Structural characterization of dioicin 1 from Phytolacca dioica L. gains novel insights into phylogenetic relationships of Phytolaccaceae type 1 RIPs

Russo, Rosita; Severino, Valeria; Parente, Augusto; Maro, Antimo Di

doi:10.1016/j.bbrc.2015.06.003

Cited by 6 publications

(3 citation statements)

References 38 publications

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“…Chemical fragmentation of pheasant apo‐Mb (100 μg) with cyanogen bromide (CNBr) was carried out as previously described (Di Maro et al, ). Apo‐Mb (100 μg) was digested with trypsin in 0.1 M Tris•Cl, pH 8.5, containing 20 mM CaCl 2 , and 10% acetonitrile (Russo, Chambery, Severino, Parente, & Di Maro, ). Weak acid hydrolysis of apo‐Mb was performed in 2% formic acid (FA) in boiling water (100°C) for 2 hr to obtain cleavages at the N‐terminus of aspartic acid residues (Seo et al, ).…”

Section: Methodsmentioning

confidence: 99%

Myoglobin from common pheasant (Phasianus colchicus L.): Purification and primary structure characterization

et al. 2017

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Myoglobin (Mb) is a monomeric hemoprotein involved in dioxygen storage and transport in skeletal muscles and heart. Mb, containing the heme pigment, is present in large amount in meat, thus influencing meat color and consumer choice. Here, the primary structure of Mb isolated from muscle of Phasianus colchicus L. was determined by using a comparative peptide mapping approach based on MALDI-TOF mass spectrometry. This strategy allowed the determination of common pheasant Mb primary sequence, which resulted identical to the chicken Mb, as also confirmed by intact molecular mass determination by ESI/Q-TOF mass spectrometry. Indeed, the accurate molecular mass (17,290.50 Da) of common pheasant Mb was found to be in good agreement with that of chicken Mb (17,290.86 Da). Finally, the 3D model of common pheasant Mb was predicted by homology modeling. Overall, in this study we confirmed that chicken, turkey and common pheasant, belonging to the Galliformes order, share the same Mb sequence. Practical applicationsConsidering the economic importance of game meat consumption, our result may be interesting for meat industry, providing useful information for the determination of species-specific differences in color and color stability compared to other poultry species.

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Section: Methodsmentioning

confidence: 99%

Myoglobin from common pheasant (Phasianus colchicus L.): Purification and primary structure characterization

et al. 2017

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“…The Grand Average Hydropathy (GRAVY) value of a protein is calculated by summing the hydropathy values of all its amino acids as shown in Table S1 , then dividing the result by the number of residues in the protein sequence (Li et al 2020 ; Ragucci et al 2021 ). The GRAVY indices of the ribosome inactivating protein (RIP) proteins range from 0.78 to 0.854, indicating that virtually all of the RIP proteins studied in this study are hydrophobic (Russo et al 2015 ; Moghadam et al 2016 ). However, RIP protein functional and physicochemical characterization was also carried out, as well as transmembrane or TM region identification, followed by the prediction of disulfide bonding pairs, and so on.…”

Section: Discussionmentioning

confidence: 87%

In-silico analysis of ribosome inactivating protein (RIP) of the Cucurbitaceae family

Maqsood,

Sumrin,

Ali

et al. 2024

AMB Expr

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Ribosome-inactivating proteins (RIPs) are highly active N-glycosidases that depurinate both bacterial and eukaryotic rRNAs, halting protein synthesis during translation. Found in a diverse spectrum of plant species and tissues, RIPs possess antifungal, antibacterial, antiviral, and insecticidal properties linked to plant defense. In this study, we investigated the physiochemical properties of RIP peptides from the Cucurbitaceae family through bioinformatics approaches. Molecular weight, isoelectric point, aliphatic index, extinction coefficient, and secondary structures were analyzed, revealing their hydrophobic nature. The novelty of this work lies in the comprehensive examination of RIPs from the Cucurbitaceae family and their potential therapeutic applications. The study also elucidated the binding interactions of Cucurbitaceae RIPs with key biological targets, including Interleukin-6 (IL-6). Strong hydrogen bond interactions between RIPs and these targets suggest potential for innovative insilico drug design and therapeutic applications, particularly in cancer treatment. Comprehensive analysis of bond lengths using Ligpolt + software provides insights for optimizing molecular interactions, offering a valuable tool for drug design and structural biology studies.

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“…Since then, many others type-1 RIPs were isolated from Phytolaccaceae species such as Phytolacca dodecandra L'Herit [26], Phytolacca heterotepala H. Walter [27,28], Phytolacca insularis [29] Nakai, and Phytolacca dioica L. [30]. In particular, from seeds and from adult and young leaves of P. dioica plant, three (PD-S1-3; [31,32]), four (PD-L1-4; [33,34]), and two (dioicin 1 and 2; [35][36][37]) type-1 RIPs, respectively, were isolated and extensively characterized. On the other hand, biological and antipathogenic activities [6] and a possible source of antimicrobial peptides [38,39] have been recently reported for type-1 RIPs from P. dioica.…”

Section: Introductionmentioning

confidence: 99%

Antiviral Activity of PD-L1 and PD-L4, Type 1 Ribosome Inactivating Proteins from Leaves of Phytolacca dioica L. in the Pathosystem Phaseolus vulgaris–Tobacco Necrosis Virus (TNV)

Bulgari

Ragucci

Faoro

et al. 2020

Toxins

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Using the pathosystem Phaseolus vulgaris–tobacco necrosis virus (TNV), we demonstrated that PD-L1 and PD-L4, type-1 ribosome inactivating proteins (RIPs) from leaves of Phytolacca dioica L., possess a strong antiviral activity. This activity was exerted both when the RIPs and the virus were inoculated together in the same leaf and when they were inoculated or applied separately in the adaxial and abaxial leaf surfaces. This suggests that virus inhibition would mainly occur inside plant cells at the onset of infection. Histochemical studies showed that both PD-L1 and PD-L4 were not able to induce oxidative burst and cell death in treated leaves, which were instead elicited by inoculation of the virus alone. Furthermore, when RIPs and TNV were inoculated together, no sign of H2O2 deposits and cell death were detectable, indicating that the virus could have been inactivated in a very early stage of infection, before the elicitation of a hypersensitivity reaction. In conclusion, the strong antiviral activity is likely exerted inside host cells as soon the virus disassembles to start translation of the viral genome. This activity is likely directed towards both viral and ribosomal RNA, explaining the almost complete abolition of infection when virus and RIP enter together into the cells.

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Structural characterization of dioicin 1 from Phytolacca dioica L. gains novel insights into phylogenetic relationships of Phytolaccaceae type 1 RIPs

Cited by 6 publications

References 38 publications

Myoglobin from common pheasant (Phasianus colchicus L.): Purification and primary structure characterization

Myoglobin from common pheasant (Phasianus colchicus L.): Purification and primary structure characterization

In-silico analysis of ribosome inactivating protein (RIP) of the Cucurbitaceae family

Antiviral Activity of PD-L1 and PD-L4, Type 1 Ribosome Inactivating Proteins from Leaves of Phytolacca dioica L. in the Pathosystem Phaseolus vulgaris–Tobacco Necrosis Virus (TNV)

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