Protein folding modulates the chemical reactivity of a Gram-positive adhesin

Force-regulated chaperone activity of BiP/ERdj3 is opposite to their homologs DnaK/DnaJ

Polypeptide chains experience mechanical tension while translocating through cellular tunnels, which are subsequently folded by molecular chaperones. However, interactions between tunnel-associated chaperones and these emerging polypeptides under force is not completely understood. Our investigation focused on mechanical chaperone activity of two tunnel-associated chaperones, BiP and ERdj3 both with and without mechanical constraints and comparing them with their cytoplasmic homologs: DnaK and DnaJ. While BiP/ERdj3 have been observed to exhibit robust foldase activity under force, DnaK/DnaJ showed holdase function. Importantly, the tunnel-associated chaperones (BiP/ERdj3) transitioned to a holdase state in the absence of force, indicating a force-dependent chaperone behavior. This chaperone-driven folding event in the tunnel generated an additional mechanical energy of up to 54 zJ, potentially aiding protein translocation. Our findings align with strain theory, where chaperones with higher intrinsic deformability act as mechanical foldases (BiP, ERdj3), while those with lower deformability serve as holdases (DnaK and DnaJ). This study thus elucidates the differential mechanically regulated chaperoning activity and introduces a novel perspective on co-translocational protein folding.

Single-molecule magnetic tweezers to probe the equilibrium dynamics of individual proteins at physiologically relevant forces and timescales

The reversible unfolding and refolding of proteins is a regulatory mechanism of tissue elasticity and signalling used by cells to sense and adapt to extracellular and intracellular mechanical forces. However, most of these proteins exhibit low mechanical stability, posing technical challenges to the characterization of their conformational dynamics under force. Here, we detail step-by-step instructions for conducting single-protein nanomechanical experiments using ultra-stable magnetic tweezers, which enable the measurement of the equilibrium conformational dynamics of single proteins under physiologically relevant low forces applied over biologically relevant timescales. We report the basic principles determining the functioning of the magnetic tweezer instrument, review the protein design strategy and the fluid chamber preparation and detail the procedure to acquire and analyze the unfolding and refolding trajectories of individual proteins under force. This technique adds to the toolbox of single-molecule nanomechanical techniques and will be of particular interest to those interested in proteins involved in mechanosensing and mechanotransduction. The procedure takes 4 d to complete, plus an additional 6 d for protein cloning and production, requiring basic expertise in molecular biology, surface chemistry and data analysis.

Molecular Mechanism of Interaction between DNA Aptamer and Receptor-Binding Domain of Severe Acute Respiratory Syndrome Coronavirus 2 Variants Revealed by Steered Molecular Dynamics Simulations

The ongoing SARS-CoV-2 pandemic has underscored the urgent need for versatile and rapidly deployable antiviral strategies. While vaccines have been pivotal in controlling the spread of the virus, the emergence of new variants continues to pose significant challenges to global health. Here, our study focuses on a novel approach to antiviral therapy using DNA aptamers, short oligonucleotides with high specificity and affinity for their targets, as potential inhibitors against the spike protein of SARS-CoV-2 variants Omicron and JN.1. Our research utilizes steered molecular dynamics (SMD) simulations to elucidate the binding mechanisms of a specifically designed DNA aptamer, AM032-4, to the receptor-binding domain (RBD) of the aforementioned variants. The simulations reveal detailed molecular insights into the aptamer-RBD interaction, demonstrating the aptamer's potential to maintain effective binding in the face of rapid viral evolution. Our work not only demonstrates the dynamic interaction between aptamer-RBD for possible antiviral therapy but also introduces a computational method to study aptamer-protein interactions.

Decoding Biomechanical Cues Based on DNA Sensors

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Ester Bond: Chemically Labile Yet Mechanically Stable

Due to the dynamic nature of ester linkages, ester-bond-containing materials are well known for their outstanding degradability and stimuli responsiveness. However, whether ester hydrolysis is affected by mechanical forces remains unclear. Here, we develop a single-molecule assay to quantitatively study the force-dependent ester hydrolysis using an engineered circular permutant protein with a caged ester bond as a model. Our single-molecule force spectroscopy results show that the ester hydrolysis rate is surprisingly insensitive to forces, with a ∼7 s-1 dissociation rate that remains almost unchanged in the force range of 80 to 200 pN. Quantum calculations reveal that the ester hydrolysis involves an intermediate state formed by either H3O+- or OH--bonded tetrahedral intermediates. The measured ester-hydrolysis kinetics at the single-molecule level may primarily correspond to the rupture of these intermediate states. However, the rate-limiting step appears to be the formation of the tetrahedral intermediates, which cannot be quantitatively characterized in our experiments. Nonetheless, based on the quantum calculations, this step is also insensitive to applied forces. Altogether, our study suggests that the ester bond is chemically labile yet mechanically stable, serving as the basis for the design of responsive materials using ester bonds as mechanically inert units.

Using a Dynamic Hydrophilization Strategy to Achieve Nanodispersion, Full Wetting, and Precise Delivery of Hydrophobic Pesticide

Various strategies have been developed to improve the applicability of hydrophobic pesticides for better effectiveness in agriculture. However, existing formulations of hydrophobic pesticides still suffer from complicated processing, abused organic solvents, indispensable surfactants, or inescapable ecotoxicity, which strictly limit their applications. Herein, a dynamic covalent bond tailored pesticide (fipronil) amphiphile is constructed to address the above issues, which accomplishes the nanodispersion, full wetting, and precise delivery without organic solvents, surfactants, and materials simultaneously. By introducing a hydrophilic ligand on the hydrophobic fipronil through an imine bond, the cleavable fipronil amphiphile (FPP) exhibits superior water solubility and can even self-assemble into micelles at higher concentrations, which can be directly applied in powder form without organic solvents. Attributed to the suitable hydrophilic/hydrophobic ratio, FPP achieves full wetting and effective deposition on superhydrophobic rice leaves without surfactants. Moreover, benefiting from the unique dynamic nature of the imine bond, FPP maintains good storage stability while sensitively releasing back to fipronil under the humidity and pH trigger, consequently implementing the precise delivery for nontarget Apis cerana and target Chilo suppressalis without materials. To our knowledge, this dynamic covalent bond tailored amphiphile strategy is the first idea that simultaneously takes the dispersibility, wettability, and responsiveness of hydrophobic pesticides into account, providing a possibility to control the entire journey of field application and even promising to be incorporated into the synthesis process, thus paving the way for modern sustainable agriculture.

S373P Mutation Stabilizes the Receptor-Binding Domain of the Spike Protein in Omicron and Promotes Binding

A cluster of several newly occurring mutations on Omicron is found at the β-core region of the spike protein's receptor-binding domain (RBD), where mutation rarely happened before. Notably, the binding of SARS-CoV-2 to human receptor ACE2 via RBD happens in a dynamic airway environment, where mechanical force caused by coughing or sneezing occurs. Thus, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to measure the stability of RBDs and found that the mechanical stability of Omicron RBD increased by ∼20% compared with the wild type. Molecular dynamics (MD) simulations revealed that Omicron RBD showed more hydrogen bonds in the β-core region due to the closing of the α-helical motif caused primarily by the S373P mutation. In addition to a higher unfolding force, we showed a higher dissociation force between Omicron RBD and ACE2. This work reveals the mechanically stabilizing effect of the conserved mutation S373P for Omicron and the possible evolution trend of the β-core region of RBD.

Acrylate-functionalized porphyrin-covalent organic framework for bacterial-targeted and reaction-enhanced synergistic phototherapy/chemotherapy toward sterilization and wound healing

Porphyrinic covalent organic frameworks (COFs) have emerged as prospective materials in photodynamic and photothermal sterilization. However, it is still a great challenge to construct an efficient COF-based sterilizing agent with good photothermal and photodynamic properties and bacterial targeting ability. Herein, we report a multifunctional porphyrin-COF for bacterial-targeted and reaction-enhanced synergistic phototherapy/chemotherapy for sterilization and wound healing. The ordered crystal structure of the porphyrin-COF not only effectively avoids the self-aggregation-induced quenching of the porphyrin monomer, but also facilitates the storage and transport of singlet oxygen. The acrylate substituent in the other monomer serves as a bacterial targeting moiety and the in situ reaction site with the sulfhydryl group of the bacterial surface protein via a Michael addition reaction, thus fixing the bacteria on the surface of COF and making them lose the colonization ability. Furthermore, the bonding of COF and bacteria further amplifies the therapeutic efficiency of phototherapy. Therefore, the developed multifunctional sterilization platform not only provides a new strategy for the design of novel bactericidal materials but also broadens the biological applications of COF-based materials.

Chemical reaction-mediated covalent localization of bacteria

Methods capable of manipulating bacterial colonization are of great significance for modulating host-microbiota relationships. Here, we describe a strategy of in-situ chemical reaction-mediated covalent localization of bacteria. Through a simple one-step imidoester reaction, primary amino groups on bacterial surface can be converted to free thiols under cytocompatible conditions. Surface thiolation is applicable to modify diverse strains and the number of introduced thiols per bacterium can be easily tuned by varying feed ratios. These chemically reactive bacteria are able to spontaneously bond with mucous layer by catalyst-free thiol-disulfide exchange between mucin-associated disulfides and newly converted thiols on bacterial surface and show thiolation level-dependent attachment. Bacteria optimized with 9.3 × 10⁷ thiols per cell achieve 170-fold higher attachment in mucin-enriched jejunum, a challenging location for gut microbiota to colonize. As a proof-of-concept application for microbiota transplantation, covalent bonding-assisted localization of an oral probiotic in the jejunum generates an improved remission of jejunal mucositis. Our findings demonstrate that transforming bacteria with a reactive surface provides an approach to chemically control bacterial localization, which is highly desirable for developing next-generation bacterial living bioagents.

Histidine-Specific Bioconjugation for Single-Molecule Force Spectroscopy

Atomic force microscopy (AFM) based single-molecule force spectroscopy (SMFS) is a powerful tool to study the mechanical properties of proteins. In these experiments, site-specific immobilization of proteins is critical, as the tether determines the direction and amplitude of forces applied to the protein of interest. However, existing methods are mainly based on thiol chemistry or specific protein tags, which cannot meet the need of many challenging experiments. Here, we developed a histidine-specific phosphorylation strategy to covalently anchor proteins to an AFM cantilever tip or the substrate via their histidine tag or surface-exposed histidine residues. The formed covalent linkage was mechanically stable with rupture forces of over 1.3 nN. This protein immobilization method considerably improved the pickup rate and data quality of SMFS experiments. We further demonstrated the use of this method to explore the pulling-direction-dependent mechanical stability of green fluorescent protein and the unfolding of the membrane protein archaerhodopsin-3.

Mechanical Stabilization of a Bacterial Adhesion Complex

The adhesions between Gram-positive bacteria and their hosts are exposed to varying magnitudes of tensile forces. Here, using an ultrastable magnetic tweezer-based single-molecule approach, we show the catch-bond kinetics of the prototypical adhesion complex of SD-repeat protein G (SdrG) to a peptide from fibrinogen β (Fgβ) over a physiologically important force range from piconewton (pN) to tens of pN, which was not technologically accessible to previous studies. At 37 °C, the lifetime of the complex exponentially increases from seconds at several pN to ∼1000 s as the force reaches 30 pN, leading to mechanical stabilization of the adhesion. The dissociation transition pathway is determined as the unbinding of a critical β-strand peptide (“latch” strand of SdrG that secures the entire adhesion complex) away from its binding cleft, leading to the dissociation of the Fgβ ligand. Similar mechanical stabilization behavior is also observed in several homologous adhesions, suggesting the generality of catch-bond kinetics in such bacterial adhesions. We reason that such mechanical stabilization confers multiple advantages in the pathogenesis and adaptation of bacteria.

Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin

Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.

Nanolab in a Cell: Crystallization-Induced In Situ Self-Assembly for Cancer Theranostic Amplification

Conducting crystallization-assisted self-assembly in living biosystems to obtain large-size nanoparticles and achieve a specific physiological purpose remains an appealing yet significantly challenging task. In this study, we designed Au(I)-disulfide nanosheets containing an aggregation-induced emission photosensitizer, namely, NSs@TTVP, which exhibited pH-responsive crystallization-driven self-assembly capability in lysosomes of cancer cells and tumor tissues of mice. The crystallization process endowed NSs@TTVP with a microscale morphology, stronger fluorescence output, and highly enhanced reactive oxygen species production efficiency. The in vivo results demonstrated that NSs@TTVP shows both long-term retention in tumors and extensive destruction to cancer cells, making it supremely powerful for fluorescence imaging-guided tumor tracking and inhibition.

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling

HaloTag labeling technology has introduced unrivaled potential in protein chemistry and molecular and cellular biology. A wide variety of ligands have been developed to meet the specific needs of diverse applications, but only a single protein tag, DhaAHT, is routinely used for their incorporation. Following a systematic kinetic and computational analysis of different reporters, a tetramethylrhodamine- and three 4-stilbazolium-based fluorescent ligands, we showed that the mechanism of incorporating different ligands depends both on the binding step and the efficiency of the chemical reaction. By studying the different haloalkane dehalogenases DhaA, LinB, and DmmA, we found that the architecture of the access tunnels is critical for the kinetics of both steps and the ligand specificity. We showed that highly efficient labeling with specific ligands is achievable with natural dehalogenases. We propose a simple protocol for selecting the optimal protein tag for a specific ligand from the wide pool of available enzymes with diverse access tunnel architectures. The application of this protocol eliminates the need for expensive and laborious protein engineering.

Single-Molecule Force Spectroscopy Reveals the Dynamic HgS Coordination Site in the De Novo-Designed Metalloprotein α3DIV

The de novo-designed metalloprotein α3DIV binds to mercury via three cysteine residues under dynamic conditions. An unusual trigonal three-coordinate HgS3 site is formed in the protein in basic solution, whereas a linear two-coordinate HgS2 site is formed in acidic solution. Furthermore, it is unknown whether the two coordinated cysteines in the HgS2 site are fixed or not, which may lead to more dynamics. However, the signal for HgS2 sites with different cysteines may be similar or may be averaged and indistinguishable. To circumvent this problem, we adopt a single-molecule approach to study one mercury site at a time. Using atomic force microscopy-based single-molecule force spectroscopy, the protein is unfolded, and the HgS site is ruptured. The results confirm the formation of HgS3 and HgS2 sites at different pH values. Moreover, it is found that any two of the three cysteines in the protein bind to mercury in the HgS2 site.

Direct Observation of the Mechanical Role of Bacterial Chaperones in Protein Folding

Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.

Nonexponential kinetics in captured in sequential unfolding of polyproteins over a range of loads

While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L₈ under varying loads, specifically high (150, 100 ​pN) and moderate-low (45, 30, 20 ​pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.

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Poly-L₈ unfolding shows nonexponential kinetics at forces ranging from 150 to 20 ​pN.

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Different phenomenological trends are observed for the dwell-time distributions.

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The unfolding events were shown to be dependent and not identically distributed.

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Free energy analysis reveals elastic impact and hierarchy in the unfolding barriers.

Molecular basis for inhibition of adhesin-mediated bacterial-host interactions through a peptide-binding domain

Infections typically begin with pathogens adhering to host cells. For bacteria, this adhesion can occur through specific ligand-binding domains. We identify a 20-kDa peptide-binding domain (PBD) in a 1.5-MDa RTX adhesin of a Gram-negative marine bacterium that colonizes diatoms. The crystal structure of this Ca²⁺-dependent PBD suggests that it may bind the C termini of host cell-surface proteins. A systematic peptide library analysis reveals an optimal tripeptide sequence with 30-nM affinity for the PBD, and X-ray crystallography details its peptide-protein interactions. Binding of the PBD to the diatom partner of the bacteria can be inhibited or competed away by the peptide, providing a molecular basis for inhibiting bacterium-host interactions. We further show that this PBD is found in other bacteria, including human pathogens such as Vibrio cholerae and Aeromonas veronii. Here, we produce the PBD ortholog from A. veronii and demonstrate, using the same peptide inhibitor, how pathogens may be prevented from adhering to their hosts.

Enzymatic Protein-Protein Conjugation through Internal Site Verified at the Single-Molecule Level

Enzymes are widely used for protein ligation because of their efficient and site-specific connections under mild conditions. However, many enzymatic ligations are restricted to connections between protein termini while protein-protein conjugation at a specific internal site is limited. Previous work has found that Sortase A (SrtA) conjugates small molecules/peptides to a pilin protein at an internal lysine site via an isopeptide bond. Herein, we apply this noncanonical ligation property of SrtA for protein-protein conjugation at a designed YPKH site. Both a small protein domain, I27, and a large protein, GFP, were ligated at the designed internal site. Moreover, besides characterization by classic methods at the ensemble level, the specific ligation site at the interior YPKH motif is unambiguously verified by atomic force microscopy-based single-molecule force spectroscopy, showing the characteristic unfolding signature at the single-molecule level. Finally, steered molecular dynamics simulations also agreed with the results.

An ester bond underlies the mechanical strength of a pathogen surface protein

Gram-positive bacteria can resist large mechanical perturbations during their invasion and colonization by secreting various surface proteins with intramolecular isopeptide or ester bonds. Compared to isopeptide bonds, ester bonds are prone to hydrolysis. It remains elusive whether ester bonds can completely block mechanical extension similarly to isopeptide bonds, or whether ester bonds dissipate mechanical energy by bond rupture. Here, we show that an ester-bond containing stalk domain of Cpe0147 is inextensible even at forces > 2 nN. The ester bond locks the structure to a partially unfolded conformation, in which the ester bond remains largely water inaccessible. This allows the ester bond to withstand considerable mechanical forces and in turn prevent complete protein unfolding. However, the protecting effect might be reduced at non-physiological basic pHs or low calcium concentrations due to destabilizing the protein structures. Inspired by this design principle, we engineer a disulfide mutant resistant to mechanical unfolding under reducing conditions.

Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

SARS-CoV-2 has been spreading around the world for the past year. Recently, several variants such as B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), which share a key mutation N501Y on the receptor-binding domain (RBD), appear to be more infectious to humans. To understand the underlying mechanism, we used a cell surface-binding assay, a kinetics study, a single-molecule technique, and a computational method to investigate the interaction between these RBD (mutations) and ACE2. Remarkably, RBD with the N501Y mutation exhibited a considerably stronger interaction, with a faster association rate and a slower dissociation rate. Atomic force microscopy (AFM)-based single-molecule force microscopy (SMFS) consistently quantified the interaction strength of RBD with the mutation as having increased binding probability and requiring increased unbinding force. Molecular dynamics simulations of RBD-ACE2 complexes indicated that the N501Y mutation introduced additional π-π and π-cation interactions that could explain the changes observed by force microscopy. Taken together, these results suggest that the reinforced RBD-ACE2 interaction that results from the N501Y mutation in the RBD should play an essential role in the higher rate of transmission of SARS-CoV-2 variants, and that future mutations in the RBD of the virus should be under surveillance.

Protein nanomechanics in biological context

How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.

Highly Dynamic Polynuclear Metal Cluster Revealed in a Single Metallothionein Molecule

Human metallothionein (MT) is a small-size yet efficient metal-binding protein, playing an essential role in metal homeostasis and heavy metal detoxification. MT contains two domains, each forming a polynuclear metal cluster with an exquisite hexatomic ring structure. The apoprotein is intrinsically disordered, which may strongly influence the clusters and the metal-thiolate (M-S) bonds, leading to a highly dynamic structure. However, these features are challenging to identify due to the transient nature of these species. The individual signal from dynamic conformations with different states of the cluster and M-S bond will be averaged and blurred in classic ensemble measurement. To circumvent these problems, we combined a single-molecule approach and multiscale molecular simulations to investigate the rupture mechanism and chemical stability of the metal cluster by a single MT molecule, focusing on the Zn₄S₁₁ cluster in the α domain upon unfolding. Unusual multiple unfolding pathways and intermediates are observed for both domains, corresponding to different combinations of M-S bond rupture. None of the pathways is clearly preferred suggesting that unfolding proceeds from the distribution of protein conformational substates with similar M-S bond strengths. Simulations indicate that the metal cluster may rearrange, forming and breaking metal-thiolate bonds even when MT is folded independently of large protein backbone reconfiguration. Thus, a highly dynamic polynuclear metal cluster with multiple conformational states is revealed in MT, responsible for the binding promiscuity and diverse cellular functions of this metal-carrier protein.

Pioglitazone Inhibits Metal Cluster Transfer of mitoNEET by Stabilizing the Labile Fe-N Bond Revealed at Single-Bond Level

Outer mitochondrial membrane protein mitoNEET (mNT) is a target of the type 2 diabetes drug pioglitazone. It contains a labile Fe₂S₂(His)₁(Cys)₃ metal cluster with a single Fe-N(His87) coordinating bond and can transfer its cluster to acceptor proteins. Previous ensemble studies showed that pioglitazone's binding inhibited the transfer by stabilizing the cluster, and histidine 87 may be the key mediator. Here we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to study the unfolding process of mNT dimer in the absence and presence of pioglitazone, which can distinguish the binding effect for different regions of a protein. By developing a two-step strategy using different mNT monomers with respective purification tags, we solve the problem that the classic polyprotein formation disables the mNT to dimerize. As a result, a polyprotein including a stable, naturally noncovalently bound mNT homodimer is obtained, which is required for reliable AFM measurement and pioglitazone binding. Then, the dissociation rate (k_off) of the metal cluster was measured, showing a 10-fold decrease upon pioglitazone binding, while the other parts decreased only 3-fold, verifying that pioglitazone mainly stabilizes the cluster. Moreover, when the Fe(III)-N(His87) bond was ruptured, this effect for the remaining Fe₂S₂(Cys)₃ intermediate largely disappeared. Consequently, AFM results revealed that pioglitazone inhibited the metal cluster transfer of mNT by stabilizing the labile Fe(III)-N(His87) bond. In addition, an alternative method to build a natural, noncovalently bound protein dimer or complex for reliable single-molecule measurement was developed.