Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1

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.

Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

“…In addition, the missing amino acid (residues range: 67-78, 96-98, 143-155, 177-186, 247-260, 329-334, 444-448, 455-490, 501-502, 621-639, 673-686, 812-814, and 829-852) coordinates in the structure of SARS-CoV-2 spike glycoprotein were built using the swissmodel (Figure 1) [61]. Molecular dynamics simulations were carried on the model systems as per the standardized pipelines [62][63][64] (detailed method explained in the supplementary materials; File S1). The GROMACS 4.6.5 [65] program (GROMACS; Groningen Machine for Chemical Simulations, University of Groningen, Groningen, The Netherlands) was used to perform MD calculations assigning the CHARMM27 forcefield [66].…”

Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site

“…In addition, the missing amino acids (residues range: 67-78, 96-98, 143-155, 177-186, 247-260, 329-334, 444-448, 455-490, 501-502, 621-639, 673-686, 812-814, and 829-852) coordinates in the structure of SARS-CoV-2 spike glycoprotein were built using the swissmodel (Figure 1) [60]. Molecular dynamics simulations (MD) were carried on the model systems as per standardized pipelines [61][62][63] (detailed method explained in the supplementary materials). The GROMACS 4.6.5 [64] program (GROMACS; Groningen Machine for Chemical Simulations) was used to perform MD calculations assigning the CHARMM27 forcefield [65].…”

Nonsense-Mediated mRNA Decay: Pathologies and the Potential for Novel Therapeutics

“…The UPF1 protein has a conserved cysteine-histidine-rich domain (CH-domain), followed by two RecA-like domains (RecA1 and RecA2; helicase region), and a SQ (serine-glutamine) domain ( Figure 1b) [33,34]. From the structural analysis it is known that binding of UPF2/UPF3 protein to the CH-domain of UPF1 activates UPF1 ATPase and the helicase activities [35] ( Figure 2).…”