Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favorability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB)versus Thr(HB)-Asn(nHB). Significantly (p < or = 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi1 conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi1 and chi2 conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favorability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http://www.rubic.rdg.ac.uk/betapairprefsparallel/).

Amino acid pairing preferences in parallel beta-sheets in proteins

Statistical approaches have been applied to examine amino acid pairing preferences within parallel beta-sheets. The main chain hydrogen bonding pattern in parallel beta-sheets means that, for each residue pair, only one of the residues is involved in main chain hydrogen bonding with the strand containing the partner residue. We call this the hydrogen bonded (HB) residue and the partner residue the non-hydrogen bonded (nHB) residue, and differentiate between the favourability of a pair and that of its reverse pair, e.g. Asn(HB)-Thr(nHB) versus Thr(HB)-Asn(nHB). Significantly (p <= 0.000001) favoured pairings were rationalised using stereochemical arguments. For instance, Asn(HB)-Thr(nHB) and Arg(HB)-Thr(nHB) were favoured pairs, where the residues adopted favoured chi(1) rotamer positions that allowed side-chain interactions to occur. In contrast, Thr(HB)-Asn(nHB) and Thr(HB)-Arg(nHB) were not significantly favoured, and could only form side-chain interactions if the residues involved adopted less favourable chi(1) conformations. The favourability of hydrophobic pairs e.g. Ile(HB)-Ile(nHB), Val(HB)-Val(nHB) and Leu(HB)-Ile(nHB) was explained by the residues adopting their most preferred chi(1) and chi(2) conformations, which enabled them to form nested arrangements. Cysteine-cysteine pairs are significantly favoured, although these do not form intrasheet disulphide bridges. Interactions between positively and negatively charged residues were asymmetrically preferred: those with the negatively charged residue at the HB position were more favoured. This trend was accounted for by the presence of general electrostatic interactions, which, based on analysis of distances between charged atoms, were likely to be stronger when the negatively charged residue is the HB partner. The Arg(HB)-Asp(nHB) interaction was an exception to this trend and its favourability was rationalised by the formation of specific side-chain interactions. This research provides rules that could be applied to protein structure prediction, comparative modelling and protein engineering and design. The methods used to analyse the pairing preferences are automated and detailed results are available (http:// www.rubic.rdg.ac.uk/betapairprefsparallel/). (c) 2005 Elsevier Ltd. All rights reserved.

Amino-acid cycling drives nitrogen fixation in the legume - Rhizobium symbiosis

The biological reduction of atmospheric N-2 to ammonium (nitrogen fixation) provides about 65% of the biosphere's available nitrogen. Most of this ammonium is contributed by legume rhizobia symbioses(1), which are initiated by the infection of legume hosts by bacteria (rhizobia), resulting in formation of root nodules. Within the nodules, rhizobia are found as bacteroids, which perform the nitrogen fixation: to do this, they obtain sources of carbon and energy from the plant, in the form of dicarboxylic acids(2,3). It has been thought that, in return, bacteroids simply provide the plant with ammonium. But here we show that a more complex amino-acid cycle is essential for symbiotic nitrogen fixation by Rhizobium in pea nodules. The plant provides amino acids to the bacteroids, enabling them to shut down their ammonium assimilation. In return, bacteroids act like plant organelles to cycle amino acids back to the plant for asparagine synthesis. The mutual dependence of this exchange prevents the symbiosis being dominated by the plant, and provides a selective pressure for the evolution of mutualism.

Supramolecular peptide helix from a novel double turn forming peptide containing a beta-amino acid

A single-crystal X-ray diffraction study of the terminally protected tetrapeptide Boc-beta-Ala-Aib-Leu-Aib-OMe 1 (Aib: alpha-aminoisobutyric acid; beta-Ala: beta-Alanine) reveals that it adopts a new type of double turn structure which self-associates to form a unique supramolecular helix through intermolecular hydrogen bonds. Scanning electron microscopic studies show that peptide 1 exhibits amyloid-like fibrillar morphology in the solid state. (C) 2003 Elsevier Science Ltd. All rights reserved.

Dipeptide nanotubes, with n-terminally located omega-amino acid residues, that are stable proteolytically, thermally, and over a wide range of pH

Two dipeptides containing an N-terminally positioned omega-amino acid residue (beta-alanine/delta-amino valeric acid) self-assembles to form nanotubes in the solid state as well as in aqueous solution. In spite of having hollow nanotubular structures in the solid state and in solution, their self-assembling nature in these two states are different and this leads to the formation of different internal diameters of these nanotubes in solution and in solid state structure. These nanotubes are stable proteolytically, thermally, and over a wide range of pH values (1-13). The role of water molecules in nanotube formation has been investigated in the solid state. These nanotubes can be considered as a new class of dipeptide nanotubes as they are consisting of N-terminally located protease resistant omega-amino acid residues and C-terminally positioned alpha-amino acid residues. These dipeptides can form an interesting class of short peptidic structure that can give rise to stable nanotubular structure upon self-assembly and these nanotubes can be explored in future for potential nanotechnological applications.

Ring-rearrangement metathesis of bicyclic amino acid derivatives

In this letter, we describe the ring-rearrangement metathesis (RRM) of bicyclic amino acid derivatives. The procedure is of use for the synthesis of constrained amino acid and peptide derivatives with potential as reverse-turn inducers. (c) 2005 Elsevier Ltd. All rights reserved.

Synthesis of a novel class of chiral polyaromatic amide dendrimers bearing an amino acid derived C-3-symmetric core

Chiral polyaromatic amide dendrimers incorporating a C-3-core have been prepared as potential catalysts for asymmetric reactions. (C) 2002 Elsevier Science Ltd. All rights reserved.

Chiral poly(aromatic amide ester) dendrimers bearing an amino acid derived C-3-symmetric core: synthesis and properties

The effect of hyperbranched macromolecular architectures (dendrimers) upon chirality has received significant attention in recent years in the light of the proposal of amplification of chirality. In particular, several studies have been carried out on the chiroptical properties of dendrimers that contain a chiral core and achiral branches in order to determine if the chirality of the central core can be transmitted to the distal. region of the macromolecule. In addition to interest of a pure academic nature, the presence of such chiral conformational order would be extremely useful in the development of asymmetric catalysts. In this paper, a novel class of chiral dendrimers is described - these perfect hyperbranched macromolecules have been prepared by a convergent route by the coupling of a chiral central core based upon tris(2-aminoethyl)amine and poly(aromatic amide ester) dendritic branches. The chiral properties of these dendrimers have been investigated by detailed optical rotation studies and circular dichroism analysis; the results of these studies are described herein. (C) Wiley-VCH Verlag GmbH Co.

Casein and whey exert different effects on plasma amino acid profiles, gastrointestinal hormone secretion and appetite

Protein, generally agreed to be the most satiating macronutrient, may differ in its effects on appetite depending on the protein source and variation in digestion and absorption. We investigated the effects of two milk protein types, casein and whey, on food intake and subjective ratings of hunger and fullness, and on postprandial metabolite and gastrointestinal hormone responses. Two studies were undertaken. The first study showed that energy intake from a buffet meal ad libitum was significantly less 90 min after a 1700 kJ liquid preload containing 48 g whey, compared with an equivalent casein preload (P<0.05). In the second study, the same whey preload led to a 28 % increase in postprandial plasma amino acid concentrations over 3 h compared with casein (incremental area under the curve (iAUC), P<0.05). Plasma cholecystokinin (CCK) was increased by 60 % (iAUC, P<0.005), glucagon-like peptide (GLP)-1 by 65 % (iAUC, P<0.05) and glucose-dependent insulinotropic polypeptide by 36 % (iAUC, P<0.01) following the whey preload compared with the casein. Gastric emptying was influenced by protein type as evidenced by differing plasma paracetamol profiles with the two preloads. Greater subjective satiety followed the whey test meal (P<0.05). These results implicate post-absorptive increases in plasma amino acids together with both CCK and GLP-1 as potential mediators of the increased satiety response to whey and emphasise the importance of considering the impact of protein type on the appetite response to a mixed meal.

Effects of genotype and environment on free amino acid levels in wheat grain: implications for acrylamide formation during processing

Acrylamide forms from free asparagine and reducing sugars during cooking, with asparagine concentration being the key parameter determining the formation in foods produced from wheat flour. In this study free amino acid concentrations were measured in the grain of varieties Spark and Rialto and four doubled haploid lines from a Spark x Rialto mapping population. The parental and doubled haploid lines had differing levels of total free amino acids and free asparagine in the grain, with one line consistently being lower than either parent for both of these factors. Sulfur deprivation led to huge increases in the concentrations of free asparagine and glutamine, and canonical variate analysis showed clear separation of the grain samples as a result of treatment (environment, E) and genotype (G) and provided evidence of G x E interactions. Low grain sulfur and high free asparagine concentration were closely associated with increased risk of acrylamide formation. G, E, and G x E effects were also evident in grain from six varieties of wheat grown at field locations around the United Kingdom in 2006 and 2007. The data indicate that progress in reducing the risk of acrylamide formation in processed wheat products could be made immediately through the selection and cultivation of low grain asparagme varieties and that further genetically driven improvements should be achievable. However, genotypes that are selected should also be tested under a range of environmental conditions.

Free-amino acid profiles of thua nao, a Thai fermented soybean

Thua nao, a rich source of free-amino acids, is a fermented soybean, usually used as seasoning or flavouring enhancer in northern Thailand. Free-amino acids (FAA) of unfermented/cooked soybeans, thua nao, fermented by pure Bacillus subtilis TN51 (TNB51), and a naturally fermented product (TNMX), were investigated by pre-column derivatisation with 9-fluorenylmethyl chloroformate, followed by reversed-phase HPLC. Total FAA and essential amino acids were found at significantly higher concentrations in TNB51 thua nao than in TNMX thua nao (naturally fermented). Both fermented thua nao had much higher concentrations of FAA than had their unfermented counterparts. With respect to taste-enhancing FAA, typical bitter attributes of thua nao came mainly from hydrophobic and basic FAA, whereas an umami attribute came predominantly from acidic FAA.

Asymmetric phase-transfer-catalyzed synthesis of five-membered cyclic gamma-Amino acid precursors

The first example of an intramolecular enantioselective Michael addition of nitronates onto conjugated systems utilizing a chiral phase-transfer catalyst is described. A range of five-membered gamma-nitro esters with up to three stereocentres have been prepared and the relative and absolute configurations proven by chemical and crystallographic methods. The products are rapidly obtained and are precursors to five-membered cyclic gamma-amino acids.

A β-amino acid modified heptapeptide containing a designed recognition element disrupts fibrillization of the amyloid β-peptide

We study the complex formation of a peptide betaAbetaAKLVFF, previously developed by our group, with Abeta(1–42) in aqueous solution. Circular dichroism spectroscopy is used to probe the interactions between betaAbetaAKLVFF and Abeta(1–42), and to study the secondary structure of the species in solution. Thioflavin T fluorescence spectroscopy shows that the population of fibers is higher in betaAbetaAKLVFF/Abeta(1–42) mixtures compared to pure Abeta(1–42) solutions. TEM and cryo-TEM demonstrate that co-incubation of betaAbetaAKLVFF with Abeta(1–42) causes the formation of extended dense networks of branched fibrils, very different from the straight fibrils observed for Abeta(1–42) alone. Neurotoxicity assays show that although betaAbetaAKLVFF alters the fibrillization of Abeta(1–42), it does not decrease the neurotoxicity, which suggests that toxic oligomeric Abeta(1–42) species are still present in the betaAbetaAKLVFF/Abeta(1–42) mixtures. Our results show that our designed peptide binds to Abeta(1–42) and changes the amyloid fibril morphology. This is shown to not necessarily translate into reduced toxicity.