Chemical Properties Of Proteins Research Articles

Research Progress on the Mechanism of the Impact of Myofibrillar Protein Oxidation on the Flavor of Meat Products.

Myofibrillar proteins primarily consist of myosin, actin, myogenin, and actomyosin. These proteins form complex networks within muscle fibers and are crucial to the physical and chemical properties of meat. Additionally, myofibrillar proteins serve as significant substrates for the adsorption of volatile flavor compounds, including aldehydes, alcohols, ketones, and sulfur and nitrogen compounds, which contribute to the overall flavor profile of meat products. A series of chemical reactions occur during the processing, storage, and transportation of meat products. Oxidation is one of the most significant reactions. Oxidative modification can alter the physical and chemical properties of proteins, ultimately impacting the sensory quality of meat products, including flavor, taste, and color. In recent years, considerable attention has been focused on the effects of protein oxidation on meat quality and its regulation. This study investigates the impact of myofibrillar protein oxidation on the sensory attributes of meat products by analyzing the oxidation processes and the factors that initiate myofibrillar protein oxidation. Additionally, it explores the control of myofibrillar protein oxidation and its implications on the sensory properties of meat products, providing theoretical insights relevant to meat processing methods and quality control procedures.

Effects of microgels fabricated by microfluidic on the stability, antioxidant, and immunoenhancing activities of aquatic protein

Aquatic products are considered a potential source of novel bioactive proteins, which are used as therapeutic drugs for the treatment of different diseases (such as oxidative stress, immunocompromised, and inflammation), as well as nutraceuticals and cosmetics. However, the physical and chemical properties of proteins are unstable, and they are easily denatured by the influence of external high temperature and polar pH during processing, resulting in the loss of their functional activity. Herein, Fenneropenaeus chinensis water-soluble protein (FCWP) and Lateolabrax japonicus water-soluble protein (LJWP) were encapsulated within spherical biopolymer microgels composed of pectin and chitosan produced by the microfluidic device. The encapsulated samples remained inside the microgels when they were exposed to upper gastrointestinal but were released when they were exposed to simulated colonic fluid due to the hydrolysis effect by enzymes secreted by the colonic microflora. The results showed that microgels improve the thermal stability of FCWP and LJWP due to the interaction between polysaccharides and proteins in the microgels. In addition, microgels encapsulation did not affect the antioxidant and immunoenhancing activities of FCWP and LJWP. In summary, these microgels are suitable for oral colon-specific delivery in functional foods and supplements.

Twelve Years of Genome-Wide Association Studies of Human Protein N-Glycosylation

Most human-secreted and membrane-bound proteins have covalently attached oligosaccharide chains or glycans. Glycosylation influences the physical and chemical properties of proteins, as well as their biological functions. Unsurprisingly, alterations in protein glycosylation have been implicated in a growing number of human diseases, and glycans are increasingly being considered as potential therapeutic targets, an essential part of therapeutics, and biomarkers. Although glycosylation pathways are biochemically well-studied, little is known about the networks of genes that guide the cell- and tissue-specific regulation of these biochemical reactions in humans in vivo. The lack of a detailed understanding of the mechanisms regulating glycome variation and linking the glycome to human health and disease is slowing progress in clinical applications of human glycobiology. Two of the tools that can provide much sought-after knowledge of human in vivo glycobiology are human genetics and genomics, which offer a powerful data-driven agnostic approach for dissecting the biology of complex traits. This review summarizes the current state of human populational glycogenomics. In Section 1, we provide a brief overview of the N-glycan’s structural organization, and in Section 2, we give a description of the major blood plasma glycoproteins. Next, in Section 3, we summarize, systemize, and generalize the results from current N-glycosylation genome-wide association studies (GWASs) that provide novel knowledge of the genetic regulation of the populational variation of glycosylation. Until now, such studies have been limited to an analysis of the human blood plasma N-glycome and the N-glycosylation of immunoglobulin G and transferrin. While these three glycomes make up a rather limited set compared with the enormous multitude of glycomes of different tissues and glycoproteins, the study of these three does allow for powerful analysis and generalization. Finally, in Section 4, we turn to genes in the established loci, paying particular attention to genes with strong support in Section 5. At the end of the review, in Sections 6 and 7, we describe special cases of interest in light of new discoveries, focusing on possible mechanisms of action and biological targets of genetic variation that have been implicated in human protein N-glycosylation.

Using the Noncanonical Metallo-Amino Acid [Cu(II)(2,2'-Bipyridin-5-yl)]-alanine to Study the Structures of Proteins.

Genetic code expansion allows modification of the physical and chemical properties of proteins by the site-directed insertion of noncanonical amino acids. Here we exploit this technology for measuring nanometer-scale distances in proteins. (2,2'-Bipyridin-5-yl)alanine was incorporated into the green fluorescent protein (GFP) and used as an anchoring point for Cu(II) to create a spin-label. The incorporation of (2,2'-bipyridin-5-yl)alanine directly into the protein resulted in a high-affinity binding site for Cu(II) capable of outcompeting other binding positions in the protein. The resulting Cu(II)-spin label is very compact and not larger than a conventional amino acid. By using 94 GHz electron paramagnetic resonance (EPR) pulse dipolar spectroscopy we have been able to determine accurately the distance between two such spin-labels. Our measurements revealed that GFP dimers can adopt different quaternary conformations. The combination of spin-labeling using a paramagnetic nonconventional amino acid with high-frequency EPR techniques resulted in a sensitive method for studying the structures of proteins.

Graph Signal Processing on protein residue networks helps in studying its biophysical properties

Understanding the physical and chemical properties of proteins is vital, and many efforts have been made to study the emergent properties of the macro-molecules as a combination of long chains of amino acids. Here, we present a graph signal processing based approach to model the biophysical property of proteins. For each protein inter-residue proximity-based network is used as basis graph and the respective amino acid properties are used as node-signals. Signals on nodes are decomposed on network’s Laplacian eigenbasis using graph Fourier transformations. We found that the intensity in low-frequency components of graph signals of residue features could be used to model few biophysical properties of proteins. Specifically, using our approach, we could model protein folding-rate, globularity and fraction of alpha-helices and beta-sheets. Our approach also allows amalgamation of different types of chemical and graph theoretic properties of residue to be used together in a multi-variable regression model to predict biophysical properties.

The H-D-isotope effect of heavy water affecting ligand-mediated nanoparticle formation in SANS and NMR experiments.

An isotopic effect of normal (H2O) vs. heavy water (D2O) is well known to fundamentally affect the structure and chemical properties of proteins, for instance. Here, we correlate the results from small angle X-ray and neutron scattering (SAXS, SANS) with high-resolution scanning transmission electron microscopy to track the evolution of CdS nanoparticle size and crystallinity from aqueous solution in the presence of the organic ligand ethylenediaminetetraacetate (EDTA) at room temperature in both H2O and D2O. We provide evidence via SANS experiments that exchanging H2O with D2O impacts nanoparticle formation by changing the equilibria and dynamics of EDTA clusters in solution as investigated by nuclear magnetic resonance analysis. The colloidal stability of the CdS nanoparticles, covered by a layer of [Cd(EDTA)]2- complexes, is significantly reduced in D2O despite the strong stabilizing effect of EDTA in suspensions of normal water. Hence, conclusions about nanoparticle formation mechanisms from D2O solutions reveal limited transferability to reactions in normal water due to isotopic effects, which thus need to be discussed for contrast match experiments.

DIGE Analysis of Clinical Specimens.

Two-dimensional difference gel electrophoresis (2D-DIGE) is an elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2D-GE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The use of an internal pooled standard makes 2D-DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. Technical limitations of this technique (i.e., underrating of low abundant, high molecular mass and integral membrane proteins) are counterbalanced by the incomparable separation power which allows proteoforms and unknown PTM (posttranslational modification) identification. Moreover, the image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

An antibody-free enrichment approach enabled by reductive glutaraldehydation for monomethyllysine proteome analysis.

Protein lysine monomethylation is an important post-translational modification participated in regulating many biological processes. There is growing interest in identifying these methylation events. However, the introduction of one methyl group on lysine residues has negligible effect on changing the physical and chemical properties of proteins or peptides, making enriching and identifying monomethylated lysine (Kme1) proteins or peptides extraordinarily challenging. In this study, we proposed an antibody-free chemical proteomics approach to capture Kme1 peptides from complex protein digest. By exploiting reductive glutaraldehydation, 5-aldehyde-pentanyl modified Kme1 residues and piperidine modified primary amines were generated at the same time. The peptides with aldehyde modified Kme1 residues were then enriched by solid-phase hydrazide chemistry. This chemical proteomics approach was validated by using several synthetic peptides. It was demonstrated that it can enrich and detect Kme1 peptide from peptide mixture containing 5000-fold more bovine serum albumin tryptic digest. Besides, we extended our approach to profile Kme1 using heavy methyl stable isotope labeling by amino acids in cell culture (hmSILAC) labeled Jurkat T cells and Hela cells. Totally, 29 Kme1 sites on 25 proteins were identified with high confidence and 11 Kme1 sites were identified in both two types cells. This is the first antibody-free chemical proteomics approach to enrich Kme1 peptides from complex protein digest, and it provides a potential avenue for the analysis of methylome.

The Change in the Structure and Functionality of Ferritin during the Production of Pea Seed Milk.

Understanding the effect of thermal treatment on the physical and chemical properties of protein and its mechanisms has important theoretical implications in food science. Pea seed ferritin (PSF) is an iron storage protein naturally occurring in pea seeds, which represents a promising iron supplement. However, how thermal processing affects the structure and function of PSF remains unknown. In this work, during the production of pea seed milk, we investigated the effect of thermal treatments at boiling temperature for two different times (5 and 10 min), respectively, on the structure and function of PSF. The results demonstrated that thermal treatment resulted in a pronounced change in the primary, secondary, and tertiary structure, iron content, and iron oxidation activity of PSF. However, the shell-like structure of PSF can be kept during the processing of pea seed milk. Interestingly, upon thermal treatment, both thermal-treated samples exhibit larger higher iron absorption rate by Caco-2 than untreated PSF at the same protein concentration. Such an investigation provides a better understanding of the relationship between the structure and function of food protein, as affected by thermal treatment.

Generating new protein sequences by using dense network and attention mechanism.

Protein engineering uses de novo protein design technology to change the protein gene sequence, and then improve the physical and chemical properties of proteins. These newly generated proteins will meet the needs of research better in properties and functions. The Dense-AutoGAN model is based on GAN, which is combined with an Attention mechanism to generate protein sequences. In this GAN architecture, the Attention mechanism and Encoder-decoder can improve the similarity of generated sequences and obtain variations in a smaller range on the original basis. Meanwhile, a new convolutional neural network is constructed by using the Dense. The dense network transmits in multiple layers over the generator network of the GAN architecture, which expands the training space and improves the effectiveness of sequence generation. Finally, the complex protein sequences are generated on the mapping of protein functions. Through comparisons of other models, the generated sequences of Dense-AutoGAN verify the model performance. The new generated proteins are highly accurate and effective in chemical and physical properties.

CURRENT USE OF NANOPROTEIN AND APPLICATION IN THE DEVELOPMENT OF FOOD PRODUCTS FOR FUNCTIONAL AND NUTRITIONAL BENEFITS

In the last few decades, there has been a growing interest in the production of Nano protein particles from food protein. The term Nanotechnology refers to the formation of materials, devices, and systems by manipulating their matter into a length scale of ~1-100 nm. Nanoparticles can be formed from various types of materials like metals, polysaccharides, and proteins. Biological protein-based nanoparticles made from whey, soy, corn zein are advantageous for health and possess relatively low cost. For the production of Nano protein, the physical and chemical properties of proteins can be modified for specific food and make the protein applicable for biotechnological purposes. Specific structure and number of functional groups in protein that are responsible for the physicochemical properties are selectively modified during the preparation of Nano protein. Nano protein particles are used in a wide range of settings and it replaces many particles which are not biocompatible and exerts a negative effect on the environment. In the food industry Nano protein is a revolutionary fact to maintain the color, flavor, and nutritive value of food. Various types of natural and synthetic nanoparticles are available in the food and pharmacological industry but among them, protein-based nanoparticles are widely used because of their size and relatively easy method of preparation. These nanoparticles are used in the loading and delivery of physiologically active compounds like nutraceuticals. Nano protein formation is also helped to combat global food security challenges which are related to the increased global population, unstable world economy, and climate changes.

Clustering and Differentiation of glr-3 Gene Function and Its Homologous Proteins

In order to adapt to the low temperature environment, organisms transmitexcitement to the central system through the thermal sensing system, whichis a classic reflex reaction. The cold receptor GLR-3 perceives cold and produces cold avoidance behavior through peripheral sensory neurons ASER.In order to further understand the gene encoding of the cold sensing glr-3gene and the evolution of its homologous gene group function and proteinfunction, the nucleotide sequence and amino acid sequence of the glr-3gene and its homologous gene in 24 species were obtained and compared.By clustering with the GRIK2 gene sequence of Rana chensinensis, the bioinformatics method was used to predict and sequence analyze the change ofgene, evolution rate, physical and chemical properties of protein, glycosylation sites, phosphorylation sites, secondary structure and tertiary structureof protein. The analysis results show that the glr-3 gene and its homologousgene have obvious positive selection effect. The protein prediction analysisshowed that the glr-3 gene and its homologous genes encoded proteinsin these 25 species were hydrophilic proteins, and the proportion of sidechains of aliphatic amino acids was high. The transmembrane helix waswidespread and there were more N-glycosylation sites and O-glycosylationsites. The protein phosphorylation sites encoded were serine, threonine andtyrosine phosphorylation sites. Secondary structure prediction showed thatthe secondary structure units of the encoded protein were α-helix, β-turn,random coil and extended chain, and the proportion of α-helix was the largest. This study provides useful information on the evolution and function ofthe cold sensing gene glr-3 and its homologous genes.

Mechanism of interactions between \u03b1-conotoxin RegIIA and carbohydrates at the human \u03b13\u03b24 nicotinic acetylcholine receptor

Conotoxins are marine peptide toxins from marine cone snails. The α-conotoxin RegIIA can selectively act on human (h) α3β4 nicotinic acetylcholine receptor (nAChR), and is an important lead for drug development. The high-resolution cryo-electron microscopy structure of the α3β4 nAChR demonstrates several carbohydrates are located near the orthosteric binding sites, which may affect α-conotoxin binding. Oligosaccharide chains can modify the physical and chemical properties of proteins by changing the conformation, hydrophobicity, quality and size of the protein. The purpose of this study is to explore the effect of oligosaccharide chains on the binding modes and activities of RegIIA and its derivatives at hα3β4 nAChRs. Through computational simulations, we designed and synthesized RegIIA mutants at position 14 to explore the importance of residue H14 to the activity of the peptide. Molecular dynamics simulations suggest that the oligosaccharide chains affect the binding of RegIIA at the hα3β4 nAChR through direct interactions with H14 and by affecting the C-loop conformation of the binding sites. Electrophysiology studies on H14 analogues suggest that in addition to forming direct interactions with the carbohydrates, the residue might play an important role in maintaining the conformation of the peptide. Overall, this study further clarifies the structure–activity relationship of α-conotoxin RegIIA at the hα3β4 nAChR and, also provides important experimental and theoretical basis for the development of new peptide drugs.

Analytical Techniques for Structural Characterization of Proteins in Solid Pharmaceutical Forms: An Overview.

Therapeutic proteins as biopharmaceuticals have emerged as a very important class of drugs for the treatment of many diseases. However, they are less stable compared to conventional pharmaceuticals. Their long-term stability in solid forms, which is critical for product performance, depends heavily on the retention of the native protein structure during the lyophilization (freeze-drying) process and, thereafter, in the solid state. Indeed, the biological function of proteins is directly related to the tertiary and secondary structure. Besides physical stability and biological activity, conformational stability (three-dimensional structure) is another important aspect when dealing with protein pharmaceuticals. Moreover, denaturation as loss of higher order structure is often a precursor to aggregation or chemical instability. Careful study of the physical and chemical properties of proteins in the dried state is therefore critical during biopharmaceutical drug development to deliver a final drug product with built-in quality that is safe, high-quality, efficient, and affordable for patients. This review provides an overview of common analytical techniques suitable for characterizing pharmaceutical protein powders, providing structural, and conformational information, as well as insights into dynamics. Such information can be very useful in formulation development, where selecting the best formulation for the drug can be quite a challenge.

Fluorescent Cadmium Chalcogenide Nanoclusters in Ubiquitin

Fluorescent semiconductor nanoclusters (FNCs) have received much attention by many scientists due to their attractive functions and features. However, the traditional organometallic chemical synthesis routes for such FNCs require harsh reaction conditions in organic solvents, which limit their use in biological applications. Therefore, developing synthesis strategies for the fabrication of FNCs by association with proteins under mild reaction conditions is pivotal to improve their functionalities. In addition, understanding the effect of structural and chemical properties of proteins on the synthesis mechanism of FNCs is one of the key points, which eventually enables to control and tune the photophysical properties of FNCs. The purpose of this study is to introduce the syntheses of cadmium selenide nanocluster (CdSeNC) and cadmium sulfide nanocluster (CdSNC) by using ubiquitin, a small cysteine‐free protein, and investigating their properties via spectroscopic and microscopic methods. It is shown that significant changes in the protein structure as well as in its oligomerization occur upon the formation of the highly hydrated FNCs.

Adaptive Evolution of Chalcone Isomerase Superfamily in Fagaceae.

Chalcone Isomerase (CHI) catalyzes the biosynthesis of flavonoids and secondary metabolism in plants. Currently, there is no systematic analysis of CHIs gene family in Fagaceae which is available. In this study, twenty-two CHI proteins were identified in five species of the Fagaceae family. The CHI superfamily in Fagaceae can be classified into three subfamilies and five groups using phylogenetic analysis, analysis of physicochemical properties, and structural prediction. Results indicated that serine (Ser) and isoleucine (Ile) residues determine the substrate preferred by active Type I Fagaceae CHI, and the chalcone isomerase-like (CHIL) of Fagaceae had active site residues. Adaptive analysis of CHIs showed that CHIs are subject to selection pressure. The active CHI gene of Fagaceae was located in the cytoplasm, and it had the typical gene structure of CHI and contains four exons. All the twenty-two identified CHIs had the conserved domain motif 3, and the different groups had their own structural characteristics. In the process of fatty acid binding protein (FAP) evolution to CHIL and CHI, the physical and chemical properties of proteins also had significant differences in addition to changes in protein functions.

Bioinformatics analysis of <italic>SnRK</italic> gene family and its relation with seed oil content of <italic>Brassica napus</italic> L.

<p indent=0mm>Sucrose non-fermenting-1-related protein kinase (SnRK) is a widely existed serine/threonine protein kinase in plants, which is involved in the regulation of biological processes such as signal transduction, stress response and seed growth. In order to explore the mechamism of the <italic>SnRK</italic> gene families and its influence on the seed oil content of<italic> Brassica napus </italic>L., <italic>BnSnRK </italic>gene family system evolution, gene structure, physical and chemical properties of protein, conservative motif, protein secondary structure, <italic>cis</italic>-element and subcellular localization prediction were analyzed, and<italic> BnSnRK</italic> genes affecting oil content of seeds were screened by candidate genes association analysis, haplotype analysis and qRT-PCR. The results showed that 92<italic> BnSnRK</italic> members were identified and divided into three subgroups, distributed on 19 chromosomes of <italic>Brassica napus </italic>L. The physical and chemical properties of proteins were significantly different among subgroups. Most genes had 7–14 exons; the motifs of the same subfamily were more similar in distribution. The<italic> BnSnRK</italic> family was mainly expressed in the cytoplasm. 12 family members related to the oil content were screened out by association analysis in rapeseed. Genes<italic> BnaC02g10730D</italic> might negatively regulate seed oil content, while genes <italic>BnaA07g12290D</italic>, <italic>BnaA10g22850D</italic>,<italic> BnaA08g18050D</italic>, and <italic>BnaC04g44390D</italic> might positively regulate seed oil content of <italic>Brassica napus</italic> L. There were significant differences in seed oil content under different environments, and 12 oil-related members all contained MYB, MYC and ABA response elements. Environment-specific oil-related genes might be related to plant abiotic stress response. This study provides a theoretical basis for<italic> BnSnRK </italic>gene functional verification and breeding.

Improvements in chemical carriers of proteins and peptides.

The successful intracellular delivery of biologically active proteins and peptides plays an important role for therapeutic applications. Indeed, protein/peptide delivery could overcome some problems of gene therapy, for example, controlling the expression levels and the integration of transgene into the host cell genome. Thus, protein/peptide drug delivery showed a promising and safe approach for treatment of cancer and infectious diseases. Due to the unique physical and chemical properties of proteins, their production (e.g., isolation, purification & formulation) and delivery represented significant challenges in pharmaceutical studies. Modification in the structural moieties of these protein/peptide drugs could improve their solubility, stability, crystallinity, lipophilicity, enzymatic susceptibility and targetability, and subsequently, therapies and cures against various diseases. Using the structural modification of protein/peptide, their delivery provided overall higher success rates including high specificity, high activity, bioreactivity and safety. Recently, biotechnological and pharmaceutical companies have tried to find novel techniques for the modifications and improve delivery systems/carriers. However, each carrier has its own benefits and drawbacks, and an appropriate carrier is often established by the physicochemical properties of protein or peptide, the ideal route of injection, and clinical characteristics of therapy. In this review, an attempt was made to give an overview on the chemical carriers for proteins and peptides as well as the recent advances in this field.

Genome-wide identification and expression analysis of brassinosteroid action-related genes during the shoot growth of moso bamboo.

Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles in a range of plant growth and development processes. BR action includes active BR formation by a complex biosynthesis process and driving BR biological function through signal transduction. Although the characterization of several BR action-related genes has been conducted in a few model plants, systematic information about these genes in bamboo is still lacking. We identified 64 genes related to BR action from the genome of moso bamboo (Phyllostachys edulis), including twenty that participated in BR biosynthesis and forty-four involved in BR signal transduction. The characteristics of all these candidate genes were identified by bioinformatics methods, including the gene structures, basic physical and chemical properties of proteins, conserved domains and evolutionary relationships. Based on the transcriptome data, the candidate genes demonstrated different expression patterns, which were further validated by qRT-PCR using templates from bamboo shoots with different heights. Thirty-four positive and three negative co-expression modules were identified by 44 candidate genes in the newly emerging bamboo shoot. The gene expression patterns and co-expression modules of BR action-related genes in bamboo shoots indicated that they might function to promote bamboo growth through BR biosynthesis and signal transduction processes. This study provides the first step towards the cloning and functional dissection of the role of BR action-related genes in moso bamboo, which also presents an excellent opportunity for genetic engineering using the candidate genes to improve bamboo quantity and quality.

Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network

Prediction of protein-protein interactions (PPIs) is of great significance. To achieve this, we propose a novel computational method for PPIs prediction based on a similarity network fusion (SNF) model for integrating the physical and chemical properties of proteins. Specifically, the physical and chemical properties of protein are the protein amino acid mutation rate and its hydrophobicity, respectively. The amino acid mutation rate is extracted using a BLOSUM62 matrix, which puts the protein sequence into block substitution matrix. The SNF model is exploited to fuse protein physical and chemical features of multiple data by iteratively updating each original network. Finally, the complementary features from the fused network are fed into a label propagation algorithm (LPA) for PPIs prediction. The experimental results show that the proposed method achieves promising performance and outperforms the traditional methods for the public dataset of H. pylori, Human, and Yeast. In addition, our proposed method achieves average accuracy of 76.65%, 81.98%, 84.56%, 84.01% and 84.38% on E. coli, C. elegans, H. sapien, H. pylori and M. musculus datasets, respectively. Comparison results demonstrate that the proposed method is very promising and provides a cost-effective alternative for predicting PPIs. The source code and all datasets are available at http://pan.baidu.com/s/1dF7rp7N.