Biology subjects

Hamid, M.

Publications and source records attributed to Hamid, M..

3 recordsLinked to original sources

bioRxiv2025

Conservation of the hydrogen-bond network in bacterial response regulators

The bacterial response regulator (RR) superfamily is activated by single aspartyl phosphorylation to modulate a distant target binding surface for diverse functions. The enteric CheY RRs, which represent the chemotaxis subfamily, have been extensively characterized. Their native, chemical or genetically-altered crystal structures have revealed an essential role for water-mediated hydrogen bonds (H-bonds) in activation. Here, we use molecular dynamics (MD) to compare the protein-water H-bond network in basal and in-silico phosphorylated conformations. We supplement the MD with energy frustration profiles for atomic structures and models from selected RR superfamily representatives. The energetically frustrated phosphorylation pocket consists of the conserved aspartate triad for phosphorylation, plus associated structural waters and residues for Mg2+ ion coordination. It orchestrates the H-bond network characterized here in atomic detail. The network has an energetically stable core. Its plastic nodes switch bonding states coupled to loop flexibility and sidechain rotations. Mutual information revealsthat the long-range, dynamic networks respond to single H-bond transitions. The network centrality of the phosphorylation pocket, connected to the target binding surface by water-mediated channels via the conserved switch residues (T87, K109), increases upon phosphorylation. Analysis of other RR representatives suggests this design is a generic feature of RR allostery with subtle, function-dependent differences. The water contribution may prove critical for the design of specific RR sub-family specific, allosteric inhibitors.

biophysics↗

bioRxiv2025

An AlphaFold guided model for the evolution of the CaMKII interactome

The neuronal functions of mammalian calcium calmodulin (Ca2+.CAM) dependent protein kinase II (CaMKII) are orchestrated by an interactome of multiple CaMKII-protein interactions when Ca2+.CAM opens the kinase domain to bind Ca2+ response regulators and substrates to its regulatory helix and C-lobe, respectively. We analyzed over forty 3D-atomic structures and models of CaMKII-target complexes to track the evolution of the neuronal CaMKII interactome over three model organisms and the early metazoan Trichoplax adhaerans. We report the conservation of the molecular interactome based on binding surface overlap, energy frustration and fold evolution. Transcriptome databases informed on Ca2+ CaMKII response regulation and colocalization with substrates. The activation machinery was invariant, but the co-expression of CaMKII and its substrates relative to the mammalian isoform was progressively reduced in simpler organisms. We propose CaMKII architecture for autoinhibition, Ca2+ response and substrate association was formed for neurosecretion, then specialized for synaptic signalling with the -isoform.

neuroscience↗

bioRxiv2022

The Solvation of the E. coli CheY Phosphorylation SiteMapped by XFMS

The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.

biochemistry↗