HDAC Inhibitors as Epigenetic Regulators

Subsequent studies expanded the peptide substrates tested to include changes in residues P8 to P5.15,16 These studies of BACE1 subsite specificity provide a cleavage sequence profile that can be adapted for bioinformatic studies. Though the precise physiological function of BACE1 remains elusive, some have suggested that it acts as a sheddase.17 Despite its relatively loose specificity, only a handful of in vivo BACE1 substrates have been identified, primarily through top down approaches. in cell surface protein-protein interactions. strong class=”kwd-title” Keywords: bioinformatics, BACE1, protease, Alzheimers disease, protease substrates Introduction BACE1 (memapsin 2, -secretase, Asp 2 ELN484228 protease) is a Type I membrane-bound aspartyl protease. It is highly expressed ELN484228 in the brain and pancreas, and the bulk of the enzyme, including catalytic domain, is extracytoplasmic (extracellular or luminal), with a short C-terminal tail containing a cell trafficking domain that directs it to ELN484228 the trans-Golgi network and endosomes.1 Just over ten years ago it was identified by several groups as the protease responsible for the initial cleavage of the amyloid precursor protein (APP, also a Type I membrane protein) in the brain.2C6 Subsequent cleavage of APP within its transmembrane domain by -secretase, a novel aspartyl protease protein complex with multiple membrane spanning -helices, yields short peptide fragments primarily consisting of 40 or 42 amino acids termed amyloid- (A). Aggregation of the A peptides forms plaques in the brain which are one of the hallmark pathological features of Alzheimers disease (AD). The precise ELN484228 mechanisms by which these A peptides exert their pathogenic effects in the brain are unknown, but soluble oligomers of A have been shown to be involved in the synaptic dysfunction associated with AD.7 Due to its association with the production of A and with AD, BACE1 has gained significant attention as an attractive AD therapeutic target for at least two reasons. Firstly, since it is the first protease to cleave APP on the pathway leading to A formation, inhibiting it precludes -secretase cleavage from leaving APP to be processed via the non-pathogenic -secretase pathway. Secondly, BACE1 knockout mice showed a mild, albeit complex phenotype and no detectable A in the brain, whereas knocking out -secretase was embryonic lethal.8C13 As is the case with many other aspartyl proteases, BACE1 has a relatively open active site and fairly loose specificity Turner et al initially reported the S1PR2 subsite specificity for BACE1 by measuring the second order rate constant for the peptide hydrolysis within pools of octapeptide libraries, in which seven residues were held constant while substituting one of the 19 standard amino acids (cysteine omitted) for the remaining residue.14 This was initially done for each of the P4 to P1 and P1 to P4 residues. Subsequent studies expanded the peptide substrates tested to include changes in residues P8 to P5.15,16 These studies of BACE1 subsite specificity provide a cleavage sequence profile that can be adapted for bioinformatic studies. Though the precise physiological function of BACE1 remains elusive, some have suggested that it acts as a sheddase.17 Despite its relatively loose specificity, only a handful of in vivo BACE1 substrates have been identified, primarily through top down approaches. As mentioned above, APP is a known physiological BACE1 substrate. Another extensively characterized BACE1 substrate is the growth factor Neuregulin-1 (NRG1), a Type I membrane protein expressed on the surface of axons that interacts with the ErbB family of receptor tyrosine kinases. NRG1 is involved in the stimulation of Schwann cell proliferation and ultimately myelination.18,19 This connection between BACE1 and NRG1 is borne out in the observation of hypo myelination in BACE1?/? knockout mice.20 Another set of proteins identified as BACE1 substrates are the beta-subunits of voltage gated sodium channels (VGSC).21,22 Wong et al demonstrated that BACE1 knockout cell lines showed a 50% reduction in the proteolytic processing responsible for the generation of the C-terminal fragment (CTF) of 1 1, 2, 3, and 4 VGSC subunits, but the residual 40%C50% activity suggests that other proteases are.