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01-12-2019 | Original Article | Issue 1/2019

Network Modeling Analysis in Health Informatics and Bioinformatics 1/2019

Protein crystallization screening using enhanced associative experimental design

Journal:
Network Modeling Analysis in Health Informatics and Bioinformatics > Issue 1/2019
Authors:
Mahesh Kumar Juttu, Marc L. Pusey, Ramazan S. Aygun
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Abstract

Protein crystallization screening helps determine factors (e.g., salts, pH of buffers, ionic strengths, temperature, and type of precipitants) that are favorable for the formation of a large protein crystal suitable for X-ray crystallography. While existing commercial screens may not generate crystalline outcomes for difficult proteins, their outcomes could be used for recommending novel screens. Current methods for protein crystallization screening such as associative experimental design (AED) process only cocktails having one chemical per reagent while ignoring cocktails with multiple chemicals per reagent. To analyze cocktails having multiple chemicals per reagent, we propose enhanced associative experimental design (AED) that recommends novel crystallization conditions by analyzing the content of successful preliminary crystallization conditions. In wet lab experiments, our enhanced AED (AED\(^+\)) yielded ten new crystalline conditions for Tt189 (Nucleoside diphosphate kinase) in addition to 20 crystalline conditions generated by AED. Moreover, our AED+ allows pairing of crystalline or likely lead outcome with a non-crystalline outcome to generate novel crystalline conditions overcoming the limitation of AED requiring at least two good cocktails having at least one coming reagent.

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