SPECIAL ISSUE ARTICLE Structural insights on P31‐43, a gliadin peptide able to promote an innate but not an adaptive response in celiac disease Luisa Calvanese 1 | Merlin Nanayakkara 2 | Rosita Aitoro 2 | Marina Sanseverino 3 | Anna Lucia Tornesello 4 | Lucia Falcigno 1,5 | Gabriella D'Auria 1,5 | Maria Vittoria Barone 2 1 CIRPeB, University of Naples Federico II, 80134 Naples, Italy 2 Department of Translational Medical Science (section of Pediatrics) and ELFID (European Laboratory for the Investigation of Food Induced Diseases), University Federico II, 80131 Naples, Italy 3 INBIOS srl Via P. Castellino, 80131 Naples, Italy 4 Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori “Fondazione G. Pascale”—IRCCS, Naples, Italy 5 Department of Pharmacy, University of Naples Federico II, 80134 Naples, Italy Correspondence Prof. Gabriella D'Auria, Department of Pharmacy, via Mezzocannone 16, 80134 Naples, Italy. Email: gabriella.dauria@unina.it Inflammation of intestinal tissue in patients affected by celiac disease (CD) originates from the adaptive and innate immune responses elicited by the undigested gliadin fragments through molecular mechanisms not yet completely described. Undigested A‐gliadin peptide P31‐43 is central to CD pathogenesis, entering enterocytes in vesicular compartments by endocytosis and inducing an innate immune response in CD intestinal mucosa. This study focused on the reasons why P31‐43 does not behave as adaptive immunogenic agent. Once obtained by NMR analysis, the three‐ dimensional model of P31‐43 was used to implement a series of in silico experiments aimed to explore the ability of the peptide to interact with HLA‐DQ2 and the corre- sponding receptor onto T cells. Our results show that P31‐43 is a poor ligand for DQ2 and/or T‐cell receptor. This study was also aimed to investigate, from a structural point of view, the previous experimental findings by which P31‐43 is able to enhance the phosphorylation level of the protein ERK2, while some P31‐43 Ala‐mutants decrease or totally inhibit that process. The molecular models of P31‐43, P31‐43 P36A, and F37A mutants were used for in silico docking experiments onto the ERK2 structure. The experiments support the hypothesis that P31‐43 F37A works as an ERK2 phosphorylation inhibitor because it binds to the ERK2 phosphorylation site. This study reports on the structural properties of so far never NMR character- ized gliadin peptides relevant in CD and explores details about their mechanisms of action. KEYWORDS celiac disease, docking simulations, ERK, gliadin peptide, HLA‐DQ2, P31‐43, solution NMR, T‐cell receptor 1 | INTRODUCTION In the intestine and particularly in the enterocytes, nutrients are mod- ulators of various cellular functions and may be involved in tissue inflammation and immune response. Dietary proteins are often not completely digested by the intestinal proteases, and residual peptides can have biological effects. Peptide fragments from poorly digested gliadin, alimentary protein present in wheat, barley, and rye, cause the immune‐mediated disorder known as celiac disease (CD) in susceptible individuals. 1 CD clinical manifestations, which can vary greatly and are different in children and adults, include enteropathy, severe villous atrophy, intraepithelial lymphocytes infiltration, and crypt hyperplasia. CD shows a strong genetic predisposition that is associated mainly with class II human histocompatibility leukocyte antigen (HLA) DQ2 2 and DQ8. 3 Molecular mechanisms associated with CD pathology are not completely deciphered. 4,5 However, some molecular pathways are well assessed and indicate that the undigested gliadin peptides, once Received: 20 December 2018 Revised: 12 February 2019 Accepted: 13 February 2019 DOI: 10.1002/psc.3161 J Pep Sci. 2019;e3161. https://doi.org/10.1002/psc.3161 © 2019 European Peptide Society and John Wiley & Sons, Ltd. wileyonlinelibrary.com/journal/psc 1 of 10