Abstract
Nonsense-mediated mRNA decay (NMD) is a quality control mechanism that recognizes post-transcriptionally abnormal transcripts and mediates their degradation. The master regulator of NMD is UPF1, an enzyme with intrinsic ATPase and helicase activities. The cancer genomic sequencing data has identified frequently mutated residues in the CH-domain and ATP-binding site of UPF1. In silico screening of UPF1 stability change as a function over 41 cancer mutations has identified five variants with significant effects: K164R, R253W, T499M, E637K, and E833K. To explore the effects of these mutations on the associated energy landscape of UPF1, molecular dynamics simulations (MDS) were performed. MDS identified stable H-bonds between residues S152, S203, S205, Q230/R703, and UPF2/AMPPNP, and suggest that phosphorylation of Serine residues may control UPF1-UPF2 binding. Moreover, the alleles K164R and R253W in the CH-domain improved UPF1-UPF2 binding. In addition, E637K and E833K alleles exhibited improved UPF1-AMPPNP binding compared to the T499M variant; the lower binding is predicted from hindrance caused by the side-chain of T499M to the docking of the tri-phosphate moiety (AMPPNP) into the substrate site. The dynamics of wild-type/mutant systems highlights the flexible nature of the ATP-binding region in UPF1. These insights can facilitate the development of drug discovery strategies for manipulating NMD signaling in cell systems using chemical tools.
Highlights
Non-sense mediated mRNA decay (NMD) is a quality-control checkpoint that detects and eliminates aberrant messenger RNAs with premature termination codons (PTCs) [1,2,3]
The cancer genomic sequencing data suggests that residues in the ATP-binding site and CH-domain (i.e., UPF2 interacting interface) of the up frameshift 1 (UPF1) protein are frequently mutated, and we assessed the effects of those mutations on UPF1using in silico methodologies
The most promising key residues of UPF1 were identified by molecular dynamics simulations (MDS) and were in common in forming hydrogen bond interactions with UPF2 or AMPPNP as follows: S152, S203, S205, and Q230 or R703, respectively
Summary
Non-sense mediated mRNA decay (NMD) is a quality-control checkpoint that detects and eliminates aberrant messenger RNAs (mRNAs) with premature termination codons (PTCs) [1,2,3]. The NMD complex can modulate the phenotypic outcome of genetic disorders caused by PTCs. Several studies have identified the existence of a transient ribosome associated complex containing eukaryotic release factor 1 (eRF1)-eRF3, up frameshift 1 (UPF1), ATP-dependent RNA helicase DEAH box polypeptide 34 (DHX34), and suppressor with morphological effect on genitalia 1 complex (SMG1C; containing SMG1 and its regulators SMG8 and SMG9) [4,5,6,7,8,9]. DHX34 dissociates DHX34-UPF1-SMG1C from ribosome-associated eRF1-eRF3 and promotes its association with UPF2-UPF3-EJC (exon junction complex) [5,9]. This may result in translation termination leading to the dissociation of the individual ribosomal subunits, release factors, and nascent protein. The UPF2 protein binds with the N-terminal domain of the UPF1 protein, and releases this domain from the central core of UPF1 [9,10,11]
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