MICROFLUIDIC TOOLS FOR STUDYING THE SPECIFIC BINDING, ADSORPTION, AND DISPLACEMENT OF PROTEINS AT INTERFACES

Impact of pH-dependent dynamics of human serum proteins on dialysis membranes: Cryptographic structure assessment, synchrotron imaging of membrane-protein adsorption, and molecular docking studies

Proteins are fundamental to biochemical processes and critical in hemodialysis. This study investigates the impact of pH on human serum albumin (HSA), fibrinogen (FB), and transferrin (TRF) interactions with polyarylethersulfone (PAES) hemodialysis membranes. A multi-method approach was utilized, including protein crystallography for structural insights, hydration layer analysis to explore solvation and interaction potentials, molecular docking using AutoDock 4.0 for binding affinity simulations, and in-situ X-ray synchrotron SR-μCT imaging to observe protein deposition dynamics. Molecular docking revealed that PAES demonstrated superior binding energies and interaction patterns with FB and TRF compared to cellulose triacetate (CTA), facilitated by specific hydrogen bonding within a water shell. CTA displayed weaker, hydration-sensitive interactions varying with pH. Imaging studies indicated that FB showed higher adsorption at pH 6 than at pH 7.2, predominantly in the middle membrane regions. Similarly, HSA and TRF exhibited increased adsorption at pH 6, suggesting a stronger affinity under acidic conditions. Mixed protein solutions also indicated higher adsorption at pH 6, emphasizing an increased risk of membrane fouling. These findings highlight the crucial role of pH in modulating protein-membrane interactions and enhancing the efficacy of hemodialysis. A deeper understanding of hydration environments and their effects on protein binding affinities provides valuable insights for optimizing membrane design and performance. Clinically, this research suggests that fine-tuning pH during hemodialysis could mitigate protein fouling on membranes, thereby improving procedural efficiency and potentially leading to better patient outcomes through enhanced dialysis effectiveness.

The concept of protein folding/unfolding and its impacts on human health

Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.

Phase Separation of Intrinsically Disordered Proteins

There is growing interest in the topic of intracellular phase transitions that lead to the formation of biologically regulated biomolecular condensates. These condensates are membraneless bodies formed by phase separation of key protein and nucleic acid molecules from the cytoplasmic or nucleoplasmic milieus. The drivers of phase separation are referred to as scaffolds whereas molecules that preferentially partition into condensates formed by scaffolds are known as clients. Recent advances have shown that it is possible to generate physical and functional facsimiles of many biomolecular condensates in vitro. This is achieved by titrating the concentration of key scaffold proteins and solution parameters such as salt concentration, pH, or temperature. The ability to reproduce phase separation in vitro allows one to compare the relationships between information encoded in the sequences of scaffold proteins and the driving forces for phase separation. Many scaffold proteins include intrinsically disordered regions whereas others are entirely disordered. Our focus is on comparative assessments of phase separation for different scaffold proteins, specifically intrinsically disordered linear multivalent proteins. We highlight the importance of coexistence curves known as binodals for quantifying phase behavior and comparing driving forces for sequence-specific phase separation. We describe the information accessible from full binodals and highlight different methods for-and challenges associated with-mapping binodals. In essence, we provide a wish list for in vitro characterization of phase separation of intrinsically disordered proteins. Fulfillment of this wish list through key advances in experiment, computation, and theory should bring us closer to being able to predict in vitro phase behavior for scaffold proteins and connect this to the functions and features of biomolecular condensates.

Artefacts at the liquid interface and their impact in miniaturized biochemical assay

Droplet microfluidic technology has the potential to significantly reduce reagent use, and therefore, lower costs of assays employed in drug discovery campaigns. In addition to the reduction in costs, this technology can also reduce evaporation and contamination which are often problems seen in miniaturized microtitre plate formats. Despite these advantages, we currently advise caution in the use of these microfluidic approaches as there remains a lack of understanding of the artefacts of the systems such as reagent partitioning from droplet to carrier oil and interaction of the biological reagents with the water-oil interface. Both types of artefact can lead to inaccurate and misleading data. In this paper, we present a study of the partitioning of a number of drug-like molecules in a range of oils and evidence of protein binding at the water-oil interface which results in reduced activity of a cytochrome P450 enzyme. Data presented show that the drug-like molecules partitioned the least into fluorocarbon oils and the interaction of the 1A2 cytochrome at the water-oil interface resulted in a lower or complete absence of enzyme activity. This loss of activity of cytochrome 1A2 could be restored by the use of secondary blocking proteins although changes in the pharmacology of known 1A2 inhibitors were observed. The artefacts described here due to reagents partitioning into the carrier oil or protein binding at the water-oil interface significantly impact the potential use of these microfluidic systems as a means to carry out miniaturized biological assays, and further work is needed to understand the impact and reduction of these phenomena.

Quantitative heterogeneous immunoassays in protein modified polydimethylsiloxane microfluidic channels for rapid detection of disease biomarkers

Conventional detection of disease biomarkers employs techniques such as lateral-flow assays or central laboratory-based enzyme-linked immunosorbent assays (ELISA). Miniaturization and performance improvement of such traditional immunoassays using microfluidic technologies has proved promising in producing rapid, sensitive and automated next-generation immunosensors for quantitative diagnoses in the point-of-care setting. In this article a poly(dimethylsiloxane) (PDMS)-based immunosensor is presented for rapid detection of C-reactive protein. PDMS is selected in part because of the vast popularity of using PDMS as a material for microfluidic devices and in part because of the challenge of obtaining a stable surface coating with PDMS for immunosensing applications. Practical procedures for fabrication, surface modification, and preservation of the microfluidic immuno-chips as well as detailed descriptions of performing the microfluidic heterogeneous assay are presented.

A microfluidic biosensor based on competitive protein adsorption for thyroglobulin detection

We report a microfluidic sensing platform for the detection of thyroglobulin (Tg) using competitive protein adsorption. Serum Tg is a highly specific biomarker for residual thyroid tissue, recurrence and metastases after treatment for differentiated thyroid cancer (DTC). Conventional Tg detection techniques require complicated immobilization of antibodies and need to form a sandwich assay using additional secondary antibodies to enhance the sensitivity. We present a fundamentally different sensing technique without using antibody immobilization on a microfluidic platform. We engineer two surfaces covered by two known proteins, immunoglobulin G (IgG) and fibrinogen, with different affinities onto the surfaces. The microfluidic device offers a selective protein sensing by being displaced by a target protein, Tg, on only one of the surfaces. By utilizing the competitive protein adsorption, Tg displaces a weakly bound protein, IgG; however, a strongly bound protein, fibrinogen, is not displaced by Tg. The surface plasmon resonance (SPR) sensorgrams show that five human serum proteins, albumin, haptoglobin, IgG, fibrinogen and Tg, have different adsorption strengths to the surface and the competitive adsorption of individuals controls the exchange sequence. The adsorption and exchange are evaluated by fluorescent labeling of these proteins. Tg in a protein mixture of albumin, haptoglobin, and Tg is selectively detected based on the exchange reaction. By using the technique, we obviate the need to rely on antibodies as a capture probe and their attachment to transducers.

In situ synthesis of lipopeptides as versatile receptors for the specific binding of nanoparticles and liposomes to solid-supported membranes

A detailed study of the in situ coupling of small peptides such as CGGH6 (H6) and CGWK8 (K8) to maleimide functionalized phospholipid bilayers is presented. Individually addressable microstructured membranes are employed to unequivocally probe the conjugation. The in situ coupling of peptides via a terminal cysteine moiety to maleimide functionalized phospholipids is shown to be a convenient and versatile way to selectively fabricate peptide-modified phospholipid bilayers serving as specific receptor platforms for functionalized vesicles and nanoparticles. Specific binding of functional vesicles to the peptide-modified bilayers is achieved by either histidine complexation with Ni-NTA-DOGS containing vesicles or electrostatic interaction between positively charged oligolysine bearing lipopeptides and negatively charged POPC/POPG vesicles. Peptide receptors are also found to be easily accessible from the aqueous phase and not buried within the membrane interior.

Microfluidic Protein Patterning on Silicon Nitride Using Solvent Extracted Poly(dimethylsiloxane) Channels

Biomolecular patterning is essential for the creation of sensing motifs that rely on receptor-ligand binding for selectivity. Microfluidic devices have the potential to aid in the development of simple, robust methods for biomolecular patterning and therefore contribute to the generation of protein, DNA, and cell microarrays. In microfluidic patterning, the choice of both substrate and microfluidic channel material is essential for control of both the receptor binding for maximal signal generation as well as non-specific adsorption that acts as chemical noise. In this study, polystyrene, glass, silicon nitride, and poly(dimethylsiloxane) (PDMS) were evaluated as substrates for protein patterning using two types of PDMS microchannels for patterning, native PDMS and solvent-extracted PDMS (E-PDMS). E-PDMS microfluidic channels resulted in better patterning characteristics than native PDMS channels as determined by a higher fluorescence intensity of immobilized protein on all substrate types tested. Microfluidic patterning was then applied to perform two- and four-layer immunoassays.

Total internal reflection with fluorescence correlation spectroscopy

Total internal reflection-fluorescence correlation spectroscopy (TIR-FCS) is an emerging technique that is used to measure events at or near an interface, including local fluorophore concentrations, local translational mobilities and the kinetic rate constants that describe the association and dissociation of fluorophores at the interface. TIR-FCS is also an extremely promising method for studying dynamics at or near the basal membranes of living cells. This protocol gives a general overview of the steps necessary to construct and test a TIR-FCS system using either through-prism or through-objective internal reflection geometry adapted for FCS. The expected forms of the autocorrelation function are discussed for the cases in which fluorescent molecules in solution diffuse through the depth of the evanescent field, but do not bind to the surface of interest, and in which reversible binding to the surface also occurs.

Glass surfaces grafted with high-density poly(ethylene glycol) as substrates for DNA oligonucleotide microarrays

Surfaces carrying a dense layer of poly(ethylene glycol) (PEG) were prepared, characterized, and tested as substrates for DNA oligonucleotide microarrays. PEG bis(amine) with a molecular weight of 2000 was grafted onto silanized glass slides bearing aldehyde groups. After grafting, the terminal amino groups of the PEG layer were derivatized with the heterobifunctional cross-linker succinimidyl 4-[p-maleimidophenyl]butyrate to permit the immobilization of thiol-modified DNA oligonucleotides. The stepwise chemical modification was validated with X-ray photoelectron spectroscopy. Goniometry indicated that the PEG grafting procedure reduced surface inhomogeneities present after the silanization step, while atomic force microscopy and ellipsometry confirmed that the PEG layer was dense and monomolecular. Hybridization assays using DNA oligonucleotides and fluorescence imaging showed that PEG grafting improved the yield in hybridization 4-fold compared to non-PEGylated maleimide-derivatized surfaces. In addition, the PEG layer reduced the nonspecific adsorption of DNA by a factor of up to 13, demonstrating that surfaces with a dense PEG layer represent suitable substrates for DNA oligonucleotide microarrays.