In Situ Kinase Profiling Reveals Functionally Relevant Properties of Native Kinases

SummaryProtein kinases are intensely studied mediators of cellular signaling, yet important questions remain regarding their regulation and in vivo properties. Here, we use a probe-based chemoprotemics platform to profile several well studied kinase inhibitors against >200 kinases in native cell proteomes and reveal biological targets for some of these inhibitors. Several striking differences were identified between native and recombinant kinase inhibitory profiles, in particular, for the Raf kinases. The native kinase binding profiles presented here closely mirror the cellular activity of these inhibitors, even when the inhibition profiles differ dramatically from recombinant assay results. Additionally, Raf activation events could be detected on live cell treatment with inhibitors. These studies highlight the complexities of protein kinase behavior in the cellular context and demonstrate that profiling with only recombinant/purified enzymes can be misleading

What Does Database Federation Mean To Crystallography?

Syntax Notation version 1 (ASN.1). Thus data is either collected directly in ASN.1, through, for example, direct deposition of sequences to the NCBI, or converted from other formats with programs specific to each database. (These programs are, however, built from the same library of tools.) SRS, on the other hand, uses an Object Data Definition (ODD) which is a generic data definition language used to describe the representation found for example in a PDB entry or GenBank sequence entry, or the flat file representations of approximately 80 other biological databases for that matter [13]. Once the ODD for a specific type of data is defined, the same code is used to perform the parsing and indexing by first reading the ODD definition for a particular database. Figure 1 gives a view of some of the databases accessible through SRS characterized by the type of information available. Entrez takes this indexing idea a step further with the concept of neighbors. Neighbors provide hypertext l..

WHAT DOES DATABASE FEDERATION MEAN TO CRYSTALLOGRAPHY?

More than ever crystallographers are faced with using a variety of databases, each with its own content, organization and query interface. Database federation offers the promise of a unified view of these disparate data and detailed query through a single easy to use interface available via the World Wide Web. This paper discusses current progress towards database federation in molecular biology and uses the Protein Kinase Resource (PKR) as an example. The paper concludes that while we are a long way from achieving the computer scientist’s view of database federation, there are useful resources available today. These resources and what we can expect in the future are introduced. Throughout emphasis is placed on the importance of better computer-readable annotation for achieving true database federation. 1