Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G

Probing the Epidermal Growth Factor Receptor under Piconewton Mechanical Compressive Force Manipulations

Studying the relationship among protein structure, dynamics, and function under external compressive forces offers valuable insights. While extensive research has focused on manipulating protein dynamics and ligand-receptor interactions under pulling forces, the exploration of protein conformational changes under compressive forces has been limited. In this study, we investigate the response of unliganded epidermal growth factor receptor (EGFR) monomers, liganded EGF-EGFR monomers, and dimers when exposed to external compressive forces using a home-modified AFM setup with an ultrasoft AFM tip. We observed that both ligand-bound and unbound EGFR proteins can undergo spontaneous tertiary structural rupture under piconewton-level compressive forces, a previously hidden protein behavior that may play a significant role in protein cell signaling. The magnitudes of the threshold compressive forces obtained in our study lie in the range of tens and hundreds of piconewtons (pN), which is accessible within a live biological system. Moreover, we developed a kinetic model to exhibit that only a fraction of the uniaxial compressive force exerted by the AFM tip affects the internal tension that causes a pseudopulling force within the protein before it undergoes the tertiary structural rupture. This calculated fraction ranged from 0.45 to 0.65, depending on the protein type and the approach velocity of the AFM tip. Additionally, we employed molecular dynamics (MD) simulations, particularly Steered MD (SMD) simulations along with Umbrella Sampling (US), to investigate the dynamics of unliganded and liganded EGFR in the presence of external compressive forces. These MD simulation results offer valuable insights into the flexibilities and unfolding behaviors of both liganded and unliganded EGFR proteins when subjected to external compressive forces.

Trimethylamine N-oxide-derived zwitterion coating for polyurethane ureteral stents prevents encrustation formation

A ureteral stent with strong resistance to proteins, bacteria, and multivalent ions is crucial for the safe treatment of urologic diseases. Generally, the proteins, bacteria, and multivalent ions present in urine tend to bind to the stent surface, leading to aggregation, nucleation, and subsequent stent encrustation. Stent encrustation can induce or exacerbate urinary tract infections and obstructions, thereby seriously harming kidney function. Although hydrophilic coatings on ureteral stents can reduce the binding of proteins, bacteria, and multivalent ions, encrustation still occurs. To date, preventing stent encrustation formation remains a significant challenge. Here, we grafted dense trimethylamine oxide (TMAO)-derived zwitterionic polymers onto the stent surface via a branched amplification strategy. These zwitterions can strongly bind water molecules, forming a stable hydration layer that repels proteins, bacteria, and multivalent ions from adhering to the surface of the polyurethane ureteral stent, thus rendering the stent anti-encrustation. The results showed that the TMAO-derived zwitterion-coated stents exhibited a significantly reduced encrustation weight (13.8% of the original polyurethane stent) and demonstrated good safety. This approach offers a promising method for enhancing stent encrustation resistance. STATEMENT OF SIGNIFICANCE: This study successfully developed a TMAO-derived zwitterionic coating on the surface of a polyurethane stent, creating a superhydrophilic surface with a minimal contact angle of 5.2o. This surface effectively shields the stent from interactions with proteins, bacteria, and multivalent ions in urine, demonstrating favorable anti-protein adsorption and antibacterial adhesion properties. The superhydrophilic surface formed by the TMAO-derived zwitterionic coating on the stents (PTMAO-s) provides strong anti-fouling resistance and enhanced anti-encrustation properties. Under identical conditions, the encrustation resistance of PTMAO-s is approximately 7.2-fold greater than that of original polyurethane stents (PU), 3.6-fold greater than Bard commercial stents, and 2.1-fold greater than betaine-coated stents (PSBG-s).

pH-induced changes in IgE molecules measured by atomic force microscopy

The environment surrounding proteins is tightly linked to its dynamics, which can significantly influence the conformation of proteins. This study focused on the effect of pH conditions on the ultrastructure of Immunoglobulin E (IgE) molecules. Herein, the morphology, height, and area of IgE molecules incubated at different pH were imaged by atomic force microscopy (AFM), and the law of IgE changes induced by pH value was explored. The experiment results indicated that the morphology, height and area of IgE molecules are pH dependent and highly sensitive. In particular, IgE molecules were more likely to present small-sized ellipsoids under acidic conditions, while IgE molecules tend to aggregate into large-sized flower-like structures under alkaline conditions. In addition, it was found that the height of IgE first decreased and then increased with the increase of pH, while the area of IgE increased with the increase of pH. This work provides valuable information for further study of IgE, and the methodological approach used in this study is expected to developed into AFM to investigate the changes of IgE molecules mediated by other physical and chemical factors. RESEARCH HIGHLIGHTS: The ultrastructure of IgE molecules is pH dependent and highly sensitive. IgE molecules were tend to present small-sized ellipsoids under acidic pH. Alkaline pH drives IgE self-assembly into flower-like aggregates.

Tailored Microcantilever Optimization for Multifrequency Force Microscopy

Microcantilevers are at the heart of atomic force microscopy (AFM) and play a significant role in AFM-based techniques. Recent advancements in multifrequency AFM require the simultaneous excitation and detection of multiple eigenfrequencies of microcantilevers to assess more data channels to quantify the material properties. However, to achieve higher spatiotemporal resolution there is a need to optimize the structure of microcantilevers. In this study, the architecture of the cantilever with gold nanoparticles using a dip-coating method is modified, aiming to tune the higher eigenmodes of the microcantilever as integer multiples of its fundamental frequency. Through the theoretical methodology and simulative model, that integer harmonics improve the coupling in multifrequency AFM measurements is demonstrated, leading to enhanced image quality and resolution. Furthermore, via the combined theoretical-experimental approach, the interplay between induced mass and stiffness change of the modified cantilever depending on the attached particle location, size, mass, and geometry is found. To validate the results of this predictive model, tapping-mode AFM is utilized and bimodal Amplitude Modulation AFM techniques to examine and quantify the impact of tuning higher-order eigenmodes on the imaging quality of a polystyrene-polymethylmethacrylate (PS-PMMA) block co-polymer assembly deposited on a glass slide and Highly Ordered Pyrolytic Graphite (HOPG).

Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires

Helical homopolymers of multiheme cytochromes catalyze biogeochemically significant electron transfers with a reported 10 3 -fold variation in conductivity. Herein, classical molecular dynamics and hybrid quantum/classical molecular mechanics are used to elucidate the structural determinants of the redox potentials and conductivities of the tetra-, hexa-, and octaheme outer-membrane cytochromes E, S, and Z, respectively, from Geobacter sulfurreducens . Second-sphere electrostatic interactions acting on minimally polarized heme centers are found to regulate redox potentials over a computed 0.5-V range. However, the energetics of redox conduction are largely robust to the structural diversity: Single-step electronic couplings (⟨H mn ⟩), reaction free energies , and reorganization energies (λ mn ) are always respectively <|0.026|, <|0.26|, and between 0.5 - 1.0 eV. With these conserved parameter ranges, redox conductivity differed by less than a factor of 10 among the 'nanowires' and is sufficient to meet the demands of cellular respiration if 10 2 - 10 3 'nanowires' are expressed. The 'nanowires' are proposed to be differentiated by the protein packaging to interface with a great variety of environments, and not by conductivity, because the rate-limiting electron transfers are elsewhere in the respiratory process. Conducting-probe atomic force microscopy measurements that find conductivities 10 3 -10 6 -fold more than cellular demands are suggested to report on functionality that is either not used or not accessible under physiological conditions. The experimentally measured difference in conductivity between Omc- S and Z is suggested to not be an intrinsic feature of the CryoEM-resolved structures.