Crystal structure of PD‐L1, a ribosome inactivating protein from <i>Phytolacca dioica</i> L. Leaves with the property to induce DNA cleavage

Ruggiero, Alessia; Maro, Antimo Di; Severino, Valeria; Berisio, Rita

doi:10.1002/bip.21260

Cited by 12 publications

(4 citation statements)

References 49 publications

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“…Residue numbering is according to the structure of Thricosanthin. The IDL motif present in the Saporin is peculiar, and it is found one helix-turn before to those of Thricosantin and the RIP from M. charantia ; ( C ) 3D structure superposition between RIP from Phytolacca americana chain A (pdb code: 1J1Q; in orange), RIP from Iris hollandica chain A (pdb code 3MVG: in purple) and RIP from Phytolacca dioica chain A (pdb code: 3H5K; in pink) [ 80 ]. The structures belong to Cluster 3 (3 RIPs), whose members are characterized by the I, D, L motif in the αhelix 6.…”

Section: Figurementioning

confidence: 99%

Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins

Giansanti

Flavell

Angelucci

et al. 2018

Toxins

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Plant Ribosome-inactivating proteins (RIPs) including the type I RIP Saporin have been used for the construction of Immunotoxins (ITxs) obtained via chemical conjugation of the toxic domain to whole antibodies or by generating genetic fusions to antibody fragments/targeting domains able to direct the chimeric toxin against a desired sub-population of cancer cells. The high enzymatic activity, stability and resistance to conjugation procedures and especially the possibility to express recombinant fusions in yeast, make Saporin a well-suited tool for anti-cancer therapy approaches. Previous clinical work on RIPs-based Immunotoxins (including Saporin) has shown that several critical issues must be taken into deeper consideration to fully exploit their therapeutic potential. This review focuses on possible combinatorial strategies (chemical and genetic) to augment Saporin-targeted toxin efficacy. Combinatorial approaches may facilitate RIP escape into the cytosolic compartment (where target ribosomes are), while genetic manipulations may minimize potential adverse effects such as vascular-leak syndrome or may identify T/B cell epitopes in order to decrease the immunogenicity following similar strategies as those used in the case of bacterial toxins such as Pseudomonas Exotoxin A or as for Type I RIP Bouganin. This review will further focus on strategies to improve recombinant production of Saporin-based chimeric toxins.

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Section: Figurementioning

confidence: 99%

Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins

Giansanti

Flavell

Angelucci

et al. 2018

Toxins

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“…Regarding this activity, nigrin-RP1 and nigrin-RP2 showed very different behaviors, so the differences between both proteins must be more than just a difference in the glycosylation pattern. Many RIPs do not present this activity, which is related to a different configuration in the structure near the active site that allows the accommodation of the supercoiled DNA of the plasmids [19,63].…”

Section: Discussionmentioning

confidence: 99%

Structure and Biological Properties of Ribosome-Inactivating Proteins and Lectins from Elder (Sambucus nigra L.) Leaves

Iglesias

Russo

Valletta

et al. 2022

Toxins

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Ribosome-inactivating proteins (RIPs) are a group of proteins with rRNA N-glycosylase activity that catalyze the removal of a specific adenine located in the sarcin–ricin loop of the large ribosomal RNA, which leads to the irreversible inhibition of protein synthesis and, consequently, cell death. The case of elderberry (Sambucus nigra L.) is unique, since more than 20 RIPs and related lectins have been isolated and characterized from the flowers, seeds, fruits, and bark of this plant. However, these kinds of proteins have never been isolated from elderberry leaves. In this work, we have purified RIPs and lectins from the leaves of this shrub, studying their main physicochemical characteristics, sequences, and biological properties. In elderberry leaves, we found one type 2 RIP and two related lectins that are specific for galactose, four type 2 RIPs that fail to agglutinate erythrocytes, and one type 1 RIP. Several of these proteins are homologous to others found elsewhere in the plant. The diversity of RIPs and lectins in the different elderberry tissues, and the different biological activities of these proteins, which have a high degree of homology with each other, constitute an excellent source of proteins that are of great interest in diagnostics, experimental therapy, and agriculture.

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“…Best crystals of PD-L1 were obtained using the macro-seeding technique as described. 15 Crystals suitable for X-ray diffraction experiments were obtained after the transfer of needles to a pre-equilibrated solution containing 10 mg mL À1 PD-L1, 0.16 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate (pH 6.5), 24% (w/v) polyethylene glycol 8000, 3 mM adenine.…”

Section: Crystallization Data Processing and Structure Refinementmentioning

confidence: 99%

The role of the glycan moiety on the structure–function relationships of PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves

Severino¹,

Maro²,

Marasco

et al. 2010

Mol. BioSyst.

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N-glycosylation is one of the major naturally occurring covalent co-translational modifications of proteins in plants, being involved in proteins structure, folding, stability and biological activity. In the present work the influence of carbohydrate moieties on the structure-function relationships of type 1 ribosome-inactivating proteins (RIPs) was investigated. To this aim, PD-Ls, RIPs isolated from Phytolacca dioica L. leaves, differing for their glycosylation degree, were used as an experimental system. In particular, comparative structural and biological analyses were performed using native and unglycosylated recombinant PD-L1, the most glycosylated P. dioica RIP isoform. The glycans influence on protein synthesis inhibition and adenine polynucleotide glycosidase activity was investigated. The interaction with adenine, the product of the de-adenylation reaction, was also investigated for native and recombinant PD-L1 by fluorescence spectroscopy. Furthermore, the crystal structure of PD-L1 in complex with adenine was determined. Our data confirm that the absence of glycan moieties did not affect the biological activity in terms of protein synthesis inhibition. However, the removal of carbohydrate chains significantly increased the deadenylation capability, likely as a consequence of the increased accessibility of substrates to the active site pocket. Furthermore, preliminary data on cellular uptake showed that all PD-L isoforms were internalized and, for the first time, that the vesicular distribution within cells could be influenced by the protein glycosylation degree.

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Crystal structure of PD‐L1, a ribosome inactivating protein from Phytolacca dioica L. Leaves with the property to induce DNA cleavage

Cited by 12 publications

References 49 publications

Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins

Strategies to Improve the Clinical Utility of Saporin-Based Targeted Toxins

Structure and Biological Properties of Ribosome-Inactivating Proteins and Lectins from Elder (Sambucus nigra L.) Leaves

The role of the glycan moiety on the structure–function relationships of PD-L1, type 1 ribosome-inactivating protein from P. dioica leaves

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