Imprinted polymers assisting protein crystallization

Preparation and Characterization of Metal-Organic Framework Coatings for Improving Protein Crystallization Screening

Modifying crystallization plates can significantly impact the success rate and quality of protein crystal growth, making it a helpful strategy in protein crystallography. However, appropriate methods for preparing nano-sized particles with a high specific surface area and strategies for applying these nanoparticles to form suitable coatings on crystallization plate surfaces still need to be clarified. Here, we utilized both an ultrasonic crusher and a high-pressure homogenizer to create a nano metal-organic framework (MOF), specifically HKUST-1, and introduced a solvent evaporation method for producing MOF coatings on 96-well crystallization plates to induce protein crystal growth. The morphology of MOF coatings on the resin surface of the plate well was characterized using optical and scanning electron microscopy. Compared to the control group, crystallization screening experiments on nine proteins confirmed the effectiveness of plates with MOF coatings. Applying MOF coatings to crystallization plates is an easy-to-use, time-efficient, and potent tool for initiating crystallization experiments.

Molecularly Imprinted Polymer-Based Sensors for the Detection of Skeletal- and Cardiac-Muscle-Related Analytes

Molecularly imprinted polymers (MIPs) are synthetic polymers with specific binding sites that present high affinity and spatial and chemical complementarities to a targeted analyte. They mimic the molecular recognition seen naturally in the antibody/antigen complementarity. Because of their specificity, MIPs can be included in sensors as a recognition element coupled to a transducer part that converts the interaction of MIP/analyte into a quantifiable signal. Such sensors have important applications in the biomedical field in diagnosis and drug discovery, and are a necessary complement of tissue engineering for analyzing the functionalities of the engineered tissues. Therefore, in this review, we provide an overview of MIP sensors that have been used for the detection of skeletal- and cardiac-muscle-related analytes. We organized this review by targeted analytes in alphabetical order. Thus, after an introduction to the fabrication of MIPs, we highlight different types of MIP sensors with an emphasis on recent works and show their great diversity, their fabrication, their linear range for a given analyte, their limit of detection (LOD), specificity, and reproducibility. We conclude the review with future developments and perspectives.

Heterogeneous Nucleation in Protein Crystallization

Protein crystallization was first discovered in the nineteenth century and has been studied for nearly 200 years. Protein crystallization technology has recently been widely used in many fields, such as drug purification and protein structure analysis. The key to successful crystallization of proteins is the nucleation in the protein solution, which can be influenced by many factors, such as the precipitating agent, temperature, solution concentration, pH, etc., among which the role of the precipitating agent is extremely important. In this regard, we summarize the nucleation theory of protein crystallization, including classical nucleation theory, two-step nucleation theory, and heterogeneous nucleation theory. We focus on a variety of efficient heterogeneous nucleating agents and crystallization methods as well. The application of protein crystals in crystallography and biopharmaceutical fields is further discussed. Finally, the bottleneck of protein crystallization and the prospect of future technology development are reviewed.

Protein Crystals Nucleated and Grown by Means of Porous Materials Display Improved X-ray Diffraction Quality

Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass (“Naomi’s Nucleant”), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.

Application of Polymers as a Tool in Crystallization-A Review

The application of polymers as a tool in the crystallization process is gaining more and more interest among the scientific community. According to Web of Science statistics the number of papers dealing with “Polymer induced crystallization” increased from 2 in 1990 to 436 in 2020, and for “Polymer controlled crystallization”—from 4 in 1990 to 344 in 2020. This is clear evidence that both topics are vivid, attractive and intensively investigated nowadays. Efficient control of crystallization and crystal properties still represents a bottleneck in the manufacturing of crystalline materials ranging from pigments, antiscalants, nanoporous materials and pharmaceuticals to semiconductor particles. However, a rapid development in precise and reliable measuring methods and techniques would enable one to better describe phenomena involved, to formulate theoretical models, and probably most importantly, to develop practical indications for how to appropriately lead many important processes in the industry. It is clearly visible at the first glance through a number of representative papers in the area, that many of them are preoccupied with the testing and production of pharmaceuticals, while the rest are addressed to new crystalline materials, renewable energy, water and wastewater technology and other branches of industry where the crystallization process takes place. In this work, authors gathered and briefly discuss over 100 papers, published in leading scientific periodicals, devoted to the influence of polymers on crystallizing solutions.

X-ray crystallographic studies of RoAb13 bound to PIYDIN, a part of the N-terminal domain of C-C chemokine receptor 5

C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.

Theoretical and experimental investigation of protein crystal nucleation in pores and crevices

The nucleation ability of pores is explained using the equilibration between the cohesive energy maintaining the integrity of a crystalline cluster and the destructive energy tending to tear it up. It is shown that to get 3D crystals it is vital to have 2D crystals nucleating in the pores first. By filling the pore orifice, the 2D crystal nuclei are more stable because their peripheries are protected from the destructive action of water molecules. Furthermore, the periphery of the 2D crystal is additionally stabilized as a result of its cohesion with the pore wall. The understanding provided by this study combining theory and experiment will facilitate the design of new nucleants.

Protein crystallisation with air bubble templates: case of gas–liquid–solid interfaces

Crystal formation on air bubble–liquid interface, as soft template to efficiently prompt nucleation of proteins.

Molecularly Imprinted Synthetic Antibodies: From Chemical Design to Biomedical Applications

Billions of dollars are invested into the monoclonal antibody market every year to meet the increasing demand in clinical diagnosis and therapy. However, natural antibodies still suffer from poor stability and high cost, as well as ethical issues in animal experiments. Thus, developing antibody substitutes or mimics is a long-term goal for scientists. The molecular imprinting technique presents one of the most promising strategies for antibody mimicking. The molecularly imprinted polymers (MIPs) are also called "molecularly imprinted synthetic antibodies" (MISAs). The breakthroughs of key technologies and innovations in chemistry and material science in the last decades have led to the rapid development of MISAs, and their molecular affinity has become comparable to that of natural antibodies. Currently, MISAs are undergoing a revolutionary transformation of their applications, from initial adsorption and separation to the rising fields of biomedicine. Herein, the fundamental chemical design of MISAs is examined, and then current progress in biomedical applications is the focus. Meanwhile, the potential of MISAs as qualified substitutes or even to transcend the performance of natural antibodies is discussed from the perspective of frontier needs in biomedicines, to facilitate the rapid development of synthetic artificial antibodies.

Charged polymeric additives affect the nucleation of lysozyme crystals

Charged polymers (PGA and PL) interact with lysozyme and then promote the heterogeneous nucleation of the crystals.

Peculiarities of Protein Crystal Nucleation and Growth

This paper reviews investigations on protein crystallization. It aims to present a comprehensive rather than complete account of recent studies and efforts to elucidate the most intimate mechanisms of protein crystal nucleation. It is emphasized that both physical and biochemical factors are at play during this process. Recently-discovered molecular scale pathways for protein crystal nucleation are considered first. The bond selection during protein crystal lattice formation, which is a typical biochemically-conditioned peculiarity of the crystallization process, is revisited. Novel approaches allow us to quantitatively describe some protein crystallization cases. Additional light is shed on the protein crystal nucleation in pores and crevices by employing the so-called EBDE method (equilibration between crystal bond and destructive energies). Also, protein crystal nucleation in solution flow is considered.

Antibody Biomimetic Material Made of Pyrrole for CA 15-3 and Its Application as Sensing Material in Ion-Selective Electrodes for Potentiometric Detection

This work reports a very simple approach for creating a synthetic antibody against any protein of interest and its application in potentiometric transduction. The selected protein was Breast Cancer Antigen (CA 15-3), which is implicated in breast cancer disease and used to follow-up breast cancer patients during treatment. The new material with antibody-like properties was obtained by molecular-imprinting technology, prepared by electropolymerizing pyrrol (Py, 5.0 × 10-3 mol/L) around Breast Cancer Antigen (CA 15-3) (100 U/mL) on a fluorine doped tin oxide (FTO) conductive glass support. Cyclic voltammetry was employed for this purpose. All solutions were prepared in 4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer, of pH 6.5. The biomarker was removed from the imprinted sites by chemical action of ethanol. The biomimetic material was then included in poly vinyl chloride (PVC) plasticized membranes to act as potentiometric ionophore, having or not a lipophilic ionic additive added. The corresponding selective electrodes were evaluated by calibration curves (in buffer and in synthetic serum) and by selectivity testing. The best analytical performance was obtained by selective electrodes including the plastic antibody and no lipophilic additive. The average limits of detection were 1.07 U/mL of CA 15-3, with a linear response from 1.44 to 13.2 U/mL and a cationic slope of 44.5 mV/decade. Overall, the lipophilic additives yielded no advantage to the overall potentiometric performance. The application of the MIP-based electrodes to the analysis of spiked synthetic serum showed precise and accurate results.

Protein crystal nucleation in pores

The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials.

A Capped Dipeptide Which Simultaneously Exhibits Gelation and Crystallization Behavior

Short peptides capped at their N-terminus are often highly efficient gelators, yet notoriously difficult to crystallize. This is due to strong unidirectional interactions within fibers, resulting in structure propagation only along one direction. Here, we synthesize the N-capped dipeptide, benzimidazole-diphenylalanine, which forms both hydrogels and single crystals. Even more remarkably, we show using atomic force microscopy the coexistence of these two distinct phases. We then use powder X-ray diffraction to investigate whether the single crystal structure can be extrapolated to the molecular arrangement within the hydrogel. The results suggest parallel β-sheet arrangement as the dominant structural motif, challenging existing models for gelation of short peptides, and providing new directions for the future rational design of short peptide gelators.

Preparation of molecularly imprinted polymers for the recognition of proteins via the generation of peptide-fragment binding sites by semi-covalent imprinting and enzymatic digestion

An acryloyl protein was copolymerized with a crosslinker, followed by enzymatic digestion, yielding protein imprinted polymers bearing peptide-fragment binding sites.

Preparation of metallic pivot-based imprinted monoliths with a hydrophilic macromonomer

The hydrophilic macromonomer oligo(ethyleneglycol) methyl ether methacrylate (OEG) was introduced into a metal ion-mediated MIP matrix to achieve good selectivity and less hydrophobic character.

Uniform core–shell molecularly imprinted polymers: a correlation study between shell thickness and binding capacity

A model of core–shell MIPs was constructed to evaluate the correlation between shell thickness and binding capacity.

Advances in nanocrystallography as a proteomic tool

In order to overcome the difficulties and hurdles too much often encountered in crystallizing a protein with the conventional techniques, our group has introduced the innovative Langmuir-Blodgett (LB)-based crystallization, as a major advance in the field of both structural and functional proteomics, thus pioneering the emerging field of the so-called nanocrystallography or nanobiocrystallography. This approach uniquely combines protein crystallography and nanotechnologies within an integrated, coherent framework that allows one to obtain highly stable protein crystals and to fully characterize them at a nano- and subnanoscale. A variety of experimental techniques and theoretical/semi-theoretical approaches, ranging from atomic force microscopy, circular dichroism, Raman spectroscopy and other spectroscopic methods, microbeam grazing-incidence small-angle X-ray scattering to in silico simulations, bioinformatics, and molecular dynamics, has been exploited in order to study the LB-films and to investigate the kinetics and the main features of LB-grown crystals. When compared to classical hanging-drop crystallization, LB technique appears strikingly superior and yields results comparable with crystallization in microgravity environments. Therefore, the achievement of LB-based crystallography can have a tremendous impact in the field of industrial and clinical/therapeutic applications, opening new perspectives for personalized medicine. These implications are envisaged and discussed in the present contribution.

Epitope imprinted polyethersulfone beads by self-assembly for target protein capture from the plasma proteome

Self-assembly techniques were applied to fabricate epitope imprinted polyethersulfone beads for target protein capture from the plasma proteome.