Biomolecule imprinting: Developments in mimicking dynamic natural recognition systems

The principle of molecular imprinting has repeatedly been proven a successful and effective means of creating sites of specific recognition within polymers. After almost three decades of development, we finally have some evidence of large molecule imprinting. In this review, the authors aim to bring the molecular imprinting community up-to-date. We describe here some of the new and innovative work that endeavours to take molecular imprinting away from its chromatographic, synthetic past and make use of this technique in new, exciting and developing fields, such as drug delivery, biotechnology, biosensors, protein/drug recognition and in the development of novel materials. The main discussion analyses a variety of different two-dimensional and three-dimensional approaches recently developed for the recognition of larger molecules or biomolecules, such as proteins, viruses and cells, and how the traditional imprinting methods have been adapted to suit the mass transfer requirements of these biological templates. We also review a relatively new technique that has emerged from the imprinting approach, which aims to develop novel materials from the imprints of biological materials.     

Molecular imprinting of nitrophenol and hydroxybenzoic acid isomers: effect of molecular structure and acidity on imprinting

Three nitrophenol isomer-imprinted polymers were prepared under the same conditions using 4-vinylpyridine as a functional monomer. Different recognition capacities for template molecules were observed for the three polymers. Another imprinting system with stronger acidity than nitrophenol isomers, 2-hydroxybenzoic acid (salicylic acid) and 4-hydroxybenzoic acid, was imprinted using 4-vinylpyridine or acrylamide as functional monomer respectively. Both 4-hydroxybenzoic acid-imprinted polymers using the two monomers showed recognition ability for the template molecule. However, when acrylamide was chosen as functional monomer, the salicylic acid-imprinted polymer showed very weak recognition for the template molecule, whereas strong recognition ability of the resultant polymer for salicylic acid was observed with 4-vinylpyridine as functional monomer. It seems that the structure and acidity of template molecules is responsible for the difference in recognition, by influencing the formation and strength of interaction between template molecule and functional monomer during the imprinting process. An understanding of the mechanism of molecular imprinting and molecular recognition of MIPs will help to predict the selectivity of MIPs on the basis of template molecule properties.     

An innovative approach to molecularly imprinted capillaries for polar templates by grafting polymerization

Molecularly imprinted polymers have been successfully used as selective stationary phases in capillary electrophoresis. Notwithstanding, this technique suffers from several drawbacks as the loss of molecular recognition properties in aqueous media and the lack of feasibility for imprinted systems directed towards highly polar templates soluble in aqueous environments only. Thus, the preparation of imprinted polymers for highly polar, water-soluble analytes, represents a challenge. In this work, we present an innovative approach to overcome these drawbacks. It is based on a surface molecular imprinting technique that uses preformed macromonomers as both functional recognition elements and cross-linking agents. A poly-2-hydroxyethyl-co-methacrylic acid linear polymer was grafted from the surface of silica capillaries. The grafted polymer was exhaustively esterified with methacrylic anhydride to obtain polyethylendimethacrylate-co-methacrylic acid linear chains. Then, as a proof of concept, an adequate amount of a very polar template like penicillin V was added in a hydro-organic mixture, and a thin layer of imprinted polymer was obtained by cross-linking the polymer linear chains. The binding behaviour of the imprinted and non-imprinted capillaries was evaluated in different separation conditions in order to assess the presence of template selectivity and molecular recognition effects. The experimental results clearly show that this innovative kind of imprinted material can be easily obtained in very polar polymerization environments and that it is characterized by enhanced molecular recognition properties in aqueous buffers and good selectivity towards the template and strictly related molecules.     

Multiple Protein-immobilized Phospholipid Polymer Nanoparticles: Effect of Spacer Length on Residual Enzymatic Activity and Molecular Diagnosis

We report the development of phosphorylcholine (PC) group-covered nanoparticles for multiple immobilization reactions; the surface of these nanoparticles facilitates bioreactions such as enzymatic reactions and molecular diagnoses. The nanoparticles were covered with a bioconjugate PC group containing a polymer backbone, and their surface properties were as follows: (1) suppression of nonspecific protein adsorption and (2) stabilization of immobilized biomolecules. In this study, biomolecules were immobilized on PC-covered nanoparticles by using different spacer lengths between the polymer backbone and biomolecules. The stability of the immobilized biomolecules was evaluated using horseradish peroxidase-labeled IgG, and the bioconjugate nanoparticles were stored at 4, 25, and 40 °C. The residual enzymatic activity of the peroxidase was monitored at a particular time. On the other hand, to test the role of these nanoparticles in molecular diagnosis, we used IgG-conjugated nanoparticles and the fluorescence resonance energy transfer (FRET) phenomenon. The IgG molecules were labeled with either donor or acceptor molecules, and each labeled IgG was simultaneously immobilized on the PC-covered nanoparticles. These labeled IgG molecules induce the FRET phenomenon upon capture of the target antigen provided they are in close proximity. The resulting fluorescence was readable via the FRET phenomenon. In the present study, C-reactive protein (CRP) was used as the target antigen, and the effect of the spacer length is discussed. The bioconjugated nanoparticles covered with PC groups are promising tools for tuning bioreactions.     

Inorganic nanoparticles for multimodal molecular imaging

Multimodal molecular imaging can offer a synergistic improvement of diagnostic ability over a single imaging modality. Recent development of hybrid imaging systems has profoundly impacted the pool of available multimodal imaging probes. In particular, much interest has been focused on biocompatible, inorganic nanoparticle-based multimodal probes. Inorganic nanoparticles offer exceptional advantages to the field of multimodal imaging owing to their unique characteristics, such as nanometer dimensions, tunable imaging properties, and multifunctionality. Nanoparticles mainly based on iron oxide, quantum dots, gold, and silica have been applied to various imaging modalities to characterize and image specific biologic processes on a molecular level. A combination of nanoparticles and other materials such as biomolecules, polymers, and radiometals continue to increase functionality for in vivo multimodal imaging and therapeutic agents. In this review, we discuss the unique concepts, characteristics, and applications of the various multimodal imaging probes based on inorganic nanoparticles.     

Fragment molecular orbital calculations for biomolecules

Exploring biomolecule behavior, such as proteins and nucleic acids, using quantum mechanical theory can identify many life science phenomena from first principles. Fragment molecular orbital (FMO) calculations of whole single particles of biomolecules can determine the electronic state of the interior and surface of molecules and explore molecular recognition mechanisms based on intermolecular and intramolecular interactions. In this review, we summarized the current state of FMO calculations in drug discovery, virology, and structural biology, as well as recent developments from data science.     

Characterizing rare-event property distributions via replicate molecular dynamics simulations of proteins

As computational resources increase, molecular dynamics simulations of biomolecules are becoming an increasingly informative complement to experimental studies. In particular, it has now become feasible to use multiple initial molecular configurations to generate an ensemble of replicate production-run simulations that allows for more complete characterization of rare events such as ligand-receptor unbinding. However, there are currently no explicit guidelines for selecting an ensemble of initial configurations for replicate simulations. Here, we use clustering analysis and steered molecular dynamics simulations to demonstrate that the configurational changes accessible in molecular dynamics simulations of biomolecules do not necessarily correlate with observed rare-event properties. This informs selection of a representative set of initial configurations. We also employ statistical analysis to identify the minimum number of replicate simulations required to sufficiently sample a given biomolecular property distribution. Together, these results suggest a general procedure for generating an ensemble of replicate simulations that will maximize accurate characterization of rare-event property distributions in biomolecules.     

Use of biomolecular templates for the fabrication of metal nanowires

The nano-scale spatial organization of metallic and other inorganic materials into 1D objects is a key task in nanotechnology. Nano-scale fibers and tubes are very useful templates for such organization because of their inherent 1D organization. Fibrillar biological molecules and biomolecular assemblies are excellent physical supports on which to organize the inorganic material. Furthermore, these biological assemblies can facilitate high-order organization and specific orientation of inorganic structures by their utilization of highly specific biological recognition properties. In this minireview, I will describe the use of biomolecules and biomolecular assemblies, including DNA, proteins, peptides, and even viral particles, which are excellent templates for 1D organization of inorganic materials into wires. This ranges from simple attempts at electroless deposition on inert biological templates to the advanced use of structural motifs and specific protein-DNA interactions for nano-bio-lithography as well as the fabrication of multilayer organic and inorganic composites. The potential technological applications of these hybrid biological-inorganic assemblies will be discussed.     

Reversibly switchable DNA nanocompartment on surfaces

Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartments on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartments are used to encage molecules, switched by the collective effect of Watson–Crick base-pairing interactions. This effect is used to perform molecular recognition. Furthermore, we found that ‘fuel’ strands with single-base variation cannot afford an efficient closing of nanocompartments, which allows highly sensitive label-free DNA array detection. Our results suggest that DNA nanocompartments can be used as building blocks for complex biomaterials because its core functions are independent of substrates and mediators.     

The possible role of soluble salts in chemical evolution

Summary A model is proposed for a prebiotic environment in which concentration, condensation, and chemical evolution of biomolecules could have taken place. The main reactions expected of proteins, nucleic acids, lipids, and some of their precursors in this environment are examined.The model is based on our previously developed concept of a fluctuating system in which hydration and dehydration processes take place in a cyclic manner. In the present model, however, high concentrations of soluble salts, such as chlorides and sulfates, are taken into account, whereas previously a more or less salt-free system had been assumed. Thus the preponderance of surfaces of soluble salts is implied, even though sparingly soluble minerals, such as clay minerals or quartz, are also present.During the dehydration stage biomolecules tend to leave the solution and concentrate at certain microenvironments, such as in micelles and aggregates, at the liquid-gas surface and, possibly, at the emerging solid surfaces. Moreover, in these brines, and especially during the last stages of dehydration, high temperatures are attainable, which may enhance certain reactions between the organic molecules, and result in a net increase of condensation over degradation.In the dehydrated state, solid-state condensation and synthesis reactions are possible in which the surface of soluble salts may serve as a catalyst. Several reports in the literature support this hypothesis. Hydration brings about dissolution of the minerals and redistribution of the biomolecules. In such a system, evolutionary processes like those postulated by White (1980) and by Lahav and White (1980) are possible. Moreover, since several soluble salts of known geological occurrence are optically active in their crystalline state, the involvement of the model system in the selection and evolution of chiral organic compounds should also be considered. In addition, organic molecules in the above microenvironments are also expected to undergo selective interactions based on factors such as molecular pattern and chiral recognition and hydrophobicity. The proposed system emphasizes the need to develop the theoretical background and experimental methods for the study of interactions among biomolecules in the presence of high salt concentrations and solid surfaces of soluble salts, as well as interactions between the biomolecules and these surfaces.     

Bioimprinting strategies: From soft lithography to biomimetic sensors and beyond

Imprinting is a straightforward, yet a reliable technique to develop dynamic artificial recognition materials—so called as synthetic antibodies. Surface imprinting strategies such as soft lithography allow biological stereotyping of polymers and sol–gel phases to prepare extremely selective receptor layers, which can be combined with suitable transducer systems to develop high performance biomimetic sensors. This article presents an overview of the remarkable technical advancements in the field of surface bioimprinting with particular emphasis on surface imprinted bioanalyte detection systems and their applications in rapid bioanalysis and biotechnology. Herein, we discuss a variety of surface imprinting strategies including soft lithography, template immobilization, grafting, emulsion polymerization, and others along with their biomimetic sensor applications, merits and demerits. The pioneering research works on surface patterned biosensors are described with selected examples of detecting biological agents ranging from small biomolecules and proteins to living cells and microorganisms.     

Recent Development of Quinoxaline Based Polymers/Small Molecules for Organic Photovoltaics

Among the various molecular designs developed for the synthesis of conjugated polymers and small molecules for optoelectronic applications, the donor: acceptor (D–A) approach is the most widely explored method over the past decades. Through the covalent linkage of electron‐rich and electron‐deficient units, a plethora of medium‐low band gap materials has been developed and tested in organic photovoltaic devices. In particular, the quinoxaline aromatic structure and its derivatives are among the most studied electron deficient aromatic units used in D–A structures. Quinoxaline based materials are endowed with characteristics that are useful for large scale production in real world applications, such as easy synthetic procedures and excellent stability in air. Moreover, the use of quinoxaline based polymers/small molecules in bulk heterojunction (BHJ) devices led to power conversion efficiencies over 9%. Considering the potential of quinoxaline based materials, this review gathers together quinoxaline based polymers and small molecules reported in the literature during the last 5 years, summarizing and discussing the structure‐properties relationships for this class of organic semiconductors, aiming to serve as a background and to promote efforts for the further development of new quinoxaline derivatives with improved and advanced properties for future applications.     

Protein-polymer conjugates: synthetic approaches by controlled radical polymerizations and interesting applications

Protein-polymer conjugates are of interest to researchers in diverse fields. Attachment of polymers to proteins results in improved pharmacokinetics, which is important in medicine. From an engineering standpoint, conjugates are exciting because they exhibit properties of both the biomolecules and synthetic polymers. This allows the activity of the protein to be altered or tuned, anchoring to surfaces, and supramolecular self-assembly. Thus, there is broad interest in straightforward synthetic methods to prepare protein-polymer conjugates. Controlled radical polymerization (CRP) techniques have emerged as excellent strategies to make conjugates because the resulting polymers have narrow molecular weight distributions, targeted molecular weights, and attach to specific sites on proteins. Herein, recent advances in the synthesis and application of protein-polymer conjugates by CRP are highlighted.     

Protein semi-synthesis: new proteins for functional and structural studies

Our ability to alter and control the structure and function of biomolecules, and of proteins in particular, will be of utmost importance in order to understand their respective biological roles in complex systems such as living organisms. This challenge has prompted the development of powerful modern techniques in the fields of molecular biology, physical biochemistry and chemical biology. These fields complement each other and their successful combination has provided unique insights into protein structure and function at the level of isolated molecules, cells and organisms. Chemistry is without doubt most suited for introducing subtle changes into biomolecules down to the atomic level, but often struggles when it comes to large targets, such as proteins. In this review, we attempt to give an overview of modern and broadly applicable techniques that permit chemical synthesis to be applied to complex protein targets in order to gain control over their structure and function. As will be demonstrated, these approaches offer unique possibilities in our efforts to understand the molecular basis of protein functioning in vitro and in vivo. We will discuss modern synthetic reactions that can be applied to proteins and give examples of recent highlights. Another focus of this review will be the application of inteins as versatile protein engineering tools.     

Molecular simulation for predicting the rheological properties of polymer melts

ABSTRACT

Bottom-up prediction that links materials chemistry to their properties is a constant theme in polymer simulation. Rheological properties are particularly challenging to predict because of the extended time scales involved as well as large uncertainty in the stress output from molecular simulation. This review focuses on the application of molecular simulation in the prediction of such properties, including approaches solely based on molecular simulation and its integration with rheological models. Most attention is given to the prediction of quantitative properties, in particular, those most studied such as shear viscosity and linear viscoelasticity. Studies on the fundamental understanding of rheology are referenced only when they are directly relevant to the property prediction. The review starts with an overview of the major methods for extracting rheological properties from molecular simulation, using bead-spring chain models as a sandbox system. It then discusses materials-specific prediction using chemically-realistic models, including systematically coarse-grained models that allow the mapping between scales. Finally, integrating molecular simulation with rheological models extends the prediction to highly entangled polymers. Recent development of several multiscale predictive frameworks allowed the successful prediction of rheological properties from the chemical structure for polymers of experimentally relevant molecular weights.     

Mechanical equilibrium,a prerequisite to unveil auxetic properties in molecular compounds

The unique physical properties of auxetic compounds make them very attractive materials. Nevertheless, no synthesised materials known to exhibit negative Poisson’s ratio at the molecular level have been made. One way to explore such compounds is to predict potential candidates prior to their synthesis. To achieve it, multi-atom simulation is a powerful predicting tool. However, the lack of existing systems means that the crucial step of validation cannot be carried out. This paper aims to provide a procedure to predict the auxeticity of proposed molecular systems. The strategy is based on first revealing the determinant step in reaching the mechanical equilibrium of existing isotropic compounds such as polymers, or organic glasses, to compute efficiently mechanical properties. The Poisson’s ratio is found in good agreement with experimental data. The procedure is thus modified to be applied to anisotropic compounds, liquid crystals. The agreement with experimental behaviour allowed us to extrapolate the procedure to potentially auxetic compounds, thus offering great opportunities to reveal auxetic properties prior to the synthesis of the molecules.     

Hyaluronan and its catabolic products in tissue injury and repair.

Hyaluronan is an unbiquitous glycosaminoglycan present in most tissues. Under homeostatic conditions hyaluronan exists as a high molecular mass polymer that has important roles in tissue structural integrity. Under conditions of stress such as following tissue injury, hyaluronan becomes depolymerized and lower molecular mass polymers are generated. The biological properties of these hyaluronan fragments appear to be distinct from the larger precursor molecules. This review examines the biological role of hyaluronan fragments in tissue injury and repair.     

Structure and interactions of aggrecans: statistical thermodynamic approach

Weak polyelectrolytes tethered to cylindrical surfaces are investigated using a molecular theory. These polymers form a model system to describe the properties of aggrecan molecules, which is one of the main components of cartilage. We have studied the structural and thermodynamical properties of two interacting aggrecans with a molecular density functional theory that incorporates the acid-base equilibrium as well as the molecular properties: including conformations, size, shape, and charge distribution of all molecular species. The effect of acidity and salt concentration on the behavior is explored in detail. The repulsive interactions between two cylindrical-shaped aggrecans are strongly influenced by both the salt concentration and the pH. With increasing acidity, the polyelectrolytes of the aggrecan acquire charge and with decreasing salt concentration those charges become less screened. Consequently the interactions increase in size and range with increasing acidity and decreasing salt concentration. The size and range of the forces offers a possible explanation to the aggregation behavior of aggrecans and for their ability to resist compressive forces in cartilage. Likewise, the interdigitation of two aggrecan molecules is strongly affected by the salt concentration as well as the pH. With increasing pH, the number of charges increases, causing the repulsions between the polymers to increase, leading to a lower interdigitation of the two cylindrical polymer layers of the aggrecan molecules. The low interdigitation in charged polyelectrolytes layers provides an explanation for the good lubrication properties of polyelectrolyte layers in general and cartilage in particular.     

Label-enhanced surface plasmon resonance applied to label-free interaction analysis of small molecules and fragments

Surface plasmon resonance (SPR) is a well-established method for studying interactions between small molecules and biomolecules. In particular, SPR is being increasingly applied within fragment-based drug discovery; however, within this application area, the limited sensitivity of SPR may constitute a problem. This problem can be circumvented by the use of label-enhanced SPR that shows a 100-fold higher sensitivity as compared with conventional SPR. Truly label-free interaction data for small molecules can be obtained by applying label-enhanced SPR in a surface competition assay format. The enhanced sensitivity is accompanied by an increased specificity and inertness toward disturbances (e.g., bulk refractive index disturbances). Label-enhanced SPR can be used for fragment screening in a competitive assay format; the competitive format has the added advantage of confirming the specificity of the molecular interaction. In addition, label-enhanced SPR extends the accessible kinetic regime of SPR to the analysis of very fast fragment binding kinetics. In this article, we demonstrate the working principles and benchmark the performance of label-enhanced SPR in a model system—the interaction between carbonic anhydrase II and a number of small-molecule sulfonamide-based inhibitors.