A model-based approach for mining membrane protein crystallization trials.
BACKGROUND
Membrane proteins are known to play crucial roles in various cellular functions. Information about their function can be derived from their structure, but knowledge of these proteins is limited, as their structures are difficult to obtain. Crystallization has proved to be an essential step in the determination of macromolecular structure. Unfortunately, the bottleneck is that the crystallization process is quite complex and extremely sensitive to experimental conditions, the selection of which is largely a matter of trial and error. Even under the best conditions, it can take a large amount of time, from weeks to years, to obtain diffraction-quality crystals. Other issues include the time and cost involved in taking multiple trials and the presence of very few positive samples in a wide and largely undetermined parameter space. Therefore, any help in directing scientists' attention to the hot spots in the conceptual crystallization space would lead to increased efficiency in crystallization trials.


RESULTS
This work is an application case study on mining membrane protein crystallization trials to predict novel conditions that have a high likelihood of leading to crystallization. We use suitable supervised learning algorithms to model the data-space and predict a novel set of crystallization conditions. Our preliminary wet laboratory results are very encouraging and we believe this work shows great promise. We conclude with a view of the crystallization space that is based on our results, which should prove useful for future studies in this area.
Asur
Sitaram
S
Department of Computer Science and Engineering, Ohio State University, USA. srini@cse.ohio-state.edu
Raman
Pichai
P
Otey
Matthew Eric
ME
Parthasarathy
Srinivasan
S
D000465:Algorithms; D003198:Computer Simulation; D003460:Crystallization / Q000379:methods*; D003461:Crystallography / Q000379:methods; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry / Q000648:ultrastructure; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods*
D008565:Membrane Proteins; D046912:Multiprotein Complexes