Amino acid sequence analysis of the neuronal type II calmodulin-dependent protein kinase by tandem mass spectrometry

Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching

Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures. Graphical Abstract ᅟ.

Regulation and role of brain calcium/calmodulin-dependent protein kinase II

Ca2+/calmodulin-dependent protein kinase II (CaMKII) exhibits a broad substrate specificity and regulates diverse responses to physiological changes of intracellular Ca2+ concentrations. Five isozymic subunits of the highly abundant brain kinase are encoded by four distinct genes. Expression of each gene is tightly regulated in a cell-specific and developmental manner. CaMKII immunoreactivity is broadly distributed within neurons but is discretely associated with a number of subcellular structures. The unique regulatory properties of CaMKII have attracted a lot of attention. Ca2+/calmodulin-dependent autophosphorylation of a specific threonine residue (alpha-Thr286) within the autoinhibitory domain generates partially Ca(2+)-independent CaMKII activity. Phosphorylation of this threonine in CaMKII is modulated by changes in intracellular Ca2+ concentrations in a variety of cells, and may prolong physiological responses to transient increases in Ca2+. Additional residues within the calmodulin-binding domain are autophosphorylated in the presence of Ca2+ chelators and block activation by Ca2+/calmodulin. This Ca(2+)-independent autophosphorylation is very rapid following prior Ca2+/calmodulin-dependent autophosphorylation at alpha-Thr286 and generates constitutively active, Ca2+/calmodulin-insensitive CaMKII activity. Ca(2+)-independent autophosphorylation of CaMKII also occurs at a slower rate when alpha-Thr286 is not autophosphorylated and results in inactivation of CaMKII. Thus, Ca(2+)-independent autophosphorylation of CaMKII generates a form of the kinase that is refractory to activation by Ca2+/calmodulin. CaMKII phosphorylates a wide range of neuronal proteins in vitro, presumably reflecting its involvement in the regulation of diverse functions such as postsynaptic responses (e.g. long-term potentiation), neurotransmitter synthesis and exocytosis, cytoskeletal interactions and gene transcription. Recent evidence indicates that the levels of CaMKII are altered in pathological states such as Alzheimer's disease and also following ischemia.

Calmodulin-dependent protein kinase II. Kinetic studies on the interaction with substrates and calmodulin

The kinetic reaction mechanism of calmodulin (CaM)-dependent protein kinase II (CaM-kinase II), including the regulatory mechanism by CaM, was studied by using microtubule-associated protein 2 (MAP2) as substrate under steady-state conditions. The detailed kinetic analyses of the phosphorylation of MAP2 and its inhibitions by the reaction products and by an ATP analogue, 5'-adenylylimidodiphosphate, revealed the rapid-equilibrium random mechanism. In the absence of Ca2+, CaM-kinase II was inactivated by incubation with ATP. The inactivation rate was dependent on the concentrations of ATP and MAP2, suggesting that these substrates can bind to the enzyme even in the absence of Ca2+/CaM. The activation of the enzyme by CaM reached the maximum when about 10 mol of CaM bound to 1 mol of CaM-kinase II, indicating the stoichiometry of the binding of one CaM to one subunit of the enzyme. The enzyme activity as a function of the concentration of CaM showed a sigmoidal curve. The concentration of CaM required for the half-maximal activation was dependent on the concentration of ATP at a fixed concentration of MAP2, although the Hill coefficient was unaffected by the concentration of ATP. A possible reaction mechanism of CaM-kinase II, including the phosphorylation of MAP2 by the enzyme and the binding of CaM to the enzyme, is discussed.

A monoclonal antibody against brain calmodulin-dependent protein kinase type II detects putative conformational changes induced by Ca2+-calmodulin

A mouse monoclonal IgG1 antibody has been generated against the soluble form of the calmodulin-dependent protein kinase type II. This antibody recognizes both the soluble and cytoskeletal forms of the enzyme, requiring Ca2+ (EC50 = 20 microM) for the interaction. Other divalent cations such as Zn2+, Mn2+, Cd2+, Co2+, and Ni2+ will substitute for Ca2+, while Mg2+ and Ba2+ will not. The antibody reacts with both the alpha- and beta-subunits on Western blots in a similar Ca2+-dependent fashion but with a lower sensitivity. The affinity of the antibody for the kinase is 0.13 nM determined by displacement of 125I Bolton-Hunter-labeled kinase with unlabeled enzyme. A variety of other proteins including tubulin do not compete for antibody binding. The Mr 30,000 catalytic fragment obtained by proteolysis of either the soluble or the cytoskeletal form of the kinase fails to react with the antibody. Calmodulin and antibody reciprocally potentiate each other's interaction with the enzyme. This is illustrated both by direct binding studies and by a decrease of the Kmapp for calmodulin and an increase in the Vmax for the autophosphorylation reaction of the enzyme. The antibody thus appears to recognize and stabilize a conformation of the kinase which favors calmodulin binding although it does not itself activate the kinase in the absence of calmodulin. Since the Mr 30,000 catalytic fragment of the kinase is not immunoreactive, either the antibody combining site of the kinase must be present in the noncatalytic portion of the protein along with the calmodulin binding site or proteolysis interferes with the putative Ca2+-dependent conformational change.(ABSTRACT TRUNCATED AT 250 WORDS)