Tuning the amino acid sequence of minimalist peptides to present biological signals via charge neutralised self assembly

Nanofibrous materials yielded by the self-assembly of peptides are rich in potential; particularly for the formation of scaffolds that mimic the landscape of the host environment of the cell. Here, we report a novel methodology to direct the formation of supramolecular structures presenting desirable amino acid sequences by the self-assembly of minimalist peptides which cannot otherwise yield the desired scaffold structures under biologically relevant conditions. Through the rational modification of the pK?, we were able to optimise ordered charge neutralised assembly towards in vivo conditions.

Binding affinities of amino acid analogues at the charged aqueous titania interface : implications for titania-binding peptides

Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

Structural classification of proteins through amino acid sequence using interval type-2 fuzzy logic system

This paper introduces a new multi-output interval type-2 fuzzy logic system (MOIT2FLS) that is automatically constructed from unsupervised data clustering method and trained using heuristic genetic algorithm for a protein secondary structure classification. Three structure classes are distinguished including helix, strand (sheet) and coil which correspond to three outputs of the MOIT2FLS. Quantitative properties of amino acids are used to characterize the twenty amino acids rather than the widely used computationally expensive binary encoding scheme. Amino acid sequences are parsed into learnable patterns using a local moving window strategy. Three clustering tasks are performed using the adaptive vector quantization method to derive an equal number of initial rules for each type of secondary structure. Genetic algorithm is applied to optimally adjust parameters of the MOIT2FLS with the purpose of maximizing the Q3 measure. Comprehensive experimental results demonstrate the strong superiority of the proposed approach over the traditional methods including Chou-Fasman method, Garnier-Osguthorpe-Robson method, and artificial neural network models.

Analysis and prediction of major blood proteins based on their amino acid and dipeptide composition

A method has been developed for predicting blood proteins using the SVM based machine learning approach. In this prediction method a two-step strategy was deployed to predict blood proteins and their subclasses. We have developed models of blood proteins and achieved the maximum accuracies of 90.57% and 91.39% with Matthews correlation coefficient (MCC) of 0.89 and 0.90 using single amino acid and dipeptide composition respectively. Furthermore, the method is able to predict major subclasses of blood proteins; developed based on amino acid (AC) and dipeptide composition (DC) with a maximum accuracy 90.38%, 92.83%, 87.41%, 92.52% and 85.27%, 89.07%, 94.82%, 86.31 for albumin, globulin, fibrinogen, and regulatory proteins respectively. All modules were trained, tested, and evaluated using the five-fold cross-validation technique.

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

The operation of many nanostructured biomolecular sensors and catalysts critically hinges on the manipulation of non-covalent adsorption of biomolecules on unfunctionalised noble-metal nanoparticles (NMNPs). Molecular-level structural details of the aqueous biomolecule/NMNP interface are pivotal to the successful realisation of these technologies, but such experimental data are currently scarce and challenging to obtain. Molecular simulations can generate these details, but are limited by the assumption of non-preferential adsorption to NMNP features. Here, via first principles calculations using a vdW-DF functional, and based on nanoscale sized NMNPs, we demonstrate that adsorption preferences to NP features vary with adsorbate chemistry. These results show a clear distinction between hydrocarbons, that prefer adsorption to facets over edges/vertices, over heteroatomic molecules that favour adsorption onto vertices over facets. Our data indicate the inability of widely used force-fields to correctly capture the adsorption of biomolecules onto NMNP surfaces under aqueous conditions. Our findings introduce a rational basis for the development of new force-fields that will reliably capture these phenomena.

Organotin(IV) complexes derived from proteinogenic amino acid: Synthesis, structure and evaluation of larvicidal efficacy on Anopheles stephensi mosquito larvae

Five new organotin(IV) complexes of composition [Bz2SnL1]n (1), [Bz3SnL1HH2O] (2), [Me2SnL2H2O] (3), [Me2SnL3] (4) and [Bz3SnL3H]n (5) (where L1 = (2S)-2-([(E)-(4-hydroxypentan-2-ylidene)]amino)-4-methylpentanoate, L2 = (rac)-2-([(E)-1-(2-hydroxyphenyl)methylidene]amino)-4-methylpentanoate and L3 = (2S)- or (rac)-2-([(E)-1-(2-hydroxyphenyl)ethylidene]amino)-4-methylpentanoate) were synthesized and characterized using 1H NMR, 13C NMR, 119Sn NMR and infrared spectroscopic techniques. The crystal structure of 2 reveals a distorted trigonal-bipyramidal geometry around the tin atom where the oxygen atoms of the carboxylate ligand and a water ligand occupy the axial positions, while the three benzyl ligands are located at the equatorial positions. On the other hand, the analogous derivative of enantiopure L3H (5) consists of polymeric chains, in which the ligand-bridged tin atoms adopt the same trans-Bz3SnO2 trigonal-bipyramidal configuration and are now coordinated to a phenolic oxygen atom instead of H2O. In 2, the OH hydrogen of the ketoimine substituent has moved to the nearby nitrogen atom while in the salicylidene derivative 5, the OH is located almost midway between the phenolic oxygen atom and the nitrogen atom of the C=N group. For the dibenzyltin derivative 1, a polymeric chain structure is observed as a result of a long intermolecular SnO bond involving the exocyclic carbonyl oxygen atom from the tridentate ligand of a neighbouring tin-complex unit. The tin atom in this complex has distorted octahedral coordination geometry. In contrast, the racemic dimethyltin(IV) complexes 3 and 4 display discrete monomeric structures with a distorted octahedral- and trigonal-bipyramidal geometry, respectively. The structures show that the coordination mode of the Schiff base ligand depends primarily on the number of bulky benzyl ligands (R) at the tin atom, as indeed found in the structures of related complexes where R = phenyl. With three bulky R groups, the tridentate chelating O,N,O coordination mode is preferred, whereas with fewer or less bulky R ligands, only the carboxylate and hydroxy groups are involved, which leads to polymers. Larvicidal efficacies of two of the new tribenzyltin(IV) complexes (2 and 5) were assessed on the second larval instar of Anopheles stephensi mosquito larvae and compared with two triphenyltin(IV) analogues, [Ph3SnL1H]n and [Ph3SnL3H]n. The results demonstrate that the compounds containing Sn-Ph ligands are more effective than those with Sn-Bz ligands.

Protecting skeletal muscle with protein and amino acid during periods of disuse

Habitual sedentary behavior increases risk of chronic disease, hospitalization and poor quality of life. Short-term bed rest or disuse accelerates the loss of muscle mass, function, and glucose tolerance. Optimizing nutritional practices and protein intake may reduce the consequences of disuse by preserving metabolic homeostasis and muscle mass and function. Most modes of physical inactivity have the potential to negatively impact the health of older adults more than their younger counterparts. Mechanistically, mammalian target of rapamycin complex 1 (mTORC1) signaling and muscle protein synthesis are negatively affected by disuse. This contributes to reduced muscle quality and is accompanied by impaired glucose regulation. Simply encouraging increased protein and/or energy consumption is a well-intentioned, but often impractical strategy to protect muscle health. Emerging evidence suggests that leucine supplemented meals may partially and temporarily protect skeletal muscle during disuse by preserving anabolism and mitigating reductions in mass, function and metabolic homeostasis.

Amino acids and endurance exercise

Provides information on a study which examined the role of amino acids during endurance exercise and the implications for sports nutrition and performance. Description of amino acid utilization during exercise; Function of glutamine; Cardiovascular function of L-arginine.

Selective determination of amino acids using flow injection analysis coupled with chemiluminescence detection

The determination of the amino acids proline, histidine, tyrosine, arginine, phenylalanine and tryptophan using flow injection analysis (FIA) with chemiluminescence detection is described. Proline was the only amino acid to exhibit chemiluminescence with the tris(2,2-bipyridyl)ruthenium(III) reaction at pH 10. While, histidine was found to selectively enhance the reaction of luminol with Mn(II) salts in a basic medium. Acidic potassium permanganate chemiluminescence was able to selectively determine tyrosine at pH 6.75. Low pressure separations using a C18 guard column allowed the simultaneous determination of tyrosine and tryptophan or phenylalanine and tryptophan with acidic potassium permanganate and copper(II)–amino acid–hydrogen peroxide chemiluminescence, respectively. Precision for each method was less than 3.9% (R.S.D.) for five replicates of a standard (1×10−5 M) and the detection limits ranged between 4×10−9 and 7×10−6 M. Preliminary investigations revealed that the methodology developed was able to selectively determine the individual amino acids in an equimolar mixture of the 20 naturally occurring amino acids.

Strategies and methods for the attachment of amino acids and peptides to chiral [n]polynorbornane templates

A versatile synthesis of amino acid and peptide functionalised [n]polynorbornane scaffolds is described. The frameworks are constructed using the stereoselective and regioselective cycloaddition of suitably functionalised chiral cyclobutene epoxides with similar norbornenes. The strategies employed allow a range of topologies to be accessed and a number of regioselectively addressable linkage points to be accommodated.

Retention of essential amino acids during extrusion of protein and reducing sugars

This research investigates the retention of essential amino acid profiles of products during the extrusion of proteins and reducing sugars. Animal proteins (egg and milk protein at 10 and 30% levels) and reducing sugars (fructose and galactose at 0, 2, and 8% levels), with pregelatinized wheat flour, were extruded at 110 and 125 °C product temperatures and feed moistures of 19 and 23.5% for egg protein and 13.75 and 16% for milk protein. The nutritional property analyzed was essential amino acid retention, and sugar retention was also considered to understand the relationship of sugars with retention of amino acids. Lysine showed the lowest retention (up to 40%) of all the essential amino acids. Retention of other essential amino acids varied from 80 to 100% in most situations. Apart from lysine,  tryptophan, threonine, and methionine were found to be significantly changed (P < 0.05) with processing conditions. Increased protein and sugar levels resulted in a significant degradation of lysine. Greater lysine retention was found at a lower temperature and higher feed moisture. Results of sugar retention also showed similar patterns. The products made from fructose had greater lysine retention than products made from galactose with any type of protein. The outcomes of this research suggested that the combination of milk protein and fructose at a lower temperature and higher feed moisture is most favorable for developing high-protein extruded products.

Relationships of nicotianamine and other amino acids with nickel, zinc and iron in Thlaspi hyperaccumulators

Experimental evidence suggests that nicotianamine (NA) is involved in the complexation of metal ions in some metal-hyperaccumulating plants. Closely-related nickel (Ni)- and zinc (Zn)-hyperaccumulating species were studied to determine whether a correlation exists between the Ni and Zn concentrations and NA in foliar tissues. A liquid chromatography–mass spectrometry (LC-MS) procedure was developed to quantify the NA and amino acid contents using the derivatizing agent 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate. A strong correlation emerged between Ni and NA, but not between Zn and NA. Concentrations of NA and l-histidine (His) also increased in response to higher Ni concentrations in the hydroponic solution supplied to a serpentine population of Thlaspi caerulescens. An inversely proportional correlation was found between the iron (Fe) and Ni concentrations in the leaves. Correlations were also found between Zn and asparagine. The results obtained in this study suggest that NA is involved in hyperaccumulation of Ni but not Zn. The inverse proportionality between the Ni and Fe concentrations in the leaf may suggest that Ni and Fe compete for complexation to NA.