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Proteins are widely consumed for their nutritional benefits, and they possess many applications such as emulsifiers, foaming agents, fat replacers, and thickeners which aid in obtaining the desired rheology and texture of food products. Moreover, the formation of protein–carbohydrate complex can further enhance the functional properties. Hence, the present study investigated the effect of ultrasonic cavitation in the formation of soy protein-rice starch complexes. Ultrasound treatment at 60% amplitude (450 W) combined with heat treatment formed complexes with enhanced solubility, water holding, and foaming properties compared to raw soy protein isolates. Further, sonication preserved the crystalline nature of the complexes formed. The molecular docking studies performed using 11 S protein (1FXZ) indicate the formation of the hydrogen bonds of shorter distances between glutamine (GLN) and leucine (LEU) amino acids with the OH group of rice starch. The complexes formed had excellent functional properties, which increased their scope of application in the food industry. [ABSTRACT FROM AUTHOR]

The relevance of the study is due to the need to improve the technology for processing peas and beans of domestic selection into plant-based drinks and their use in technologies for alternative products of complex raw materials for healthy, functional and specialized nutrition of various population groups. The purpose of the work is to study the influence of the developed technological modes of bioactivation on the nutritional and biological value, functional and technological properties of the protein-carbohydrate complex of pea and bean grains. The work examines the results of studies of changes occurring in pea grains bred at the Bashkir Research Institute of Agriculture and beans bred at the Omsk State Agrarian University during their bioactivation using the Smart Sprouter "Rosinka" installation, in particular the biochemical composition and inhibitory activity of grain of the studied varieties, a protein complex and amino acid composition, protein digestibility in vitro, functional and technological properties of the protein-carbohydrate complex of grain. The research has been carried out using generally accepted, modern instrumental methods for analyzing the properties of raw materials and finished products. It has been established that the use of the developed technological parameters of bioactivation leads to modification of the functional and technological properties of the structure-forming nutrients of grain, intensive accumulation of all amino acids, with the exception of threonine, make it possible to increase the protein content in pea grain by 15.32 % and beans by 14.96 %, relative to the initial values increase the degree of compliance of pea and bean grain protein with the FAO/WHO reference protein by 4.48 and 17.53 %, reduce the activity of grain protease inhibitors by 19.76 and 26.12 %, increase the digestibility of grain protein by 7.77 and 5.85 %. The research results prove the feasibility of using bioactivated pea and bean grains for the production of alternative products with a complex raw material composition, including plant-based drinks and products in the "dairy alternatives" segment.

Protein-carbohydrate interactions occur naturally in glycoproteins which are highly stable in nature and are involved in various food complexes and can enhance the quality and functional properties of foods. In the current study, we characterized the protein-carbohydrate complex formed between commercial soy protein isolate and rice starch using different treatments namely heat treatment alone, ultrasound treatment alone, combination of ultrasound and heat treatment and mixing alone. The structural data obtained using circular dichroism indicated that during the complex formation, the α-helix values were reduced by a maximum of 67% compared to soy protein isolate alone. The crystalline nature of the complexes formed by ultrasound treatment preserved the techno-functional properties as compared to complexes formed by heat treatments. The FTIR analysis of the complexes formed indicated the formation of glycosidic bond. Molecular docking analysis revealed the interaction between the complexes occurred due to hydrogen bonds which make the proteins more stable in nature thus enhancing their denaturation temperature. Glutamine, Proline and Arginine present in the D subunit of 7S 3AUP interacts with the starch molecule. The obtained results suggest that sonication combined with heat treatment led to higher interaction between the soy proteins isolate and rice starch.

Protein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability to model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural and biophysical data in order to train and validate a new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function. Information on both protein and carbohydrate complementarity, in terms of shape and chemistry, was captured using graph-based structural signatures. Across both training and independent test sets, we achieved comparable Pearson's correlations of 0.72 under cross-validation [root mean square error (RMSE) of 1.58 Kcal/mol] and 0.67 on the independent test (RMSE of 1.72 Kcal/mol), providing confidence in the generalisability and robustness of the final model. Similar performance was obtained across mono-, di- and oligosaccharides, further highlighting the applicability of this approach to the study of larger complexes. We show CSM-carbohydrate significantly outperformed previous approaches and have implemented our method and make all data freely available through both a user-friendly web interface and application programming interface, to facilitate programmatic access at http://biosig.unimelb.edu.au/csm%5fcarbohydrate/. We believe CSM-carbohydrate will be an invaluable tool for helping assess docking poses and the effects of mutations on protein-carbohydrate affinity, unravelling important aspects that drive binding recognition. [ABSTRACT FROM AUTHOR]

Protein–carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein–carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein–carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein–carbohydrate complexes belonging to six categories of protein–carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149 kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein–Carbohydrate Affinity Predictor, for predicting the binding affinity of protein–carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera. [ABSTRACT FROM AUTHOR]

Summary MGG_03307 is a lectin isolated from Magnaporte oryzae , a fungus that causes devastating rice blast disease. Its function is associated with protecting M. oryzae from the host immune response in plants. To provide the structural basis of how MGG_03307 protects the fungus, crystal structures of its CVNH-LysM module were determined in the absence and presence of GlcNAc-containing cell wall chitin constituents, which can act as pathogen-associated molecular patterns. Our structures revealed that glycan binding is accompanied by a notable conformational change in the LysM domain and that GlcNAc 3 and GlcNAc 4 are accommodated similarly. GlcNAc 5 and GlcNAc 6 interact with the LysM domain in multiple conformations, as evidenced by solution nuclear magnetic resonance studies. No dimerization of MoCVNH3 via its LysM domain was observed upon binding to GlcNAc 6 , unlike in multiple LysM domain-containing proteins. Importantly, we define a specific consensus binding mode for the recognition of GlcNAc oligomers by single LysM domains. [ABSTRACT FROM AUTHOR]

Protein-carbohydrate interactions occur naturally in glycoproteins which are highly stable in nature and are involved in various food complexes and can enhance the quality and functional properties of foods. In the current study, we characterized the protein-carbohydrate complex formed between commercial soy protein isolate and rice starch using different treatments namely heat treatment alone, ultrasound treatment alone, combination of ultrasound and heat treatment and mixing alone. The structural data obtained using circular dichroism indicated that during the complex formation, the α-helix values were reduced by a maximum of 67% compared to soy protein isolate alone. The crystalline nature of the complexes formed by ultrasound treatment preserved the techno-functional properties as compared to complexes formed by heat treatments. The FTIR analysis of the complexes formed indicated the formation of glycosidic bond. Molecular docking analysis revealed the interaction between the complexes occurred due to hydrogen bonds which make the proteins more stable in nature thus enhancing their denaturation temperature. Glutamine, Proline and Arginine present in the D subunit of 7S 3AUP interacts with the starch molecule. The obtained results suggest that sonication combined with heat treatment led to higher interaction between the soy proteins isolate and rice starch., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

Structural biology plays a key role in understanding how networks of protein interactions with their partners are organized at the atomic level. In this review, we show that NMR is a very efficient method to solve 3D structures of protein – RNA and protein–carbohydrate complexes of high quality. We explain the importance of studying such interactions and describe the main steps that are required to determine structures of these types of complexes by NMR. Finally, we show that X-ray crystallography and NMR are complementary methods and briefly report on advantages and disadvantages of each approach.

Simian virus 40 (SV40) has been a paradigm for understanding attachment and entry of nonenveloped viruses, viral DNA replication, and virus assembly, as well as for endocytosis pathways associated with caveolin and cholesterol. We find by glycan array screening that SV40 recognizes its ganglioside receptor GM1 with a quite narrow specificity, but isothermal titration calorimetry shows that individual binding sites have a relatively low affinity, with a millimolar dissociation constant. The high-resolution crystal structure of recombinantly produced SV40 capsid protein, VP1, in complex with the carbohydrate portion of GM1, reveals that the receptor is bound in a shallow solvent-exposed groove at the outer surface of the capsid. Through a complex network of interactions, VP1 recognizes a conformation of GM1 that is the dominant one in solution. Analysis of contacts provides a structural basis for the observed specificity and suggests binding mechanisms for additional physiologically relevant GM1 variants. Comparison with murine Polyomavirus (Polyoma) receptor complexes reveals that SV40 uses a different mechanism of sialic acid binding, which has implications for receptor binding of human polyomaviruses. The SV40-GM1 complex reveals a parallel to cholera toxin, which uses a similar cell entry pathway and binds GM1 in the same conformation. [ABSTRACT FROM AUTHOR]

The 3D structure of a complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed synthetic heparin hexasaccharide has been determined by NMR spectroscopy. This hexasaccharide can substitute natural heparins in FGF-1 mitogenesis assays, in spite of not inducing any apparent dimerization of the growth factor. The use of this well defined synthetic heparin analogue has allowed us to perform a detailed NMR structural analysis of the heparin–FGF interaction, overcoming the limitations of NMR to deal with the high molecular mass and heterogeneity of the FGF-1 oligomers formed in the presence of natural heparin fragments. Our results confirm that glycosaminoglycans induced FGF-1 dimerization either in a cis or trans disposition with respect to the heparin chain is not an absolute requirement for biological activity. [ABSTRACT FROM AUTHOR]

Trehalose (α-d-glucopyranosyl-1,1-α-d-glucopyranose) is a non-reducing diglucoside found in various organisms that serves as a carbohydrate reserve and as an agent that protects against a variety of physical and chemical stresses. Deinococcus radiodurans possesses an alternative biosynthesis pathway for the synthesis of trehalose from maltooligosaccharides. This reaction is mediated by two enzymes: maltooligosyltrehalose synthase (MTSase) and maltooligosyltrehalose trehalohydrolase (MTHase). Here, we present the 1.1Å resolution crystal structure of MTHase. It consists of three major domains: two β-sheet domains and a conserved glycosidase (β/α)8 barrel catalytic domain. Three subdomains consisting of short insertions were identified within the catalytic domain. Subsequently, structures of MTHase in complex with maltose and trehalose were obtained at 1.2Å and 1.5Å resolution, respectively. These structures reveal the importance of the three inserted subdomains in providing the key residues required for substrate recognition. Trehalose is recognised specifically in the +1 and +2 binding subsites by an extensive hydrogen-bonding network and a strong hydrophobic stacking interaction in between two aromatic residues. Moreover, upon binding to maltose, which mimics the substrate sugar chain, a major concerted conformational change traps the sugar chain in the active site. The presence of magnesium in the active site of the MTHase–maltose complex suggests that MTHase activity may be regulated by divalent cations. [Copyright &y& Elsevier]

Protein-carbohydrate interactions play a major role in several cellular and biological processes. Elucidating the factors influencing the binding affinity of protein-carbohydrate complexes and predicting their free energy of binding provide deep insights for understanding the recognition mechanism. In this work, we have collected the experimental binding affinity data for a set of 389 protein-carbohydrate complexes and derived several structure-based features such as contact potentials, interaction energy, number of binding residues and contacts between different types of atoms. Our analysis on the relationship between binding affinity and structural features revealed that the important factors depend on the type of the complex based on number of carbohydrate and protein chains. Specifically, binding site residues, accessible surface area, interactions between various atoms and energy contributions are important to understand the binding affinity. Further, we have developed multiple regression equations for predicting the binding affinity of protein-carbohydrate complexes belonging to six categories of protein-carbohydrate complexes. Our method showed an average correlation and mean absolute error of 0.731 and 1.149 kcal/mol, respectively, between experimental and predicted binding affinities on a jackknife test. We have developed a web server PCA-Pred, Protein-Carbohydrate Affinity Predictor, for predicting the binding affinity of protein-carbohydrate complexes. The web server is freely accessible at https://web.iitm.ac.in/bioinfo2/pcapred/. The web server is implemented using HTML and Python and supports recent versions of major browsers such as Chrome, Firefox, IE10 and Opera., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Background: Protein-carbohydrate interactions play vital roles in several biological processes in living organisms. The comparative analysis of binding site residues along with stabilizing residues in protein-carbohydrate complexes provides ample insights to understand the structure, function and recognition mechanism., Objective: The main objective of this study is to identify and analyze the residues, which are involved in both folding and binding of the protein-carbohydrate complexes., Methods: We have identified the stabilizing residues using the knowledge of hydrophobicity, longrange interactions and conservation, as well as binding site residues using a distance cutoff of 3.5Å between any heavy atoms in protein and ligand. Residues, which are common in stabilizing and binding, are termed as key residues. These key resides are analyzed with various sequence and structure based parameters such as frequency of occurrence, surrounding hydrophobicity, longrange order and conservation score., Results: In this work, we have identified 2.45% binding site residues in a non-redundant dataset of 1130 complexes using distance-based criteria and 7.07% stabilizing residues using the concepts of hydrophobicity, long-range interactions and conservation of residues. Further, 5.9% of binding and 2.04% of stabilizing residues are common to each other, which are termed as key residues. The key residues have been analysed based on protein classes, carbohydrate types, gene ontology functional classifications, amino acid preference and structure-based parameters. We found that all-β, α+β and α/β have more key residues than other protein classes and most of the KRs are present in β-strands, which shows their importance in stability and binding of complexes. On the ligand side, Lsaccharide has the highest number of key residues and it has a high percentage of KRs in SRs and BRs than other carbohydrate types. Further, polar and charged residues have a high tendency to serve as key residues. Classifications based on gene ontology terms revealed that Lys is preferred in all the three groups: molecular functions, biological processes and cellular components. Key residues have 6 to 9 contacts within the protein and make only one contact with the carbohydrate ligand. These contacts are dominant to form polar-nonpolar contacts followed by the contacts between charged atoms. Further, the influence of sequence and structural parameters such as surrounding hydrophobicity, solvent accessibility, secondary structure, long-range order and conservation score has been discussed., Conclusion: The results obtained in the present work provide deep insights for understanding the interplay between stability and binding in protein-carbohydrate complexes., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.)