James M. Murphy 2026-11-05
James M. Murphy is a researcher in protein signaling and the functions of pseudokinases, kinase-like protein domains with altered residues normally associated with catalysis. In a 2014 collaborative study, James M. Murphy and colleagues developed a thermal shift assay to classify 31 pseudokinase protein domains according to their binding of nucleotides and metal ions.[ref]
A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties by James M. Murphy and others. Abstract and classification results; Biochemical Journal 457, 323–334, 2014
The key distinction is between binding and chemical activity. A protein may bind ATP without efficiently transferring its phosphate group. The thermal shift assay measures changes in thermal stability associated with binding, while an ordinary kinase activity assay can register activity from a small contaminating protein kinase. The study found four binding classes, including pseudokinases with no detectable binding and others whose binding depended on metal ions. This showed why the label pseudokinase cannot substitute for testing an individual protein.[ref]
A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties by James M. Murphy and others. Abstract: four nucleotide/cation-binding classes and contamination caveat; Experimental: thermal-shift assays
Pseudokinase 2026-11-05
A pseudokinase is a protein kinase-like protein domain that lacks one or more conserved residues usually important for conventional phosphoryl-transfer catalysis. The term identifies an atypical kinase-like structure and sequence; it does not by itself establish that the domain is biologically useless, unable to bind ATP, or incapable of every catalytic reaction. Such domains can regulate other proteins through binding and conformational effects.[ref]
A systematic biochemical study used thermal-shift measurements to examine nucleotide and ion binding in thirty-one pseudokinase domains. Binding properties differed: many showed no detectable nucleotide binding, while others bound nucleotides with different requirements for divalent ions. The results challenged the shortcut of assigning the same biochemical behavior to every atypical domain.[ref]
A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties by James M. Murphy and others. Abstract and Figures2–4: assay and four binding classes
For an assay example, suppose adding ATP reproducibly changes a purified domain's thermal unfolding curve. That supports an interaction under the assay conditions; it does not yet demonstrate transfer of a phosphate group to a substrate. Conversely, detecting phosphorylation in a protein preparation does not establish which protein catalyzed it: a small contaminating protein kinase can matter. Binding and catalytic assays therefore require different controls.[ref]
A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties by James M. Murphy and others. Abstract: thermal-shift method and contaminating-kinase problem
The useful question is what the particular pseudokinase does in its molecular context. Sequence-based expectations guide experiments, but measurements must distinguish nucleotide recognition, chemical turnover and downstream signaling.