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Emerald Bio has gained a breadth of expertise in structural biology for drug discovery which we'd like to share with our partners. Our drug discovery webinar series is designed to show you important trends on a broad level, and to give you tips to help you succeed. Sign up for our upcoming 50 minute webinars, or view prerecorded ones at your leisure. Also, if you'd like an individualized consultation, contact us.

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Tools for the Expression and Crystallization of Membrane Proteins

Date: Nov 12, 2012
Time: 4pm - 5pm EST
Jim Fairman, Ph.D.

describe the imageMembrane proteins are important targets in the pharmaceutical industry, and compose an estimated 50 to 60 percent of potential novel drug targets.  In addition, approximately 40 percent of prescription drug molecules currently on the market target the GPCR family of membrane proteins.  Determination of structural information on these targets is of immense benefit, as it enables pharmaceutical companies to further fill their drug development pipeline with structure-based drug design.  However, membrane proteins are notoriously difficult to express, purify, and crystallize.  Thus any information about their structure is of high value.  In this webinar we will present and discuss some tools that Emerald Bio uses for the expression and crystallization of membrane proteins.  In particular, we will cover fluorescence coupled size exclusion chromatography (FSEC) and its application to expression and detergent solubility screening of membrane proteins.  We will also review the fluorescence recovery after photobleaching (FRAP) method and its relevance to improving crystallization conditions of membrane proteins in the lipidic cubic phase.

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MTPP Focus on Molecular Biology: Implementing a Parallel Processing Approach to Construct Design and Expression Testing

Date: Jul 17, 2012
Time: 11:00 – 11:50 AM PDT
Amy Raymond, Ph.D.

Technological advances in the forms of new tools and procedures have revolutionized access to protein structure determination by X-ray crystallography by dramatically lowering time and cost. These tools and procedures enable structural biologists to rapidly advance protein crystallography projects by allowing the researcher to select multiple target constructs and prosecute them in parallel, thus compressing the gene-to-protein part of the gene-to-structure pathway. Learn how this can be accomplished through High Throughput methodologies for parallel cloning.  By putting your gene into a variety contexts followed by screening the array of constructs for expression and solubility, you will gain critical insights as to which constructs will provide the highest return on investment at the preparative scale. In this webinar, several case studies will be used to illustrate how concepts from the Multi-Target Parallel Processing™ platform (MTPP) at Emerald BioStructures can be applied in moderate sized laboratories. Topics included will be:

  • Structure-guided construct design

  • High Throughput/Parallel cloning strategies

  • Use of structure-specific proteases and fusion partners as screening tools

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Seawater Phage Metaproteomics or: Dark Matter, It’s Not Just for Astronomers Anymore

Date: Jun 19, 2012
Time: 11:00 – 11:50 AM PDT
Don Lorimer, Project Leader

Abstract:  Despite centuries of discovery, most of our planet’s biodiversity remains unknown. Characterizing this diversity is a fundamental goal of biology and has very important practical applications.  For example, discovering new enzymes and new metabolic pathways could potentially lead to new medicines, new biomaterials, and certainly new tools for biotechnology.  Emerald BioStructures is currently involved in an NSF funded project led by Dr. Forest Rohwer (San Diego State University) to address this goal by determining the structure of proteins from viruses living in the world’s oceans. This is particularly difficult because the vast majority of open reading frames (ORFs) identified in these viruses are so widely disparate it is not possible to align them with any other protein of known function. These ORFs are therefore referred to as “Dark Matter” because the corresponding protein structures and functions are completely unknown.  Emerald is using its Multi-Target Parallel Processing (MTPP) platform to process hundreds of Dark Matter proteins with completely unknown structure and function.  We will present the processes for expressing, purifying, crystallizing, and determining the structure of viral metagenomic proteins. The unique challenges this approach demands along with the solutions that Emerald has developed with our collaborators will be discussed. In addition, the structures of several viral Dark Matter proteins will be presented including one which possesses a novel protein fold.

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Membrane Protein Crystallization Using Lipidic Mesophases and Bicelles

Date: May 15, 2012
Time: 11:00 – 11:50 AM PDT
Timothy Craig, Ph.D. and James Fairman, Ph.D.

The crystallization of membrane proteins such as G- Protein Coupled Receptors (GPCR) and Ion Channels in detergent micelles has traditionally been difficult. Advanced mesophase crystallization technologies present an attractive option for the crystallization of membrane proteins of all types. Recent successes in G- Protein Coupled Receptor crystallization using lipidic mesophases has led to a resurgence of interest in mesophase crystallography. In this webinar, we will explain the basis for lipidic cubic phase (LCP) and Bicelle crystallization techniques as well as how to interpret the results of these experiments. We will also talk about LCP-FRAP, a useful method for rapidly pre-screening crystallization conditions using small amounts of fluorescently labeled protein. Topics included will be:

  • Lipidic Cubic Phase Crystallization

  • Bicelle-based Crystallization

  • LCP-FRAP Precrystallization Screening

  • Interpreting LCP Crystallization Experiments

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Complementing Biophysical and Structural Methods for Drug Discovery with Capillary Electrophoresis

Date: Apr 17, 2012
Time: 11:00 – 11:50 AM PDT
Speaker: Dallas Hughes, Consultant, Selcia Discovery

Structure-based techniques such as fragment-based drug discovery (FBDD) are well-recognized and successful alternatives to high throughput screening. FBDD requires assays that can detect weak affinity fragment/target interactions, and must be able to tolerate high concentrations of test fragments. Selcia has developed a capillary electrophoresis method (CEFrag™) to detect weak fragment interactions with protein targets in solution. The method requires low reagent usage and no chemical modification or immobilization of the target protein.
CEFrag is a microscale, high resolution, separation technique that can be used either as a primary screen or as an orthogonal screening tool to confirm fragment hits obtained by other methods. The principle of the technique uses CE to detect a reduced interaction of a probe ligand with its target protein in the presence of a binding fragment. The competitive nature of this interaction ensures that fragment “hits” bind in a defined manner and avoids the problem of false positives caused by non-specific binding. Case studies of different targets screened against the Selcia fragment library using CEFrag will be presented and comparisons to orthogonal methods will be discussed.

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Multi-Target Parallel Processing or, How to Turn a Dozen New Targets into a SBDD Pipeline in Less Than a Year

Date: Mar 20, 2012
Time: 11:00 – 11:50 AM PDT
Bart Staker, Ph.D.

The advances of structural genomics technology have revolutionized the time and cost of protein structure determination by X-ray crystallography. New tools and procedures are available today which enable structural biologists to rapidly advance protein crystallography projects involving sets of six or more targets. The essence of this success can be distilled into the concept of selecting multiple target constructs and prosecuting them in parallel. In this free 45 minute webinar, several case studies will be used to illustrate how concepts from the multi-target parallel processing platform at Emerald BioStructures can be applied in moderate sized laboratories. We will discuss the structure determination of multiple targets from the methylerythritol phosphate (MEP) pathway from Pseudomonas aerurginosa and Klebsiella pneumonia. Additionally we will discuss how single target poor crystallization hits can be rapidly improved by creating multiple derivative constructs. Topics included will be:

  • Multi-target selection for protein structure based methods

  • Expression system selection, parallel screening and purification

  • Optimizing crystallization and expression properties through construct design

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Antibody-Antigen and Protein-Nucleic Acid Complexes for X-Ray Crystallography

Date: Feb 21, 2012
Time: 11:00 – 11:50 AM PDT
Alex Burgin, Ph.D. and Doug Davies, Ph.D.

Many biological macromolecules derive their function from interactions with other macromolecules. Understanding these interactions is crucial for developing therapeutics.  Emerald BioStructures is a structural biology Contract Research Organization with extensive experience in elucidating macromolecular complexes including antibody-antigen and protein-nucleic acid complexes. In this Webinar, Emerald scientists will discuss some of the practical issues involved in preparing macromolecular complexes for crystallization and X-ray diffraction experiments. For antibody complexes, issues of Fab preparation, complex formation and analysis will be discussed. Protein-nucleic acid complex formation will be discussed with an emphasis on sourcing and optimizing oligonucleotides for crystallization, with numerous case studies included. This webinar should be of interest to X-ray crystallographers and researchers looking to collaborate with X-ray crystallographers to solve novel macromolecular complex structures.

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Applying Ligand-observe NMR Spectroscopy to Enable Fragment-based Lead Discovery

Date: Nov 15, 2011
Time: 11:00 – 11:50 AM PST
Darren Begley, Ph.D.

Nuclear magnetic resonance (NMR) spectroscopy can provide fast, powerful, and versatile techniques for atomic-level resolution studies of protein-ligand interactions. NMR methods are well-suited to monitor and characterize small molecule-macromolecule interactions for weak-binding compounds, such as those used in fragment-based screening. Data acquired by NMR for protein-ligand interactions in solution can be particularly valuable in cases where structural information on a macromolecular complex is either difficult or impossible to obtain.

In this webinar, several case studies will be used to illustrate information obtainable by NMR, and highlight some of the advantages in using NMR-based, hit-to-lead strategies in comparison to other biophysical methods. We’ll discuss some of the practical aspects of ligand-observe NMR methods for fragment-based screening and lead discovery, including:

•         NMR sample preparation and library assembly
•         Data acquisition and NMR spectra interpretation for primary fragment-based screens
•         Follow-up experiments for hit characterization

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GPCR Expression for Biophysical and Structural Studies

Date: Oct 18, 2011
Time: 11:00 – 11:50 AM PDT
Peter Nollert, Ph.D.

GPCRs (G-protein coupled receptors) play a critical role in cellular signaling at the cell membrane. Although this class of transmembrane proteins has long been identified  as a premier drug target, the availability of samples in quantities and qualities that are sufficient for biophysical and structural studies is often limited. Recent advances in structural and biophysical characterization for a select set of GPCRs have demonstrated that these proteins are indeed amenable to such studies. What are the tools that have enabled the preparation of GPCRs for such studies? This webinar provides insight into the latest advances in methods and techniques that Emerald Biostructures and other membrane protein experts have employed for the expression of this important target molecule class for structural and biophysical methods.

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Using Structural Biology to Exploit Allosteric and Protein: Protein Interactions in Drug Discovery

Date: Sep 20, 2011
Time: 11:00 – 11:50 AM PDT
Alex Burgin, Ph.D.

Abstract: Although traditional structure based drug design has focused on the development of active site inhibitors, considerable efforts are now being devoted to develop small molecule drugs that modulate enzyme activity at allosteric sites.  These allosteric modulators have several important advantages over traditional active site inhibitors.  For example, allosteric modulators can be much more potent than competitive inhibitors when substrate concentrations are high since they do not have to compete with substrate for binding.  In addition, allosteric modulators can often be much more selective than active site inhibitors against enzyme superfamilies with highly conserved active sites.  In this webinar, we will review some of the advantages of allosteric modulators compared to traditional competitive inhibitors using several structurally characterized examples.  In addition, we will provide a description of how structural insights were used to develop the first allosteric modulators of PDE4 and how these small molecules modulate specific protein: protein interactions in vivo.  The important technical aspects of obtaining the first ligand-bound regulatory domain will also be emphasized.  By reviewing several examples of allostery and describing a specific example in some detail (PDE4), we hope to provide a paradigm for how structural biology can enable the discovery of this important class of small molecules.

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