Graphene Quantum Dots as Nucleants for Protein Crystallization

Abstract

Structural analysis of proteins using X-ray crystallography is crucial for discovering their biochemical functionalities. However, growing X-ray-quality crystals of proteins is often a challenging task that requires complicated and tedious processes, especially for the formation of crystalline seeds in the early stage of the process. In the present study, graphene quantum dots (GQDs) were investigated as a nanomaterial nucleant for protein crystallization in the aspects of the process accelerations and their possible underlying mechanisms, where lysozyme was employed for a model system. Compared to that without GQDs, dramatically faster formation of crystalline seeds was observed in the presence of GQDs within 2 h of incubation. The hydrodynamic size of lysozyme increased by about 30% when GQDs were included according to dynamic light scattering measurements, implying a possible binding of GQDs to the protein. X-ray diffraction analysis of lysozyme crystals also implies the possible binding of GQDs to the protein by showing reduced thermal B-factors when GQDs were included, suggesting flexibility reducing interactions of GQDs with random coil sites. In spite of the prevalent existence of GQDs in the crystal, the X-ray structural analysis cell parameters of lysozyme grown with GQDs showed negligible differences compared to those grown without GQDs, suggesting that GQDs might be an ideal nucleant for protein crystallization.

Silica Nanoparticles-Induced Lysozyme Crystallization: Effects of Particle Sizes

“…The crystal formed at such conditions is considered to exhibit a tetragonal morphology [21][22][23][24]. As stated in other works, no significant effect on the structure of lysozyme crystals was discovered when nanoparticles such as gold particles or carbon quantum dots (GQDs) were used as nucleating agents [12,25]. Therefore, it is speculated here that the addition of nanoparticles may not alter the lysozyme crystal assembly process and that the lysozyme crystals obtained belong to a tetragonal morphology.…”

Practical techniques for protein crystallization: additive assistance and external field intensification

“…32,33 ILs, MIPs, and DESs are important additives having more effective properties which are different from those of traditional additives, such as degradability and designability. Some other additives have been reported for protein crystallization, such as graphene quantum dots, 45 carbon-nanotube-based materials, 46 and rough well surfaces. 47 There are detailed reviews of this subject.…”

Heterogeneous Nucleation in Protein Crystallization

“…It has been reported that nanomaterials in the form of aggregates or films could improve the crystallization efficiency of all proteins [ 58 , 59 ]. Nanodiamond (ND) is a kind of carbon-based nanomaterial that has extensive biological application potential [ 60 ]. One such application is to promote the nucleation of protein crystals in aqueous solutions ( Figure 5 ) [ 59 ].…”