Octamer formation in lysozyme solutions at the initial crystallization stage detected by small-angle neutron scattering

A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis

Lack of controls and understanding in nucleation, which proceeds crystal growth and other phase transitions, has been a bottleneck challenge in chemistry, materials, biology, and other fields. The exemplary needs for better methods for biomacromolecule crystallization include (1) synthesizing crystals for high-resolution structure determinations in fundamental research and (2) tuning the crystal habit and thus the corresponding properties in materials and pharmaceutical applications. Herein, a deterministic method is established capable of sustaining the nucleation and growth of a single crystal using the protein lysozyme as a prototype. The supersaturation is localized at the interface between a sample and a precipitant solution, spatially confined by the tip of a single nanopipette. The exchange of matter between the two solutions determines the supersaturation, which is controlled by electrokinetic ion transport driven by an external potential waveform. Nucleation and subsequent crystal growth disrupt the ionic current limited by the nanotip and are detected. The nucleation and growth of individual single crystals are measured in real time. Electroanalytical and optical signatures are elucidated as feedbacks with which active controls in crystal quality and method consistency are achieved: five out of five crystals diffract at a true atomic resolution of up to 1.2 Å. As controls, those synthesized under less optimized conditions diffract poorly. The crystal habits during the growth process are tuned successfully by adjusting the flux. The universal mechanism of nano-transport kinetics, together with the correlations of the diffraction quality and crystal habit with the crystallization control parameters, lay the foundation for the generalization to other materials systems.

The Relationship of Precursor Cluster Concentration in a Saturated Crystallization Solution to Long-Range Order During the Transition to the Solid Phase

A model for the transition from disordered liquid state to the solid phase has been proposed based on establishing a correlation between the concentration of precursor clusters in a saturated solution and the features of solid phase formation. The validity of the model has been verified experimentally by simultaneously studying the oligomeric structure of lysozyme protein solutions and the peculiarities of solid phase formation from these solutions. It was shown that no solid phase is formed in the absence of precursor clusters (octamers) in solution; perfect monocrystals are formed at a small concentration of octamers; mass crystallization is observed with an increasing degree of supersaturation (and concentration of octamers); further increase in octamer concentration leads to the formation of an amorphous phase.

Identification of the Precursor Cluster in the Crystallization Solution of Proteinase K Protein by Molecular Dynamics Methods

It is known that precursor clusters appear in solution prior to protein crystallization. For proteinase K, as it was found by SAXS, such clusters are dimers, but the accuracy of the method did not allow for determining its type. In this work, the behavior of six possible types of precursor clusters was simulated by the molecular dynamics technique. Stability analysis revealed the most probable type of dimer formed in the proteinase K solution before its crystallization. SAXS data modelling also supported the MD calculations. The dynamics of this precursor cluster was modeled at three temperatures: 20, 30, and 40 °C. At 40 °C, an abnormal increase in the stability of the thermophilic proteinase K was found.

Influence of Chlorides of Mono- and Divalent Metals on the Oligomeric Composition of Lysozyme Crystallization Solutions and Further Crystal Growth

Abstract

The influence of the precipitant type (LiCl, NaCl, KCl, NiCl2, and CuCl2) on the formation of oligomers (dimers and octamers) in lysozyme crystallization solutions at two protein concentrations has been investigated by small-angle X-ray scattering (SAXS). The same solutions have been used to grow crystals in order to reveal the influence of the oligomeric composition on the crystal growth. The data obtained in this and previous studies on the influence of precipitant concentration yield an inversely proportional dependence of the total content of octamers and dimers on the cation atomic number, which is in agreement with the increase in the ion activity in the lyotropic series for Li+, Na+, and K+ and the increase in the ionic radius for Li+, Na+, K+, Ni2+, and Cu2+. It is shown that a decrease in the protein concentration in a crystallization solution leads to a decrease in octamer volume fraction at an invariable volume fraction of dimers and reduces the probability of crystal formation.

The binding of precipitant ions in the tetragonal crystals of hen egg white lysozyme

The bonds between lysozyme molecules and precipitant ions in single crystals grown with chlorides of several metals are analysed on the basis of crystal structure data. Crystals of tetragonal hen egg lysozyme (HEWL) were grown with chlorides of several alkali and transition metals (LiCl, NaCl, KCl, NiCl₂ and CuCl₂) as precipitants and the three-dimensional structures were determined at 1.35 Å resolution by X-ray diffraction method. The positions of metal and chloride ions attached to the protein were located, divided into three groups and analysed. Some of them, in accordance with the recently proposed and experimentally confirmed crystal growth model, provide connections in protein dimers and octamers that are precursor clusters in the crystallization lysozyme solution. The first group, including Cu⁺², Ni⁺² and Na⁺¹ cations, binds specifically to the protein molecule. The second group consists of metal and chloride ions bound inside the dimers and octamers. The third group of ions can participate in connections between the octamers that are suggested as building units during the crystal growth. The arrangement of chloride and metal ions associated with lysozyme molecule at all stages of the crystallization solution formation and crystal growth is discussed.Communicated by Ramaswamy H. Sarma.