Single-crystal – oriented-crystal – and epitaxy growth processes; – Processes of growth from liquid or supercritical state – Having growth from a solution comprising a solvent which is...
Reexamination Certificate
2000-08-02
2004-11-02
Kunemund, Robert (Department: 1765)
Single-crystal, oriented-crystal, and epitaxy growth processes;
Processes of growth from liquid or supercritical state
Having growth from a solution comprising a solvent which is...
C117S069000, C117S927000
Reexamination Certificate
active
06811608
ABSTRACT:
FIELD OF THE INVENTION
This invention relates to the crystallization of molecules, in particular, to a method and system for capturing a large number of crystallization trial observations and creating a relational database based on the trial observations.
BACKGROUND OF THE INVENTION
Macromolecular x-ray crystallography is an essential aspect of modern drug discovery and molecular biology. Using x-ray crystallographic techniques, the three-dimensional structures of biological macromolecules, such as proteins, nucleic acids, and their various complexes, can be determined at practically atomic level resolution. The enormous value of three-dimensional information has led to a growing demand for innovative products in the area of protein crystallization, which is currently the major rate limiting step in x-ray structure determination.
One of the first and most important steps of the x-ray crystal structure determination of a target macromolecule is to grow large, well diffracting crystals with the macromolecule. As techniques for collecting and analyzing x-ray diffraction data have become more rapid and automated, crystal growth has become a rate limiting step in the structure determination process.
Vapor diffusion is the most widely used technique for crystallization in modern macromolecular x-ray crystallography. In this technique, a small volume of the macromolecule sample is mixed with an approximately equal volume of a crystallization solution. The resulting drop of liquid (containing macromolecule and dilute crystallization solution) is sealed in a chamber with a much larger reservoir volume of the crystallization solution. The drop is kept separate from the reservoir, either by hanging from a glass cover slip or by sitting on a tiny pedestal. Over time, the crystallization drop and the reservoir solutions equilibrate via vapor diffusion of the volatile species. Supersaturating concentrations of the macromolecule are achieved, resulting in crystallization in the drop when the appropriate reservoir solution is used.
The process of growing biological macromolecule crystals remains, however, a highly empirical process. Macromolecular crystallization is a hyperdimensional phenomena, dependent on a host of experimental parameters including pH, temperature, and the concentration of salts, macromolecules, and the particular precipitating agent (of which there are hundreds). A sampling of this hyperspace, via thousands of crystallization trials, eventually leads to the precise conditions for crystal growth. Thus, the ability to rapidly and easily generate many crystallization trials is important in determining the right conditions for crystallization. Also, since so many multidimensional data points are generated in these crystallization trials, it is imperative that the experimenter be able to accurately record and analyze the data so that promising conditions are pursued, while no further time, resources, and effort are spent on negative conditions.
Recently, an international protein structure initiative has taken shape with the goal of determining the three dimensional structures of all representative protein folds. This massive undertaking in structural biology which may some day rival the human genome sequencing project in size and scope, is estimated to require a minimum of 100,000 x-ray structure determinations of newly discovered proteins for which no structural information is currently available or predicted. For perspective, the total number of reported novel crystal structures determined to date (spanning nearly 50 years of work) is only approximately 10,000.
Using existing methods for the crystallization of proteins (random screens of conditions) the protein structure initiative will require a minimum of approximately 100 million crystallization trials. In addition the biological information gleaned from genomic research in the protein structure initiative are expected to create even more demand for structural information. Specifically, the biotechnology and pharmaceutical industries are estimated to require upwards of ten fold more protein crystallization experiments (one billion) as a result of research and structure based drug design and the use of crystallized therapeutic proteins. This would require that each of the approximately 500 macromolecular crystallography labs worldwide be responsible for setting up approximately 2000 crystallization trials every working day of the year for five years. Currently, there is no known device available for collecting for analysis macromolecular crystallization data on this scale. Thus, there is a need for a device that permits the efficient capture and storing of large amounts of crystallization trial data information.
SUMMARY OF THE INVENTION
The present invention is directed to a providing a system and method for capturing large amounts of crystallization trial data and storing the captured data in a relational database for subsequent analysis. The preferred implementation of the present invention includes software having a plurality of database managers. Preferably, the database managers include a trial manager, a solution manager, a matrix manager, a compound buffer manager, a chemical manager, an apparatus manager, a subunit manager, a macromolecule manager, a macromolecule formulation manager, a complex macromolecule formulation manager, a manufacturer manager, a collaborator manager, a project manager, and a user manager. Preferably, the software also includes query tools for mining the database and a database object manager for managing database objects. To assist a user of the database, preferably, the software also includes a help tool for managing help documentation. In essence, the software provides a crystallographer with a graphical user interface (GUI) to facilitate the entry of relevant data into a relational database. In addition, to the software, the presently preferred implementation of the present invention includes a trial observation system; i.e., a microscope for viewing the results of crystallization trials; and, preferably, a positioning mechanism for positioning the results of multiple crystallization trials within the observation area of the trial observation system.
In accordance with other aspects of this invention, the software resides in a computer having a central processing unit (CPU) and a memory.
In accordance with further aspects of the invention, the trial manager includes a sequence of executable steps that causes the computer to launch “builders” to guide the user through the initial setup of the trials in order to arrive at the ultimate goal of collecting crystallization trial data for storage in a relational database. The builders include a crystallization trial builder that, in its normal mode, captures all aspects of a crystallization trial in which all crystallization drops receive the same composition of macromolecule formulations and other solutions together with a specified volume of crystallant from each of the crystallants that comprise a specified crystallization matrix. A GUI builder takes the user through all necessary steps required to set up a crystallization trial.
In accordance with further aspects of this invention, the information captured by the crystallization, trial builder includes, but is not limited to information such as: a unique trial ID, a project name, gas purge information (specifies the use of gasses to bathe the crystallization setup), temperature (the temperature at which the crystallization trial will be conducted), temperature units, reservoir volume, reservoir volume units, preparation date, an oil overlay specification (oil can be chosen and the volume specified for the placement of oil on top of the crystallization drop or on top of the reservoir solution), oil overlay units, the order of addition and volume of macromolecule formulations and other solutions that are added to the crystallization drop including the volume of the crystallant that is added to the crystallization drop, barcode IDs for each crystallization apparatus that is used in the trial
Dunn Paul M.
Fleuchaus Lucius B. C. A.
Kim Hidong
Stewart Lansing J.
Christensen O'Connor Johnson & Kindness PLLC
Emerald Biostructures, Inc.
Kunemund Robert
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