Sequence–Conformation Relationship of Zwitterionic Peptide Brushes: Theories and Simulations

RNA Translocation through Protein Nanopores: Interlude of the Molten RNA Globule

Direct translocation of RNA with secondary structures using single-molecule electrophoresis through protein nanopores shows significant fluctuations in the measured ionic current, in contrast to unstructured single-stranded RNA or DNA. We developed a multiscale model combining the oxRNA model for RNA with the 3-dimensional Poisson-Nernst-Planck formalism for electric fields within protein pores, aiming to map RNA conformations to ionic currents as RNA translocates through three protein nanopores: α-hemolysin, CsgG, and MspA. Our findings reveal three distinct stages of translocation (pseudoknot, melting, and molten globule) based on contact maps and current values. Two translocation modes emerge: fast and slow. In the fast mode, the speed is determined by the electric field, independent of pore geometry. In the slow mode, the molten globule stage is the rate-determining factor in slowing the translocation, instead of the previous paradigm of melting of the base pairs. Using these insights, we propose a neural network framework to identify and reconstruct RNA secondary structures from ionic current windows. We find that the electric field distribution, not the nanopore geometry, drives the molten globule stage. Our results explain the large current fluctuations. These results provide a fundamental understanding of the role of secondary and tertiary structures in the translocation of RNA in direct RNA translocation platforms based on single-molecule electrophoresis. This work offers design rules for new protein pores and real-time imaging of the secondary structures of RNA.

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a "brush" surrounding each NF. Precisely how the tails' variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Zwitterionic Peptides: From Mechanism, Design Strategies to Applications

Zwitterionic peptides, as a type of peptide composed of charged residues, are electrically neutral, which combine the advantages of zwitterionic materials and biological peptides, exhibiting hydrophilicity and programmable properties. As attractive candidates for resisting nonspecific adsorption of biomacromolecules and microorganisms, zwitterionic peptides have been applied in materials science, biomedicine, and biochemistry over the past decade. In this review, the development of zwitterionic peptides has been systematically outlined and analyzed, including their mechanisms, structure-function relationships, and design strategies. Furthermore, this review emphasizes and discusses their recent applications for developing functional coatings, biosensors, drug delivery systems, and engineering proteins. Finally, future research perspectives and challenges of zwitterionic peptides are also prospected and discussed. This review is intended to provide clarity and insight into the design and applications of zwitterionic peptides.

Sustained antibacterial release of zwitterionic globular hyperbranched polymer dots intercalated into layered double hydroxides

This study introduces zwitterionic hyperbranched polymer (HBP) dots intercalated into layered double hydroxides (LDHs) for sustained antibacterial release. The proposed zwitterionic HBPs possess a three-dimensional spherical structure; unconventional blue fluorescent luminescence; water solubility; abundant COOH, amine, and amide functional groups; anionic exchangeability for intercalating into LDH interlayers; and sustained-release antibacterial activity. The intercalation for the layered nanomaterials was determined by adding different weight ratios of HBPs to Mg-Al LDHs to investigate the changes in the interlayer distance. X-ray diffraction revealed that the LDH layer spacing increased from 8.6 to 25.5 Å, effectively expanding the interlayer spacing with increasing HBP intercalation. Additionally, Fourier-transform infrared spectroscopy revealed the functional groups of the intercalated nanohybrids. Because the peripheral functional groups of HBPs are amino (-NH2) groups, preliminary evaluations revealed that pristine HBPs exhibited antibacterial properties. We further examined the antibacterial properties of the HBP/LDH nanohybrids. The results showed that HBPs combined with LDHs' controllable release properties can effectively achieve long-term sustained antibacterial release.

Design, preparation, and characterization of lubricating polymer brushes for biomedical applications

The lubrication modification of biomedical devices significantly enhances the functionality of implanted interventional medical devices, thereby providing additional benefits for patients. Polymer brush coating provides a convenient and efficient method for surface modification while ensuring the preservation of the substrate's original properties. The current research has focused on a "trial and error" method to finding polymer brushes with superior lubricity qualities, which is time-consuming and expensive, as obtaining effective and long-lasting lubricity properties for polymer brushes is difficult. This review summarizes recent research advances in the biomedical field in the design, material selection, preparation, and characterization of lubricating and antifouling polymer brushes, which follow the polymer brush development process. This review begins by examining various approaches to polymer brush design, including molecular dynamics simulation and machine learning, from the fundamentals of polymer brush lubrication. Recent advancements in polymer brush design are then synthesized and potential avenues for future research are explored. Emphasis is placed on the burgeoning field of zwitterionic polymer brushes, and highlighting the broad prospects of supramolecular polymer brushes based on host-guest interactions in the field of self-repairing polymer brush applications. The review culminates by providing a summary of methodologies for characterizing the structural and functional attributes of polymer brushes. It is believed that a development approach for polymer brushes based on "design-material selection-preparation-characterization" can be created, easing the challenge of creating polymer brushes with high-performance lubricating qualities and enabling the on-demand creation of coatings. STATEMENT OF SIGNIFICANCE: Biomedical devices have severe lubrication modification needs, and surface lubrication modification by polymer brush coating is currently the most promising means. However, the design and preparation of polymer brushes often involves "iterative testing" to find polymer brushes with excellent lubrication properties, which is both time-consuming and expensive. This review proposes a polymer brush development process based on the "design-material selection-preparation-characterization" strategy and summarizes recent research advances and trends in the design, material selection, preparation, and characterization of polymer brushes. This review will help polymer brush researchers by alleviating the challenges of creating polymer brushes with high-performance lubricity and promises to enable the on-demand construction of polymer brush lubrication coatings.

Designed Polyhydroxyproline Helical Peptide with Ultrarobust Antifouling Capability for Electrochemical Sensing in Diverse Complex Biological Fluids

Developing a generalized strategy for the nonfouling detection of biomarkers in diverse biological fluids presents a significant challenge. Herein, a polyhydroxyproline helical peptide (PHHP) was designed and adopted to fabricate electrochemical microsensors capable of detecting targets in various biological media. The PHHP possessed unique properties such as strong hydrophilicity, rigid structure, and lack of ionizable side-chain groups. Compared with common zwitterionic peptides (ZIPs), the PHHP exhibited similar antifouling capability but exceptional stability, allowing its antifouling performance to be unaffected by environmental alteration. The PHHP can prevent biofouling even in fluctuating pH conditions, high ionic strength environments, and the presence of high-valence ions and resist the protease hydrolysis. The PHHP-modified carbon fiber microelectrode was further immobilized with an aptamer to construct an antifouling microsensor for cortisol detection across diverse biofluids, and the microsensor exhibited acceptable accuracy and higher sensitivity than the ELISA method. In addition, different biological samples of mice were collected in situ using a microsensing device, and cortisol levels were analyzed in each specifically tailored region. This nonfouling sensing strategy based on PHHP allows a comprehensive assessment of biomarkers in both spatial and temporal dimensions in diverse biological environments, holding promising potential for early disease diagnosis and real-time health monitoring.

Electroresponse of weak polyelectrolyte brushes

End-tethered polyelectrolytes are widely used to modify substrate properties, particularly for lubrication or wetting. External stimuli, such as pH, salt concentration, or an electric field, can induce profound structural responses in weak polyelectrolyte brushes, which can be utilized to further tune substrate properties. We study the structure and electroresponsiveness of weak polyacid brushes using an inhomogeneous theory that incorporates both electrostatic and chain connectivity correlations at the Debye-Hückel level. Our calculation shows that a weak polyacid brush swells under the application of a negative applied potential, in agreement with recent experimental observation. We rationalize this behavior using a scaling argument that accounts for the effect of the surface charge. We also show that the swelling behavior has a direct influence on the differential capacitance, which can be modulated by the solvent quality, pH, and salt concentration.