Predicting recombinant protein expression experiments using molecular dynamics simulation

Available online 2 October 2014Soluble expression of de novo-designed proteins in Escherichia coli (E. coli) remains empirical. For given experimental conditions expression success is determined in part by protein primary sequence. This has been previously explored with varying success using a variety of statistical solubility prediction tools though without taking fold stability into account. In the present study, the three-dimensional structure of proteins in molecular dynamics (MD) simulations is used to predict expression as a new approach with a set of four-helix bundles. Stability-related parameters for ten structures were determined in a thermal unfolding MD simulation and used to build statistical models with a support vector machine (SVM) classifier. The most accurate models were identified by their performance on five independent four-helix bundle sequences. The final model provided accurate classification prediction for this test set and was successfully applied in a model challenge with two newly designed sequences. The combination of simulation-derived parameters and an SVM classifier has potential to predict recombinant expression outcome for this set of four-helix bundles. With further development, this approach of utilizing higher-dimensional protein structural information to predict expression may have potential to advance recombinant biotechnology through modern computational and statistical science.Andrea Schaller, Natalie K.Connors, Stefan A. Oelmeier, Jürgen Hubbuch, Anton P.J. Middelber

Computational study of elements of stability of a four-helix bundle protein biosurfactant

Biosurfactants are surface-active molecules produced principally by microorganisms. They are a sustainable alternative to chemically-synthesized surfactants, having the advantages of being non-toxic, highly functional, eco-friendly and biodegradable. However they are currently only used in a few industrial products due to costs associated with production and purification, which exceed those for commodity chemical surfactants. DAMP4, a member of a four-helix bundle biosurfactant protein family, can be produced in soluble form and at high yield in Escherichia coli, and can be recovered using a facile thermal phase-separation approach. As such, it encompasses an interesting synergy of biomolecular and chemical engineering with prospects for low-cost production even for industrial sectors. DAMP4 is highly functional, and due to its extraordinary thermal stability it can be purified in a simple two-step process, in which the combination of high temperature and salt leads to denaturation of all contaminants, whereas DAMP4 stays stable in solution and can be recovered by filtration. This study aimed to characterize and understand the fundamental drivers of DAMP4 stability to guide further process and surfactant design studies. The complementary use of experiments and molecular dynamics simulation revealed a broad pH and temperature tolerance for DAMP4, with a melting point of 122.4 °C, suggesting the hydrophobic core as the major contributor to thermal stability. Simulation of systematically created in silico variants of DAMP4 showed an influence of number and location of hydrophilic mutations in the hydrophobic core on stability, demonstrating a tolerance of up to three mutations before a strong loss in stability occurred. The results suggest a consideration of a balance of stability, functionality and kinetics for new designs according to their application, aiming for maximal functionality but at adequate stability to allow for cost-efficient production using thermal phase separation approaches.Andrea Schaller, Natalie K. Connors, Mirjana Dimitrijev Dwyer, Stefan A. Oelmeier, Jürgen Hubbuch, Anton P.J. Middelber

Evidence for the Interactions Occurring Between Ionic Liquids and Tetraethylene Glycol in Binary Mixtures and Aqueous Biphasic Systems

The well-recognized advantageous properties of poly(ethylene glycol)s (PEGs) and ionic liquids (ILs) in the context of an increasing demand for safe and efficient biotechnological processes has led to a growing interest in the study of their combinations for a wide range of procedures within the framework of green chemistry. Recently, one of the most promising and attractive applications has been the novel IL/polymer-based aqueous biphasic systems (ABS) for the extraction and purification of biomolecules. There still lacks, however, a comprehensive picture of the molecular phenomena that control the phase behavior of these systems. In order to further delve into the interactions that govern the mutual solubilities between ILs and PEGs and the formation of PEG/IL-based ABS, H-1 NMR spectroscopy in combination with classical molecular dynamics (MD) simulations performed for binary mixtures of tetraethylene glycol (TEG) and 1-alkyl-3-methylimidazolium-chloride-based ILs and for the corresponding ternary TEG/IL/water solutions, at T = 298.15 K, were employed in this work. The results of the simulations show that the mutual solubilities of the ILs and TEG are mainly governed by the hydrogen bonds established between the chloride anion and the -OH group of the polymer in the binary systems. Additionally, the formation of IL/PEG-based ABS is shown to be controlled by a competition between water and chloride for the interactions with the hydroxyl group of TEG