Biology subjects

Boggon, T. J.

Publications and source records attributed to Boggon, T. J..

5 recordsLinked to original sources

bioRxiv2025

Clinically observed RASA1 missense mutants exhibit diverse RasGAP protein behaviors

The RASA1 gene is mutated in cerebrovascular disorders and cancer, yet how the resulting mutations in the GTPase Activating Protein, RasGAP (p120RasGAP, RASA1) dysregulate signaling remains poorly understood. Here, we catalogue currently reported disease-associated mutations in RASA1 and assess their impact on RasGAP protein in vitro. On mapping these mutations onto experimental structures and structural models of RasGAP we identify regions that suggest functional impact. We assess key mutations within these regions for their effects on protein expression, thermal stability, and their interactions with a known binding partner, p190RasGAP. We then assess Michaelis-Menten kinetics of the mutant RasGAP proteins towards Ras. Together, we find that disease-associated RasGAP mutations classify into a panel of distinct classes based on their mode of dysregulation. We demonstrate that protein stability is necessary but not sufficient for full catalytic activity and that destabilizing mutations across the length of the protein can disrupt this function, but that the C2 domain appears to be unique in its role of regulating GAP activity by mechanisms other than destabilization involving the interactions of specific residues.

biochemistry↗

bioRxiv2025

Optimized conditions for GTP loading of Ras

Ras and the small GTPase group are essential for myriad cellular processes and cycle between GDP- and GTP-loaded states to allow stringent control of downstream signaling pathways. Biochemical studies of small GTPases can therefore require a specific nucleotide-bound state. Small GTPases possess basal intrinsic activity to process GTP into GDP plus inorganic phosphate, therefore in vitro exchange of GDP for GTP is necessary for assays on GTP-loaded states. Here, we assess the methodology of in vitro nucleotide exchange for soluble H-Ras. We begin by describing a protocol to quantify the nucleotide bound content of H-Ras using anion exchange chromatography and use this protocol to investigate optimal strategies for loading Ras with GTP by assessing the effects of time, temperature, H-Ras concentration, magnesium, excess nucleotide, and isoform identity. We continue by considering storage of GTP-loaded H-Ras and present optimal conditions to minimize intrinsic GTP hydrolysis. Finally, we conclude by investigating the nucleotide composition of recombinantly expressed H-Ras encompassing cancer mutations at residues Gly12, Gly13, and Gln61. We therefore describe methodology to quantitatively analyze the nucleotide content of small GTPases and their mutants, and demonstrate conditions to achieve efficient GTP loading of Ras.

biochemistry↗

bioRxiv2025

Nickel binding to a split ATCUN motif in c-Src SH3 domain facilitates crystallization

Numerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions. Here, we report a unique crystal structure of Src SH3 domain in trigonal space group H32 to 1.45 [A] resolution. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules. This study provides an example of metal binding by N-terminal protein residues that contrasts the amino terminal copper and nickel binding (ATCUN) motif and is an alternative avenue for crystallization of the Src SH3 domain. STRUCTURED ABSTRACTO_ST_ABSIntroductionC_ST_ABSNumerous X-ray crystal structures of the c-Src SH3 domain have provided a large sampling of atomic-level information for this important signaling domain. Multiple crystal forms have been reported, with variable crystal lattice contacts and chemical crystallization conditions. Materials and MethodsWe crystallize the c-Src SH3 domain in a crystallization buffer containing NiCl2. ResultsA unique crystal structure of Src SH3 domain in trigonal space group H32 to 1.45 [A] resolution is determined. Crystal packing and anomalous scattering reveal that this crystal form is mediated by two ordered nickel ions provided by the crystallization buffer. Nickel coordination occurs in a 2:2 stoichiometry which dimerizes two SH3 domain monomers across a pseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, a surface-exposed histidine residue, and ordered water molecules. DiscussionThis study provides an example of metal-mediated crystallization and metal binding by N-terminal protein residues that contrasts the amino terminal copper and nickel binding (ATCUN) motif. ConclusionAlternative avenues for helps widen the potential for future crystallography-based studies of the c-Src SH3 domain.

biochemistry↗

bioRxiv2024

The C2 domain augments Ras GTPase Activating Protein catalytic activity

Regulation of Ras GTPases by GTPase activating proteins (GAP) is essential for their normal signaling. Nine of the ten GAPs for Ras contain a C2 domain immediately proximal to their canonical GAP domain, and in RasGAP (p120GAP, p120RasGAP; RASA1) mutation of this domain is associated with vascular malformations in humans. Here, we show that the C2 domain of RasGAP is required for full catalytic activity towards Ras. Analysis of the RasGAP C2-GAP crystal structure, AlphaFold models, and sequence conservation reveal direct C2 domain interaction with the Ras allosteric lobe. This is achieved by an evolutionarily conserved surface centered around RasGAP residue R707, point mutation of which impairs the catalytic advantage conferred by the C2 domain in vitro. In mice, R707C mutation phenocopies the vascular and signaling defects resulting from constitutive disruption of the RASA1 gene. In SynGAP, mutation of the equivalent conserved C2 domain surface impairs catalytic activity. Our results indicate that the C2 domain is required to achieve full catalytic activity of Ras GTPase activating proteins.

biochemistry↗

bioRxiv2023

Distinct functional constraints driving conservation of the cofilin N-terminal regulatory tail

Cofilin family proteins have essential roles in remodeling the cytoskeleton through filamentous actin depolymerization and severing. The short unstructured N-terminal region of cofilin is critical for actin binding and harbors the major site of inhibitory phosphorylation. Atypically for a disordered sequence, the N-terminal region is highly conserved, but the aspects of cofilin functionality driving this conservation are not clear. Here, we screened a library of 16,000 human cofilin N-terminal sequence variants for their capacity to support growth in S. cerevisiae in the presence or absence of the upstream regulator LIM kinase. Results from the screen and subsequent biochemical analysis of individual variants revealed distinct sequence requirements for actin binding and regulation by LIM kinase. While the presence of a serine, rather than threonine, phosphoacceptor residue was essential for phosphorylation by LIM kinase, the native cofilin N-terminus was otherwise a suboptimal LIM kinase substrate. This circumstance was not due to sequence requirements for actin binding and severing, but rather appeared primarily to maintain the capacity for phosphorylation to inactivate cofilin. Overall, the individual sequence requirements for cofilin function and regulation were remarkably loose when examined separately, but collectively restricted the N-terminus to sequences found in natural cofilins. Our results illustrate how a regulatory phosphorylation site can balance potentially competing sequence requirements for function and regulation.

molecular biology↗