Quantification of Binary Diffusion in Protein Crystals

Characterization of Guest DNA Transport and Adsorption within Host Porous Protein Crystals

Nucleic acid transport through protein-based pores is a well-characterized phenomenon due in part to advancements in nanopore sequencing. A less studied area is nucleic acid transport through extended protein-based channels, where the additional surface area and increased contact time allow for the study of prolonged binding interactions. Porous protein crystals composed of "CJ", a putative polyisoprenoid-binding protein from Campylobacter jejuni, represent a favorable, highly ordered material for studying DNA transport and binding/unbinding along protein-based channels. These crystals adopt a hexagonal prism habit and contain a densely packed hexagonal array of 13 nm diameter axial nanopores that run from the top to the bottom of the crystal. After cross-linking, the crystals are easily manipulated for experimentation. An adsorption isotherm between host crystals and guest double-stranded 8 base pair DNA (8mer) revealed a high equilibrium adsorption constant of 206 ± 30 L/g. Fluorescence confocal microscopy tracked the loading of guest DNA into host crystals predominately along the major axial crystal nanopores. Four different computational models based on the finite volume (FV) method were assessed to model the transport process for guest 8mer and 15mer dsDNA loading into empty host crystals in terms of fundamental parameters, such as the intrapore diffusion constant. Fitting the models to the data revealed that the most basic FV model sufficed to describe the observed loading behavior, characterized by a single effective diffusion coefficient. Leveraging Fick's first law, we more directly fit a numerical range for the observed intrapore diffusion coefficient as a function of time, position within the crystal, and relative guest concentration. This new transport analysis strategy was applied to both out-of-equilibrium loading and fluorescence recovery after photobleaching (FRAP) experiments. The intrapore diffusion constants are comparable between 8mer and 15mer dsDNA and were found to be 2 orders of magnitude faster for DNA loading into empty crystals than that observed in FRAP experiments, which averaged (10 ± 4) × 10-11 cm2/s.

In Situ Absorption and Fluorescence Microspectroscopy Investigation of the Molecular Incorporation Process into Single Nanoporous Protein Crystals

Protein crystals exhibit distinct three-dimensional structures, which contain well-ordered nanoporous solvent channels, providing a chemically heterogeneous environment. In this paper, the incorporation of various molecules into the solvent channels of native hen egg-white lysozyme crystals was demonstrated using fluorescent dyes, including acridine yellow G, rhodamine 6G, and eosin Y. The process was evaluated on the basis of absorption and fluorescence microspectroscopy at a single-crystal level. The molecular loading process was clearly visualized as a function of time, and it was determined that the protein crystals could act as nanoporous materials. It was found that the incorporation process is strongly dependent on the molecular charge, leading to heterogeneous molecular aggregation, which suggests host-guest interaction of protein crystals from the viewpoint of nanoporous materials.

Imaging Ca2+ Concentration and pH in Nanopores/Channels of Protein Crystals

Protein crystals are nanoporous materials. Despite this important characteristic, little is known about the conditions in the pores, also called channels. Here, we describe a method to study the calcium concentration and pH in the nanopores of thaumatin and lysozyme crystals. We load the crystal nanopores with fluorescent indicators and then perfuse the crystals with solutions of different calcium concentrations and pH while reading out the crystal's fluorescence intensity with confocal microscopy. By calibrating the fluorescence signal, we can determine the calcium concentration and pH in the nanopores. For the pH in thaumatin nanopores measured with the ratiometric pH sensor SNARF-1, we find a -0.7 pH shift compared to the bath pH corresponding to a fivefold higher proton concentration. This is similar to the -0.3 pH shift found in lysozyme nanopores. With single-wavelength probes, we find that the calcium concentration in thaumatin crystal nanopores is the same as in the bath, whereas it is 0.24 times lower in lysozyme nanopores. Summarizing, our experiments show that calcium concentration and pH in the nanopores of protein crystals can deviate significantly from that in the bath. In general, the described method can be applied for testing a wide range of ion or small-molecule concentrations in transparent nanoporous materials not only with ratiometric but also with single wavelength fluorescent indicators.

Preparation of a cross-linked porous protein crystal containing Ru carbonyl complexes as a CO-releasing extracellular scaffold

Protein crystals generally are stable solid protein assemblies. Certain protein crystals are suitable for use as nanovessels for immobilizing metal complexes. Here we report the preparation of ruthenium carbonyl-incorporated cross-linked hen egg white lysozyme crystals (Ru·CL-HEWL). Ru·CL-HEWL retains a Ru carbonyl moiety that can release CO, although a composite of Ru carbonyl-HEWL dissolved in buffer solution (Ru·HEWL) does not release CO. We found that treatment of cells with Ru·CL-HEWL significantly increased nuclear factor kappa B (NF-κB) activity as a cellular response to CO. These results demonstrate that Ru·CL-HEWL has potential for use as an artificial extracellular scaffold suitable for transport and release of a gas molecule.

Modeling the mechanical response of tetragonal lysozyme crystals

We investigate the temperature- and humidity-dependent mechanical response of tetragonal lysozyme crystals using a continuum-based crystal plasticity model calibrated with existing experimental data. The effects of temperature and intracrystalline water are incorporated in the elastic constant of the protein crystal as well as the critical resolved shear stress on the slip planes in the crystal plasticity model. The critical resolved shear stresses have been deduced from Vickers microhardness test data corresponding to different temperatures and states of hydration. Compression analyses have then been carried out along different crystallographic directions of lysozyme crystals which reveal that their mechanical response is highly anisotropic and orientation dependent, being purely elastic along the [110] direction but elastoplastic along the [100] and [212] directions. An interesting observation is that an increase in temperature and the amount of intracrystalline water molecules leads to a decrease in the critical resolved shear stress of the slip systems resulting in softening of the crystal. The analysis presented in this paper may be applied to the study of other protein crystal systems as well as their optimal design for biotechnological applications.

Molecular dynamics simulations for water and ions in protein crystals

The spatial and temporal properties of water and ions in bionanoporous materials-protein crystals-have been investigated using molecular dynamics simulations. Three protein crystals are considered systematically with different morphologies and chemical topologies: tetragonal lysozyme, orthorhombic lysozyme, and tetragonal thermolysin. It is found that the thermal fluctuations of C(alpha) atoms in the secondary structures of protein molecules are relatively weak due to hydrogen bonding. The solvent-accessible surface area per residue is nearly identical in the three protein crystals; the hydrophobic and hydrophilic residues in each crystal possess approximately the same solvent-accessible surface area. Water distributes heterogeneously and has different local structures within the biological nanopores of the three protein crystals. The mobility of water and ions in the crystals is enhanced as the porosity increases and also by the fluctuations of protein atoms particularly in the two lysozyme crystals. Anisotropic diffusion is found preferentially along the pore axis, as experimentally observed. The anisotropy of the three crystals increases in the order: tetragonal thermolysin < tetragonal lysozyme < orthorhombic lysozyme.

Exchange dynamics at the interface of nanoporous materials with their surroundings

The evolution of transient concentration profiles in nanoporous materials is shown to provide direct information about the rate of molecular exchange at the interface of these materials with the surrounding atmosphere. This includes the quantitation of a surface permeability and, related with each other, of the sticking factor, i.e., of the probability that a molecule colliding with the external surface from the outside atmosphere, will in fact enter the genuine pore system of the material under study. Owing to the recent introduction of interference microscopy to this type of systems, the relevant experimental evidence has become directly accessible and is applied to two model systems which are found to differ notably in their interface dynamics.

Advanced protein crystallization using water-soluble ionic liquids as crystallization additives

The application of five water-soluble, halogen-free, alkylammonium-based ionic liquids (ILs) as additives for advanced crystallization of lysozyme was investigated. Their biocompatibility was determined by long-term measurement of the overall mean relative enzyme activities. These were maximally reduced by about 10-15% when up to 200 g IL l(-1) was added. Sitting-drop vapor diffusion crystallization experiments revealed that the addition of some of the ILs led to less crystal polymorphism and precipitation was avoided reliably even at larger NaCl concentrations. The addition of ILs tended to result in larger crystals. The kinetics of lysozyme crystallization were significantly enhanced using ILs as crystallization additives, e.g. by a factor of 5.5 when 100 g ethanolammonium formate l(-1 )was added. ILs with "soft" anions, such as formate or glycolate, were superior to ILs with "hard" anions, like nitrate.

Solute transport in orthorhombic lysozyme crystals: a molecular simulation study

Long-time equilibrium molecular dynamics simulations were performed to study the passage of a substrate, L: -arabinose, through nanopores of orthorhombic hen egg white lysozyme crystals. Cross-linked protein crystals (CLPC), as novel biological nanoporous media, consist of an extensive regular matrix of chiral solvent-filled nanopores via which ions and solutes, e.g. sugars and amino acids, travel in and out. We studied the diffusive motion of arabinose inside protein channels. The computed diffusion coefficients within the crystal were orders of magnitudes lower relative to the diffusion coefficient of the solute in water. This study is valuable for understanding the nature of solute-protein interactions and transport phenomena in CLPCs and provides an understanding of biocatalytic and bioseparation processes using CLPC.