Emerald Biostructures, Incorporated

University of Washington

Decode Biostructures, Inc.

Lansing J Stewart

Hidong Kim

Kathryn Hjerrild

Paul M Dunn

Alex Burgin

Robin Clark

Alexandrina Muntianu

Lucius B C A Fleuchaus

Steven H Sarfaty

John W Walchli

Wim G J Hol

Pieces of software and databases are used to facilitate the design and synthesis of genes. The synthesis techniques allow identification, quantification, transcription, translation, and manipulation of portions of the gene sequence represented as 0's and 1's in a computing system. These pieces of software and databases compile constraint information provided by a user to create synthetic genes to express proteins lacking disordered or variable regions and containing surface mutations that promote solubility and/or crystallization. Regions of the gene sequence that do not form stable structures can be removed and replaced by a short biological linker to improve crystallization of proteins.

Gene synthesis software

This invention relates to crystallization based assays for identifying ligands that bind to a macromolecule.

Screening methods for identifying ligands

A matrix mixing robot includes a plurality of precision pumps (such as precision syringe pumps), a distributor and a processor system. Each pump, under the control of the processor system, draws an associated stock solution from a stock solution source, and pumps the drawn stock solution out through an outlet. The distributor, also under the control of the processor system, directs a stock solution from a particular pump outlet to a selected solution receptacle. A multi-port distribution valve may be associated with each precision pump. Each valve, under control of the processor system, can connect its associated pump to one the pump's inlets or outlets.

Robot for mixing crystallization trial matrices

Disclosed is a system and a method for depositing crystallization observations into a relational database. The system includes a computer, microscope, and a headset having a microphone and headphones. Crystallization observations are deposited into the database by verbal commands. Verbal commands also drive the crystallization apparatus plates to position the apparatus wells within the microscope field of vision. The system is integrated with a software application which enables the user to build the trials, matrices, solutions, and macromolecules to be used in the crystallization trials. The user is guided through the crystallization trial setup by a multitude of managers and builders of the software application. The software application also provides numerous tools to query the database and display results in a multitude of formats.

Method and system for creating a crystallization results database

In one aspect, the present invention provides crystallization solutions useful for crystallizing proteins and other molecules, especially macromolecules. In a presently preferred embodiment, the crystallization solutions of the invention are combined as four crystallization solution sets. Each of the four crystallization solution sets includes forty eight different crystallization solutions. Each individual crystallization solution includes a precipitant and a buffer, and optionally includes at least one additive. In another aspect, the present invention provides kits including a plurality of crystallization solutions of the present invention and at least one crystallization plate that preferably includes a plurality of reservoirs. Preferably the crystallization solutions are disposed within the reservoirs of the crystallization plates.

Crystallization media

The present invention provides a crystallization unit including a solvent reservoir in gaseous communication with a plurality of chambers. Preferably, a plurality of crystallization units are arrayed in the form of a crystallization tray. A first preferred embodiment of the present invention provides a crystallization tray 10 including a rectangular array of crystallization units 26. Each crystallization unit includes a central reservoir 28 and four drop chambers 32 arranged in a cruciform configuration around central reservoir 28. Each drop chamber 32 is connected to central reservoir 28 by a diffusion channel 30. Each drop chamber 32 also includes a shoulder which is capable of supporting a cover slip from which a drop of solution, containing the substance to be crystallized, can be suspended. A second preferred embodiment of the present invention is identical to the first preferred embodiment except that central reservoir 28 is divided into four equal sections by dividers extending vertically from the bottom of central reservoir 28.

Growing community of inventors

Bainbridge Island, WA, United States of America

Lansing J Stewart