Bench Marks

The baculovirus expression vector system has been widely used to produce proteins originating from both prokaryotic and eukaryotic sources. It offers easy cloning techniques and abundant viral propagation, and since it is based on an insect cell environment, it provides eukaryotic posttranslational modification machinery. Surface modifications of the viral capsid enable specific targeting. Such modifications can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. In the March issue of Cold Spring Harbor Protocols, Christian Oker-Blom and colleagues provide a suite of articles detailing the use of baculovirus-based display and gene delivery systems. Their protocol for Creation of Baculovirus Display Libraries is a featured article for March, and is freely available, along with nearly 90 other featured articles.

The recent explosion in the availability and variety of fluorescent proteins, new organic dyes and quantum dots has been a driving force in the growing use of Total Internal Reflection Fluorescence Microscopy (TIRFM). TIRFM only illuminates molecules that are within a thin volume near the coverslip surface of a specimen and not those deeper in solution. This allows for an unparalleled signal-to-noise ratio and tremendous resolution. In the March issue of Cold Spring Harbor Protocols, Samara Reck-Peterson, Nathan Derr and Nico Stuurman present Imaging Single Molecules Using Total Internal Reflection Fluorescence Microscopy (TIRFM), which includes an overview of the theory behind TIRFM, considerations for TIRFM setup and purification/labeling of proteins, and a discussion of new techniques for imaging single molecules with super-resolution localization. In addition, the group offers step-by-step protocols for Determining Single-Molecule Intensity as a Function of Power Density and Imaging Single Molecular Motor Motility with TIRFM. An example of TIRFM imaging of single dynein molecules labeled with TMR (green) moving along axonemal microtubules labeled with Cy5 (red) can be seen here.

The use of recombinant proteins, antibodies, small molecules, or nucleic acids as affinity reagents is a simple yet powerful strategy to study the protein/bait interactions that drive biological processes. Analysis via mass spectrometry rather than western blotting extends the identification of interactors, often allowing detection of thousands of proteins from complex mixtures. But this increased sensitivity can lead to problems distinguishing specific interactions from background noise. In the March issue of Cold Spring Harbor Protocols, Shao-En Ong from the Broad Institute of MIT and Harvard presents Unbiased Identification of Protein/Bait Interactions Using Biochemical Enrichment and Quantitative Proteomics. This method uses quantitative proteomics approaches to compare enrichment with the bait of interest against samples using control baits to allow sensitive detection and discrimination of specific protein/bait interactions. As one of March’s featured articles, it is freely available to subscribers and non-subscribers alike.