If We Could But Peek Inside the Cell …Quantifying, Characterizing and Visualizing Protein:Protein  Interactions

14231183 WB MS Protein Interactions Hero Image 600x214Robert Hooke first coined the term “cell” after observing  plant cell walls through a light microscope—little empty chambers, fixed in time and space. However,  cells are anything but fixed.

Cells are dynamic: continually responding to a shifting context of time, environment, and signals from within and without. Interactions between the macromolecules within cells, including proteins, are ever changing—with complexes forming, breaking up, and reforming in new ways. These interactions provide a temporal and special framework for the work of the cell, controlling gene expression, protein production, growth, cell division and cell death.

Visualizing and measuring these fluid interactions at the level of the cell without perturbing them is the goal of every cell biologist.

A recent article by Thomas Machleidt et al. published in ACS Chemical Biology, describes a new technology that brings us closer to being able to realize that goal. Continue reading “If We Could But Peek Inside the Cell …Quantifying, Characterizing and Visualizing Protein:Protein  Interactions”

Uncovering Protein Autoinhibition Using NanoBRET™ Technology

13305818-protein ligandIntroducing new assays or technologies is meant to make it easier for you to perform research and craft experiments to test hypotheses. However, scientists are creative people, and new technologies or assays may just be the catalyst for a crucial experiment or new data you are seeking. In the case of a recent Proceedings of the National Academy of Sciences USA article, Wang et al. used the principle of our NanoBRET™ assay to understand how ERK1/2 phosphorylation of Rabin8, a guanine nucleotide exchange factor, influenced its configuration and subsequent activation of Rab8, a protein that regulates exocytosis. Continue reading “Uncovering Protein Autoinhibition Using NanoBRET™ Technology”

Detecting Inhibition of Protein Interactions in vivo

Protein Interactions with NanoBRETIn a paper published in the September issue of ACS Medicinal Chemistry Letters, researchers from GlaxoSmithKline in the UK and Germany report on the discovery, binding mode and structure:activity relationship of a new, potent BRPF1 (bromodomain and PHD finger containing protein family) inhibitor. This paper came to our attention as it is one of the first publications to apply Promega NanoBRET technology in an vivo assay that reversibly measures the interaction of protein partners. The technology enabled the identification of a novel inhibitor compound that disrupts the chromatin binding of this relatively unstudied class of bromodomain proteins.

What exactly are bromodomains and why do they matter?
Bromodomains are regions (~100 amino acids) within chromatin regulator proteins that recognize and “read” acetylated lysine residues on histones. These acetylated lysines act as docking stations for regulatory protein complexes via binding of the bromodomain region. Because of their role in chromatin binding and gene regulation, bromodomains have attracted interest as potential targets for anti-cancer treatments. Although some bromodomain-containing proteins (e.g., those in the bromodomain and extraterminal domain (BET) subfamily) are well characterized and have been identified as potential therapeutic targets, others are less well understood. Continue reading “Detecting Inhibition of Protein Interactions in vivo”

Tools for Observing Protein Behaviors Inside Cells

nanoluchomepageimageIn this BioCompare video, Promega scientist, Dr. Keith Wood, explains how the smaller, brighter and sensitive NanoLuc® Luciferase allows scientists to observe protein behaviors inside cells, including rare events. See how a luciferase can now be used to investigate protein activities as well as for traditional luciferase genetic reporter assays.

http://www.biocompare.com/Life-Science-Videos/156795-Tools-for-Analysis-of-Protein-Behavior-In-Living-Cells/?arev=true

Site-specific copy number variations in cancer: A story begins to unfold

Designed by Nick Klein for ISO-form, courtesy of Promega.
Designed by Nick Klein for ISO-form, courtesy of Promega.

Tumor cells are characterized by many features: including uncontrolled proliferation, to loss of contact inhibition, acquired chromosomal instability and gene copy number changes among them. Some of those copy number changes are site-specific, but very little is known about the mechanisms or proteins involved in creating site-specific copy number changes. In a recently published Cell paper, Black and colleagues, propose a mechanism for site-specific copy number variations involving histone methylation proteins and replication complexes.

Previous work from Klang et al. had shown that local amplification of chromosomal regions occurs during S phase and that chromatin structure plays a critical role in this amplification (2), and other work by Black and colleagues (3) implicated KDM4A in changing timing of replication by altering chromatin accessibility in specific regions. Other research also had shown that KDM4A protein levels influence replication initiation and that KDM4A has a role in some DNA damage response pathways (4,5).  Looking at the body of work, Black et al. hypothesized that KDM4A, with its roles in replication, might possibly provide link into the mechanism of site-specific copy number variation in cancer. Continue reading “Site-specific copy number variations in cancer: A story begins to unfold”

Basic Biology Matters

crop image2Every scientific paper is the story of a journey from an initial hypothesis to a final conclusion. It may take months or years and consists of many steps taken carefully one at a time. The experiments are repeated, the controls verified, the negative and positive results analyzed until the story finally makes sense. Sometimes the end of the story confirms the hypothesis, sometimes it is a surprise. A paper published last week in Cell describes a study where a team of researchers investigating one problem in basic biology (how one component of a signaling complex works), found an unexpected and potentially significant application in a different field (cancer research).

The paper, published in the June 6 issue of Cell, describes a previously unknown interaction between two cellular proteins—the transcription factor HIF1A and the cyclin-dependent kinase CDK8—in the regulation of genes associated with cellular survival under low-oxygen conditions. An accompanying press release describes how the discovery of a role for CDK8 in this process may have implications for cancer research, as CDK8 may be a potential target for drugs to combat “hypoxic” tumors. Continue reading “Basic Biology Matters”

Cell-Free Expression Applications: Characterization of Viral-Mediated Diseases

INFECTION IS BY TRANSCRIPTION OF THE VIRAL DNA INTO THE GENETIC MATERIAL OF THE HOST CELL, SO ANTIBODY TEST ING CAN DIAGNOSE AIDS. MORE SIGNIFICANTLY, IF THE PERCENTAGE OF LYMPHOCYTES THAT ARE CD4+ IS ABOVE 500 PER CUBIC MM THERE IS BETTER PROGNOSIS FOR TREATMENT. HERE THE VIRUS IS BUDDING FROM THE T CELL AS PART OF ITS PROLIFERATION AFTER INFECTING THE T CELL. AIDS VIRUS DIGITIZED TEM COLOR ENHANCED

The characterization of viral mediated diseases is critical to promote the overall welfare of humans or animals. Initial research focused on the interpretation the genomic content (i.e., DNA or RNA based) of the selected virus. The next step is to better understand the proteins that are encoded by this content and their interaction with the host proteome.
The following citations illustrate the use of cell-free protein expression to facilitate this research. Continue reading “Cell-Free Expression Applications: Characterization of Viral-Mediated Diseases”

Variations on the Two-Hybrid Assay

puzzle_lightThe use of reporter genes for simple analysis of promoter activity (promoter bashing) is a well known practice. However, there are many other elegant applications of reporter technologies. One such application is illustrated in the paper by Zheng et al., published in the Sept. 2008 issue of Cancer Research. These researchers from the Hormel Institute at the University of Minnesota showed that the cyclin-dependent kinase cdk3 phosphorylates the transcription factor ATF1 and enhances its transcriptional and transactivation activity. The observed cdk/ATF1 signaling was shown to have an important role in cell proliferation and transformation. To do this they used several variations of a reporter-based two-hybrid assay. Continue reading “Variations on the Two-Hybrid Assay”

Understanding the Flexi® Vector Terminology

pFN6A (HQ) Flexi® VectorWe work hard for our customers. Our various research groups are trying to find better, quicker and easier ways to purify DNA manually or using automation, to assay cell viability or apoptosis and yes, even to clone and express your protein of interest. Our Flexi® Cloning System is a simple and powerful method of directional cloning with a wide array of vectors suitable for many downstream uses, including adding protein expression tags, studying mammalian protein interactions, performing in vitro expression and expressing fusion proteins. Continue reading “Understanding the Flexi® Vector Terminology”