Disentangling protein-silica interactions

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.

Confining a Protein-Containing Water Nanodroplet inside Silica Nanochannels

Incorporation of biological systems in water nanodroplets has recently emerged as a new frontier to investigate structural changes of biomolecules, with perspective applications in ultra-fast drug delivery. We report on the molecular dynamics of the digestive protein Pepsin subjected to a double confinement. The double confinement stemmed from embedding the protein inside a water nanodroplet, which in turn was caged in a nanochannel mimicking the mesoporous silica SBA-15. The nano-bio-droplet, whose size fits with the pore diameter, behaved differently depending on the protonation state of the pore surface silanols. Neutral channel sections allowed for the droplet to flow, while deprotonated sections acted as anchoring piers for the droplet. Inside the droplet, the protein, not directly bonded to the surface, showed a behavior similar to that reported for bulk water solutions, indicating that double confinement should not alter its catalytic activity. Our results suggest that nanobiodroplets, recently fabricated in volatile environments, can be encapsulated and stored in mesoporous silicas.

Supramolecular Organization in Confined Nanospaces

Empty spaces are abhorred by nature, which immediately rushes in to fill the void. Humans have learnt pretty well how to make ordered empty nanocontainers, and to get useful products out of them. When such an order is imparted to molecules, new properties may appear, often yielding advanced applications. This review illustrates how the organized void space inherently present in various materials: zeolites, clathrates, mesoporous silica/organosilica, and metal organic frameworks (MOF), for example, can be exploited to create confined, organized, and self-assembled supramolecular structures of low dimensionality. Features of the confining matrices relevant to organization are presented with special focus on molecular-level aspects. Selected examples of confined supramolecular assemblies - from small molecules to quantum dots or luminescent species - are aimed to show the complexity and potential of this approach. Natural confinement (minerals) and hyperconfinement (high pressure) provide further opportunities to understand and master the atomistic-level interactions governing supramolecular organization under nanospace restrictions.

Enzymes immobilized in mesoporous silica: a physical-chemical perspective

Mesoporous materials as support for immobilized enzymes have been explored extensively during the last two decades, primarily not only for biocatalysis applications, but also for biosensing, biofuels and enzyme-controlled drug delivery. The activity of the immobilized enzymes inside the pores is often different compared to that of the free enzymes, and an important challenge is to understand how the immobilization affects the enzymes in order to design immobilization conditions that lead to optimal enzyme activity. This review summarizes methods that can be used to understand how material properties can be linked to changes in enzyme activity. Real-time monitoring of the immobilization process and techniques that demonstrate that the enzymes are located inside the pores is discussed by contrasting them to the common practice of indirectly measuring the depletion of the protein concentration or enzyme activity in the surrounding bulk phase. We propose that pore filling (pore volume fraction occupied by proteins) is the best standard for comparing the amount of immobilized enzymes at the molecular level, and present equations to calculate pore filling from the more commonly reported immobilized mass. Methods to detect changes in enzyme structure upon immobilization and to study the microenvironment inside the pores are discussed in detail. Combining the knowledge generated from these methodologies should aid in rationally designing biocatalyst based on enzymes immobilized in mesoporous materials.

Phenanthrene binding by humic acid-protein complexes as studied by passive dosing technique

This work investigated the binding behavior of phenanthrene by humic acids (HA-2 and HA-5), proteins (bovine serum albumin (BSA)), lysozyme and pepsin), and their complexes using a passive dosing technique. All sorption isotherms were fitted well with Freundlich model and the binding capability followed an order of HA-5 > HA-2 > BSA > pepsin > lysozyme. In NaCl solution, phenanthrene binding to HA-BSA complexes was much higher than the sum of binding to individual HA and BSA, while there was no enhancement for HA-pepsin. Positively charged lysozyme slightly lowered phenanthrene binding on both HAs due to strong aggregation of HA-lysozyme complexes, leading to reduction in the number of binding sites. The binding enhancement by HA-BSA was observed under all tested ion species and ionic strengths. This enhancement can be explained by unfolding of protein, reduction of aggregate size and formation of HA-BSA complexes with favorable conformations for binding phenanthrene.

Structure and biological activity of glasses and ceramics

Biomaterials for repairing and regenerating parts of the human body play a key role in contemporary medicine, and have an increasing impact in modern society. Given the importance of orthopaedic medicine (bone is the second most replaced organ after blood), bioactive glasses and ceramics represent a key reference to guide technological advances in this field. Their established role in current biomedical applications has already led many research groups worldwide to look into their structural properties, with a view to identifying the molecular basis of their biological activity. As the efforts directed towards this crucial and exciting direction continue to increase, it is now timely to review the situation, in order to guide future investigations on structure-bioactivity relationships. In this introductory article, the field is reviewed, to provide an appropriate context for the contributions to this Theme Issue.