Biology subjects

Tunon, I.

Publications and source records attributed to Tunon, I..

3 recordsLinked to original sources

bioRxiv2026

Molecular Determinants of Sequence-Dependent N-glycosylation by the Human Oligosaccharyltransferase

Protein N-glycosylation is catalysed by the oligosaccharyltransferase (OST) complex, yet how local sequon composition controls substrate selection by human OST remains poorly understood. Here we combine atomistic molecular dynamics, alchemical free-energy calculations, in cellulo glycosylation assays and human glycoproteome analysis to define the molecular basis of sequence-dependent N-glycosylation. We built, to our knowledge, the first atomistic model of human OST with both the lipid-linked oligosaccharide donor and an acceptor peptide simultaneously accommodated in a catalytically competent complex. Simulations show that conserved STT3 motifs stabilize the acceptor Asn and explain how substitutions at positions 0, +1 and +2 alter binding and productive geometry. Cellular assays in HEK 293T cells validate the predicted loss of glycosylation for N0Q sequon, +1 Pro and the +2 hierarchy Thr > Ser >> Cys. Analysis of 14,800 human glycosites confirms these rules at proteome scale.

biochemistry↗

bioRxiv2025

Molecular basis of noncanonical complement C3 activation by histamine

For fifty years the tick-over mechanism has been considered responsible for priming the activation of the complement systems alternative pathway through the reaction of a nucleophilic water molecule with C3 yielding C3(H2O), even though the exclusivity of this role has been challenged by the existence of extrinsic proteases that can cleave circulating C3 into C3b. Here we show that the biogenic amine histamine can activate C3 by reacting with the internal thioester bond yielding a novel species that is equivalent to C3(H2O), which we have called C3h. Histamine activation of C3 occurs significantly faster than the water-mediated tick-over reaction, leading to the accelerated release of the C3a anaphylatoxin moiety, contributing to inflammation. Importantly, C3h can form an active C3 convertase enzyme that, together with the released C3a, can amplify complement activation and inflammatory responses. These results offer insight into the priming of the complement system activation and support the existence of direct crosstalk between histamine-releasing processes and complement activation.

biochemistry↗

bioRxiv2019

Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: a QM/MM study

Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results show that the base-assisted mechanism is preferred over the substrate-assisted pathway, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity.

bioinformatics↗