Optimization of crystallization conditions for biological macromolecules

On-the-fly resolution enhancement in X-ray protein crystallography using electric field

X-ray crystallography has tremendously served structural biology by routinely providing high-resolution 3D structures of macromolecules. The extent of information encoded in the X-ray crystallography is proportional to which resolution the crystals diffract and the structure can be refined to. Therefore, there is a continuous effort to obtain high-quality crystals, especially for those proteins, which are considered difficult to crystallize into high-quality protein crystals of suitable sizes for X-ray crystallography. Efforts in enhancing the resolution in X-ray crystallography have also been made by optimizing crystallization protocols using external stimuli such as an electric field and magnetic field during the crystallization. Here, we present the feasibility of on-the-fly post-crystallization resolution enhancement of the protein crystal diffraction by applying a high-voltage electric field. The electric field between 2 and 11 kV/cm, which was applied after mounting the crystals in the beamline, resulted in the enhancement of the resolution. The crystal diffraction quality improved progressively with the exposure time. Moreover, we also find that upto defined electric field threshold, the protein structure remains largely unperturbed, a conclusion further supported by molecular dynamics simulations.

Automated Nanoliter Volume Assay Optimization on a Cost-Effective Microfluidic Disc

Optimizing multireagent assays often requires successive titration of individual components until the optimal combination of conditions is achieved. This process is time-consuming, laborious, and often expensive since parallelized experimentation requires bulk consumption of reagents. Microfluidics presents a solution through miniaturization of standard processes by reducing reaction volume, executing multiple parallel workflows, and enabling automation. While single-digit microliter reactions can be effective, scaling to nanoliter volumes without employing droplets is difficult. We describe a cost-effective, customizable centrifugal microdisc for optimizing assays pertinent to a broad array of applications. An automated two-stage metering process leverages tunable, laser-actuated valves that retain defined fluidic volumes upon opening and meter discrete nanoliter volumes into downstream architecture. We demonstrate that ∼150 nL volumes could be metered and tuned for specific applications. We illustrate the potential for controlled metering of up to four reagents with high parallelization for rapid, cost-effective assay optimization with minimal manual intervention.

Development of novel antimicrobials with engineered endolysin LysECD7-SMAP to combat Gram-negative bacterial infections

BACKGROUND

Among the non-traditional antibacterial agents in development, only a few targets critical Gram-negative bacteria such as carbapenem-resistant Pseudomonas aeruginosa, Acinetobacter baumannii or cephalosporin-resistant Enterobacteriaceae. Endolysins and their genetically modified versions meet the World Health Organization criteria for innovation, have a novel mode of antibacterial action, no known bacterial cross-resistance, and are being intensively studied for application against Gram-negative pathogens.

METHODS

The study presents a multidisciplinary approach, including genetic engineering of LysECD7-SMAP and production of recombinant endolysin, its analysis by crystal structure solution following molecular dynamics simulations and evaluation of antibacterial properties. Two types of antimicrobial dosage forms were formulated, resulting in lyophilized powder for injection and hydroxyethylcellulose gel for topical administration. Their efficacy was estimated in the treatment of sepsis, and pneumonia models in BALB/c mice, diabetes-associated wound infection in the leptin receptor-deficient db/db mice and infected burn wounds in rats.

RESULTS

In this work, we investigate the application strategies of the engineered endolysin LysECD7-SMAP and its dosage forms evaluated in preclinical studies. The catalytic domain of the enzyme shares the conserved structure of endopeptidases containing a putative antimicrobial peptide at the C-terminus of polypeptide chain. The activity of endolysins has been demonstrated against a range of pathogens, such as Klebsiella pneumoniae, A. baumannii, P. aeruginosa, Staphylococcus haemolyticus, Achromobacter spp, Burkholderia cepacia complex and Haemophylus influenzae, including those with multidrug resistance. The efficacy of candidate dosage forms has been confirmed in in vivo studies. Some aspects of the interaction of LysECD7-SMAP with cell wall molecular targets are also discussed.

CONCLUSIONS

Our studies demonstrate the potential of LysECD7-SMAP therapeutics for the systemic or topical treatment of infectious diseases caused by susceptible Gram-negative bacterial species and are critical to proceed LysECD7-SMAP-based antimicrobials trials to advanced stages.

Spectroscopic insights into multi-phase protein crystallization in complex lysate using Raman spectroscopy and a particle-free bypass

Protein crystallization as opposed to well-established chromatography processes has the benefits to reduce production costs while reaching a comparable high purity. However, monitoring crystallization processes remains a challenge as the produced crystals may interfere with analytical measurements. Especially for capturing proteins from complex feedstock containing various impurities, establishing reliable process analytical technology (PAT) to monitor protein crystallization processes can be complicated. In heterogeneous mixtures, important product characteristics can be found by multivariate analysis and chemometrics, thus contributing to the development of a thorough process understanding. In this project, an analytical set-up is established combining offline analytics, on-line ultraviolet visible light (UV/Vis) spectroscopy, and in-line Raman spectroscopy to monitor a stirred-batch crystallization process with multiple phases and species being present. As an example process, the enzyme Lactobacillus kefir alcohol dehydrogenase (LkADH) was crystallized from clarified Escherichia coli (E. coli) lysate on a 300 mL scale in five distinct experiments, with the experimental conditions changing in terms of the initial lysate solution preparation method and precipitant concentration. Since UV/Vis spectroscopy is sensitive to particles, a cross-flow filtration (cross-flow filtration)-based bypass enabled the on-line analysis of the liquid phase providing information on the lysate composition regarding the nucleic acid to protein ratio. A principal component analysis (PCA) of in situ Raman spectra supported the identification of spectra and wavenumber ranges associated with productspecific information and revealed that the experiments followed a comparable, spectral trend when crystals were present. Based on preprocessed Raman spectra, a partial least squares (PLS) regression model was optimized to monitor the target molecule concentration in real-time. The off-line sample analysis provided information on the crystal number and crystal geometry by automated image analysis as well as the concentration of LkADH and host cell proteins (HCPs) In spite of a complex lysate suspension containing scattering crystals and various impurities, it was possible to monitor the target molecule concentration in a heterogeneous, multi-phase process using spectroscopic methods. With the presented analytical set-up of off-line, particle-sensitive on-line, and in-line analyzers, a crystallization capture process can be characterized better in terms of the geometry, yield, and purity of the crystals.

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.

Fast fragment and compound screening pipeline at the Swiss Light Source

Crystallography-based fragment screening is a highly effective technique employed in structure-based drug discovery to expand the range of lead development opportunities. It allows screening and sorting of weakly binding, low molecular mass fragments, which can be developed into larger high-affinity lead compounds. Technical improvements at synchrotron beamlines, design of innovative libraries mapping chemical space efficiently, effective soaking methods and enhanced data analysis have enabled the implementation of high-throughput fragment screening pipelines at multiple synchrotron facilities. This widened access to CBFS beyond the pharma industry has allowed academic users to rapidly screen large quantities of fragment-soaked protein crystals. The positive outcome of a CBFS campaign is a set of structures that present the three-dimensional arrangement of fragment-protein complexes in detail, thereby providing information on the location and the mode of interaction of bound fragments. Through this review, we provide users with a comprehensive guide that sets clear expectations before embarking on a crystallography-based fragment screening campaign. We present a list of essential pre-requirements that must be assessed, including the suitability of your current crystal system for a fragment screening campaign. Furthermore, we extensively discuss the available methodological options, addressing their limitations and providing strategies to overcome them. Additionally, we provide a brief perspective on how to proceed once hits are obtained. Notably, we emphasize the solutions we have implemented for instrumentation and software development within our Fast Fragment and Compound Screening pipeline. We also highlight third-party software options that can be utilized for rapid refinement and hit assessment.

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson-Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.

Through Diffusion Measurements of Molecules to a Numerical Model for Protein Crystallization in Viscous Polyethylene Glycol Solution

Protein crystallography has become a popular method for biochemists, but obtaining high-quality protein crystals for precise structural analysis and larger ones for neutron analysis requires further technical progress. Many studies have noted the importance of solvent viscosity for the probability of crystal nucleation and for mass transportation; therefore, in this paper, we have reported on experimental results and simulation studies regarding the use of viscous polyethylene glycol (PEG) solvents for protein crystals. We investigated the diffusion rates of proteins, peptides, and small molecules in viscous PEG solvents using fluorescence correlation spectroscopy. In high-molecular-weight PEG solutions (molecular weights: 10,000 and 20,000), solute diffusion showed deviations, with a faster diffusion than that estimated by the Stokes–Einstein equation. We showed that the extent of the deviation depends on the difference between the molecular sizes of the solute and PEG solvent, and succeeded in creating equations to predict diffusion coefficients in viscous PEG solutions. Using these equations, we have developed a new numerical model of 1D diffusion processes of proteins and precipitants in a counter-diffusion chamber during crystallization processes. Examples of the application of anomalous diffusion in counter-diffusion crystallization are shown by the growth of lysozyme crystals.

Structural and biophysical characterization of Tribbles homolog 1

Tribbles proteins are pervasive pseudokinases in cellular signaling. They play a major role in the differentiation of myeloid cells, hepatocytes and adipocytes, and more widely in immune function, metabolism and cancer. Like many other pseudokinases, an inherent lack of catalytic activity has meant that a specialized cadre of techniques has been required to investigate Tribbles function. A prerequisite to most in vitro biochemistry has been robust methods for purifying useful quantities of Tribbles protein, which can sometimes exhibit non-optimal behavior upon recombinant expression. For instance, structural studies of the Tribbles family have largely focused on TRIB1, in part because of more readily available protein. Here we describe methods we have developed to routinely produce milligram quantities of TRIB1, and specific considerations when employing TRIB1 protein for various downstream analyses. Namely, we describe preparation and crystallization of TRIB1 for structural studies, and using fluorescence polarization and isothermal titration calorimetry to analyze interactions with TRIB1. We hope that applying these considerations can facilitate further understanding of TRIB1 function, specifically, and can be selectively applied to improve studies of other Tribbles proteins and pseudokinases more generally.

The FUSION protein crystallization screen

The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.

Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury

Objective:

This research aims to study the target specificity of selective bioactive compounds in complexing with the human angiotensin-converting enzyme (hACE2) receptor to impede the severe acute respiratory syndrome coronavirus 2 influx mechanism resulting in cardiac injury and depending on the receptor’s active site properties and quantum tunneling.

Materials and Methods:

A library of 120 phytochemical ligands was prepared, from which 5 were selected considering their absorption, distribution, metabolism, and excretion (ADMET) and quantitative structure–activity relationship (QSAR) profiles. The protein active sites and belonging quantum tunnels were defined to conduct supramolecular docking of the aforementioned ligands. The hydrogen bond formation and hydrophobic interactions between the ligand–receptor complexes were studied following the molecular docking steps. A comprehensive molecular dynamic simulation (MDS) was conducted for each of the ligand–receptor complexes to figure out the values – root mean square deviation (RMSD) (Å), root mean square fluctuation (RMSF) (Å), H-bonds, Cα, solvent accessible surface area (SASA) (Ų), molecular surface area (MolSA) (Ų), Rg (nm), and polar surface area (PSA) (Å). Finally, computational programming and algorithms were used to interpret the dynamic simulation outputs into their graphical quantitative forms.

Results:

ADMET and QSAR profiles revealed that the most active candidates from the library to be used were apigenin, isovitexin, piperolactam A, and quercetin as test ligands, whereas serpentine as the control. Based on the binding affinities of supramolecular docking and the parameters of molecular dynamic simulation, the strength of the test ligands can be classified as isovitexin > quercetin > piperolactam A > apigenin when complexed with the hACE2 receptor. Surprisingly, serpentine showed lower affinity (−8.6 kcal/mol) than that of isovitexin (−9.9 kcal/mol) and quercetin (−8.9 kcal/mol). The MDS analysis revealed all ligands except isovitexin having a value lower than 2.5 Ǻ. All the test ligands exhibited acceptable fluctuation ranges of RMSD (Å), RMSF (Å), H-bonds, Cα, SASA (Ų), MolSA (Ų), Rg (nm), and PSA (Å) values.

Conclusion:

Considering each of the parameters of molecular optimization, docking, and dynamic simulation interventions, all of the test ligands can be suggested as potential targeted drugs in blocking the hACE2 receptor.

Engineering of tissue inhibitor of metalloproteinases TIMP-1 for fine discrimination between closely-related stromelysins MMP-3 and MMP-10

Matrix metalloproteinases (MMPs) have long been known as key drivers in the development and progression of diseases, including cancer and neurodegenerative, cardiovascular, and many other inflammatory and degenerative diseases, making them attractive potential drug targets. Engineering selective inhibitors based upon tissue inhibitors of metalloproteinases (TIMPs), endogenous human proteins that tightly yet nonspecifically bind to the family of MMPs, represents a promising new avenue for therapeutic development. Here, we used a counter-selective screening strategy for directed evolution of yeast-displayed human TIMP-1 to obtain TIMP-1 variants highly selective for the inhibition of MMP-3 in preference over MMP-10. As MMP-3 and MMP-10 are the most similar MMPs in sequence, structure, and function, our results thus clearly demonstrate the capability for engineering full-length TIMP proteins to be highly selective MMP inhibitors. We show using protein crystal structures and models of MMP-3-selective TIMP-1 variants bound to MMP-3 and counter-target MMP-10 how structural alterations within the N-terminal and C-terminal TIMP-1 domains create new favorable and selective interactions with MMP-3 and disrupt unique interactions with MMP-10. While our MMP-3-selective inhibitors may be of interest for future investigation in diseases where this enzyme drives pathology, our platform and screening strategy can be employed for developing selective inhibitors of additional MMPs implicated as therapeutic targets in disease.

Prediction and Modeling of Protein–Protein Interactions Using “Spotted” Peptides with a Template-Based Approach

Protein–peptide interactions (PpIs) are a subset of the overall protein–protein interaction (PPI) network in the living cell and are pivotal for the majority of cell processes and functions. High-throughput methods to detect PpIs and PPIs usually require time and costs that are not always affordable. Therefore, reliable in silico predictions represent a valid and effective alternative. In this work, a new algorithm is described, implemented in a freely available tool, i.e., “PepThreader”, to carry out PPIs and PpIs prediction and analysis. PepThreader threads multiple fragments derived from a full-length protein sequence (or from a peptide library) onto a second template peptide, in complex with a protein target, “spotting” the potential binding peptides and ranking them according to a sequence-based and structure-based threading score. The threading algorithm first makes use of a scoring function that is based on peptides sequence similarity. Then, a rerank of the initial hits is performed, according to structure-based scoring functions. PepThreader has been benchmarked on a dataset of 292 protein–peptide complexes that were collected from existing databases of experimentally determined protein–peptide interactions. An accuracy of 80%, when considering the top predicted 25 hits, was achieved, which performs in a comparable way with the other state-of-art tools in PPIs and PpIs modeling. Nonetheless, PepThreader is unique in that it is able at the same time to spot a binding peptide within a full-length sequence involved in PPI and model its structure within the receptor. Therefore, PepThreader adds to the already-available tools supporting the experimental PPIs and PpIs identification and characterization.

Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach

Lassa hemorrhagic fever, caused by Lassa mammarenavirus (LASV) infection, accumulates up to 5000 deaths every year. Currently, there is no vaccine available to combat this disease. In this study, a library of 200 bioactive compounds was virtually screened to study their drug-likeness with the capacity to block the α-dystroglycan (α-DG) receptor and prevent LASV influx. Following rigorous absorption, distribution, metabolism, and excretion (ADME) and quantitative structure-activity relationship (QSAR) profiling, molecular docking was conducted with the top ligands against the α-DG receptor. The compounds chrysin, reticuline, and 3-caffeoylshikimic acid emerged as the top three ligands in terms of binding affinity. Post-docking analysis revealed that interactions with Arg76, Asn224, Ser259, and Lys302 amino acid residues of the receptor protein were important for the optimum binding affinity of ligands. Molecular dynamics simulation was performed comprehensively to study the stability of the protein-ligand complexes. In-depth assessment of root-mean-square deviation (RMSD), root mean square fluctuation (RMSF), polar surface area (PSA), B-Factor, radius of gyration (Rg), solvent accessible surface area (SASA), and molecular surface area (MolSA) values of the protein-ligand complexes affirmed that the candidates with the best binding affinity formed the most stable protein-ligand complexes. To authenticate the potentialities of the ligands as target-specific drugs, an in vivo study is underway in real time as the continuation of the research.

Stick, stretch, and scan imaging method for DNA and filaments

Biomolecules and organelles usually undergo changes to their structure or form as a result of mechanical stretching or stimulation. It is critical to be able to observe these changes and responses, which trigger mechano-chemical coupling or signal transduction. Advanced techniques have been developed to observe structure and form during manipulation; however, these require sophisticated methods. We have developed a simple approach to observe fine structure after stretching without fluorophore labeling. DNAs or molecules on the cell surface were bound to magnetic microbeads, followed by stretching with a magnetic field. After fixing, staining, and drying, the samples were examined by scanning electron microscopy with no need to build a functional surface with complex processes. Straight DNAs were observed rather than random-walk-like loose polymers. In our cellular experiment, the magnetic beads were bound to a Jurkat cell and formed a rosette which was later stuck to the substrate. A 41.3 μm filament on the base of a filopodium was pulled out via integrin from a cell. Therefore, our method can reveal long structures up to hundreds of micrometers at nanometer resolution after stretching or twisting. Our approach could have wide applications in structure–function studies of biomolecules, and in mechanobiology and cell biology when diffraction cannot used.

Magnetic force was applied to stretch single DNAs and cells which were stuck to magnetic beads and substrates via simple conjugation methods. Scanning electron microscopy images show that the filopodia of cells were pulled to extraordinary length.

Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization

Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.

Expression, purification and X-ray crystal diffraction analysis of alcohol dehydrogenase 1 from Artemisia annua L

Alcohol dehydrogenase 1 identified from Artemisia annua (AaADH1) is a 40 kDa protein that predominately expressed in young leaves and buds, and catalyzes dehydrogenation of artemisinic alcohol to artemisinic aldehyde in artemisinin biosynthetic pathway. In this study, AaADH1 encoding gene was subcloned into vector pET-21a(+) and expressed in Escherichia coli. BL21(DE3), and purified by Co²⁺ affinity chromatography. Anion exchange chromatography was performed until the protein purity reached more than 90%. Crystallization of AaADH1 was conducted for further investigation of the molecular mechanism of catalysis, and hanging-drop vapour diffusion method was used in experiments. The results showed that the apo AaADH1 crystal diffracted to 2.95 Å resolution, and belongs to space group P1, with unit-cell parameters, a = 77.53 Å, b = 78.49 Å, c = 102.44 Å, α = 71.88°, β = 74.02°, γ = 59.97°. The crystallization condition consists of 0.1 M Bis-Tris pH 6.0, 13% (w/v) PEG 8000 and 5% (v/v) glycerol.

Design of metal-mediated protein assemblies via hydroxamic acid functionalities

The self-assembly of proteins into sophisticated multicomponent assemblies is a hallmark of all living systems and has spawned extensive efforts in the construction of novel synthetic protein architectures with emergent functional properties. Protein assemblies in nature are formed via selective association of multiple protein surfaces through intricate noncovalent protein-protein interactions, a challenging task to accurately replicate in the de novo design of multiprotein systems. In this protocol, we describe the application of metal-coordinating hydroxamate (HA) motifs to direct the metal-mediated assembly of polyhedral protein architectures and 3D crystalline protein-metal-organic frameworks (protein-MOFs). This strategy has been implemented using an asymmetric cytochrome cb₅₆₂ monomer through selective, concurrent association of Fe³⁺ and Zn²⁺ ions to form polyhedral cages. Furthermore, the use of ditopic HA linkers as bridging ligands with metal-binding protein nodes has allowed the construction of crystalline 3D protein-MOF lattices. The protocol is divided into two major sections: (1) the development of a Cys-reactive HA molecule for protein derivatization and self-assembly of protein-HA conjugates into polyhedral cages and (2) the synthesis of ditopic HA bridging ligands for the construction of ferritin-based protein-MOFs using symmetric metal-binding protein nodes. Protein cages are analyzed using analytical ultracentrifugation, transmission electron microscopy and single-crystal X-ray diffraction techniques. HA-mediated protein-MOFs are formed in sitting-drop vapor diffusion crystallization trays and are probed via single-crystal X-ray diffraction and multi-crystal small-angle X-ray scattering measurements. Ligand synthesis, construction of HA-mediated assemblies, and post-assembly analysis as described in this protocol can be performed by a graduate-level researcher within 6 weeks.

Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl-esters.

Analysis of Binding Modes of Antigen-Antibody Complexes by Molecular Mechanics Calculation

Antibodies are one of the most important protein molecules in biopharmaceutics. Due to the recent advance in technology for producing monoclonal antibodies, many structural data are available on the antigen-antibody complexes. To characterize the molecular interaction in antigen-antibody recognition, we computationally analyzed 500 complex structures by molecular mechanics calculations. The presence of Ser and Tyr is markedly large in the complementarity-determining regions (CDRs). Although Ser is abundant in CDRs, its contribution to the binding score is not large. Instead, Tyr, Asp, Glu, and Arg significantly contribute to the molecular interaction from the viewpoint of the binding score. The decomposition of the binding score suggests that the hydrophilic interaction is predominant in all CDRs compared with the hydrophobic one. The contribution of the heavy chain is larger than that of the light chain. In particular, H2 and H3 largely contribute to the binding interaction. Tyr is a main contributing residue both in H2 and H3. The positively charged residue Arg also significantly contributes to the binding score in H3, while the contribution of Lys is small. The appearance of Ser is remarkable in H2, and Asp is abundant in H3. The non-charged polar residues, Thr, Asn, and Gln, appear much in H2, compared to appearing in H3. The negatively charged residues Asp and Glu significantly contribute to the binding score in H3. The contributions of Phe and Trp are not large in spite that the aromatic residues are capable of making the π-π or CH-π interaction. Gly is commonly abundant both in H2 and H3. The average distance of the shortest direct hydrogen bond between the antigen and antibody is longer than that of the hydrogen bonds observed in the complexes between compounds and their target proteins. Therefore, the antigen-antibody interface is not so tight as the compound-target protein interface. The calculation of shape complementarity is consistent with the result of the hydrogen bonds in that the fitness of the antigen-antibody contact is not so high as that of the compound-target protein contact. There exist many water molecules at the antigen-antibody interface. These findings suggest that Tyr, Asp, Glu, and Arg are rich in H3 and work as major contributors for the interaction with the antigen. Ser, Thr, Asn, and Gln are rich in H2 and support the interaction with enhancing molecular fitness. Gly is helpful in increasing flexibility and geometrical diversity. Because the antigen-antibody binding is fundamentally hydrophilic-driven, the non-polar residues are unfavorable for mediating the contact even for the aromatic residues such as Phe and Trp.

The tetrameric structure of the novel haloalkane dehalogenase DpaA from Paraglaciecola agarilytica NO2

Haloalkane dehalogenases (EC 3.8.1.5) are microbial enzymes that catalyse the hydrolytic conversion of halogenated compounds, resulting in a halide ion, a proton and an alcohol. These enzymes are used in industrial biocatalysis, bioremediation and biosensing of environmental pollutants or for molecular tagging in cell biology. The novel haloalkane dehalogenase DpaA described here was isolated from the psychrophilic and halophilic bacterium Paraglaciecola agarilytica NO2, which was found in marine sediment collected from the East Sea near Korea. Gel-filtration experiments and size-exclusion chromatography provided information about the dimeric composition of the enzyme in solution. The DpaA enzyme was crystallized using the sitting-drop vapour-diffusion method, yielding rod-like crystals that diffracted X-rays to 2.0 Å resolution. Diffraction data analysis revealed a case of merohedral twinning, and subsequent structure modelling and refinement resulted in a tetrameric model of DpaA, highlighting an uncommon multimeric nature for a protein belonging to haloalkane dehalogenase subfamily I.

Augmentation of Neurotoxicity of Anticancer Drugs by X-Ray Irradiation

BACKGROUND

In order to investigate the combination effect of anticancer drugs and X-ray irradiation on neurotoxic side-effects (neurotoxicity), a method that provides homogeneously X-ray-irradiated cells was newly established.

MATERIALS AND METHODS

PC12 cell suspension was irradiated by X-ray (0.5 Gy) in serum-supplemented medium, immediately inoculated into 96-microwell plates and incubated overnight. The medium was replaced with fresh serum-depleted medium containing 50 ng/ml nerve growth factor to induce differentiation toward nerve-like cells with characteristic neurites according to the overlay method without changing the medium. The differentiated cells were treated by anticancer drugs as well as antioxidants, oxaliplatin or bortezomib, and the viable cell number was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide method.

RESULTS

Antioxidants and anticancer drugs were cytotoxic to differentiating PC12 cells. Combination of anticancer drugs and X-ray irradiation slightly reduced cell viability.

CONCLUSION

The present 'population irradiation method' may be useful for the investigation of the combination effect of X-ray irradiation and any pharmaceutical drug.

A review of solvent freeze-out technology for protein crystallization

In this review, we summarize important advances in solvent freeze-out (SFO) technology for protein crystallization, including the background of SFO, its fundamental principle, and some crucial conditions and factors for optimizing SFO technology.

Structure of odorant binding proteins and chemosensory proteins determined by X-ray crystallography

OBPs and CSPs are small soluble proteins used by organisms as shuttle to transport odorant molecules between air and the membrane-embedded receptors. Deciphering the interactions of these proteins with their ligands at a molecular level may give clue on the function and specificity of the olfactory chain. To reach this goal, protein crystallography is very helpful with more than hundred entries available in the protein data bank (PDB). In this chapter, we present the peculiarities of OBPs and CSPs concerning their crystallization and 3D structure determination by X-ray diffraction.

Structure Determination of the Transactivation Domain of p53 in Complex with S100A4 Using Annexin A2 as a Crystallization Chaperone

To fully understand the environmental factors that influence crystallization is an enormous task, therefore crystallographers are still forced to work "blindly" trying as many crystallizing conditions and mutations to improve crystal packing as possible. Numerous times these random attempts simply fail even when using state-of-the-art techniques. As an alternative, crystallization chaperones, having good crystal-forming properties, can be invoked. Today, the almost exclusively used such protein is the maltose-binding protein (MBP) and crystallographers need other widely applicable options. Here, we introduce annexin A2 (ANXA2), which has just as good, if not better, crystal-forming ability than the wild-type MBP. Using ANXA2 as heterologous fusion partner, we were able to solve the atomic resolution structure of a challenging crystallization target, the transactivation domain (TAD) of p53 in complex with the metastasis-associated protein S100A4. p53 TAD forms an asymmetric fuzzy complex with the symmetric S1004 and could interfere with its function.

Crystallographic Studies of Triosephosphate Isomerase from Schistosoma mansoni

Protein structure determination by X-ray crystallography guides structure-function and rational drug design studies. Helminths cause devastating diseases, including schistosomiasis that affects over one-third of the human population. Trematodes from the genus Schistosoma heavily depend on glycolysis; thus enzymes involved in this metabolic pathway are potential drug targets. Here we present a protocol to obtain crystal structures of recombinantly expressed triosephosphate isomerase from S. mansoni (SmTPI) that diffracted in house to a resolution of 2 Å.

Controlled protein crystal nucleation in microreactors: the effect of the droplet volume versus high supersaturation ratios

Control of the enhanced lysozyme nucleation under high supersaturation ratios for a broad range of droplet volumes.

Organoelement Compounds Crystallized In Situ: Weak Intermolecular Interactions and Lattice Energies

The in situ crystallization is the most suitable way to obtain a crystal of a low-melting-point compound to determine its structure via X-Ray diffraction. Herein, the intermolecular interactions and some crystal properties of low-melting-point organoelement compounds (lattice energies, melting points, etc.) are discussed. The discussed structures were divided into two groups: organoelement compounds of groups 13–16 and organofluorine compounds with other halogen atoms (Cl, Br, I). The most of intermolecular interactions in the first group are represented by weak hydrogen bonds and H···H interactions. The crystal packing of the second group of compounds is stabilized by various interactions between halogen atoms in conjunction with hydrogen bonding and stacking interactions. The data on intermolecular interactions from the analysis of crystal packing allowed us to obtain correlations between lattice energies and Hirshfeld molecular surface areas, molecular volumes, and melting points.

High-Throughput Crystallization Pipeline at the Crystallography Core Facility of the Institut Pasteur

The availability of whole-genome sequence data, made possible by significant advances in DNA sequencing technology, led to the emergence of structural genomics projects in the late 1990s. These projects not only significantly increased the number of 3D structures deposited in the Protein Data Bank in the last two decades, but also influenced present crystallographic strategies by introducing automation and high-throughput approaches in the structure-determination pipeline. Today, dedicated crystallization facilities, many of which are open to the general user community, routinely set up and track thousands of crystallization screening trials per day. Here, we review the current methods for high-throughput crystallization and procedures to obtain crystals suitable for X-ray diffraction studies, and we describe the crystallization pipeline implemented in the medium-scale crystallography platform at the Institut Pasteur (Paris) as an example.

Crystallographic approaches to study the interaction modes of PD-1- and CTLA-4-blocking antibodies

The programmed death 1 (PD-1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) are negative regulators of T-cell immune function. Removal of these "brakes" in T cells results in increased activation of the immune system and controlling and eradicating tumor. The development of immune checkpoint inhibitors (ICIs) is a revolutionary milestone in tumor immunotherapy. Obtaining the atomic structure of the human immune checkpoint receptor/ICI therapeutic antibody complex is essential for understanding its inhibition mechanism and the rational design of improved biotherapeutics. In this chapter, we describe the methods for efficient production of extracellular domain of human immune checkpoint receptors and Fv fragments of ICI therapeutic antibodies in milligram quantities sufficient for structural studies, taking examples of the PD-1/pembrolizumab Fv and CTLA-4-ipilimumab Fv complexes.

Combining random microseed matrix screening and the magic triangle for the efficient structure solution of a potential lysin from bacteriophage P68

Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.

Iterative screen optimization maximizes the efficiency of macromolecular crystallization

Advances in X-ray crystallography have streamlined the process of determining high-resolution three-dimensional macromolecular structures. However, a rate-limiting step in this process continues to be the generation of crystals that are of sufficient size and quality for subsequent diffraction experiments. Here, iterative screen optimization (ISO), a highly automated process in which the precipitant concentrations of each condition in a crystallization screen are modified based on the results of a prior crystallization experiment, is described. After designing a novel high-throughput crystallization screen to take full advantage of this method, the value of ISO is demonstrated by using it to successfully crystallize a panel of six diverse proteins. The results suggest that ISO is an effective method to obtain macromolecular crystals, particularly for proteins that crystallize under a narrow range of precipitant concentrations.

Modulating Self-Assembly of DNA Crystals with Rationally Designed Agents

This manuscript reports a strategy for controlling the crystallization kinetics and improving the quality of engineered self-assembled 3D DNA crystals. Growing large, high-quality biomacromolecule crystals is critically important for determining the 3D structures of biomacromolecules. It often presents a great challenge to structural biologists. Herein, we introduce a rationally designed agent to modulate the crystallization process. Under such conditions, fewer, but larger, crystals that yield diffraction patterns of modestly higher resolution are produced compared with the crystals from conditions without the modulating agent. We attribute the improvement to a smaller number of nuclei and slow growth rate of crystallization. This strategy is expected to be generally applicable for crystallization of other biomacromolecules.

Simulation Time Required for Diminishing the Initial Conformational Deviations among Protein Crystal Structures

Multiple crystal structures of a single kind of protein can be generally separated into several groups from their conformational deviations. A major factor causing the structural separation is the space group of crystals, in which precipitating agents have a strong influence on the packing of proteins in a crystal. In this study, we examined whether the separated groups of protein crystal structures can be merged into one group by computer simulation without a precipitating agent. The crystal structures of hen egg-white lysozyme (HEWL), myoglobin (Mb), hemoglobin (Hb), and human serum albumin (HSA) were selected as samples for molecular dynamics (MD) simulation. For example, 25 MD simulations were performed for HEWL, with 25 computational models being built from different crystal structures. Cluster analysis was applied to 25 snapshot structures obtained at the same time point from the respective simulation trajectories and the cluster analysis was repeated every 5 ns during the simulations. As a result, the separated cluster groups were basically merged into one group with only a few exceptions. In HEWL, noticeable conformational changes from the crystal structures were observed after heating. The dependence of the simulated structures on the initial crystals was diminished, and all of the clusters were merged into one group at 20 ns of MD simulation. In Mb, all of the clusters were merged into one group at 10 ns. For Hb and HSA, the time necessary for merging the structures became longer. In Hb, the initial group separation gradually became ambiguous after pre-equilibration, and the time required for diminishing the dependence on the crystal structure was 130 ns except for one cluster group. In HSA, 160 ns was necessary for all of the clusters to be merged into one group. These times provide important index for judging the equilibration of protein simulations.

Growing Protein Crystals with Distinct Dimensions Using Automated Crystallization Coupled with In Situ Dynamic Light Scattering

The automated crystallization device is a patented technique1 especially developed for monitoring protein crystallization experiments with the aim to precisely maneuver the nucleation and crystal growth towards desired sizes of protein crystals. The controlled crystallization is based on sample investigation with in situ Dynamic Light Scattering (DLS) while all visual changes in the droplet are monitored online with the help of a microscope coupled to a CCD camera, thus enabling a full investigation of the protein droplet during all stages of crystallization. The use of in situ DLS measurements throughout the entire experiment allows a precise identification of the highly supersaturated protein solution transitioning to a new phase – the formation of crystal nuclei. By identifying the protein nucleation stage, the crystallization can be optimized from large protein crystals to the production of protein microcrystals. The experimental protocol shows an interactive crystallization approach based on precise automated steps such as precipitant addition, water evaporation for inducing high supersaturation, and sample dilution for slowing induced homogeneous nucleation or reversing phase transitions.

Tailored Robust Hydrogel Composite Membranes for Continuous Protein Crystallization with Ultrahigh Morphology Selectivity

The tailored and robust hydrogel composite membranes (HCMs) with diverse ion adsorption and interfacial nucleation property are prepared and successfully used in the continuous lysozyme crystallization. Beyond the heterogeneous supporter, the HCMs functioning as an interface ion concentration controller and nucleation generator are demonstrated. By constructing accurately controlled nucleation and growth circumstances in the HCM-equipped membrane crystallizer, the target desired morphology (hexagon cube) and brand-new morphology (multiple flower shape) that differ from the ones created in the conventional crystallizer are continuously and repetitively generated with ultrahigh morphology selectivity. These tailored robust HCMs show great potential for improving current approaches to continuous protein crystallization with specific crystal targets from laboratorial research to actual engineering applications.

19F NMR as a Tool for Monitoring Individual Differentially Labeled Proteins in Complex Mixtures

The ability to monitor the behavior of individual proteins in complex mixtures has many potential uses, ranging from analysis of protein interactions in highly concentrated solutions, modeling biological fluids or the intracellular environment, to optimizing biopharmaceutical co-formulations. Differential labeling NMR approaches, which traditionally use ¹⁵N or ¹³C isotope incorporation during recombinant expression, are not always practical in cases when endogenous proteins are obtained from an organism, or where the expression system does not allow for efficient labeling, especially for larger proteins. This study proposes differential labeling of proteins by covalent attachment of ¹⁹F groups with distinct chemical shifts, giving each protein a unique spectral signature which can be monitored by ¹⁹F NMR without signal overlap, even in complex mixtures, and without any interfering signals from the buffer or other unlabeled components. Parameters, such as signal intensities, translational diffusion coefficients, and transverse relaxation rates, which report on the behavior of individual proteins in the mixture, can be recorded even for proteins as large as antibodies at a wide range of concentrations.

Characterizing metal-binding sites in proteins with X-ray crystallography

Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.

Application of Empirical Phase Diagrams for Multidimensional Data Visualization of High-Throughput Microbatch Crystallization Experiments

Protein phase diagrams are a tool to investigate the cause and consequence of solution conditions on protein phase behavior. The effects are scored according to aggregation morphologies such as crystals or amorphous precipitates. Solution conditions affect morphologic features, such as crystal size, as well as kinetic features, such as crystal growth time. Commonly used data visualization techniques include individual line graphs or phase diagrams based on symbols. These techniques have limitations in terms of handling large data sets, comprehensiveness or completeness. To eliminate these limitations, morphologic and kinetic features obtained from crystallization images generated with high throughput microbatch experiments have been visualized with radar charts in combination with the empirical phase diagram method. Morphologic features (crystal size, shape, and number, as well as precipitate size) and kinetic features (crystal and precipitate onset and growth time) are extracted for 768 solutions with varying chicken egg white lysozyme concentration, salt type, ionic strength, and pH. Image-based aggregation morphology and kinetic features were compiled into a single and easily interpretable figure, thereby showing that the empirical phase diagram method can support high-throughput crystallization experiments in its data amount as well as its data complexity.

Cromoglycate mesogen forms isodesmic assemblies promoted by peptides and induces aggregation of a range of proteins

Disodium cromoglycate (5′DSCG) belongs to a class of nonamphiphilic molecules that form nematic chromonic liquid crystals in aqueous solutions. As the concentration increases, it is believed that the molecules first form isodesmic assemblies in water, which further align to form liquid crystal phases. However, the reports on isodesmic assemblies of 5′DSCG have been scarce. Herein, we show that the presence of peptides can promote the isodesmic assembly of 5′DSCG over a broad range of concentrations before reaching the liquid crystal phase. The presence of peptides can lower the 5′DSCG concentration in the aqueous solution to ∼1.5 wt% (from 11–12 wt%, forming a nematic liquid crystal phase) for isodesmic assembly formation. This result indicates a demixing between 5′DSCG and peptides in aqueous solution. We further explored this demixing mechanism to precipitate a wide range of proteins, namely, lectin A, esterase, lipase, bovine serum albumin, trypsin, and a pilin protein from bacterium Pseudomonas aeruginosa. We found that 5′DSCG caused the aggregation of all these proteins except trypsin. These results, along with past findings, suggest that 5′DSCG isodesmic assemblies have the potential to assist in protein purification and crystallization.

5′DSCG molecules form isodesmic assembly in the presence of peptides, and cause a wide range of proteins to aggregate.

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

Solutions of lysozyme in heavy water were studied by small-angle neutron scattering (SANS) at concentrations of 40, 20 and 10 mg ml^-1 with and without the addition of precipitant, and at temperatures of 10, 20 and 30°C. In addition to the expected protein monomers, dimeric and octameric species were identified in solutions at the maximum concentration and close to the optimal conditions for crystallization. An optimal temperature for octamer formation was identified and both deviation from this temperature and a reduction in protein concentration led to a significant decrease in the volume fractions of octamers detected. In the absence of precipitant, only monomers and a minor fraction of dimers are present in solution.

Sub-Micron Polymeric Stomatocytes as Promising Templates for Confined Crystallization and Diffraction Experiments

The possibility of using sub-micrometer polymeric stomatocytes is investigated to effectuate confined crystallization of inorganic compounds. These bowl-shaped polymeric compartments facilitate confined crystallization while their glassy surfaces provide their crystalline cargos with convenient shielding from the electron beam's harsh effects during transmission electron microscopy experiments. Stomatocytes host the growth of a single nanocrystal per nanocavity, and the electron diffraction experiments reveal that their glassy membranes do not interfere with the diffraction patterns obtained from their crystalline cargos. Therefore, it is expected that the encapsulation and crystallization within these compartments can be considered as a promising template (nanovials) that hold and protect nanocrystals and protein clusters from the direct radiation damage before data acquisition, while they are examined by modern crystallography methodologies such as serial femtosecond crystallography.

Effect of nucleants in photothermally assisted crystallization

Laser-induced crystallization is emerging as a promising technique to crystallize biomolecules like amino acids and proteins. The use of external materials as nucleants and novel seeding methods open new paths for protein crystallization. We report here the results of experiments that explore the effect of nucleants on laser-based crystallization of microlitre droplets of small molecules, amino acids, and proteins. The role of parameters like solute concentration, droplet volume, type and size of the nucleant, and laser power, are systematically investigated. In addition to crystallization of standard molecules like NaCl, KCl, and glycine, we demonstrate the crystallization of negatively (l-histidine), and positively (l-aspartic acid) charged amino acids and lysozyme protein. Single crystal X-ray diffraction and Raman spectroscopy studies unequivocally indicate that the nucleants do not alter the molecular structure of glycine, hydrogen bonding patterns, and packing. Localized vaporization of the solvent near the nucleant due to photothermal heating has enabled us to achieve rapid crystallization - within 3 s - at laser intensities of 0.1 MW cm^-2, significantly lower than those reported earlier, with both saturated and unsaturated solutions. The outcome of the current experiments may be of utility in tackling various crystallization problems during the formation of crystals large enough to perform X-ray crystallography.