Description

This report explores the technological challenges faced by protein scientists when assessing biomolecular interactions in vivo and also highlights the opportunities for new techniques and products to facilitate innovative research in this area. It will provide marketing professionals and product developers with unique insights into the product preferences, preferred suppliers, level of satisfaction with the current technologies, definitions of quality and unmet needs in biomolecular interactions. By studying biomolecular interactions, life scientists hope to better understand the regulation of protein function, expression of proteins under different cellular conditions, and protein interactions with other biomolecules such as nucleic acids and ligands. In vivo methods for identifying and characterizing biomolecular interactions and complexes have greatly improved over the past few years. Traditional methods employing affinity chromatography or co-immunoprecipitation have largely been replaced by predominantly two-hybrid and phage-display systems. The most prominent two-hybrid system employed among scientists is the Yeast Two-Hybrid System-an efficient and rapid method of analysis. The Yeast Two-Hybrid System-although highly useful-challenges protein scientists with its many limitations. Existing systems present low throughput, high rates of false positives, low detection levels and poor expression stability. In addition, yeast model systems cannot process complex post-translational modifications required for proper function of many types of proteins. Recent improvements in the Yeast Two-Hybrid System include smaller vectors, low copy number vectors, vectors with multiple cloning sites, increased reporter numbers and reporters with greater sensitivity. Competitors are now developing technologies to address scientists' needs for increased transformation efficiency, higher stringency detection, decreased false positive results and high-throughput formats. In addition, two-hybrid systems have been expanded to include mammalian and bacterial two-hybrid systems. Mammalian two-hybrid systems offer a native environment for protein function as well as rapid and efficient analysis, whereas bacterial two-hybrid systems are a more familiar model system, offering higher efficiency and the ability to screen larger, more complex libraries. The final report is based on the opinions of a worldwide panel of research scientists. It provides you with the answers needed to better serve the protein science market and is available at a fraction of what it would cost to conduct a custom study similar in size and scope. Biomolecular Interactions (In Vivo Methods) is the seventh installment in our series-which details all aspects of protein research-and specifically focuses on the gene tagging methods employed by protein scientists. Hybrid systems will continue to dominate the gene tagging method for identifying biomolecular interactions and complexes. Utilizing these methods, scientists will continue to classify proteins, identify interactions between proteins and learn more about various biological functions that form larger cellular processes. As the alternatives grow, companies involved with proteomics must understand life scientists' current needs and future research goals in order to improve their products and technologies and make them more powerful. Report Highlights More than 250 researchers studying biomolecular interactions using in vivo methods participated in this survey between November 26 and December 5, 2001. The report details findings for each and every question in the survey. Below is a glimpse of some of the findings derived from different questions: • Currently, the primary technique for protein scientists involved in identifying protein-protein associations in biological systems is the yeast two-hybrid method. • "Screening a library (or libraries) to discover previously unknown binding partners of the protein of interest" is the primary application of the in vivo research performed by researchers. • To confirm the validity of in vivo protein interactions, many researchers will rely on in vitro methods over the more time-intensive, costly and invasive physiological studies with organs or whole bodies. • According to the protein scientists surveyed, the risk in using yeast two-hybrid proteomic approaches is that the systems are "prone to false positive results" and that "hybrid proteins may not fold normally." • The "ability to simultaneously detect/analyze multiple sets of protein-protein interactions in a single screening" is a major factor in influencing a researcher's decision to use an in vivo system for studying protein-protein interactions. (Electronic copy also includes 1 print copy)

Table of Contents

Section 1 Executive Overview and Introduction -Executive Overview -Key Findings -Introduction -Visualizing & Quantifying Proteins In Vivo -Identifying & Characterizing Protein Interactions In Vivo -Applications of These Different Techniques -High-throughput Screening -Technologies & Suppliers Section 2 Study Methodology and Demographics -Study Methodology -Objectives -Comments -Demographics -Market Segment -Organization Size -Laboratory Size -Region -Job Position -Area(s) of Research Section 3 Significant Findings -Visualizing & Quantifying Biomolecules In Vivo -Current and future use of technologies for visualizing and/or quantifying proteins in vivo -Detection techniques used for visualizing and/or quantifying proteins in vivo -Type of multi-color applications performed -Future plans for instrumentation Identifying & Characterizing Protein Interactions In Vivo -Current and future use of in vivo techniques for identifying and/or characterizing protein-nucleic acid interactions -Number of in vivo protein-protein interaction assays and/or library screens performed each month -Applications that use in vivo approaches for studying protein-protein interactions -Type of protein used as "bait" for in vivo protein interaction experiments -Places "bait" proteins normally localize -Origins of "bait" proteins used -Size range of "bait" proteins used -Correspondence of length of "bait" proteins to the wild-type protein under study -Most commonly used reporters and/or markers when performing in vivo protein interaction assays -Most commonly used techniques when assaying reporter activity for in vivo protein interaction assays -Most commonly used substrate when assaying reporter activity for in vivo protein-protein interaction assays -Most commonly used criteria for establishing the validity of interacting pairs -Average percentage of interacting pairs discovered to be "false positives" Technologies & Suppliers -Percentage of lab effort directed toward identifying or characterizing protein-protein interactions using in vivo methodologies -Percentage of lab effort directed toward visualizing or quantifying protein in vivo -Top-of-mind company for products/technologies for studying protein interactions in vivo -Familiarity with suppliers of products/technologies for identifying or studying protein interactions in vivo -Current and future estimated percentage of annual budget for products/instrumentation dedicated to studying protein interactions in vivo -Top factors that are most problematic when using yeast two-hybrid systems Section 4 Presentation of Survey Data -50 pages of detailed tables, full-color analytical charts and graphs highlighting the responses and findings for each of the 28 questions in the survey instrument. Section 5 Cross Tabulations of Survey Data -Over 50 questions or answer choices tabulated against Market Segment, Geographic Region, Area of Research or other relevant questions. Section 6 Appendix -Related Reports -About BioInformatics -Our Valued Clients