Protein Crystals Research Articles

A simple and effective method to remove pigments from heterologous secretory proteins expressed in Pichia pastoris

Pichia pastoris is a popular yeast host for high-level heterologous expression of proteins on an industrial scale owing to its reliable expression, robust growth, high fermentation density, and easy genetic manipulation and cultivation at a relatively low cost. Of particular interest is its high secretion efficiency for small proteins including insulin, human serum albumin, vaccines, enzymes, and llama-derived heavy-chain only antibodies (nanobodies) for pharmaceutical and research applications. However, a recurring challenge in using P. pastoris heterologous secretory proteins is the co-purification of a sticky, yellow pigment which has been identified as a tetra-benzoyl disaccharide. Current methods for pigment removal involve crystallization of the heterologous secretory protein, active carbon absorption, and chromatography using cation exchange and hydrophobic interaction. Here, we present a simple and effective method to remove the yellow pigment, demonstrated with divalent nanobodies targeting SARS-CoV-2. The method entails capturing the nanobody on an affinity column and subsequent washing with the zwitterionic detergent lauryldimethylamine N-oxide (LDAO). We anticipate the method become generally useful to remove pigments from secretion proteins produced in P. pastoris, offering a practical solution to enhance the purity of heterologous proteins in various biotechnological applications.

SYNTHESIS AND BIOLOGICAL EVALUATION OF 1H-(INDOLE-5-YL)-3-SUBSTITUTED-1,2,4-OXADIAZOLES AS NOVEL 5-LOX INHIBITORS

: A series of indolyloxadiazoles were synthesized from amidoxime and indole 3-carboxaldehyde using CAN as a catalyst and PEG as a solvent. In vitro, a 5-LOX inhibitory assay has been performed for all the synthesized compounds. Among the tested compounds, 4bf showed the highest potency (IC50 18.78 µg/ml). The synthesized compound carried out docking on the 5-LOX enzyme protein crystal structure. Compound (4bf) docked snugly into the receptor site with a score of -9.1 Kcal/mol, and it showed strong hydrogen bond interactions with two key amino acids, His368 and Asn555.

Biosynthesis of Cry5B-Loaded Sulfur Nanoparticles using Arthrobotrys oligospora Filtrate: Effects on Nematicidal Activity, Thermal Stability, and Pathogenicity against Caenorhabditis elegans.

Cry5B, a crystal protein produced by Bacillus thuringiensis (Bt), is a bionematicide with potent nematicidal activity against various plant-parasitic and free-living nematodes. This protein, however, is susceptible to destruction by ultraviolet light, proteolytic enzymes, and high temperatures. This study aims to produce Cry5B protein for bionematicidal use and improve its stability and nematicidal efficacy by loading it intoArthrobotrys oligospora-mediated sulfur nanoparticles (AO-SNPs). Based on the mortality assay, the Cry5B protein exhibited dose-dependent nematicidal activity against the model organismCaenorhabditis elegans. The nematicidal activity, thermal stability, and pathogenic effects of Cry5B-loaded AO-SNPs (Cry5B-SNPs) were compared to those of free Cry5B. After 3 h of exposure to heat at 60 °C, Cry5B-SNPs had greater nematicidal activity than free Cry5B protein, indicating the effective formulation of Cry5B-SNPs that could be used as an alternative to current nematicide delivery strategies.

Characterization of Indigenous Bacillus thuringiensis Isolates and Toxicity Analysis Against Brinjal Shoot and Fruit Borer, Leucinodes orbonalis (Guenee)

The toxins derived from Bacillus thuringiensis (Bt) exhibit significant promise in managing specific orders of harmful insects without the drawbacks in using of chemical insecticides. This study examines 20 indigenous Bt isolates, with a focus on their colony and crystal morphology, gene content, protein profiles, and toxicity against the larvae of Leucinodes orbonalis. The results revealed that all colonies were creamy white in colour with fried egg type appearance, flat surface, and undulated margin with spherical shaped crystals. PCR screening detected the existence of cry1, cry2, and vip3A genes with varying gene combinations among the isolates. Protein profiles exhibited the presence of multiple proteins with molecular weights ranging from 20 to 135 kDa, particularly ~135 and ~65 kDa represents Cry1 and Cry2 protein. In vitro bioassays against L. orbonalis revealed that four isolates T193, T339, T374, and T380 having substantial toxicity (93.33 to 100% mortality), suggesting the potential for their utilization in sustainable pest management strategies.

Electric-field-induced motion of a PDZ domain protein crystal simulated using all-atom molecular dynamics

Electric-field-induced motion of a PDZ domain protein crystal simulated using all-atom molecular dynamics

Boosting protein crystallization from liquid-liquid phase separation by increasing metastability gap

Aqueous solutions of lysozyme undergo LLPS by cooling in the presence of NaCl (0.1–0.2 M) around neutral pH. This phase transition is metastable with respect to protein crystallization. Addition of 4-(2-hydroxyethyl)-1-piperazineethanesulfonate (HEPES, 0.1 M) to these solutions triggers a rapid, reproducible and high-yield formation of tetragonal lysozyme microcrystals through LLPS even if NaCl concentration is quite low. In this work, we demonstrate that HEPES causes opposite thermodynamic effects on solubility and LLPS boundaries in the protein phase diagram, leading to broadening of metastability gap. This increases thermodynamic driving force for crystal nucleation inside protein-rich liquid phase. The observed enhancement of LLPS-based crystallization is independent of HEPES protonation state. However, crystallization output is dramatically reduced when HEPES is replaced by other organic molecules sharing same functional groups. We attribute HEPES effect on crystallization to its ability to bind lysozyme inside crystal. Replacing NaCl with phosphate buffer as LLPS inducer radically reduces crystallization, consistent with NaCl being a more effective agent for lysozyme crystallization. This work shows that protein crystallization from metastable LLPS can be successfully enhanced by combining an additive that induces LLPS with another additive that increases metastability gap.

Aldo-keto reductases 7A subfamily: A mini review

Aldo-keto reductase-7A (AKR7A) subfamily belongs to the AKR superfamily and is associated with detoxification of aldehydes and ketones by reducing them to the corresponding alcohols. So far five members of ARK7A subfamily are identified: two human members-AKR7A2 and AKR7A3, two rat members-AKR7A1 and AKR7A4, and one mouse member-AKR7A5, which are implicated in several diseases including neurodegenerative diseases and cancer. AKR7A members share similar crystal structures and protein functional domains, but have different substrate specificity, inducibility and biological functions. This review will summarize the research progress of AKR7A members in substrate specificity, tissue distribution, inducibility, crystal structure and biological function. The significance of AKR7A members in the occurrence and development of diseases will also be discussed.

Advanced isoconversional kinetic analysis: Insight in mechanisms and simulations. Successes and future

Various examples of application of advanced isoconversional kinetic analysis are discussed. The paper focuses on polymerization and crystallization mechanisms, protein denaturation and simulations in a model-free way under different temperature programs. It is shown how isoconversional kinetic analysis was developed in the recent years to gain meaningful kinetic information on changes in rate-limiting steps and was applied to multi-step processes. The complementary of the information obtained by estimating pre-exponential factors, rate constants and mathematical function that describes the reaction mechanism, in addition to the usual effective activation energy dependency, is highlighted. In addition, combination of model-free and model-based methods can be used for the elucidation of multi-step kinetics.

From femtoseconds to minutes: time-resolved macromolecular crystallography at XFELs and synchrotrons.

Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump-probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.

PEGDA hydrogel microspheres with encapsulated salt for versatile control of protein crystallization

Due to their biocompatibility and adjustable chemical structure and morphology, hydrogels have great potential in many applications, and can be used to enhance protein crystal quality and crystallization efficiency, contributing to biomedicine manufacturing. Monodispersed PEGDA hydrogel microspheres (HMSs) were synthesized using a Lego-inspired microfluidic device. The generated droplets were then UV polymerized, partially hydrolyzed with 0.1 M NaOH solution to improve their absorption capacity, and soaked in a buffer solution containing 0, 0.5, 1, 2, and 4 M NaCl. Salt-loaded HMSs were used as the medium for the enhanced crystallization of hen egg white lysozyme from aqueous solutions. Different supersaturations were achieved in the protein solutions by releasing NaCl of different concentrations from HMSs, as confirmed by electrical conductivity measurements. HMSs with or without NaCl can both provide heterogeneous nucleation sites due to their nano-porous structure and wrinkled surface. The addition of NaCl-loaded HMSs to the protein solution can also increase or decrease the supersaturation in the whole solution or locally near the HMS, leading to controllable nucleation time and crystal size distribution dependent on the NaCl concentration loaded into HMSs.

Investigation of Potential Drug Targets Involved in Inflammation Contributing to Alzheimer's Disease Progression.

Alzheimer's disease has become a major public health issue. While extensive research has been conducted in the last few decades, few drugs have been approved by the FDA to treat Alzheimer's disease. There is still an urgent need for understanding the disease pathogenesis, as well as identifying new drug targets for further drug discovery. Alzheimer's disease is known to arise from a build-up of amyloid beta (Aβ) plaques as well as tangles of tau proteins. Along similar lines to Alzheimer's disease, inflammation in the brain is known to stem from the degeneration of tissue and build-up of insoluble materials. A minireview was conducted in this work assessing the genes, proteins, reactions, and pathways that link brain inflammation and Alzheimer's disease. Existing tools in Systems Biology were implemented to build protein interaction networks, mainly for the classical complement pathway and G protein-coupled receptors (GPCRs), to rank the protein targets according to their interactions. The top 10 protein targets were mainly from the classical complement pathway. With the consideration of existing clinical trials and crystal structures, proteins C5AR1 and GARBG1 were identified as the best targets for further drug discovery, through computational approaches like ligand-protein docking techniques.

Refining Protein Envelopes with a Transition Region for Enhanced Direct Phasing in Protein Crystallography

In protein crystallography, the determination of an accurate protein envelope is of paramount importance for ab initio phasing of diffraction data. In our previous work, we introduced an approach to ascertain the protein envelope by seeking an optimal cutoff value on a weighted-average density map. In this paper, we present a significant advancement in our approach by focusing on identifying a transition region that demarcates the boundary between the protein and solvent regions, rather than relying solely on a single cutoff value. Within this transition region, we conducted a meticulous search for the protein envelope using a finer map and our proposed transition hybrid input–output (THIO) algorithm. Through this improvement, we achieved a refined protein envelope even when starting from random phases, enabling us to determine protein structures with irregular envelopes and successfully phase crystals with reduced solvent contents. To validate the efficacy of our method, we conducted tests using real diffraction data from five protein crystals, each containing solvent contents ranging from 60% to 65%. Solving these structures through conventional direct methods proved difficult due to the limited solvent content. The mean phase error obtained through our proposed method was about 30°. The reconstructed model matched with the structure in the protein data bank with a root mean square deviation (r.m.s.d.) of about 1 Å. These results serve as compelling evidence that the utilization of the proposed transition region in conjunction with the THIO algorithm contributes significantly to the construction of a reliable protein envelope. This, in turn, becomes indispensable for the direct phasing of protein crystals with lower solvent contents.

Ym1 protein crystals promote type 2 immunity

Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Although mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.

Ym1 protein crystals promote type 2 immunity.

Spontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Although mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded by Chil3 and Chil4 and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography as in vivo native crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.

Tangential flow filtration for continuous processing of crystallized proteins

Protein crystallization has the potential to provide nearly pure protein products in a single processing step. Most previous studies of protein crystallization have used centrifugation for dewatering and washing the crystallized solids, but this approach would be difficult to adopt in continuous bioprocessing operations. This study provides the first demonstration that crystallized proteins can be successfully filtered using hollow fiber tangential flow filtration (TFF) modules. Experiments were performed with human serum albumin (HSA) crystallized by the addition of trivalent CeCl3, both with and without polyethylene glycol (PEG). Greater than 85 % protein yield was achieved using 4.5 mM CeCl3 in the presence of 3 wt% PEG with the crystallization occurring in less than 20 s, which is ideal for continuous processing. The addition of PEG had minimal effect on the crystallization yield, but it did lead to the formation of larger and denser crystals and a corresponding increase in the critical flux, which is the maximum value of the flux that causes minimal increase in the transmembrane pressure (i.e., minimal fouling). Filtration experiments performed at optimal conditions were successfully run for 24 h with the transmembrane pressure remaining below 5 kPa, demonstrating the feasibility of using continuous crystallization with tangential flow filtration for the purification of high value protein products.

Determining Protein Structures Using X-Ray Crystallography.

X-ray crystallography is a robust and widely used technique that facilitates the three-dimensional structure determination of proteins at an atomic scale. This methodology entails the growth of protein crystals under controlled conditions followed by their exposure to X-ray beams and the subsequent analysis of the resulting diffraction patterns via computational tools to determine the three-dimensional architecture of the protein. However, achieving high-resolution structures through X-ray crystallography can be quite challenging due to complexities associated with protein purity, crystallization efficiency, and crystal quality.In this chapter, we provide a detailed overview of the gene to structure determination pipeline used in X-ray crystallography, a crucial tool for understanding protein structures. The chapter covers the steps in protein crystallization, along with the processes of data collection, processing, structure determination, and refinement. The most commonly faced challenges throughout this procedure are also addressed. Finally, the importance of standardized protocols for reproducibility and accuracy is emphasized, as they are crucial for advancing the understanding of protein structure and function.

The TR-icOS setup at the ESRF: time-resolved microsecond UV-Vis absorption spectroscopy on protein crystals.

The technique of time-resolved macromolecular crystallography (TR-MX) has recently been rejuvenated at synchrotrons, resulting in the design of dedicated beamlines. Using pump-probe schemes, this should make the mechanistic study of photoactive proteins and other suitable systems possible with time resolutions down to microseconds. In order to identify relevant time delays, time-resolved spectroscopic experiments directly performed on protein crystals are often desirable. To this end, an instrument has been built at the icOS Lab (in crystallo Optical Spectroscopy Laboratory) at the European Synchrotron Radiation Facility using reflective focusing objectives with a tuneable nanosecond laser as a pump and a microsecond xenon flash lamp as a probe, called the TR-icOS (time-resolved icOS) setup. Using this instrument, pump-probe spectra can rapidly be recorded from single crystals with time delays ranging from a few microseconds to seconds and beyond. This can be repeated at various laser pulse energies to track the potential presence of artefacts arising from two-photon absorption, which amounts to a power titration of a photoreaction. This approach has been applied to monitor the rise and decay of the M state in the photocycle of crystallized bacteriorhodopsin and showed that the photocycle is increasingly altered with laser pulses of peak fluence greater than 100 mJ cm-2, providing experimental laser and delay parameters for a successful TR-MX experiment.

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

Additives (ionic liquids, deep eutectic solvents, molecularly imprinted polymers) and external fields (magnetic field, electric field, ultrasonic field, shear, light field) enhance protein crystallization.

Porous protein crystals: synthesis and applications.

Large-pore protein crystals (LPCs) are an emerging class of biomaterials. The inherent diversity of proteins translates to a diversity of crystal lattice structures, many of which display large pores and solvent channels. These pores can, in turn, be functionalized via directed evolution and rational redesign based on the known crystal structures. LPCs possess extremely high solvent content, as well as extremely high surface area to volume ratios. Because of these characteristics, LPCs continue to be explored in diverse applications including catalysis, targeted therapeutic delivery, templating of nanostructures, structural biology. This Feature review article will describe several of the existing platforms in detail, with particular focus on LPC synthesis approaches and reported applications.

Theory of density waves and organization of proteins in icosahedral virus capsids.

Understanding the physical principles underlying the structural organization of the proteinaceous viral shells is of major importance to advance antiviral strategies. Here, we develop a phenomenological thermodynamic theory, which considers structures of small and middle-size icosahedral viral shells as a result of condensation of a minimum number of protein density waves on a spherical surface. Each of these irreducible critical waves has icosahedral symmetry and can be expressed as a specific series of the spherical harmonics Ylm with the same wave number l. As we demonstrate, in small viral shells self-assembled from individual proteins, the maxima of one critical density wave determine the positions of proteins, while the spatial derivatives of the second one control the protein orientations on the shell surface. In contrast to the small shells, the middle-size ones are always formed from pentamers and hexamers (referred to as capsomers). Considering all such structures deposited in the Protein Data Bank, we unexpectedly found that the positions of capsomeres in these shells correspond to the maxima of interference patterns produced by no more than two critical waves with close wave numbers. This fact allows us to explain the observed limit size of the icosahedral shells assembled from pentamers and hexamers. We also construct nonequilibrium thermodynamic potentials describing the protein crystallization and discuss the reasons behind the specific handedness of the viral shells.