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Feature Articles : Sep 1, 2006 (Vol. 26, No. 15)

Protein Crystallization in Pharma Research

Refinements of the Technology Are Taking Place Very Quickly
  • Elizabeth Lipp

While the drug pipeline narrows, pharmaceutical companies are broadening their options by ruling nothing out. Protein crystallization technology is proving to be a valuable tool.

“The trial and error involved in drug discovery is risky from a financial and scientific standpoint,” says Roland Durner, global product manager, biopharma at Tecan (www.tecan.com). “That is why our customers try a more rational approach to drug discovery.”

Protein crystallization has two roles in the pharmaceutical industry: for structural biology applications involving in silico drug design and for controlled drug delivery. In the first application, protein crystallography ascertains the 3-D structure of a molecule. Producing better quality crystals will result in more accurate 3-D protein structures. This leads to a more precise understanding of biological function and improved drug design.

Scientist-driven Innovation

“The goal of protein crystallography is to crystallize purified protein so that its 3-D structure can be determined by x-ray diffraction,” Durner notes. “The trick here is to bring the protein to crystallize. In all the common vapor diffusion approaches you need to screen for suitable crystallization conditions. This is what we help our customer do. We don’t do the analysis of the crystal but we support scientists to get crystals in the first place.”

Tecan focuses on the liquid handling of crystallization buffers and proteins, offering versatile liquid-handling platforms and flexible robotic workstations serving a full range of life science applications. Its Freedom EVO platform delivers flexibility and possibilities for expansion. Powered by CrysScreen software for experiment set-up and Freedom EVOware for robotic control, each workstation can be equipped with a wide choice of robotic arms, liquid-handling tools, and application options. CrysScreen is the company’s application-specific user interface for defining and pipetting buffers, screening grids, and for preparing complete crystallization experiments.

Tecan’s Freedom EVO protein crystallography workstation is a can be configured for semi- or complete automation of hanging drop, sitting drop, and microbatch protein crystallography experiments, according to the company. A large dynamic pipetting range enables the protein crystallography workstation to dispense both mother liquors and precious protein samples with superior accuracy and precision. For maximum capability and throughput, an array of devices, including barcode scanners, microplate sealers, dynamic light-scattering readers, incubation, and imaging systems can be integrated into the system.

The thrust of automating all processes related to protein crystallography focuses greatly on the liquid handling. “When you have a typical initial screen of several hundred different conditions, it can take a while to set up,” Durner states. “There are always liquids involved with widely differing characteristics, used in quantities varying between nanoliters to milliliters. Accurate and reproducible grid gradients of concentrations and pH need to be prepared. That is exactly what we do: We will create thousands of different conditions to screen—automatically.”

Bruker AXS (www.bruker-axs.com) is a little further down the line, after you have the crystal, says Cary Bauer, senior applications scientist, single crystal diffraction. “We recently introduced the Crystal Farm Imaging System as a means of getting in and automating the whole process of protein crystallization from start to finish.” The Crystal Farm imaging system automates protein crystallization by integrating incubation at chosen temperatures together with optical imaging of the crystal growth plates at prescheduled intervals. This accelerates the process of growing diffraction-quality protein crystals. Crystals harvested from the Crystal Farm are then characterized using a Bruker AXS Proteum x-ray system.

For high-throughput applications, this includes the latest high-brilliance Microstar x-ray source, a highly sensitive and fast readout Proteum CCD detector, as well as a BruNo robotic sample handler, Bauer explains. The system is driven by the Proteum software suite, which contains new modules for determining crystal quality. The Proteum suite provides a simple, robust interface for automated sample screening and data collection.

“The only drawback is that a person has to pick that crystal up; that is the only break in the automation chain,” says Bauer. “The next big trend will be collecting data automatically. We call this the FedEx approach to data collection.”

That break in the automation change is about to disappear with Bruker’s introduction of the Universal Micromanipulation Robot, or UMR. “It is an automated crystal looping robot,” Bauer says. “The last step in automating the entire process of x-ray crystallography is getting the crystal into a loop, which is a very small sample holder, on the order of 200 microns. The UMR is the first attempt at automating this process. We are now able to have a human drive the robot to pick up a sample. Soon, we will be able to completely automate the process and have the robot find and mount a crystal in the loop with no human intervention.

“The process of protein crystallization is very data driven,” says Paige Vinson, Ph.D., applications scientist at Thermo Electron (www.thermo.com). In this data-centric approach, data sharing, desire to glean value from all data, and the ability for companies to compete in a highly agile market place are all driving the push for pharmaceutical companies to get more value from the data they produce.

Thermo Electron hence supplies a fully automated protein crystallization system that is wrapped around an extensive set of software that was in part developed by the scientists who use it. “The Thermo system is an integrated system—plate prep, imagery, data storage—it is all connected, all together. And we focused a lot at the data end. We designed our products so that they could all be tied together in a seamless fashion, where everything runs off one database.”

In addition to accessibility to data from remote locations, challenges include network security and speed, high access rates from automation applications, database query optimization, which include heavy-weight queries from scientific users performing data mining and reporting. “Database interface must be developed for everything, including instruments and applications,” Dr. Vinson adds.

Cross Pollination of Technologies

If you thought integrated fluidic circuits were something that was strictly part of the semiconductor domain, Fluidigm (www.fluidigm.com) wants you to think again. The company is using the same fabrication methods that once went into making electronic circuits to now make devices for regulating nanoscale quantities of fluids. These devices are fabricated with a networked array of discrete pathways and intermediate switches. Instead of electrons, they move molecules of biological samples and reagents in a dazzling variety of patterns.

“By utilizing the precision of the IFC architecture rather than robotics and liquid handlers to mix together the reagents and sample, we hope to take a lot of the voodoo out of the crystallization process, relying on technology instead of trick to get the protein to crystallize,” says Kevin Farrell, TOPAZ product line manager at Fluidigm.

Fluidigm’s TOPAZ system for crystallization consists of chips, reagents, hardware, and software and it simplifies and automates nanoscale-free interface diffusion—a method that samples a broader chemical space than conventional approaches.

Coupled with automated inspection and scoring, the TOPAZ System provides a method for highly efficient discovery and a straightforward path to diffraction-quality crystals. Fluidigm continues to improve system performance through higher density chips, specialized reagent sets, and protocols in areas, such as co-crystallization, optimization, and sample preparation.

This system figured prominently in expediting the structure determination for the hemagglutinin (HA) of the H5N1 avian flu virus in June. It allows efficient identification of initial leads for solving the HA structure, explains Farrell.

“The chip technology has shown promising results in generating high-quality leads for important targets. The TOPAZ X.96 screening chips allow users to run up to 768 experiments simultaneously with less than 10 microliters of protein. This ultralow sample requirement is providing researchers with new opportunities to streamline their crystallography workflow by running more samples in parallel and in doing so improve their success rate in solving structures.

Cell-free Drug Discovery

Another factor impacting methods of drug discovery is as simple and basic as the bottom line. “Cell-free protein expression is a much faster and a more economic way to produce protein,” notes Frank Schaefer, associate director of R&D at Qiagen(www.qiagen.com). “All you need is an incubator to produce milligrams of proteins within few hours, and much of this work you can do at your benchtop. The EasyXpress Mini and Mega kits enable a streamlined workflow of successive expression screening and production steps.”

Qiagen’s systematic organization of reagent mixtures in its suites offers an effective method for finding trends that may lead to diffracting crystals. The company’s Pre-Screen Assay is arranged in three mini-grids (six conditions each), with one mini-grid for each precipitant type.

Using two concentrations of the same chemical, a direct relation can be observed between protein concentration, precipitant concentration, and precipitant chemical family. Results are divided between insoluble (precipitation in most cases) and soluble (clear drops). By analyzing the results of the assay, the concentration of protein to be used in initial screening versus most popular chemical families can be easily determined.

Each suite consists of 96 distinct screening conditions and offers a wide range of prefilled kits and bulk formats. Each Screening Suite condition is individually available as a large-volume Refill-Hit Solution.

Alternatively, stock solutions and recipes can be used to reproduce original conditions using a liquid-handling instrument. Stock solutions are also certified by detailed production reports.

A highly diffracting protein crystal is the starting point for x-ray structural analysis of proteins. “Success in crystallization has much to do with reproducibility of results. Therefore, an important point to remember is that all of our quality control data for each individual lot we produce is available online,” Schaefer notes. “This is extremely helpful for customers to track in order to ensure the reproducibility of their data.”