Primary Sequence and 3D Structure Prediction of the Plant Toxin Stenodactylin

Abstract

Stenodactylin is one of the most potent type 2 ribosome-inactivating proteins (RIPs); its high toxicity has been demonstrated in several models both in vitro and in vivo. Due to its peculiarities, stenodactylin could have several medical and biotechnological applications in neuroscience and cancer treatment. In this work, we report the complete amino acid sequence of stenodactylin and 3D structure prediction. The comparison between the primary sequence of stenodactylin and other RIPs allowed us to identify homologies/differences and the amino acids involved in RIP toxic activity. Stenodactylin RNA was isolated from plant caudex, reverse transcribed through PCR and the cDNA was amplificated and cloned into a plasmid vector and further analyzed by sequencing. Nucleotide sequence analysis showed that stenodactylin A and B chains contain 251 and 258 amino acids, respectively. The key amino acids of the active site described for ricin and most other RIPs are also conserved in the stenodactylin A chain. Stenodactylin amino acid sequence shows a high identity degree with volkensin (81.7% for A chain, 90.3% for B chain), whilst when compared with other type 2 RIPs the identity degree ranges from 27.7 to 33.0% for the A chain and from 42.1 to 47.7% for the B chain.

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

“…The best threedimensional models obtained for nigrin l, SNAlm, and SNAld are shown in Figure 8, and all showed local Distance Difference Test (lDTT) values that were much higher than 90%, which makes them suitable for characterizing the binding sites [23]. As described for ricin and other type 2 RIPs [24,25], the A chain of nigrin l consists of three folding domains. The first domain includes the N-terminal, and is composed of six antiparallel β-sheets and two α-helices in the order aAbcdeBf.…”

Techno-Functions and Safety Concerns of Plant-Based Peptides in Food Matrices

“…Within the sequence of the stenodactylin A chain, the amino acid residues Y74, Y113, E163, R166, and W200, which are critical for enzymatic activity, are usually preserved. 149 In summary, all the RIPs present in most plant-based proteins, which could have escaped the production process of PBPs, pose major safety concerns to consumers.…”

“…The A chain contains 3 cysteine residues (C9, C157, C246), and the B chain contains 12 cysteine residues which are involved in conserved intramolecular disulfide bonds. Within the sequence of the stenodactylin A chain, the amino acid residues Y74, Y113, E163, R166, and W200, which are critical for enzymatic activity, are usually preserved . In summary, all the RIPs present in most plant-based proteins, which could have escaped the production process of PBPs, pose major safety concerns to consumers.…”

A Simple, Fast and Portable Method for Electrochemical Detection of Adenine Released by Ricin Enzymatic Activity

“…The single-chain type III RIP has also been proposed, is synthesized as a proenzyme, and requires the removal of an internal peptide bond to become active [ 4 , 5 ]. Members of the type II RIP family are divided into non-toxic (e.g., ebulin, nigrin and pulchellin) and toxic (e.g., ricin, abrin, volkensin, stenodactylin, kirkiin and other plant toxins and the bacterial Shiga and Shiga-like toxins) [ 6 , 7 , 8 , 9 ].…”