Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme

Ice formation and solvent nanoconfinement in protein crystals

Ice formation within protein crystals is a major obstacle to the cryocrystallographic study of protein structure, and has limited studies of how the structural ensemble of a protein evolves with temperature in the biophysically interesting range from ∼260 K to the protein-solvent glass transition near 200 K. Using protein crystals with solvent cavities as large as ∼70 Å, time-resolved X-ray diffraction was used to study the response of protein and internal solvent during rapid cooling. Solvent nanoconfinement suppresses freezing temperatures and ice-nucleation rates so that ice-free, low-mosaicity diffraction data can be reliably collected down to 200 K without the use of cryoprotectants. Hexagonal ice (Ih) forms in external solvent, but internal crystal solvent forms stacking-disordered ice (Isd) with a near-random stacking of cubic and hexagonal planes. Analysis of powder diffraction from internal ice and single-crystal diffraction from the host protein structure shows that the maximum crystallizable solvent fraction decreases with decreasing crystal solvent-cavity size, and that an ∼6 Å thick layer of solvent adjacent to the protein surface cannot crystallize. These results establish protein crystals as excellent model systems for the study of nanoconfined solvent. By combining fast cooling, intense X-ray beams and fast X-ray detectors, complete structural data sets for high-value targets, including membrane proteins and large complexes, may be collected at ∼220-240 K that have much lower mosaicities and comparable B factors, and that may allow more confident identification of ligand binding than in current cryocrystallographic practice.

Thermal contraction of aqueous glycerol and ethylene glycol solutions for optimized protein-crystal cryoprotection

The thermal contraction of aqueous cryoprotectant solutions on cooling to cryogenic temperatures is of practical importance in protein cryocrystallography and in biological cryopreservation. In the former case, differential contraction on cooling of protein molecules and their lattice relative to that of the internal and surrounding solvent may lead to crystal damage and the degradation of crystal diffraction properties. Here, the amorphous phase densities of aqueous solutions of glycerol and ethylene glycol at T = 77 K have been determined. Densities with accuracies of <0.5% to concentrations as low as 30%(w/v) were determined by rapidly cooling drops with volumes as small as 70 pl, assessing their optical clarity and measuring their buoyancy in liquid nitrogen-argon solutions. The use of these densities in contraction matching of internal solvent to the available solvent spaces is complicated by several factors, most notably the exclusion of cryoprotectants from protein hydration shells and the expected deviation of the contraction behavior of hydration water from bulk water. The present methods and results will assist in developing rational approaches to cryoprotection and an understanding of solvent behavior in protein crystals.

Crystal Dehydration in Membrane Protein Crystallography

Crystal dehydration has been successfully implemented to facilitate the structural solution of a number of soluble and membrane protein structures over the years. This chapter will present the currently available tools to undertake controlled crystal dehydration, focusing on some successful membrane protein cases. Also discussed here will be some practical considerations regarding membrane protein crystals and the relationship between different techniques in order to help researchers to select the most suitable technique for their projects.

Analysis of tryptophan surface accessibility in proteins by MALDI-TOF mass spectrometry

Surface accessible amino acids can play an important role in proteins. They can participate in enzyme's active center structure or in specific intermolecular interactions. Thus, the information about selected amino acids' surface accessibility can contribute to the understanding of protein structure and function. In this paper, we present a simple method for surface accessibility mapping of tryptophan side chains by their chemical modification and identification by MALDI-TOF mass spectrometry. The reaction with 2-hydroxy-5-nitrobenzyl bromide, a common and highly specific covalent modification of tryptophan, seems to be very useful for this purpose. The method was tested on four model proteins with known spatial structure. In the native proteins (1) only surface accessible tryptophan side chains were found to react with the modification agent and (2) no buried one was found to react at lower reagent concentrations. These results indicate that the described method can be a potent tool for identification of surface-located tryptophan side chain in a protein of unknown conformation.

Prevention of interfacial inactivation of enzymes by coating the enzyme surface with dextran-aldehyde

Interactions between soluble enzymes and interfaces of organic solvent drops or gas bubbles have a very negative effect on the operational stability of the soluble enzymes. In this study, the formation of a hydrophilic shell around the enzyme has been attempted using dextran-aldehyde which would prevent the interaction between enzyme and hydrophobic interfaces with minimal modification of the enzyme surface. After optimizing the size of the dextran (that was found to play a critical role), three different enzymes (glucose oxidase, d-amino acid oxidase, and trypsin) have been conjugated with dextran-aldehyde and their stability towards organic-aqueous and air-liquid interfaces has been evaluated. The treatment itself proved to be very low-cost in terms of activity and was highly stabilizing for the three enzymes assayed. The conjugated preparation of the three assayed enzymes remained fully active in the presence of air-liquid interfaces for at least 10h. However, the unmodified enzymes lost more than 50% of activity within the first hour of the experiments except for trypsin which kept 38% activity after 12h while the trypsin dextran-aldehyde conjugate maintained 100% enzyme activity. Similar results were achieved in the presence of stirred organic solvent-aqueous buffer biphasic system, although in this case some activity was lost by the action of the soluble portion of the organic solvent. In fact, this treatment seems to be also effective to improve the resistance to the action of organic solvent.

Trehalose-protein interaction in aqueous solution

A variety of sugars are known to enhance the stability of biomaterials. Trehalose, a nonreducing disaccharide composed of two alpha, alpha(1 --> 1)-linked D-glucopyranose units, appears to be one of the most effective protectants. Both in vivo and in vitro, trehalose protects biostructures such as proteins and membranes from damage due to dehydration, heat, or cold. However, despite the significant amount of experimental data on this disaccharide, no clear picture of the molecular mechanism responsible for its stabilizing properties has emerged yet. Three major hypotheses (water-trehalose hydrogen-bond replacement, coating by a trapped water layer, and mechanical inhibition of the conformational fluctuations) have been proposed to explain the stabilizing effect of trehalose on proteins. To investigate the nature of protein-trehalose-water interactions in solution at the molecular level, two molecular dynamics simulations of the protein lysozyme in solution at room temperature have been carried out, one in the presence (about 0.5 M) and one in the absence of trehalose. The results show that the trehalose molecules cluster and move toward the protein, but neither completely expel water from the protein surface nor form hydrogen bonds with the protein. Furthermore, the coating by trehalose does not significantly reduce the conformational fluctuations of the protein compared to the trehalose-free system. Based on these observations, a model is proposed for the interaction of trehalose molecules with a protein in moderately concentrated solutions, at room temperature and on the nanosecond timescale.

A fully integrated protein crystallization platform for small-molecule drug discovery

Structure-based drug discovery in the pharmaceutical industry benefits from cost-efficient methodologies that quickly assess the feasibility of specific, often refractory, protein targets to form well-diffracting crystals. By tightly coupling construct and purification diversity with nanovolume crystallization, the Structural Biology Group at Syrrx has developed such a platform to support its small-molecule drug-discovery program. During the past 18 months of operation at Syrrx, the Structural Biology Group has executed several million crystallization and imaging trials on over 400 unique drug-discovery targets. Here, key components of the platform, as well as an analysis of some experimental results that allowed for platform optimization, will be described.