Search

Disordered regions of proteins are highly abundant in various biological processes, involving regulation and signaling and also in relation with cancer, cardiovascular, autoimmune diseases and neurodegenerative disorders. Hence, recognizing disordered regions in proteins is a critical task. In this paper, we presented a new feature encoding technique built from physicochemical properties of residues selected as per the chaotic structure of related protein sequence. Our feature vector has been tested with various classification algorithms on an up-to-date data set and also compared to other methods. The proposed method shows better classification performance than many methods in terms of accuracy, sensitivity and specificity. Our results suggest that the new method that links the residues and their physicochemical properties using Lyapunov exponents is highly effective in recognition of disordered regions. [ABSTRACT FROM AUTHOR]

Radioiodine labeling of peptides and proteins is routinely performed by using various oxidizing agents such as Chloramine T, Iodobeads, and Iodogen reagent and radioactive iodide (I−), although some other oxidizing agents were also investigated. The main objective of the present study was to develop and test a novel reagent, inorganic monochloramine (NH2Cl), for radioiodine labeling of new chemical entities and biomolecules which is cost-effective, easy to make and handle, and is selective to label amino acids, peptides, and proteins. The data presented in this report demonstrate that the yields of the non-radioactive iodine labeling reactions using monochloramine are >70% for an amino acid (tyrosine) and a cyclic peptide (cyclo Arg-Gly-Asp-d-Tyr-Lys, cRGDyK). No evidence of the formation of N-chloro derivatives in cRGDyK was observed, suggesting that the reagent is selective in iodinating the tyrosine residue in the biomolecules. The method was successfully translated into radioiodine labeling of amino acid, a peptide, and a protein, Bovine Serum Albumin (BSA). [ABSTRACT FROM AUTHOR]

• Supercritical fluid chromatography and enhanced fluidity liquid chromatography. • Free amino acids, peptides, proteins and nucleic acid bricks. • Mobile phases of CO 2 and co-solvent, comprising water and additives. • Detection issues and hyphenation to mass spectrometry. • Applications in foodomics, metabolomics, clinical and pharmaceutical areas. Biomolecules like proteins, peptides and nucleic acids widely emerge in pharmaceutical applications, either as synthetic active pharmaceutical ingredients, or from natural products as in traditional Chinese medicine. Liquid-phase chromatographic methods (LC) are widely employed for the analysis and/or purification of such molecules. On another hand, to answer the ever-increasing requests from scientists involved in biomolecules projects, other chromatographic methods emerge as useful complements to LC. In particular, there is a growing interest for chromatography with a mobile phase comprising pressurized carbon dioxide, which can be named either (i) supercritical (or subcritical) fluid chromatography (SFC) when CO 2 is the major constituent of the mobile phase, or (ii) enhanced fluidity liquid chromatography (EFLC) when hydro-organic or purely organic solvents are the major constituents of the mobile phase. Despite the low polarity of CO 2 , supposedly inadequate to solubilize such biomolecules, SFC and EFLC were both employed in many occasions for this purpose. This paper specifically reviews the literature related to the SFC/EFLC analysis of free amino acids, peptides, proteins, nucleobases, nucleosides and nucleotides. The analytical conditions employed for specific molecular families are presented, with a focus on the nature of the stationary phase and the mobile phase composition. We also discuss the potential benefits of combining SFC/EFLC to LC in a single gradient elution, a method sometimes designated as unified chromatography (UC). Finally, detection issues are presented, and more particularly hyphenation to mass spectrometry. [ABSTRACT FROM AUTHOR]

Water has many roles in the context of life on Earth, however throughout the universe, other liquids may be able to support the emergence of life. We looked at the ability of amino acids, peptides, a depsipeptide, and proteins to partition into a non-polar decanol phase, with and without the addition of a phase transfer agent. Partitioning evaluated using UV detection, or with HPLC coupled to either charged aerosol detection or ESI-MS. For amino acids and short peptides, phase transfer agents were used to move the biomolecules to the decanol phase, and this transfer was pH dependent. For larger molecules, phase transfer agents did not seem to affect the transfer. Both the depsipetide, valinomycin, and the protein Taq DNA polymerase had solubility in the decanol phase. Additionally, valinomycin appeared to retain its biological ability to bind to potassium ions. These results show that most terrestrial biological molecules are not compatible with non-polar solvents, but it is possible to find and perhaps evolve polymers that are functional in such phases. [ABSTRACT FROM AUTHOR]

The biological function of protein depends mainly on its tertiary structure which is determined by its amino acid sequence via the process of protein folding. Prediction of protein structure from its amino acid sequence is one of the most prominent problems in computational biology. Two basic methodologies on protein structure prediction are combined: ab initio method (3-D space lattice) and fold recognition method (hidden Markov model). The primary structure of proteins and 3-D coordinates of amino acid residues are put together in one hidden Markov model to learn the path of amino acid residues in 3-D space from the first atom to the last atom of each protein of each fold. Therefore, each model has the information of 3-D path of amino acids of each fold. The proposed method is compared to fold recognition methods which have hidden Markov model as a base of their algorithms having approaches on only amino acid sequence or secondary structure. To validate the proposed method, the models are assessed with three datasets. Results show that the proposed models outperform 7-HMM and 3-HMM in the same dataset. The face-centered cubic lattice which is the most compacted 3-D lattice reached the maximum classification accuracy in all experiments in comparison with the performance of the most effective version of optimized 3-HMM as well as the performance of the latest version of SAM 3.5. Results show that 3-D coordinates of atoms of amino acids in proteins have an important role in prediction. It also has great hidden information as compared to secondary structure of proteins in fold classification. [ABSTRACT FROM AUTHOR]

One of the most attractive areas in inorganic chemistry is the synthesis of polyoxometalates (POMs) exhibiting new properties and applications. Since the impact of POMs in biochemistry and related fields of research has increased in the last few years, there has been a special interest in this topic. Significant progress in biological applications has been made where the interaction of POMs with amino acids, peptides and proteins is relevant. Versatile POMs play a series of different roles in the interaction with these biomolecules as described in this review. Various types of interactions are established, depending on the POM shape and charge, the amino acid side chain, peptide sequence or protein structure. Experimental conditions such as temperature, acidity, solvent, etc. are also important factors that influence the binding/reactivity of POM with biomolecules, as described herein. This understanding allows the adequate design of the POM-biomolecule couple for tailoring and controlling mechanisms of action such as catalysis, inhibition, and aggregation, or the crystallising agent. [ABSTRACT FROM AUTHOR]

Purpose The purpose of this study was to composite maize, a cereal grain with low protein and lysine content, with groundnut a rich source of protein, to improve the nutritional quality of maize–groundnut composite flours and their resultant porridges.Design/methodology/approach Defatted and full fat groundnut flours were used to prepare maize–groundnut composite flours and porridges at the ratio of 100:0, 55:45, 70:30 and 85:15, respectively. They were analyzed for proximate composition, energy value, amino acid and fatty acid profiles.Findings Compositing maize with groundnut significantly (p ≤ 0.05) increased proteins from 10 per cent in maize flour to up to 21 per cent in composite porridge (denoted DFC1). The energy values for composite porridges were 434 Kcal/100 g when compared with 398 Kcal/100 g established for maize porridge alone. Lysine content was three times higher in composite flours than for maize flour, while for composite porridges, lysine was four times higher than in maize porridge. There was an increase of 35 per cent in oleic acid content when maize flour was composited with groundnut flour.Research limitations/implications Further research is required to evaluate the properties of full fat and defatted maize–groundnut porridges and their effects on consumer acceptability.Originality/value It can be concluded that compositing maize with full fat and defatted groundnut has the capability of improving the nutritional quality of cereal-based diets consequently contributing to a significant increase in nutritional security of African populations and those of other developing countries of the world. [ABSTRACT FROM AUTHOR]

How cuticular proteins (CPs) interact with chitin and with each other in the cuticle remains unresolved. We employed LC-MS/MS to identify CPs from 5–6 day-old adults of Anopheles gambiae released after serial extraction with PBS, EDTA, 2-8M urea, and SDS as well as those that remained unextracted. Results were compared to published data on time of transcript abundance, localization of proteins within structures and within the cuticle, as well as properties of individual proteins, length, pI, percent histidine, tyrosine, glutamine, and number of AAP[A/V/L] repeats. Thirteen proteins were solubilized completely, all were CPRs, most belonging to the RR-1 group. Eleven CPs were identified in both soluble fractions and the final pellet, including 5 from other CP families. Forty-three were only detected from the final pellet. These included CPRs and members of the CPAP1, CPF, CPFL, CPLCA, CPLCG, CPLCP, and TWDL families, as well as several low complexity CPs, not assigned to families and named CPLX. For a given protein, many histidines or tyrosines or glutamines appear to be potential participants in cross-linking since we could not identify any peptide bearing these residues that was consistently absent. We failed to recover peptides from the amino-terminus of any CP. Whether this implicates that location in sclerotization or some modification that prevents detection is not known. Soluble CPRs had lower isoelectric points than those that remained in the final pellet; most members of other CP families had isoelectric points of 8 or higher. Obviously, techniques beyond analysis of differential solubility will be needed to learn how CPs interact with each other and with chitin. [ABSTRACT FROM AUTHOR]

Exerting control over the size, morphology, and complexity of metal and semiconductor nanoparticles and nanostructures is a requisite for exploring novel phenomena, and the potential applications of these nanomaterials. Bottom-up colloidal chemistry syntheses can benefit from using biomolecules as active elements to influence the formation of inorganic nanoparticles. In this review, we will discuss how three main biomolecule types, (namely DNA; amino acids, peptides, and proteins; and enzymes), can affect the growth of metal and semiconductor nanoparticles. We will present and discuss the templating and non-templating roles of those biomolecules, featuring key aspects and prospects of biomolecule-assisted metal and semiconductor nanoparticle growth. [ABSTRACT FROM AUTHOR]

Although the formation mechanism of biogenically metallic nanoparticles is broadly associated to enzyme mediation, major attention has been given to the role of proteins and peptides in oxido‐reduction of metallic ions leading to these nanostructures. Among the wide range of biomolecules that can act not only as capping agents but also as non‐enzymatic agents to form nanoparticles, disulphide bridge‐containing peptides and amino acids particularly stand out. The literature proposes that they actively participate in the process of nanoparticles' synthesis, with thiols groups and disulphide bridge moieties as the reaction catalytic sites. Similarly, denaturated enzymes containing exposed S–S or S–H moieties are also able to reduce metallic ions to form nanoparticles. This mini‐review is focused on the biogenic synthesis of metallic nanoparticles such as gold, silver, copper, platinum, palladium, lead and selenium, in which proteins, peptides, reductases and even oxido‐reductases act as non‐enzymatic catalysts of the reduction reaction, opening economically and ecologically favourable perspectives in the nanoparticles synthesis field. [ABSTRACT FROM AUTHOR]

Throughout nature, self-assembly gives rise to functional supramolecular biomaterials that can perform complex tasks with extraordinary efficiency and specificity. Inspired by these examples, self-assembly is increasingly used to fabricate synthetic supramolecular biomaterials for diverse applications in biomedicine and biotechnology. Peptides are particularly attractive as building blocks for these materials because they are based on naturally derived amino acids that are biocompatible and biodegradable; they can be synthesized using scalable and cost-effective methods, and their sequence can be tailored to encode formation of diverse architectures. To endow synthetic supramolecular biomaterials with functional capabilities, it is now commonplace to conjugate self-assembling building blocks to molecules having a desired functional property, such as selective recognition of a cell surface receptor or soluble protein, antigenicity, or enzymatic activity. This review surveys recent advances in using self-assembling peptides as handles to incorporate biologically active molecules into supramolecular biomaterials. Particular emphasis is placed on examples of functional nanofibers, nanovesicles, and other nano-scale structures that are fabricated by linking self-assembling peptides to proteins and carbohydrates. Collectively, this review highlights the enormous potential of these approaches to create supramolecular biomaterials with sophisticated functional capabilities that can be finely tuned to meet the needs of downstream applications. [ABSTRACT FROM AUTHOR]