Applied genomics: integration of the technology within pharmaceutical research and development

Multiple novel technologies have recently been developed to improve the analysis of genetic sequences, to rapidly assess RNA or protein levels in relevant tissues, and to validate function of potential new drug targets. The challenge facing pharmaceutical research is one of effective integration of these new technologies in ways that can maximally affect the discovery and development pipeline. Although database mining and transcriptional profiling clearly have increased the number of putative targets, the current focus is to assign function to new gene targets in a high-throughput manner. This requires a restructuring of the classical linear progression from gene identification, functional elucidation, target validation and screen development. New approaches are called for that can make this process non-linear and high-throughput.

Cloning and expression of the human kv4.3 potassium channel

We report on the cloning and expression of hKv4.3, a fast inactivating, transient, A-type potassium channel found in both heart and brain that is 91% homologous to the rat Kv4.3 channel. Two isoforms of hKv4.3 were cloned. One is full length (hKv4.3 long), and the other has a 19 amino acid deletion (hKv4.3 short). RT-PCR shows that the brain contains both forms of the channel RNA, whereas the heart predominantly has the longer version. Both versions of the channel were expressed in Xenopus oocytes, and both contain a significant window or noninactivating current seen near potentials of -30 to -40 mV. The inactivation curve for hKv4.3 short is shifted 10 mV positive relative to hKv4.3 long. This causes the peak window current for the short version to occur near -30 mV and the peak for the longer version to be at -40 mV. There was little difference in the recovery from inactivation or in the kinetics of inactivation between the two isoforms of the channel.

Immunohistochemical localization of G protein beta1, beta2, beta3, beta4, beta5, and gamma3 subunits in the adult rat brain

The regional distributions of the G protein beta subunits (Gbeta1-beta5) and of the Ggamma3 subunit were examined by immunohistochemical methods in the adult rat brain. In general, the Gbeta and Ggamma3 subunits were widely distributed throughout the brain, with most regions containing several Gbeta subunits within their neuronal networks. The olfactory bulb, neocortex, hippocampus, striatum, thalamus, cerebellum, and brainstem exhibited light to intense Gbeta immunostaining. Negative immunostaining was observed in cortical layer I for Gbeta1 and layer IV for Gbeta4. The hippocampal dentate granular and CA1-CA3 pyramidal cells displayed little or no positive immunostaining for Gbeta2 or Gbeta4. No anti-Gbeta4 immunostaining was observed in the pars compacta of the substantia nigra or in the cerebellar granule cell layer and Purkinje cells. Immunoreactivity for Gbeta1 was absent from the cerebellar molecular layer, and Gbeta2 was not detected in the Purkinje cells. No positive Ggama3 immunoreactivity was observed in the lateral habenula, lateral septal nucleus, or Purkinje cells. Double-fluorescence immunostaining with anti-Ggamma3 antibody and individual anti-Gbeta1-beta5 antibodies displayed regional selectivity with Gbeta1 (cortical layers V-VI) and Gbeta2 (cortical layer I). In conclusion, despite the widespread overlapping distributions of Gbeta1-beta5 with Ggamma3, specific dimeric associations in situ were observed within discrete brain regions.

The 28-kDa N-terminal domain of mouse stromelysin-3 has the general properties of a weak metalloproteinase

The putative matrix metalloproteinase mouse stromelysin-3 was expressed from Escherichia coli and from a mouse myeloma cell line. In the former case a single major protein of 58-kDa was detectable by immunoblotting, but no proteolytic activity could be elicited by zymography or trypsin or organomercurial treatment as would be expected for a typical matrix metalloproteinase. In the latter case immunodetectable proteins of 55-58 and 27-28-kDa were produced. The effect of trypsin or organomercurial treatment of the 55-58-kDa forms was to generate a 51-kDa form and lower molecular mass fragments. Upon zymographic analysis only the 27-28-kDa forms showed caseinolytic activity. N-terminal sequencing and immunoblotting analysis with antibodies specific to distinct domains of stromelysin-3 indicated that the 27-28-Da stromelysin-3 forms had lost the predicted propeptide and the majority of the C-terminal domain. The purified 28-kDa form of stromelysin-3 could weakly degrade a number of extracellular matrix proteins and was inhibited by TIMP. However, the evidence that mature full-length stromelysin-3 is a metalloproteinase could not be substantiated and the precise role of this protein in vivo remains to be elucidated. By partial analogy with interstitial collagenase, one hypothesis is that stromelysin-3 with an intact C-terminal domain has specific properties for an as yet undefined substrate.

Crystallization and preliminary X-ray analysis of a truncated tissue metalloproteinase inhibitor delta 128-194 TIMP-2

Crystals of an active truncated form of a human tissue metallproteinase inhibitor (delta 128-194 TIMP-2), a protein implicated in a number of diseases of the connective tissues, have been grown in a form suitable for study by X-ray diffraction analysis. Crystals grow using polyethylene glycol 600 as a precipitant and are in space group P2(1)2(1)2, with cell dimensions a = 75.28 A, b = 100.77 A, c = 31.45 A. The asymmetric unit appears to contain two molecules of delta TIMP-2 with a Vm value of 2.3 A3/dalton. The crystals diffract to Bragg-spacings beyond 2.5 A. Native data to 3.2 A have been collected and a search for heavy-metal derivatives is in progress.