Nanodiamonds as Nucleating Agents for Protein Crystallization

Enhancing Protein Crystal Nucleation Using In Situ Templating on Bioconjugate-Functionalized Nanoparticles and Machine Learning

Although protein crystallization offers a promising alternative to chromatography for lower-cost protein purification, slow nucleation kinetics and high protein concentration requirements are major barriers for using crystallization as a viable strategy in downstream protein purification. Here, we demonstrate that nanoparticles functionalized with bioconjugates can result in an in situ template for inducing rapid crystallization of proteins at low protein concentration conditions. We use a microbatch crystallization setup to show that the range of successful crystallization conditions is expanded by the presence of functionalized nanoparticles. Furthermore, we use a custom machine learning-enabled emulsion crystallization setup to rigorously quantify nucleation parameters. We show that bioconjugate-functionalized nanoparticles can result in up to a 7-fold decrease in the induction time and a 3-fold increase in the nucleation rate of model proteins compared to those in control environments. We thus provide foundational insight that could enable crystallization to be used in protein manufacturing by reducing both the protein concentration and the time required to nucleate protein crystals.

Heterogeneous Nucleation in Protein Crystallization

Protein crystallization was first discovered in the nineteenth century and has been studied for nearly 200 years. Protein crystallization technology has recently been widely used in many fields, such as drug purification and protein structure analysis. The key to successful crystallization of proteins is the nucleation in the protein solution, which can be influenced by many factors, such as the precipitating agent, temperature, solution concentration, pH, etc., among which the role of the precipitating agent is extremely important. In this regard, we summarize the nucleation theory of protein crystallization, including classical nucleation theory, two-step nucleation theory, and heterogeneous nucleation theory. We focus on a variety of efficient heterogeneous nucleating agents and crystallization methods as well. The application of protein crystals in crystallography and biopharmaceutical fields is further discussed. Finally, the bottleneck of protein crystallization and the prospect of future technology development are reviewed.

Magnetic particles used in a new approach for designed protein crystallization

Designed protein crystallization using magnetic particles as additives in the crystallization of model case studies.

Charged polymeric additives affect the nucleation of lysozyme crystals

Charged polymers (PGA and PL) interact with lysozyme and then promote the heterogeneous nucleation of the crystals.

Ag Nanometallic Surfaces for Self-Assembled Ordered Morphologies of Zein

Nanometallic surfaces of Ag nanoparticles (NPs) catalyzed the self-aggregation behavior of zein in different ordered morphologies such as cubes, rectangles, and bars. This was studied in a ternary in situ reaction (AgNO₃ + zein + water), where zein performed the reduction as well as stabilization of Ag NPs. This reaction produced small Ag NPs of less than 10 nm predominantly bound with {111} crystal planes, which attracted the surface adsorption of zein. Surface-adsorbed zein initiated the protein seeding and converted the tertiary structure of protein into open β-pleated structure with aqueous exposed hydrophobic domains. A layered deposition of β-pleats on different crystal planes of Ag NPs derived them to nearly monodispersed cubic morphologies. The mechanistic aspects of self-aggregation of zein in the presence of nanometallic surfaces hold possible scenarios for simple and straightforward routes of protein crystallization.

Structure and Interaction of Nanoparticle-Protein Complexes

The integration of nanoparticles with proteins is of high scientific interest due to the amazing potential displayed by their complexes, combining the nanoscale properties of nanoparticles with the specific architectures and functions of the protein molecules. The nanoparticle-protein complexes, in particular, are useful in the emerging field of nanobiotechnology (nanomedicine, drug delivery, and biosensors) as the nanoparticles having sizes comparable to that of living cells can access and operate within the cell. The understanding of nanoparticle interaction with different protein molecules is a prerequisite for such applications. The interaction of the two components has been shown to result in conformational changes in proteins and to affect the surface properties and colloidal stability of the nanoparticles. In this feature article, our recent studies exploring the driving interactions in nanoparticle-protein systems and resultant structures are presented. The anionic colloidal silica nanoparticles and two globular charged proteins [lysozyme and bovine serum albumin (BSA)] have been investigated as model systems. The adsorption behavior of the two proteins on nanoparticles is found to be completely different, but they both give rise to similar phase transformation from one phase to two phase in respective nanoparticle-protein systems. The presence of protein induces the short-range and long-range attraction between the nanoparticles with lysozyme and BSA, respectively. The observed phase behavior and its dependence on various physiochemical parameters (e.g., nanoparticle size, ionic strength, and solution pH) have been explained in terms of underlying interactions.

Interfacial functional terminals enhance the heterogeneous nucleation of lysozyme crystals

A series of functional terminals were designed to interact with the flexible loop residues of lysozymes, aiming to produce quality protein crystalsviaintensified heterogeneous nucleation.

Protein crystallization: Eluding the bottleneck of X-ray crystallography

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.