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Stereo view of anionic ligand binding pockets in SM80.1. (a) Superimposition of binding pocket of two domains showing the plasticity for different ligands. (b) Pyroglutamate binding pocket with pyroglutamate (PCA) present in center surrounded by interacting residues. (c) Acetate binding pocket with acetate present in the central cavity and interacting residues are labeled in black.
Source publication
Crystal structure of a vicilin, SM80.1, was determined towards exploring its possible physiological functions. The protein was purified from Solanum melongena by combination of ammonium sulphate fractionation and size exclusion chromatography. Structure was determined ab initio at resolution of 1.5 Å by X-ray crystallography showing the three-dimen...
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Citations
... On the other hand, prolamin is an alcohol-soluble protein with a high proportion of proline and glutamine, like most cereal proteins, comprising a minor portion (less than 5%) of the total proteins Vicilin is an oligomeric protein with a trimeric structure that ranges in molecular mass from 150 to 190 kDa. Each monomer is between 50 and 70 kDa and consists of three subunits (α, β, and γ), which are linked together primarily by electrostatic forces and noncovalent hydrophobic interactions [53]. Due to the deficiency of sulfur-containing AAs, no disulfide bond is present between vicilin protein molecules. ...
... That central region is composed of β-barrels, while its extended arms are comprised of α-helices. In addition, each monomer has a core region that is established by α-helices and β-barrels extending from the core and combining with the neighboring monomers to form a trimeric structure [53]. Despite certain similarities between pulse vicilin, there is a large variance in mass, surface charge, and glycosylation of proteins. ...
... A convicilin molecule is about 70 kDa and is often found as a trimer of about 210 kDa (or 290 kDa including an N-terminal extension) comprised of three convicilin molecules or as heteromeric trimers of convicilin and vicilin ( Figure 2C). The structure and composition of convicilin are distinct from that of both legumin and vicilin, however; it contains sulfur-containing AAs, unlike vicilin, and a high charge density in the N-terminal extension [9,53,57]. ...
The ever-increasing world population and environmental stress are leading to surging demand for nutrient-rich food products with cleaner labeling and improved sustainability. Plant proteins, accordingly, are gaining enormous popularity compared with counterpart animal proteins in the food industry. While conventional plant protein sources, such as wheat and soy, cause concerns about their allergenicity, peas, beans, chickpeas, lentils, and other pulses are becoming important staples owing to their agronomic and nutritional benefits. However, the utilization of pulse proteins is still limited due to unclear pulse protein characteristics and the challenges of characterizing them from extensively diverse varieties within pulse crops. To address these challenges, the origins and compositions of pulse crops were first introduced, while an overarching description of pulse protein physiochemical properties, e.g., interfacial properties, aggregation behavior, solubility, etc., are presented. For further enhanced functionalities, appropriate modifications (including chemical, physical, and enzymatic treatment) are necessary. Among them, non-covalent complexation and enzymatic strategies are especially preferable during the value-added processing of clean-label pulse proteins for specific focus. This comprehensive review aims to provide an in-depth understanding of the interrelationships between the composition, structure, functional characteristics, and advanced modification strategies of pulse proteins, which is a pillar of high-performance pulse protein in future food manufacturing.
... Figure 6. Schematic showing the relative sizes of milk/egg proteins, plant proteins, casein micelles, and commercial plant protein isolates, with images adapted from [135][136][137][138][139][140][141][142][143][144]. Note that 7S proteins are trimers whereas the 11S proteins are hexamers, comprising two subunits. ...
... In addition to the protein source and growth conditions, an important source of variability Figure 6. Schematic showing the relative sizes of milk/egg proteins, plant proteins, casein micelles, and commercial plant protein isolates, with images adapted from [135][136][137][138][139][140][141][142][143][144]. Note that 7S proteins are trimers whereas the 11S proteins are hexamers, comprising two subunits. ...
As the plant-based food market grows, demand for plant protein is also increasing. Proteins are a major component in foods and are key to developing desired structures and textures. Seed storage proteins are the main plant proteins in the human diet. They are abundant in, for example, legumes or defatted oilseeds, which makes them an excellent candidate to use in the development of novel plant-based foods. However, they often have low and inflexible functionalities, as in nature they are designed to remain densely packed and inert within cell walls until they are needed during germination. Enzymes are often used by the food industry, for example, in the production of cheese or beer, to modify ingredient properties. Although they currently have limited applications in plant proteins, interest in the area is exponentially increasing. The present review first considers the current state and potential of enzyme utilization related to plant proteins, including uses in protein extraction and post-extraction modifications. Then, relevant opportunities and challenges are critically discussed. The main challenges relate to the knowledge gap, the high cost of enzymes, and the complexity of plant proteins as substrates. The overall aim of this review is to increase awareness, highlight challenges, and explore ways to address them.
... They are named 7S or 11S based on the sedimentation coefficient. Globulins have been studied in detail in many plant seeds such as eggplants (Solanum melongena) [11,26], soybeans (Vicia faba) [27], peas (Pisum sativum) [28] and French beans (Phaseolus vulgaris) [29]. ...
... Other than these physiological functions, the nsLTP protein from peach peel was identified as an allergen, and it was named Pru p3 [48]. The LTPs from Rosaceae fruits (peaches, apricots, cherries, plums and pears) Solanaceae (potatoes, tomatoes and eggplants) [10,26], Brassicaceae (cabbages and mustard) and even legumes and cereals are categorized as pan-allergens [49][50][51]. Unlike other plant allergens, these LTPs can trigger specific IgE antibodies, and they are, therefore, also called true food allergens [34,[52][53][54]. ...
Plants are essential for humans as they serve as a source of food, fuel, medicine, oils, and more. The major elements that are utilized for our needs exist in storage organs, such as seeds. These seeds are rich in proteins, show a broad spectrum of physiological roles, and are classified based on their sequence, structure, and conserved motifs. With the improvements to our knowledge of the basic sequence and our structural understanding, we have acquired better insights into seed proteins and their role. However, we still lack a systematic analysis towards understanding the functional diversity associated within each family and their associations with allergy. This review puts together the information about seed proteins, their classification, and diverse functional roles along with their associations with allergy.
... Our results were consistent with Al Saiqali (Table S11), who reported antimicrobial and antioxidant activity peptides from Azadirachta indica leaves [50]. Microbial infections have acquired resistance to currently available antibiotics, prompting a surge in real interest in antimicrobial protein isolation [51]. Along with bacterial infections, plant pathogenic fungi have been documented to cause significant losses to agriculturally essential crops due to root degradation, resulting in significant economic losses worldwide [52]. ...
Vicilin has nutraceutical potential and different noteworthy medicative health-promoting biotic di-versions, and it is remarkable against pathogenic microorganisms and insects. In this study, Vigna aconitifolia vicilin (VacV) has been identified and characterized from the seed of Vigna aconitifolia (Jacq.) Marechal (Moth beans). LC-MS/MS analysis of VacV provided seven random fragmented sequences comprising 238 residues, showing significant homology with already reported Vigna radiata vicilin (VraV). VacV was purified using ammonium sulfate precipitation (60%) followed by size exclusion chromatography on Hi-Load 16/60 Superdex 200 pg column and anion-exchange chromatography (Hi trap Q FF column). Purified VacV showed a major ~50 kDa band and multiple lower bands on 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) under both reduced and non-reduced conditions. After all, a three-dimensional molecular structure of VacV was predicted, which showed β-sheeted molecular conformation similar to crystallographic structure of VraV. All Vicilins from V. aconitifolia and other plants were divided into six sub-groups by phylogenetic analysis, and VacV shared a high degree of similarity with vicilins of Vigna radiata, Pisum sativum, Lupinus albus, Cicer arietinum and Glycine max. Additionally, VacV (20 μg) has sig-nificant growth inhibition against different pathogenic bacteria along strong antifungal activity (50 μg). Likewise, VacV (3.0 mg) produced significant growth reduction in Rice Weevil Sitophilus oryzae larvae after 9 days compared with control. Furthermore, by using MMT assay, the cytotoxicity effect of VacV on the growth of HepG2 liver cancerous cells was tested. VacV showed cytotoxicity against the HepG-2 line and the acquired value was 180 µg after 48 h. Finally, we performed mo-lecular docking against caspase-3 protein (PDB ID: 3DEI) for VacV bioactive receptor interface residues. Hence, our results reveal that VacV, has nutraceutical potential and moth beans can be used as a rich resource of functional foods.
... in low a nity substrate interaction with only mono-Mn 2+ binding, which compares to pyrophosphate (H 4 O 7 1−,1− P 2 ; L·H − 1 : 0.049) binding as its endogenous substrate with the potential for tri-divalent metal coordination and Alendronate (C 4 H 9 NO 7 P 2 ; -7.11 nm − 1 ) at pH 7.4, which is a Ca 2+ anionophile with a PO 4 2− NH 4+ parts-neutralized L•H − 1 at 0.081 and lesser hydrophilicity than of pyrophosphate (Fig. 5), which has similar effects on bone resorption as Zoledronate as determined in the TRAP+/calvaria micro-CT model [89]; the other sampled molecule in this class is pyroglutamate, which has been shown to be non-covalently bound to Cysteines and Histidine with part-electrotivity for Magnesium in SM80.1 [90]. ...
Introduction
Biochemical interactions occur in vivo between small solubilizing molecules and intracellular membrane proteins due to differences in intermolecular affinity. Here, this relationship is further explored by in silico modeling of partitioning solvation parameters and proportion of molecular structure lipophilicity to hydrophilicity.
Methods
The partial bond length vdWV diameter (vdWDpb, nm) is applied for correlative modeling of diameter or volume normalized fractional solubility (Log S), partition coefficient (Log P). Method I (Sf) small molecules stratified as Tier I, Tier II or Tier III are multivariate modeled based on the degree of halogenated atom substitution. Method II (Sh) small molecules are modeled by subtractive hydrophilicity. Method III is developed for improved correlation of Log S to Log P for halogen heavy atom and multiple covalent bond-containing small molecules is developed as per: Log S = (Log P + a · Log PMW vdWD HAL or NON−HAL) · vdWDpb (fract, nm). The Linternal (or external) structure · Hpolar group ⁻¹ quotient is further normalized for alternating exterior methyln−1 group (CH2) biophilicity for determination of complex small molecule interaction at the cell surface.
Results
Method 1 Tier I, II and III MW-to-vdWDpb diameter correlative solubility for halogenate substituents is - Log S · vdWDpb − 1 (Da− 1 vol) = 1.020, 1.090 and 1.227 · (- Log S · vdWDpb− 1, nm− 1 vol) – B1, 2 or 3 (R² = 0.9955, R² = 0.9999, R² = 0.9996). Method II-to-Log SPRED vdWVpb− 1 normalized correlative solubility is Log SVL · vdWVpb− 1 (nm− 1) = 2.7628 · (Log SCALC · vdWVpb− 1, nm− 1) − 0.4708 (R² = 0.9895, r = 0.995). Method III MW vdWDpb-normalized molecules and vdWDpb normalized vdWDMW Da (0.01095 · RT)⁻¹ relationship is 1.4863 (x) − 0.2615 (R² = 0.992, r = − 0.995). Based on the L · Hpolar group⁻¹, the interval range for cytosolic interaction at the periplasmic membrane is L · H− 1 > 0.057 < 0.093, and that for interaction with caveolin-associated protein is L · H− 1 0.093 < 0.297 (0.301) or with clathrin-AP is L · H− 1 0.301 ≤ (0.480) 0.497.
Conclusions
The fractional solubility-partition coefficient relationship is developed herein with partial bond length molecular diameter normalization and it is applicable to determination of small molecule solvation. The soluble small molecule structure-to-protein structure philicity relationship is determined to be predictive in sub-typing of complex linear and heterocyclic molecule cell surface interactions. There is further applicability of the findings for QSAR modeling of small molecule channel or receptor interactions.
... Globulin proteins are dominant in storage proteins of pulses. 7S vicilin-like globulins are molded principally by noncovalent interactions, which are structurally trimeric molecules with molecular mass ranging from 150 to 200 kDa (Jain et al., 2016;Tandang-Silvas et al., 2011). The lack of cysteine and methionine residues contributes to the absence of disulfide linkages. ...
... A case in point, the monomer of adzuki bean (Vigna angularis) vicilins, is in the asymmetric unit, which consists of α-helices, β-sheets, and flexible loops ( Figure 3c). The monomer can be split across a pseudo-dyad axis into two similar constituents, wherein a core region along with the extended arms exists, constructing N-and C-terminal domains (Fukuda et al., 2008;Jain et al., 2016). The core region of each domain is created by β-barrels, whereas the extended arms consist of α-helices. ...
... The core region of each domain is created by β-barrels, whereas the extended arms consist of α-helices. Each monomer also presents establishment of core region by pair of β-barrels and α-helices protruding outward from each core to collaborate with the adjacent monomers, giving rise to the construction of a trimer (Jain et al., 2016). The trimeric architectures around the threefold rotation axis are displayed in ribbon diagram (Figures 3d and 3e). ...
Consumers’ preference to have a healthy eating pattern has led to an increasing demand for more nutrient‐dense and healthier plant‐based foods. Pulse proteins are exceptional quality ingredients with potential nutritional benefits, and might act as health‐promoting agents for addressing the new‐generation foods. However, the utilization of pulse protein in foods has been hampered by its relatively poor functionality and unpleasant flavor. Protein structure modification has been proved to be a useful means to improve the functionality and flavor profile of pulse protein. This paper begins with a brief introduction of hierarchical structure of pulse protein materials to better understand the structure characteristics. A comprehensive review is presented on the current techniques including chemical and enzymatic modifications and molecular breeding on pulse protein structure and functionality/flavor. The mechanism and the limitations and the toxicological concerns of these approaches are discussed. We conclude that understanding protein structure‒functionality relationship is extremely valuable in tailoring proteins for specific functional outcomes and expanding the availability of pulse proteins. Furthermore, selective protein modification is a valuable in‐depth toolkit for generating novel protein constructs with preferable functional attributes and flavor profiles. Innovative structure modification with special focus on the molecular basis for the exquisite protein designs is a pillar of pulse protein access to the desired functionality.
... Vicilins are 7S globulin class plant seed storage proteins with no disulfide bond and structurally contain three similar subunits of 40-70 kDa (Bard et al., 2014). These proteins possess different functions and known as plant defense proteins (Jain et al., 2016). Vicilin-like peptides have similar homology with vicilin and exhibited antimicrobial and antifungal activity (Ribeiro et al., 2007;Jain et al., 2016). ...
... These proteins possess different functions and known as plant defense proteins (Jain et al., 2016). Vicilin-like peptides have similar homology with vicilin and exhibited antimicrobial and antifungal activity (Ribeiro et al., 2007;Jain et al., 2016). Capsicum baccatum L. has been reported to produce vicilin-like peptides that showed promising antifungal activity (MIC 100-200 µg/ml) (Bard et al., 2014). ...
... Vicilins are 7S globulin class plant seed storage proteins with no disulfide bond and structurally contain three similar subunits of 40-70 kDa (Bard et al., 2014). These proteins possess different functions and known as plant defense proteins (Jain et al., 2016). Vicilin-like peptides have similar homology with vicilin and exhibited antimicrobial and antifungal activity (Ribeiro et al., 2007;Jain et al., 2016). ...
... These proteins possess different functions and known as plant defense proteins (Jain et al., 2016). Vicilin-like peptides have similar homology with vicilin and exhibited antimicrobial and antifungal activity (Ribeiro et al., 2007;Jain et al., 2016). Capsicum baccatum L. has been reported to produce vicilin-like peptides that showed promising antifungal activity (MIC 100-200 µg/ml) (Bard et al., 2014). ...
The Solanaceae is an important plant family that has been playing an essential role in traditional medicine and human nutrition. Members of the Solanaceae are rich in bioactive metabolites and have been used by different tribes around the world for ages. Antimicrobial peptides (AMPs) from plants have drawn great interest in recent years and raised new hope for developing new antimicrobial agents for meeting the challenges of antibiotic resistance. This review aims to summarize the reported AMPs from plants of the Solanaceae with possible molecular mechanisms of action as well as to correlate their traditional uses with reported antimicrobial actions of the peptides. A systematic literature study was conducted using different databases until August 2019 based on the inclusion and exclusion criteria. According to literature, a variety of AMPs including defensins, protease inhibitor, lectins, thionin-like peptides, vicilin-like peptides, and snaking were isolated from plants of the Solanaceae and were involved in their defense mechanism. These peptides exhibited significant antibacterial, antifungal and antiviral activity against organisms for both plant and human host. Brugmansia, Capsicum, Datura, Nicotiana, Salpichora, Solanum, Petunia, and Withania are the most commonly studied genera for AMPs. Among these genera, Capsicum and the Solanum ranked top according to the total number of studies (35%–38% studies) for different AMPs. The mechanisms of action of the reported AMPs from Solanaceae was not any new rather similar to other reported AMPs including alteration of membrane potential and permeability, membrane pore formation, and cell aggregation. Whereas, induction of cell membrane permiabilization, inhibition of germination and alteration of hyphal growth were reported as mechanisms of antifungal activity. Plants of the Solanaceae have been used traditionally as antimicrobial, insecticidal, and antiinfectious agents, and as poisons. The reported AMPs from the Solanaceae are the products of chemical shields to protect plants from microorganisms and pests which unfold an obvious link with their traditional medicinal use. In summary, it is evident that AMPs from this family possess considerable antimicrobial activity against a wide range of bacterial and fungal pathogens and can be regarded as a potential source for lead molecules to develop new antimicrobial agents.
... The site was conserved in the phylogenetic subtree members pecan, SM80.1, Vic_CAPAN and Korean pine vicilin. The crystal structure of 7S gobulins from SM80.1, pecan, Vic_CAPAN and Korean pine showed electron density of copper at the site [14][15][16][17][18] . The presence of copper ion in Mc7S globulin was further confirmed by inductively coupled plasma mass spectroscopy (ICP-MS) ( Table S4). ...
Momordica charantia (Mc) seeds are widely used edible crop with high nutritional quality. The food and pharmaceutical industries use it as a natural anti-oxygenic agent. Herein, a ~52 kDa protein, which is a major part of seed proteome has been purified, biochemically characterized and structure has been determined. MALDI-ESI-MS identified peptide fragments and contig-deduced sequence suggested the protein to be homologous to 7S globulins. The crystal structure shows that protein has a bicupin fold similar to 7S globulins and the electron density for a copper and acetate ligand were observed in the C-terminal barrel domain. In silico study reveals that a tripeptide (VFK) from Mc7S possess a higher binding affinity for angiotensin converting enzyme (ACE) than already reported drug Lisinopril (LPR). The protein is a glycoprotein and highly stable under varying thermal and pH conditions due to its secondary structures. The DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) assay showed the protein to have an anti-oxygenic nature and can aid in scavenging free radical from sample. The protein can assist to enhance the nutritional and functional value of food by acting as a food antioxidant. Further, characterization of Mc7S required which might add in importance of Mc7S as antioxidant, anti-diabetic and anti-hypertensive.
... We were able to identify ligand bound to Vic_CAPAN (PDB ID: 5YJS) from the electron density, which was further confirmed by mass spectrometry. There are two hydrophobic pockets in Vic_CAPAN, and the C-terminal hydrophobic core was found to accommodate salicylic acid at the same position as that of acetate in SM80.1 [28]. The electron density observed in difference map after the final round of refinement before introducing ligand was equivalent to the electron density of a ring structure having functional group similar to acetate and, therefore, we initially introduced benzoic acid which fitted perfectly into the electron density. ...
... However, when we placed lauric acid at the same place, it fitted much better without any negative density after three cycles of refinement suggesting the possibility of some metabolite or ligand similar to lauric acid bound in the cavity. Moreover, the density lies in the same pocket which accommodated pyroglutamate [28] in SM80.1. The ligand omit map of Vic_CAPAN also revealed an extra density at the same position resembling that of lauric acid in N-terminal and a density for salicylic acid in C-terminal pocket (Supplementary Figure S4a,b). ...
... It was observed that only Vic_CAPAN was capable of quenching the superoxide radicals produced during the reaction in both the assays. bean-2EAA [29] and eggplant-5CAD [28] have acetate in the same pocket that accommodates salicylic acid in Vic_CAPAN. Korean pine-4LEJ [22], peanut-3S7I [30] and pecan-5E1R [23] vicilin have phosphate, sodium and (4S)-2-methyl-2,4-pentanediol in the C-terminal-binding pocket, respectively. ...
Proteins belonging to cupin superfamily are known to have critical and diverse physiological functions. However, 7S globulins family, which is also a part of cupin superfamily were undermined as only seed storage proteins. Structure determination of native protein - Vic_CAPAN from Capsicumannuum was carried out, and its physiological functions were explored after purifying the protein by ammonium sulfate precipitation followed by size exclusion chromatography. The crystal structure of vicilin determined at 2.16 Å resolution revealed two monomers per asymmetric unit which are juxtaposed orthogonal with each other. Vic_CAPAN consists predominately of β-sheets which folds to form a β-barrel structure commonly called cupin fold. Each monomer of Vic_CAPAN consists of two cupin fold domains, N-terminal and C-terminal, which accommodate two different ligands. A bound ligand was identified at the C-terminal cupin fold in the site presumably conserved for metabolites in the crystal structure. The ligand was confirmed to be salicylic acid through mass spectrometric analysis. A copper binding site was further observed near the conserved ligand binding pocket, suggesting possible superoxide dismutase activity of Vic_CAPAN which was subsequently confirmed biochemically. Vicilins from other sources did not exhibit this activity indicating functional specificity of Vic_CAPAN. Discovery of bound salicylic acid, which is a known regulator of antioxidant pathway and revelation of superoxide dismutase activity suggest that Vic_CAPAN has important role during oxidative stress. As salicylic acid changes the redox state of cell, it may act as a downstream signal for various pathways involved in plant biotic and abiotic stress rescue.
