma proteins were degraded due to hydrolysis; peptides of less than 1.04 kDa were dominant in the product when a high degree of hydrolysis was employed. [source] Oligopeptide-mediated helix stabilization of model peptides in aqueous solutionJOURNAL OF PEPTIDE SCIENCE, Issue 2 2003Yoshitaka Maeda Abstract Oligopeptide-mediated helix stabilization of peptides in hydrophobic solutions was previously found by NMR and CD spectroscopic studies. The oligopeptide included the hydrophobic amino acids found in its parent peptide and were interposed by relevant basic or acidic amino acids. The strength of the interactions depended on the amino acid sequences. However, no helix-stabilizing effect was seen for the peptides in phosphate buffer solution, because the peptides assumed a random-coil structure. In order to ascertain whether the helix-stabilizing effect of an oligopeptide on its parent peptide could operate in aqueous solution, model peptides EK17 (Ac-AEAAAAEAAAKAAAAKA-NH2) and IFM17 (Ac-AEAAAAEIFMKAAAAKA-NH2) that may assume an ,-helix in aqueous solutions were synthesized. Interactions were examined between various oligopeptides (EAAAK, KAAAE, EIFMK, KIFME, KIFMK and EYYEE) and EK17 or IFM17 in phosphate buffer and in 80% trifluoroethanol (TFE),20% H2O solutions by CD spectra. EAAAK had little effect on the secondary structures of EK17 in both buffer and TFE solutions, while KAAAE, which has the reverse amino acid sequence of EAAAK, had a marked helix-destabilizing effect on EK17 in TFE. EIFMK and KIFME were found to stabilize the ,-helical structure of EK17 in phosphate buffer solutions, whereas KIFMK and EYYEE destabilized the ,-helical structure of EK17. EIFMK and KIFME had no effect on IFM17, because unexpectedly, IFM17 had appreciable amounts of ,-sheet structure in buffer solution. It was concluded that in order for the helix-stabilizing effects to operate effectively, the following factors should be satisfied: (1) the model peptide, the ,-helical conformation of which is to be stabilized, should essentially assume an ,-helical structure by nature, and (2) the hydrophobicity of the side-chains of the oligopeptide should be high enough for the oligopeptide to perform stable specific side chain,side chain intermolecular hydrophobic interactions with the model peptide. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Comparative study on the proteolytic activities and storage globulins in seeds of Theobroma grandiflorum (Willd ex Spreng) Schum and Theobroma bicolor Humb Bonpl, in relation to their potential to generate chocolate-like aromaJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 7 2004Christoph Reisdorff Abstract The cocoa relatives T grandiflorum (cupuaçu) and T bicolor (macambo) are promising crop plants for sustainable agroforestry in the Amazon region of South America. The market for cupuaçu is expanding since the fruit flesh is utilised by the foodstuffs industry. Attempts to commercialise chocolate-like wares from the seeds have failed so far because of unreliable product quality. It is not known whether this is due to an insufficient aroma potential of cupuaçu seeds. We therefore investigated the proteolytic enzymes and the seed storage globulins which are both decisive for the formation of aroma precursors in cocoa. We found that the activities of the aspartic endopeptidase and the carboxypeptidase in T bicolor and T grandiflorum differed slightly from those in cocoa. The specificity of the carboxypeptidase for hydrophobic amino acids was quite similar across the three species, while the optimal pH of the T grandiflorum enzyme was lower than that of the other species. The qualitative and quantitative differences between the globulins indicate a lower maximum yield of aroma precursors in T grandiflorum and a higher maximum yield of aroma precursors in T bicolor, compared to cocoa. We conclude that the quality of chocolate-like products made from the studied cocoa relatives can be improved by adapting fermentation procedures to particular biochemical features of these seeds. Copyright © 2004 Society of Chemical Industry [source] Evaluating the Ability of Polyhydroxyalkanoate Synthase Mutants to Produce P(3HB -co- 3HA) from Soybean OilMACROMOLECULAR BIOSCIENCE, Issue 1 2009Takeharu Tsuge Abstract Polyhydroxyalkanoate (PHA) synthase from Pseudomonas sp 61-3 (PhaC1Ps) is able to synthesize P(3HB -co- 3HA), consisting of a 3HB unit and medium-chain-length 3HA units of 6,12 carbon atoms. Expression vectors encoding 76 PhaC1Ps mutants with an amino acid replacement at position 130, 325, 477 or 481 were individually introduced into Ralstonia eutropha. The mutant enzyme genes were evaluated in terms of their abilities to synthesize P(3HB -co- 3HA) using soybean oil as a carbon source. 20 mutants showed significantly high accumulation levels of PHA exceeding 30 wt.-% and as high as 57 wt.-%. It was found that hydrophobic amino acids at the positions are more likely to enhance accumulation of PHA in R. eutropha. [source] ABC-type amino acid uptake transporters Bgt and N-II of Anabaena sp. strain PCC 7120 share an ATPase subunit and are expressed in vegetative cells and heterocystsMOLECULAR MICROBIOLOGY, Issue 5 2008Rafael Pernil Summary Anabaena sp. strain PCC 7120 is a filamentous cyanobacterium that can fix N2 in differentiated cells called heterocysts. Anabaena open reading frames alr4167 and alr3187 encode, respectively, an ATPase subunit, BgtA, and a composite protein bearing periplasmic substrate-binding and transmembrane domains, BgtB, of an ABC-type high-affinity basic amino acid uptake transporter (Bgt). Open reading frame alr4167 is clustered with open reading frames alr4164, alr4165 and alr4166 that encode a periplasmic substrate-binding protein, NatF, and transmembrane proteins NatG and NatH respectively. The NatF, NatG, NatH and BgtA proteins constitute an ABC-type uptake transporter for acidic and neutral polar amino acids (N-II). The Bgt and N-II transport systems thus share the ATPase subunit, BgtA. These transporters together with the previously characterized ABC-type uptake transporter for proline and hydrophobic amino acids (N-I) account for more than 98% of the amino acid transport activity exhibited by Anabaena sp. strain PCC 7120. In contrast to N-I that is expressed only in vegetative cells, the Bgt and N-II systems are present in both vegetative cells and heterocysts. Whereas Bgt is dispensable for diazotrophic growth, N-II appears to contribute together with N-I to the diazotrophic physiology of this cyanobacterium. [source] Hydrolysis-improved thermosensitive polyorganophosphazenes with ,-amino-,-methoxy-poly(ethylene glycol) and amino acid esters as side groupsPOLYMER INTERNATIONAL, Issue 9 2005Sang Beom Lee Abstract A series of hydrolysis-improved thermosensitive polyorganophosphazenes with ,-amino-,-methoxy-poly(ethylene glycol) (AMPEG) and amino acid esters (AAEs) of ,N,N -systems' was synthesized, and their properties were evaluated in comparison with the thermosensitive polyorganophosphazenes with methoxy-poly(ethylene glycol) (MPEG) and AAEs of ,O,N -systems', by means of 31P NMR spectroscopy, gel permeation chromatography (GPC) and differential scanning calorimetry (DSC). Most of the present polymers showed a lower critical solution temperature (LCST) in the range 32.0,79.0 °C, depending on the kinds of AAE, length of AMPEG and the mol ratio of the two substituents. These polymers exhibited higher LCSTs and faster degradation rates than the MPEG-based polymers. The aqueous solution of poly(ethyl glycinate phosphazene)- graft -poly(ethylene glycol) [NP(GlyEt)0.94(AMPEG350)1.06]n did not show an LCST, which is presumed to be due to its high hydrophilicity, in contrast to [NP(GlyEt)1.01(MPEG350)0.99]n which showing an LCST at 77.5 °C. On the other hand, the polymers with a high content of AAE or with hydrophobic amino acids such as L -aspartic acid and L -glutamic acid, have shown a similar LCST to those of the MPEG-based polymers. The half-lives (t1/2) for hydrolysis of [NP(AMPEG350)1.06(GlyEt)0.94]n at pH 5, 7.4 and 10 were 9, 16, and 5 days, respectively, which are almost 2.5 to 4 times faster than that of the MPEG-based polymers. The LCST of the present N,N -polymers has been shown to be more influenced by salts such as NaCl (,salting-out' effect) and tetrapropylammonium bromide (TPAB) (,salting-in' effect) compared with the ,O,N -system'. Such differences of the ,N,N -systems' from the ,O,N -systems' in thermosensitivity, hydrolysis behavior and salt effect seem to be due to the higher hydrophilicity of the amino group in AMPEG. Copyright © 2005 Society of Chemical Industry [source] Mining mammalian genomes for folding competent proteins using Tat-dependent genetic selection in Escherichia coliPROTEIN SCIENCE, Issue 12 2009Hyung-Kwon Lim Abstract Recombinant expression of eukaryotic proteins in Escherichia coli is often limited by poor folding and solubility. To address this problem, we employed a recently developed genetic selection for protein folding and solubility based on the bacterial twin-arginine translocation (Tat) pathway to rapidly identify properly folded recombinant proteins or soluble protein domains of mammalian origin. The coding sequences for 29 different mammalian polypeptides were cloned as sandwich fusions between an N-terminal Tat export signal and a C-terminal selectable marker, namely ,-lactamase. Hence, expression of the selectable marker and survival on selective media was linked to Tat export of the target mammalian protein. Since the folding quality control feature of the Tat pathway prevents export of misfolded proteins, only correctly folded fusion proteins reached the periplasm and conferred cell survival. In general, the ability to confer growth was found to relate closely to the solubility profile and molecular weight of the protein, although other features such as number of contiguous hydrophobic amino acids and cysteine content may also be important. These results highlight the capacity of Tat selection to reveal the folding potential of mammalian proteins and protein domains without the need for structural or functional information about the target protein. [source] Asymmetric amino acid compositions of transmembrane ,-strandsPROTEIN SCIENCE, Issue 8 2004Aaron K. Chamberlain Abstract In contrast to water-soluble proteins, membrane proteins reside in a heterogeneous environment, and their surfaces must interact with both polar and apolar membrane regions. As a consequence, the composition of membrane proteins' residues varies substantially between the membrane core and the interfacial regions. The amino acid compositions of helical membrane proteins are also known to be different on the cytoplasmic and extracellular sides of the membrane. Here we report that in the 16 transmembrane ,-barrel structures, the amino acid compositions of lipid-facing residues are different near the N and C termini of the individual strands. Polar amino acids are more prevalent near the C termini than near the N termini, and hydrophobic amino acids show the opposite trend. We suggest that this difference arises because it is easier for polar atoms to escape from the apolar regions of the bilayer at the C terminus of a ,-strand. This new characteristic of ,-barrel membrane proteins enhances our understanding of how a sequence encodes a membrane protein structure and should prove useful in identifying and predicting the structures of trans-membrane ,-barrels. [source] A solution to the observed Z, = 2 preference in the crystal structures of hydrophobic amino acidsACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009Carl Henrik Görbitz Chiral amino acids without functional groups in their side chains (hydrophobic amino acids) systematically form crystals with two molecules in the asymmetric unit. In contrast, racemates of the same compounds form crystals with Z, = 1. The present investigation addresses the origin of this important difference between enantiomeric and racemic crystals. Through a series of ab initio calculations on infinite two-dimensional slabs, derived from crystal structures, as well as calculations on full crystal structures it is shown that it is indeed possible to explain the observed behaviour. Additionally, the (not unexpected) observation that amino acids usually form racemates in the solid phase rather than undergoing racemic separation upon crystallization is rationalized on the basis of energy calculations. [source] Molecular aggregation in selected crystalline 1:1 complexes of hydrophobic d - and l -amino acids.ACTA CRYSTALLOGRAPHICA SECTION C, Issue 6 2009The amino acid l -phenylalanine has been cocrystallized with d -2-aminobutyric acid, C9H11NO2·C4H9NO2, d -norvaline, C9H11NO2·C5H11NO2, and d -methionine, C9H11NO2·C5H11NO2S, with linear side chains, as well as with d -leucine, C9H11NO2·C6H13NO2, d -isoleucine, C9H11NO2·C6H13NO2, and d - allo -isoleucine, C9H11NO2·C6H13NO2, with branched side chains. The structures of these 1:1 complexes fall into two classes based on the observed hydrogen-bonding pattern. From a comparison with other l:d complexes involving hydrophobic amino acids and regular racemates, it is shown that the structure-directing properties of phenylalanine closely parallel those of valine and isoleucine but not those of leucine, which shares side-chain branching at C, with phenylalanine and is normally considered to be the most closely related non-aromatic amino acid. [source] Self-assembling peptides: Sequence, secondary structure in solution and film formationBIOPOLYMERS, Issue 11 2008Roberta Gambaretto Abstract Peptides of alternating charge and hydrophobic amino acids have a tendency to adopt unusually stable ,-sheet structures that can form insoluble macroscopic aggregates under physiological conditions. In this study, analogues of a well-known self-assembling peptide, characterized by the same polar/nonpolar periodicity but with different residues, were designed to study the relationship between sequence, conformation in solution and film-forming capacity in saline solution. Peptide conformation, evaluated by circular dichroism, correlated with film forming capacity observed by inverted optical microscopy after addition of saline solution and subsequent drying. We found that polar/nonpolar periodicity of several analogues is not criterion enough to induce ,-sheet and thus film formation and that conformations different from ,-sheet also allow self-assemblage. Furthermore, addition of the short adhesive sequence RGD to a known self-assembling sequence was shown to not prevent the self-assembling process. This finding might prove useful for the design of biomimetic scaffolds. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 906,915, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Influence of N-Terminal Hydrophobicity of Cationic Peptides on Thermodynamics of their Interaction with Plasmid DNACHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2009Geetha N. Goparaju There is a need to understand the thermodynamics of interaction of cationic peptides with DNA to design better peptide based non-viral gene delivery vectors. The main aim of this study was to understand the influence of N-terminal hydrophobicity of cationic amphiphilic peptides on thermodynamics of interaction with plasmid DNA. The model peptides used were TATPTD and TATPTDs modified at the N-terminal with hydrophobic amino acids. The thermodynamic binding data from isothermal titration calorimetry were compared with ethidium bromide analysis and ultrafiltration to correlate the binding parameters with the structural features of the various peptides used. It was observed that peptides having a smaller hydrophobic domain at the N-terminal have good DNA condensing ability compared with the ones with a longer hydrophobic domain. Calorimetry of peptides that reached saturation binding indicated that enthalpy and entropy are favorable for the interaction. Moreover, the interaction of these peptides with DNA appears to be predominantly electrostatic. [source] | |||||||||||||||||||||||||||||||