Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation

Proteins play a central role in all domains of life, and precise regulation of their activity is essential for understanding the related biological processes and therapeutic functions. Nucleic acid aptamers, the molecular recognition components derived from systematic evolution of ligands by exponential enrichment(SELEX), can specifically identify proteins with antibody-like recognition characteristics and help to regulate their activity. This minireview covers the SELEX-based selection of protein-binding aptamers, membrane protein analytical techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins, including membrane receptors and non-membrane proteins(thrombin as a model), as well as the potential challenges and prospects regarding aptamer-mediated protein manipulation, aiming to supply some useful information for researchers in this field.     

Sensitive targeted multiple protein quantification based on elemental detection of Quantum Dots

A generic strategy based on the use of CdSe/ZnS Quantum Dots (QDs) as elemental labels for protein quantification, using immunoassays with elemental mass spectrometry (ICP-MS), detection is presented. In this strategy, streptavidin modified QDs (QDs-SA) are bioconjugated to a biotinylated secondary antibody (b-Ab₂). After a multi-technique characterization of the synthesized generic platform (QDs-SA-b-Ab₂) it was applied to the sequential quantification of five proteins (transferrin, complement C3, apolipoprotein A1, transthyretin and apolipoprotein A4) at different concentration levels in human serum samples. It is shown how this generic strategy does only require the appropriate unlabeled primary antibody for each protein to be detected. Therefore, it introduces a way out to the need for the cumbersome and specific bioconjugation of the QDs to the corresponding specific recognition antibody for every target analyte (protein). Results obtained were validated with those obtained using UV–vis spectrophotometry and commercial ELISA Kits.     

MOEPGA: A novel method to detect protein complexes in yeast protein–protein interaction networks based on MultiObjective Evolutionary Programming Genetic Algorithm

The identification of protein complexes in protein–protein interaction (PPI) networks has greatly advanced our understanding of biological organisms. Existing computational methods to detect protein complexes are usually based on specific network topological properties of PPI networks. However, due to the inherent complexity of the network structures, the identification of protein complexes may not be fully addressed by using single network topological property. In this study, we propose a novel MultiObjective Evolutionary Programming Genetic Algorithm (MOEPGA) which integrates multiple network topological features to detect biologically meaningful protein complexes. Our approach first systematically analyzes the multiobjective problem in terms of identifying protein complexes from PPI networks, and then constructs the objective function of the iterative algorithm based on three common topological properties of protein complexes from the benchmark dataset, finally we describe our algorithm, which mainly consists of three steps, population initialization, subgraph mutation and subgraph selection operation. To show the utility of our method, we compared MOEPGA with several state-of-the-art algorithms on two yeast PPI datasets. The experiment results demonstrate that the proposed method can not only find more protein complexes but also achieve higher accuracy in terms of fscore. Moreover, our approach can cover a certain number of proteins in the input PPI network in terms of the normalized clustering score. Taken together, our method can serve as a powerful framework to detect protein complexes in yeast PPI networks, thereby facilitating the identification of the underlying biological functions.     

Proteins as functional interlayer in organic field-effect transistor

The paper summarizes and discusses the recent advances of proteins as functional interlayers in organic field-effect transistors (OFETs). Specific focus is given on the proteins integrated into the device structure, either to act as dielectric materials or to perform as the functional interlayer between the dielectric and the organic semiconductor (OSC). The main emphasis is give to the location and the specific effect of protein layers in the structure of OFETs. Besides, the possibility of amyloid serving as useful building blocks for OFET is discussed.     

A benchmark of optimally folded protein structures using integer programming and the 3D-HP-SC model

The Protein Structure Prediction (PSP) problem comprises, among other issues, forecasting the three-dimensional native structure of proteins using only their primary structure information. Most computational studies in this area use synthetic data instead of real biological data. However, the closer to the real-world, the more the impact of results and their applicability. This work presents 17 real protein sequences extracted from the Protein Data Bank for a benchmark to the PSP problem using the tri-dimensional Hydrophobic-Polar with Side-Chains model (3D-HP-SC). The native structure of these proteins was found by maximizing the number of hydrophobic contacts between the side-chains of amino acids. The problem was treated as an optimization problem and solved by means of an Integer Programming approach. Although the method optimally solves the problem, the processing time has an exponential trend. Therefore, due to computational limitations, the method is a proof-of-concept and it is not applicable to large sequences. For unknown sequences, an upper bound of the number of hydrophobic contacts (using this model) can be found, due to a linear relationship with the number of hydrophobic residues. The comparison between the predicted and the biological structures showed that the highest similarity between them was found with distance thresholds around 5.2–8.2 Å. Both the dataset and the programs developed will be freely available to foster further research in the area.     

Ultrasound-assisted immersion freezing reduces the structure and gel property deterioration of myofibrillar protein from chicken breast

The effects of air freezing (AF), immersion freezing (IF) and ultrasound-assisted immersion freezing (UF) at different power levels (125, 165, 205 and 245 W) on the structure and gel properties of the myofibrillar protein (MP) of chicken breast were investigated. UF at 165 W (UF-165) had no obvious negative impact on the primary structure of the MP and effectively reduced the change in the secondary and tertiary structure. In addition, UF-165 significantly reduced the losses in the elastic modulus (G′), gel strength, and gel water holding capacity (P < 0.05). According to low field nuclear magnetic resonance analysis, the T₂₁ and T₂₂ of the UF-165 MP gels were shorter than those of the AF and IF samples, which meant that the UF-165 reduced the mobility of the immobilized water and free water in MP gel. A scanning electron microscopy analysis showed that the appropriate ultrasonic power promoted the formation of a compact and homogeneous protein gel network. These results suggested that the appropriate ultrasonic power maintained the MP structure and reduced the loss of gel quality.     

Tridentate Schiff base and 4,4′-bipyridine coordinated di/polynuclear Cu (II) complexes: Synthesis,crystal structure,DNA/protein binding and catecholase activity

4,4′-bipyridine bridged two Cu (II) complexes, [Cu₂L¹₂(4,4′-bipy)(H₂O)₂](ClO₄)₂ ( 1 ) and [Cu₂L²₂(4,4′-bipy)]_n·(2H₂O)_n ( 2 ) (where, HL¹ = 2-[(3-methylamino-propylimino)-methyl]-phenol, H₂L² = 3-[(2-hydroxy-3-methoxy-benzylidene)-amino]-propionic acid, and 4,4′-bipy = 4,4′-bipyridine) have been synthesized and characterized by single crystal structure determination, mass spectrometry, FT-IR, electronic absorption, and emission spectroscopy. Complex 1 is dinuclear cationic compound and counter balanced by perchlorate anion, whereas complex 2 possesses 1D poly-nuclear structure. Both the complexes crystallize in monoclinic system with P2₁/c space group and the copper centers possess square pyramidal geometry. H-bonding, C-H···π, π···π interactions results the formation of two dimentional supramolecular structure for both the complexes. Interactions of complexes with bovine serum albumins (BSA) and human serum albumins (HSA) have been studied by using electronic absorption and emission spectroscopic technique. The calculated values of binding constants (K_b) are (9.22 ± 0.26) × 10⁵ L mol⁻¹ ( 1 -BSA), (7.19 ± 0.16) × 10⁵ L mol⁻¹ ( 1 -HSA), (5.05 ± 0.20) × 10⁵ L mol⁻¹ ( 2 -BSA) and (3.56 ± 0.25) × 10⁵ L mol⁻¹ ( 2 -HSA). The mechanism of serum albumins-complex interactions have been investigated by fluorescence lifetime measurement. Fluorescence spectroscopic studies indicate that both the complexes interact with calf thymas-DNA. Catecholase activity of the complexes has been studied in methanol using 3,5-di-tert-butylcatechol (3,5-DTBC) as substrate and the result show that both the complexes are active for catalytic oxidation of 3,5-DTBC to 3,5-di-tert-butylquinone (3,5-DTBQ) in presence of molecular oxygen. Calculated values of turnover numbers are 71.81 ± 1.04 h⁻¹ and 69.45 ± 0.74 h⁻¹ for 1 and 2 , respectively.     

Impact of ultrasound processing on alternative protein systems: Protein extraction,nutritional effects and associated challenges

Proteins from alternative sources including terrestrial and aquatic plants, microbes and insects are being increasingly explored to combat the dietary, environmental and ethical challenges linked primarily to conventional sources of protein, mainly meat and dairy proteins. Ultrasound (US) technologies have emerged as a clean, green and efficient methods for the extraction of proteins from alternative sources compared to conventional methods. However, the application of US can also lead to modifications of the proteins extracted from alternative sources, including changes in their nutritional quality (protein content, amino acid composition, protein digestibility, anti-nutritional factors) and allergenicity, as well as damage of the compounds associated with an increased degradation resulting from extreme US processing conditions. This work aims to summarise the main advances in US equipment currently available to date, including the main US parameters and their effects on the extraction of protein from alternative sources, as well as the studies available on the effects of US processing on the nutritional value, allergenicity and degradation damage of these alternative protein ingredients. The main research gaps identified in this work and future challenges associated to the widespread application of US and their scale-up to industry operations are also covered in detail.