Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site

Abstract

Progress in tumor sequencing and cancer databases has created an enormous amount of information that scientists struggle to sift through. While several research groups have created computational methods to analyze these databases, much work still remains in distinguishing key implications of pathogenic mutations. Here, we describe an approach to identify and evaluate somatic cancer mutations of WD40 repeat protein 5 (WDR5), a chromatin-associated protein hub. This multitasking protein maintains the functional integrity of large multi-subunit enzymatic complexes of the six human SET1 methyltransferases. Remarkably, the somatic cancer mutations of WDR5 preferentially distribute within and around an essential cavity, which hosts the WDR5 interaction (Win) binding site. Hence, we assessed the real-time binding kinetics of the interactions of key clustered WDR5 mutants with the Win motif peptide ligands of the SET1 family members (SET1 Win ). Our measurements highlight that this subset of mutants exhibits divergent perturbations in the kinetics and strength of interactions not only relative to those of the native WDR5 but also among various SET1 Win ligands. These outcomes could form a fundamental basis for future drug discovery and other developments in medical biotechnology.

Real-Time Measurement of a Weak Interaction of a Transcription Factor Motif with a Protein Hub at Single-Molecule Precision

“…In addition, it has been shown that the Win site mediates transient PPIs with dozens of proteins, including those involved in key signaling pathways, such as phosphatidylinositol 3-kinase (PI3K) and 3-phosphoinositide-dependent protein kinase 1 (PDPK1). 84 Interestingly, a high-density distribution of missense somatic cancer mutations of WDR5 occurs within and around the Win site, 85 some of which significantly alter the strength of the MLL-WDR5 interactions. 78,83,86,87 On the opposite side of the Win site, WDR5 includes the WBM binding site.…”

Evaluation of Nanopore Sensor Design Using Electrical and Optical Analyses

“…To appraise our attempt at a better understanding of these nanopores, we utilized a recently developed sensing platform that detects WD40 repeat protein 5 (WDR5), − a chromatin-associated hub. The 334-residue highly conserved WDR5 plays an essential role in the regulatory mechanisms of histone 3 lysine 4 (H3K4) mono- and dimethylation. − All our engineered nanopore sensors are equipped with a 14-residue WDR5 interaction (Win) motif ligand , of mixed-lineage leukemia 4 (MLL4 Win ) (Figure b and Table S1 in the Supporting Information). MLL4 is a member of the human MLL/SET1 methyltransferase family .…”

“…The 334-residue highly conserved WDR5 plays an essential role in the regulatory mechanisms of histone 3 lysine 4 (H3K4) mono- and dimethylation. 81 − 84 All our engineered nanopore sensors are equipped with a 14-residue WDR5 interaction (Win) motif ligand 60 , 85 of mixed-lineage leukemia 4 (MLL4 Win ) ( Figure 1 b and Table S1 in the Supporting Information). MLL4 is a member of the human MLL/SET1 methyltransferase family.…”