Protein Crystallization Screening Using Associative Experimental Design

Abstract

Protein crystallization remains a highly empirical process. The purpose of protein crystallization screening is the determination of the main factors of importance leading to protein crystallization. One of the major problems about determining these factors is that screening is often expanded to many hundreds or thousands of conditions to maximize combinatorial chemical space coverage for a successful (crystalline) outcome. In this paper, we propose a new experimental design method called “Associative Experimental Design (AED)” that provides a list of screening factors that are likely to lead to higher scoring outcomes or crystals by analyzing preliminary experimental results. We have tested AED on Nucleoside diphosphate kinase, HAD superfamily hydrolase, and nucleoside kinase proteins derived from the hyperthermophile Thermococcus thioreducens [1]. After obtaining the candidate novel conditions, we have confirmed that AED method yielded high scoring crystals after experimenting in a wet lab.