Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials

Mechanisms of Air Entraining of Proteins in Cementitious Materials

While few prior studies examined the air-entraining properties of proteins in cementitious materials, the underlying mechanisms of proteins' air entraining and the interactions between proteins and cement have not been studied in the past. The significance of this article is to address this knowledge gap by investigating the effect of proteins on relevant factors that affect air entraining in cement paste and establishing an understanding of the mechanism of air entrainment with proteins. These factors include the surface tension of pore solution, protein adsorption on cement particles, cement paste hydrophobization, and flow of fresh paste. Thirteen different proteins were used to investigate the effect of a wide range of protein characteristics on air entraining. Proteins decreased the pore solution surface tension to different degrees. At low concentrations, the adsorption of proteins on cement particles slightly affected the pore solution surface tension. Protein adsorption on cement particles showed a wide range of adsorption isotherms. Proteins generally increased the flow of paste due to electrostatic repulsion between cement particles because of the adsorption of negatively charged proteins on cement particles, as well as the ball-bearing effect of bubbles in fresh paste. The surface hydrophobicity was increased in pastes with proteins. A detailed microcomputed tomography (micro-CT) analysis showed very different air void microstructures in pastes with various proteins. While a relatively strong correlation was observed between air void porosity and surface hydrophobicity, the correlation between air void porosity and the surface tension of pore solution was weak. This indicates that the accumulation of hydrophobized cement particles on the air bubble in the fresh paste, refered to as the Pickering effect, is the main mechanism of air entraining of proteins in the paste. It was shown that a high air void porosity occurs in an intermediate range of flow.

Iron oxide magnetic aggregates: Aspects of synthesis, computational approaches and applications

Superparamagnetic magnetite nanoparticles have been central to numerous investigations in the past few decades for their use in many applications, such as drug delivery, medical diagnostics, magnetic separation, and material science. However, the properties of single magnetic nanoparticles are sometimes not sufficient to accomplish tasks where a strong magnetic response is required. In light of this, aggregated magnetite nanoparticles have been proposed as an alternative advanced material, which may expand and combine some of the advantages of single magnetic nanoparticles, including superparamagnetism, with an enhanced magnetic moment and increased colloidal stability. This review comprehensively discusses the current literature on aggregates made of magnetic iron oxide nanoparticles. This review is divided into three sections. First, the current synthetic strategies for magnetite nanoparticle aggregates are discussed, together with the influence of different stabilizers on the primary crystals and the final aggregate size and morphology. The second section is dedicated to computational approaches, such as density functional methods (which permit accurate predictions of electronic and magnetic properties and shed light on the behavior of surfactant molecules on iron oxide surfaces) and molecular dynamics simulations (which provide additional insight into the influence of ligands on the surface chemistry of iron oxide nanocrystals). The last section discusses current and possible future applications of iron oxide magnetic aggregates, including wastewater treatment, water purification, medical applications, and magnetic aggregates for materials displaying structural colors.

Albumin Retains Its Transport Function after Interaction with Cerium Dioxide Nanoparticles

The interaction of inorganic nanomaterials with biological fluids containing proteins can lead not only to the formation of a protein corona and thereby to a change in the biological activity of nanoparticles but also to a significant effect on the structural and functional properties of the biomolecules themselves. This work studied the interaction of nanoscale CeO2, the most versatile nanozyme, with human serum albumin (HSA). Fourier transform infrared spectroscopy, MALDI-TOF mass spectrometry, UV-vis spectroscopy, and fluorescence spectroscopy confirmed the formation of HSA-CeO2 nanoparticle conjugates. Changes in protein conformation, which depend on the concentration of both citrate-stabilized CeO2 nanoparticles and pristine CeO2 nanoparticles, did not affect albumin drug-binding sites and, accordingly, did not impair the HSA transport function. The results obtained shed light on the biological consequences of the CeO2 nanoparticles' entrance into the body, which should be taken into account when engineering nanobiomaterials to increase their efficiency and reduce the side effects.

Peptide adsorption on silica surfaces: Simulation and experimental insights

The understanding of interactions between proteins with silica surface is crucial for a wide range of different applications: from medical devices, drug delivery and bioelectronics to biotechnology and downstream processing. We show the application of EISM (Effective Implicit Surface Model) for discovering the set of peptide interactions with silica surface. The EISM is employed for a high-speed computational screening of peptides to model the binding affinity of small peptides to silica surfaces. The simulations are complemented with experimental data of peptides with silica nanoparticles from microscale thermophoresis and from infrared spectroscopy. The experimental work shows excellent agreement with computational results and verifies the EISM model for the prediction of peptide-surface interactions. 57 peptides, with amino acids favorable for adsorption on Silica surface, are screened by EISM model for obtaining results, which are worth to be considered as a guidance for future experimental and theoretical works. This model can be used as a broad platform for multiple challenges at surfaces which can be applied for multiple surfaces and biomolecules beyond silica and peptides.

Probing Adsorption of Dipeptides on Anatase in H2 O and D2 O: Thermodynamics and Molecular Geometry

Considering the vast importance of peptide and protein interactions with inorganic surfaces, probing hydrogen bonding during their adsorption on metal oxide surfaces is a relevant task that could shed light on the essential features of their interplay. This work is devoted to studying the dipeptides' adsorption on anatase nanoparticles (ANs) in light and heavy water to reveal differences arising upon the change of the major hydrogen bonding carrier. Thermodynamic study of six native dipeptides' adsorption on ANs in both media shows a strong influence of the solvent on the Gibbs free energy and the effect of side-chain mobile protons on the entropy of the process. The adsorption is endothermic irrespective of the medium and is entropy-driven. Computer simulations of peptide adsorption in both media shows similarity in binding via an amino group and demonstrates structural features of protonated and deuterated peptides in obtained complexes. Calculated peptide- anatase nanoparticle (AN) descriptors indicate surface oxygens as points of peptide-nanoparticle contacts.

Bare Iron Oxide Nanoparticles as Drug Delivery Carrier for the Short Cationic Peptide Lasioglossin

New drug delivery systems are a potential solution for administering drugs to reduce common side effects of traditional methods, such as in cancer therapy. Iron oxide nanoparticles (IONs) can increase the drugs’ biological activity through high binding efficiency and magnetically targeted drug delivery. Understanding the adsorption and release process of a drug to the carrier material plays a significant role in research to generate an applicable and controlled drug delivery system. This contribution focuses on the binding patterns of the peptide lasioglossin III from bee venom on bare IONs. Lasioglossin has a high antimicrobial behavior and due to its cationic properties, it has high binding potential. Considering the influence of pH, the buffer type, the particle concentration, and time, the highest drug loading of 22.7% is achieved in phosphate-buffered saline. Analysis of the desorption conditions revealed temperature and salt concentration sensitivity. The nanoparticles and peptide-ION complexes are analyzed with dynamic light scattering, zeta potential, and infrared spectroscopy. Additionally, cytotoxicity experiments performed on Escherichia coli show higher antimicrobial activity of bound lasioglossin than of the free peptide. Therefore, bare IONs are an interesting platform material for the development of drug-delivery carriers for cationic peptides.

Bio-nano interactions: binding proteins, polysaccharides, lipids and nucleic acids onto magnetic nanoparticles

The major interest in nanoparticles as an application platform for biotechnology arises from their high surface-to-volume ratio. Iron oxide nanoparticles (IONPs) are particularly appealing due to their superparamagnetic behavior, which enables bioseparation using external magnetic fields. In order to design advanced biomaterials, improve binding capacities and develop innovative processing solutions, a thorough understanding of the factors governing organic-inorganic binding in solution is critical but has not yet been achieved, given the wide variety of chemical and physical influences. This paper offers a critical review of experimental studies of the interactions between low cost IONPs (bare iron oxides, silica-coated or easily-functionalized surfaces) and the main groups of biomolecules: proteins, lipids, nucleic acids and carbohydrates. Special attention is devoted to the driving forces and interdependencies responsible of interactions at the solid-liquid interface, to the unique structural characteristics of each biomolecular class, and to environmental conditions influencing adsorption. Furthermore, studies focusing on mixtures, which are still rare, but absolutely necessary to understand the biocorona, are also included. This review concludes with a discussion of future work needed to fill the gaps in knowledge of bio-nano interactions, seeking to improve nanoparticles' targeting capabilities in complex systems, and to open the door for multipurpose recognition and bioseparation processes.

Buffer Influence on the Amino Acid Silica Interaction

Protein-surface interactions are exploited in various processes in life sciences and biotechnology. Many of such processes are performed in presence of a buffer system, which is generally believed to have an influence on the protein-surface interaction but is rarely investigated systematically. Combining experimental and theoretical methodologies, we herein demonstrate the strong influence of the buffer type on protein-surface interactions. Using state of the art chromatographic experiments, we measure the interaction between individual amino acids and silica, as a reference to understand protein-surface interactions. Among all the 20 proteinogenic amino acids studied, we found that arginine (R) and lysine (K) bind most strongly to silica, a finding validated by free energy calculations. We further measured the binding of R and K at different pH in presence of two different buffers, MOPS (3-(N-morpholino)propanesulfonic acid) and TRIS (tris(hydroxymethyl)aminomethane), and find dramatically different behavior. In presence of TRIS, the binding affinity of R/K increases with pH, whereas we observe an opposite trend for MOPS. These results can be understood using a multiscale modelling framework combining molecular dynamics simulation and Langmuir adsorption model. The modelling approach helps to optimize buffer conditions in various fields like biosensors, drug delivery or bio separation engineering prior to the experiment.

Rational Design of Iron Oxide Binding Peptide Tags

Owing to their extraordinary magnetic properties and low-cost production, iron oxide nanoparticles (IONs) are in the focus of research. In order to better understand interactions of IONs with biomolecules, a tool for the prediction of the propensity of different peptides to interact with IONs is of great value. We present an effective implicit surface model (EISM), which includes several interaction models. Electrostatic interactions, van der Waals interactions, and entropic effects are considered for the theoretical calculations. However, the most important parameter, a surface accessible area force field contribution term, derives directly from experimental results on the interactions of IONs and peptides. Data from binding experiments of ION agglomerates to different peptides immobilized on cellulose membranes have been used to parameterize the model. The work was carried out under defined environmental conditions; hence, effects because of changes, for example structure or solubility by changing the surroundings, are not included. EISM enables researchers to predict the binding of peptides to IONs, which we then verify with further peptide array experiments in an iterative optimization process also presented here. Negatively charged peptides were identified as best binders for IONs in Tris buffer. Furthermore, we investigated the constitution of peptides and how the amount and position of several amino acid side chains affect peptide-binding. The incorporation of glycine leads to higher binding scores compared to the incorporation of cysteine in negatively charged peptides.

Magnetic One-Step Purification of His-Tagged Protein by Bare Iron Oxide Nanoparticles

Magnetic separation is a promising alternative to conventional methods in downstream processing. This can facilitate easier handling, fewer processing steps, and more sustainable processes. Target materials can be extracted directly from crude cell lysates in a single step by magnetic nanoadsorbents with high-gradient magnetic fishing (HGMF). Additionally, the use of hazardous consumables for reducing downstream processing steps can be avoided. Here, we present proof of principle of one-step magnetic fishing from crude Escherichia coli cell lysate of a green fluorescent protein (GFP) with an attached hexahistidine (His6)-tag, which is used as the model target molecule. The focus of this investigation is the upscale to a liter scale magnetic fishing process in which a purity of 91% GFP can be achieved in a single purification step from cleared cell lysate. The binding through the His6-tag can be demonstrated, since no significant binding of nontagged GFP toward bare iron oxide nanoparticles (BIONs) can be observed. Nonfunctionalized BIONs with primary particle diameters of around 12 nm, as used in the process, can be produced with a simple and low-cost coprecipitation synthesis. Thus, HGMF with BIONs might pave the way for a new and greener era of downstream processing.

Progress in ligand design for monolayer-protected nanoparticles for nanobio interfaces

Ligand-functionalized inorganic nanoparticles, also known as monolayer-protected nanoparticles, offer great potential as vehicles for in vivo delivery of drugs, genes, and other therapeutics. These nanoparticles offer highly customizable chemistries independent of the size, shape, and functionality imparted by the inorganic core. Their success as drug delivery agents depends on their interaction with three major classes of biomolecules: nucleic acids, proteins, and membranes. Here, the authors discuss recent advances and open questions in the field of nanoparticle ligand design for nanomedicine, with a focus on atomic-scale interactions with biomolecules. While the importance of charge and hydrophobicity of ligands for biocompatibility and cell internalization has been demonstrated, ligand length, flexibility, branchedness, and other properties also influence the properties of nanoparticles. However, a comprehensive understanding of ligand design principles lies in the cost associated with synthesizing and characterizing diverse ligand chemistries and the ability to carefully assess the structural integrity of biomolecules upon interactions with nanoparticles.

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces

Although structures have been determined for many soluble proteins and an increasing number of membrane proteins, experimental structure determination methods are limited for complexes of proteins and solid surfaces. An economical alternative or complement to experimental structure determination is molecular simulation. Rosetta is one software suite that models protein-surface interactions, but Rosetta is normally benchmarked on soluble proteins. For surface interactions, the validity of the energy function is uncertain because it is a combination of independent parameters from energy functions developed separately for solution proteins and mineral surfaces. Here, we assess the performance of the RosettaSurface algorithm and test the accuracy of its energy function by modeling the adsorption of leucine/lysine (LK)-repeat peptides on methyl- and carboxy-terminated self-assembled monolayers (SAMs). We investigated how RosettaSurface predictions for this system compare with the experimental results, which showed that on both surfaces, LK-α peptides folded into helices and LK-β peptides held extended structures. Utilizing this model system, we performed a parametric analysis of Rosetta's Talaris energy function and determined that adjusting solvation parameters offered improved predictive accuracy. Simultaneously increasing lysine carbon hydrophilicity and the hydrophobicity of the surface methyl head groups yielded computational predictions most closely matching the experimental results. De novo models still should be interpreted skeptically unless bolstered in an integrative approach with experimental data.

Bare Iron Oxide Nanoparticles for Magnetic Harvesting of Microalgae: From Interaction Behavior to Process Realization

Microalgae continue to gain in importance as a bioresource, while their harvesting remains a major challenge at the moment. This study presents findings on microalgae separation using low-cost, easy-to-process bare iron oxide nanoparticles with the additional contribution of the upscaling demonstration of this simple, adhesion-based process. The high affinity of the cell wall for the inorganic surface enables harvesting efficiencies greater than 95% for Scenedesmus ovalternus and Chlorella vulgaris. Successful separation is possible in a broad range of environmental conditions and primarily depends on the nanoparticle-to-microalgae mass ratio, whereas the effect of pH and ionic strength are less significant when the mass ratio is chosen properly. The weakening of ionic concentration profiles at the interphase due to the successive addition of deionized water leads the microalgae to detach from the nanoparticles. The process works efficiently at the liter scale, enabling complete separation of the microalgae from their medium and the separate recovery of all materials (algae, salts, and nanoparticles). The current lack of profitable harvesting processes for microalgae demands innovative approaches to encourage further development. This application of magnetic nanoparticles is an example of the prospects that nanobiotechnology offers for biomass exploitation.

Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin

Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a) the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b) the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a) peptide receptor design; and (b) performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS) approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.