Reversible Unfolding and Folding of the Metalloprotein Ferredoxin Revealed by Single-Molecule Atomic Force Microscopy

Multiscale modeling of unfolding and bond dissociation of rubredoxin metalloprotein

Mechanical properties of proteins that have a crucial effect on their operation. This study used a molecular dynamics simulation package to investigate rubredoxin unfolding on the atomic scale. Different simulation techniques were applied, and due to the dissociation of covalent/hydrogen bonds, this protein demonstrates several intermediate states in force-extension behavior. A conceptual model based on the cohesive finite element method was developed to consider the intermediate damages that occur during unfolding. This model is based on force-displacement curves derived from molecular dynamics results. The proposed conceptual model is designed to accurately identify bond rupture points and determine the associated forces. This is achieved by conducting a thorough comparison between molecular dynamics and cohesive finite element results. The utilization of a viscoelastic cohesive zone model allows for the consideration of loading rate effects. This rate-dependent model can be further developed and integrated into the multiscale modeling of large assemblies of metalloproteins, providing a comprehensive understanding of mechanical behavior while maintaining a reduced computational cost.

Significance of the Disulfide Bridge in the Structure and Stability of Metalloprotein Azurin

Metalloproteins make up a class of proteins that incorporate metal ions into their structures, enabling them to perform essential functions in biological systems, such as catalysis and electron transport. Azurin is one such metalloprotein with copper cofactor, having a β-barrel structure with exceptional thermal stability. The copper metal ion is coordinated at one end of the β-barrel structure, and there is a disulfide bond at the opposite end. In this study, we explore the effect of this disulfide bond in the high thermal stability of azurin by analyzing both the native S-S bonded and S-S nonbonded (S-S open) forms using temperature replica exchange molecular dynamics (REMD). Similar to experimental observations, we find a 35 K decrease in denaturation temperature for S-S open azurin compared to that of the native holo form (420 K). As observed in the case of native holo azurin, the unfolding process of the S-S open form also started with disruptions of the α-helix. The free energy surfaces of the unfolding process revealed that the denaturation event of the S-S open form progresses through different sets of conformational ensembles. Subsequently, we compared the stabilities of individual β-sheet strands of both the S-S bonded and the S-S nonbonded forms of azurin. Further, we examined the contacts between individual residues for the central structures from the free energy surfaces of the S-S nonbonded form. The microscopic origin of the lowering in the denaturation temperature is further supplemented by thermodynamic analysis.

Ester Bonds for Modulation of the Mechanical Properties of Protein Hydrogels

Hydrogels are soft materials constructed of physically or chemically crosslinked polymeric net-works with abundant water. The crosslinkers, as the mechanophores that bear and respond to mechanical forces, play a critical role in determining the mechanical properties of hydrogels. Here, we use a polyprotein as the crosslinker and mechanophore to form covalent polymer hydrogels in which the toughness and fatigue fracture are controlled by the mechanical unfolding of polyproteins. The protein Parvimonas sp. (ParV) is super stable and remains folded even at forces > 2 nN; however, it can unfold under loading forces of ~100 pN at basic pH values or low calcium concentrations due to destabilization of the protein structures. Through tuning the protein unfolding by pH and calcium concentrations, the hydrogel exhibits differences in modulus, strength, and anti-fatigue fracture. We found that due to the partially unfolding of ParV, the Young's modulus decreased at pH 9.0 or in the presence of EDTA (Ethylene Diamine Tetraacetic Acid), moreover, because partially unfolded ParV can be further completely unfolded due to the mechanically rupture of ester bond, leading to the observed hysteresis of the stretching and relaxation traces of the hydrogels, which is in line with single-molecule force spectroscopy experiments. These results display a new avenue for designing pH- or calcium-responsive hydrogels based on proteins and demonstrate the relationship between the mechanical properties of single molecules and macroscopic hydrogel networks.

Role of Metal Cofactor in Enhanced Thermal Stability of Azurin

Metal cofactors are critical centers for different biochemical processes of metalloproteins, and often, this metal coordination renders additional structural stability. In this study, we explore the additional stability conferred by the copper ion on azurin by analyzing both the apo and holo forms using temperature replica exchange molecular dynamics (REMD) data. We find a 14 K decrease in denaturation temperature for apo (406 K) azurin relative to that of holo (420 K), indicating a copper ion-induced additional thermal stability for holo azurin. The unfolding of apo azurin begins with the melting of α-helix and β-sheet V, similar to that of holo form. β-Sheets IV, VII, and VIII are comparatively more stable than other β-strands and melt at higher temperatures. Similar to holo azurin, the strong hydrophobic interactions among the apolar residues in the protein core is the key factor that renders high stability to apo protein as well. We construct free energy surfaces at different temperatures to capture the major conformations along the unfolding basins of the protein. Using contact maps from different basins we show the changes in the interaction between different residues along the unfolding pathway. Furthermore, we compare the Cα root-mean-square fluctuations (Cα-RMSF) and B-factor of all residues of apo and holo forms to understand the flexibility of different regions. The concerted displacement of α-helix and β-sheets V and VI from the protein core is another distinction we observe for apo compared to the holo form, where β-sheet VI was relatively stable.

Increasing the Mechanical Stability of Polymer-Gold Interfacial Connection: A Parallel Covalent Strategy

Thiol-gold (S-Au) chemistry has been widely used in coating and functionalizing gold surfaces because it is robust and highly efficient. However, recent studies have shown that the S-Au-based self-assembled monolayers can lead to significant instability under external mechanical loading (e.g., in a swelled polymer film). Such instability limits further applications of S-Au chemistry-based functional materials. Here, we report a surface-modifying procedure based on a parallel covalent strategy. By employing dendritic macromolecules as a "middle layer" between the gold surface and polymer, the interfacial connecting strength increased by at least 350% as revealed by atomic force microscopy-based single molecule force spectroscopy (AFM-SMFS). The ultimate cleavage structure is confirmed to be an amide bond by control SMFS experiments, fluorescent microscopy, and dynamic force spectroscopy. This study/concept paves the way to prepare stable stimuli-responsive polymer brushes on solid surfaces and study mechanophores with high force stability.

Quantification of carboxylate-bridged di-zinc site stability in protein due ferri by single-molecule force spectroscopy

Carboxylate-bridged diiron proteins belong to a protein family involved in different physiological processes. These proteins share the conservative EXXH motif, which provides the carboxylate bridge and is critical for metal binding. Here, we choose de novo-designed single-chain due ferri protein (DFsc), a four-helical protein with two EXXH motifs as a model protein, to study the stability of the carboxylate-bridged di-metal binding site. The mechanical and kinetic properties of the di-Zn site in DFsc were obtained by atomic force microscopy-based single-molecule force spectroscopy. Zn-DFsc showed a considerable rupture force of ~200 pN, while the apo-protein is mechanically labile. In addition, multiple rupture pathways were observed with different probabilities, indicating the importance of the EXXH-based carboxylate-bridged metal site. These results demonstrate carboxylate-bridged di-metal site is mechanically stable and improve our understanding of this important type of metalloprotein.

The cofactor-dependent folding mechanism of Drosophila cryptochrome revealed by single-molecule pulling experiments

The link between cofactor binding and protein activity is well-established. However, how cofactor interactions modulate folding of large proteins remains unknown. We use optical tweezers, clustering and global fitting to dissect the folding mechanism of Drosophila cryptochrome (dCRY), a 542-residue protein that binds FAD, one of the most chemically and structurally complex cofactors in nature. We show that the first dCRY parts to fold are independent of FAD, but later steps are FAD-driven as the remaining polypeptide folds around the cofactor. FAD binds to largely unfolded intermediates, yet with association kinetics above the diffusion-limit. Interestingly, not all FAD moieties are required for folding: whereas the isoalloxazine ring linked to ribitol and one phosphate is sufficient to drive complete folding, the adenosine ring with phosphates only leads to partial folding. Lastly, we propose a dCRY folding model where regions that undergo conformational transitions during signal transduction are the last to fold.

Single Molecule Force Spectroscopy Studies on Metalloproteins: Opportunities and Challenges

Metalloproteins play important roles in a wide range of biological processes. Elucidating the mechanisms via which metalloproteins fold and constitute their metal centers is critical to the understanding of the functions and dynamics of metalloproteins. Owing to its superior force and length resolution, single-molecule force spectroscopy (SMFS) has evolved into a powerful tool to probe the unfolding and folding mechanisms of metalloproteins at the single level by forcing metalloproteins to unfold and then refold along a reaction coordinate defined by the applied stretching force. The folding of metalloproteins is complex and involves two interwound processes, the folding of the polypeptide chain and the constitution of the metal center. Experimental studies of the folding of metalloproteins are challenging. SMFS studies have allowed researchers to directly probe the folding and unfolding of metalloproteins at the single-molecule level and the effect of metal centers on the folding-unfolding energy landscape of metalloproteins. New mechanistic insights on the folding and unfolding of some metalloproteins have been obtained, demonstrating the power and unique advantages that SMFS techniques may offer. In this Perspective, using calcium-binding proteins and small iron-sulfur proteins as examples, I provide a concise overview of the information and insights that SMFS studies have provided to understand the folding and unfolding of metalloproteins. I also discuss the opportunities and challenges that are present in this fast-progressing area of research.

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.

Self-Healing Approach toward Catalytic Soft Robots

Soft robotics is a rapidly evolving research field that focuses on developing robots with bioinspired actuation/sensing mechanisms and highly flexible soft materials, some of which are similar to those found in living organisms. The hydrogel has the characteristics of excellent biocompatibility, softness, and elasticity, which makes it an ideal candidate material for the preparation of soft robots. Here we utilized a self-healing approach to develop a catalytically driven soft robot, which was constructed by dynamic imine bonds between modular hydrogels. One of the modules was a hydrogel formed by dynamic aldimine cross-linking of chitosan and glutaraldehyde, and the other module was a hydrogel embedded with catalase. The soft hydrogel robot moved because of catalytic reactions between the robot and environment [hydrogen peroxide (H₂O₂) fuel], giving rise to a fluidic release that supports propulsion, as inspired by the jet-propulsive mechanism in swimming dragonfly larvae. The speed of the soft robot can be mediated by adjusting the concentration of H₂O₂ and enable/disable movement based on the folding and unfolding of enzymes. In addition, the hydrogel formed by replacing glutaraldehyde with dialdehyde-functionalized PEG₂₀₀₀ had excellent elastic properties, and the soft robot based on PEG₂₀₀₀ had a higher movement speed than that based on glutaraldehyde under the same H₂O₂ concentration. Moreover, the addition of iron oxide nanoparticles can realize the magnetic guidance of the soft robot and the combination of different modules can realize different motion modes. The highly configurable self-healing catalytic soft robot holds great potential for a variety of interesting applications, including swimming robots, robot-assisted water treatment, and drug release.

Dynamic Covalent Hydrogels: Strong yet Dynamic

Hydrogels are crosslinked polymer networks with time-dependent mechanical response. The overall mechanical properties are correlated with the dynamics of the crosslinks. Generally, hydrogels crosslinked by permanent chemical crosslinks are strong but static, while hydrogels crosslinked by physical interactions are weak but dynamic. It is highly desirable to create synthetic hydrogels that possess strong mechanical stability yet remain dynamic for various applications, such as drug delivery cargos, tissue engineering scaffolds, and shape-memory materials. Recently, with the introduction of dynamic covalent chemistry, the seemingly conflicting mechanical properties, i.e., stability and dynamics, have been successfully combined in the same hydrogels. Dynamic covalent bonds are mechanically stable yet still capable of exchanging, dissociating, or switching in response to external stimuli, empowering the hydrogels with self-healing properties, injectability and suitability for postprocessing and additive manufacturing. Here in this review, we first summarize the common dynamic covalent bonds used in hydrogel networks based on various chemical reaction mechanisms and the mechanical strength of these bonds at the single molecule level. Next, we discuss how dynamic covalent chemistry makes hydrogel materials more dynamic from the materials perspective. Furthermore, we highlight the challenges and future perspectives of dynamic covalent hydrogels.

Quantification of a Neurological Protein in a Single Cell Without Amplification

Proteins are key biomolecules that not only play various roles in the living body but also are used as biomarkers. If these proteins can be quantified at the level of a single cell, understanding the role of proteins will be deepened and diagnosing diseases and abnormality will be further upgraded. In this study, we quantified a neurological protein in a single cell using atomic force microscopy (AFM). After capturing specifically disrupted-in-schizophrenia 1 (DISC1) in a single cell onto a microspot immobilizing the corresponding antibody on the surface, force mapping with AFM was followed to visualize individual DISC1. Although a large variation of the number of DISC1 in a cell was observed, the average number is 4.38 × 10³, and the number agrees with the ensemble-averaged value. The current AFM approach for the quantitative analysis of proteins in a single cell should be useful to study molecular behavior of proteins in depth and to follow physiological change of individual cells in response to external stimuli.

Force Mapping Reveals the Spatial Distribution of Individual Proteins in a Neuron

Conventional methods for studying the spatial distribution and expression level of proteins within neurons have primarily relied on immunolabeling and/or signal amplification. Here, we present an atomic force microscopy (AFM)-based nanoscale force mapping method, where Anti-LIMK1-tethered AFM probes were used to visualize individual LIMK1 proteins in cultured neurons directly through force measurements. We observed that the number density of LIMK1 decreased in neuronal somas after the cells were depolarized. We also elucidated the spatial distribution of LIMK1 in single spine areas and found that the protein predominantly locates at heads of spines rather than dendritic shafts. The study demonstrates that our method enables unveiling of the abundance and spatial distribution of a protein of interest in neurons without signal amplification or labeling. We expected that this approach should facilitate the studies of protein expression phenomena in depth in a wide range of biological systems.

New insights into the folding–unfolding mechanism and conformations of cytochrome C

Optical trapping experiments offer new insights into the folding and unfolding of cytochrome C.

Modified cytosines versus cytosine in a DNA polymerase: retrieving thermodynamic and kinetic constants at the single molecule level

DNA methylation plays key roles in various areas, such as gene expression, regulation, epigenetics, and cancers. Since 5-methylcytosine (5mC) is commonly present in methylated DNA, characterizing the binding kinetics and thermodynamics of the nucleotide to the enzymatic pocket can help to understand the DNA replication process. Furthermore, 5-carboxycytosine (5caC) is a form that appears through the iterative oxidation of 5mC, and its effect on the DNA replication process is still not well known. Here, we immobilized a DNA polymerase (DNAP) with an orientation control on a tip of an atomic force microscope (AFM), and observed the interaction between the immobilized deoxyguanosine triphosphate (dGTP) on the surface and the DNAP in the presence of a DNA duplex. The interaction probability increased as the concentration of the DNA strand, and the affinity constant between the DNAP and DNA was obtained by fitting the change. Increasing the concentration of dGTP in solution diminished the interaction probability, and a fitting allowed us to retrieve the affinity constant between dGTP and the DNAP holding the DNA in the reaction pocket. Because the dissociation constant could be obtained through the loading rate dependence of the unbinding force value, both affinity and kinetic constants for cytosine (C), 5mC, and 5caC in the DNAP were compared in the light of the steric and electronic effect of the substituents at 5-position of cytosine.

Revealing the Underestimated Anticancer Effect of Azurin by Mechanical Unfolding

As a potential anticancer agent, azurin has attracted extensive attraction among chemists, physicists, and material scientists. Its structural and unfolding/folding information has been partially understood, but some detailed information, such as the difference in the unfolding processes between apo-azurin and holo-azurin, the mechanical stability, and the role of the copper cluster in its stability, has not been addressed adequately, especially at the single-molecule level. Here, we employed AFM-based single-molecule force spectroscopy to investigate the unfolding process of azurin in the apo and holo forms under an external force. The results indicated that the unfolding processes of apo-azurin and holo-azurin are different, and holo-azurin requires a stronger force to unfold than does apo-azurin. The copper cluster exhibited a more significant impact on the stability and the folding process of holo-azurin: the copper cluster was completely broken, and the copper ion left the unfolded azurin during the unfolding process of azurin. We suspected that the presence of the disulfide bond in azurin made the unfolding of the copper cluster different from that in pseudoazurin, which is also a type I copper protein like azurin. Rarely reported in previous studies, the mechanical strength of the Cu-N(His) bond of the copper cluster was obtained in this study, which is weaker than that of most metal-S(Cys) bonds but higher than that of the Fe-N(His) bond. Altogether, our results offer a possible new scenario for azurin to widely extend its anticancer activity.

The two redox states of the human NEET proteins' [2Fe-2S] clusters

The NEET proteins constitute a unique class of [2Fe–2S] proteins. The metal ions bind to three cysteines and one histidine. The proteins’ clusters exist in two redox states; the oxidized protein (containing two Fe^III ions) can transfer the cluster to apo-acceptor protein(s), while the reduced form (containing one ferrous ion) remains bound to the protein frame. Here, we perform in silico and in vitro studies on human NEET proteins in both reduced and oxidized forms. Quantum chemical calculations on all available human NEET proteins structures suggest that reducing the cluster weakens the Fe–N^His and Fe–S^Cys bonds, similar to what is seen in other Fe–S proteins (e.g., ferredoxin and Rieske protein). We further show that the extra electron in the [2Fe–2S]⁺ clusters of one of the NEET proteins (mNT) is localized on the His-bound iron ion, consistently with our previous spectroscopic studies. Kinetic measurements demonstrate that the mNT [2Fe–2S]⁺ is released only by an increase in temperature. Thus, the reduced state of human NEET proteins [2Fe–2S] cluster is kinetically inert. This previously unrecognized kinetic inertness of the reduced state, along with the reactivity of the oxidized state, is unique across all [2Fe–2S] proteins. Finally, using a coevolutionary analysis, along with molecular dynamics simulations, we provide insight on the observed allostery between the loop L2 and the cluster region. Specifically, we show that W75, R76, K78, K79, F82 and G85 in the latter region share similar allosteric characteristics in both redox states.

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.

Nonrefoldability is Pervasive Across the E. coli Proteome

Decades of research on protein folding have primarily focused on a subset of small proteins that can reversibly refold from a denatured state. However, these studies have generally not been representative of the complexity of natural proteomes, which consist of many proteins with complex architectures and domain organizations. Here, we introduce an experimental approach to probe protein refolding kinetics for whole proteomes using mass spectrometry-based proteomics. Our study covers the majority of the soluble E. coli proteome expressed during log-phase growth, and among this group, we find that one-third of the E. coli proteome is not intrinsically refoldable on physiological time scales, a cohort that is enriched with certain fold-types, domain organizations, and other biophysical features. We also identify several properties and fold-types that are correlated with slow refolding on the minute time scale. Hence, these results illuminate when exogenous factors and processes, such as chaperones or cotranslational folding, might be required for efficient protein folding.

Nanomechanical Phenotypes in Cardiac Myosin-Binding Protein C Mutants That Cause Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is a disease of the myocardium caused by mutations in sarcomeric proteins with mechanical roles, such as the molecular motor myosin. Around half of the HCM-causing genetic variants target contraction modulator cardiac myosin-binding protein C (cMyBP-C), although the underlying pathogenic mechanisms remain unclear since many of these mutations cause no alterations in protein structure and stability. As an alternative pathomechanism, here we have examined whether pathogenic mutations perturb the nanomechanics of cMyBP-C, which would compromise its modulatory mechanical tethers across sliding actomyosin filaments. Using single-molecule atomic force spectroscopy, we have quantified mechanical folding and unfolding transitions in cMyBP-C domains targeted by HCM mutations that do not induce RNA splicing alterations or protein thermodynamic destabilization. Our results show that domains containing mutation R495W are mechanically weaker than wild-type at forces below 40 pN and that R502Q mutant domains fold faster than wild-type. None of these alterations are found in control, nonpathogenic variants, suggesting that nanomechanical phenotypes induced by pathogenic cMyBP-C mutations contribute to HCM development. We propose that mutation-induced nanomechanical alterations may be common in mechanical proteins involved in human pathologies.

Nanoaggregates Derived from Amyloid-beta and Alpha-synuclein Characterized by Sequential Quadruple Force Mapping

Overlapping of Alzheimer's disease and Parkinson's disease is associated with the formation of hetero-oligomers derived from amyloid-beta and alpha-synuclein. However, the structural identity of the hetero-oligomer has yet to be elucidated, particularly at high resolution. Here, with atomic force microscopy, the surface structure of hetero-oligomer was examined with four AFM tips tethering one of the selected antibodies recognizing N-terminus or C-terminus of each peptide. All aggregates were found to be hetero-oligomers, and probability of recognizing the termini is higher than that for the homo-oligomers, suggesting that the termini of the former have a greater tendency to be located at the surface or the termini have more freedom to be recognized, probably through loose packing. The methodology in this study provides us with a new approach to elucidate the structure of such aggregates at the single-molecule level, allowing the exploration of other intrinsically disordered proteins frequently found in nature.

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.

Recombination of 2Fe-2S Ferredoxins Reveals Differences in the Inheritance of Thermostability and Midpoint Potential

Recombination can be used in the laboratory to overcome component limitations in synthetic biology by creating enzymes that exhibit distinct activities and stabilities from native proteins. To investigate how recombination affects the properties of an oxidoreductase that transfers electrons in cells, we created ferredoxin (Fd) chimeras by recombining distantly related cyanobacterial and cyanomyophage Fds (53% identity) that present similar midpoint potentials but distinct thermostabilities. Fd chimeras having a wide range of amino acid substitutions retained the ability to coordinate an iron-sulfur cluster, although their thermostabilities varied with the fraction of residues inherited from each parent. The midpoint potentials of chimeric Fds also varied. However, all of the synthetic Fds exhibited midpoint potentials outside of the parental protein range. Each of the chimeric Fds could also support electron transfer between Fd-NADP reductase and sulfite reductase in Escherichia coli, although the chimeric Fds varied in the expression required for similar levels of cellular electron transfer. These results show how Fds can be diversified through recombination and reveal differences in the inheritance of thermostability and electrochemical properties. Furthermore, they illustrate how electron transfer efficiencies of chimeric Fds can be rapidly evaluated using a synthetic metabolic pathway.

Ultrahigh Adhesion Force Between Silica-Binding Peptide SB7 and Glass Substrate Studied by Single-Molecule Force Spectroscopy and Molecular Dynamic Simulation

Many proteins and peptides have been identified to effectively and specifically bind on certain surfaces such as silica, polystyrene and titanium dioxide. It is of great interest, in many areas such as enzyme immobilization, surface functionalization and nanotechnology, to understand how these proteins/peptides bind to solid surfaces. Here we use single-molecule force spectroscopy (SMFS) based on atomic force microscopy to directly measure the adhesion force between a silica-binding peptide SB7 and glass surface at single molecule level. SMFS results show that the adhesion force of a single SB7 detaching from the glass surface distributes in two populations at ~220 pN and 610 pN, which is higher than the unfolding forces of most mechanically stable proteins and the unbinding forces of most stable protein-protein interactions. Molecular dynamics simulation reveals that the electrostatic interactions between positively charged arginine residues and the silica surface dominates the binding of SB7 on silica. Our study provides experimental evidence and molecular mechanism at the single-molecule level for the SB7-based immobilization of proteins on silica-based surface, which is able to withstand high mechanical forces, making it an ideal fusion tag for silica surface immobilization or peptide-base adhesive materials.

Role of the copper ion in pseudoazurin during the mechanical unfolding process

Metalloproteins require the corresponding metal cofactors to exert their proper function. The presence of metal cofactors in the metalloprotein makes it more difficult to investigate its folding and unfolding process. In this study, we employed atomic-force-microscopy-based single-molecule force spectroscopy to reveal the unfolding process of pseudoazurin (PAZ) that belongs to blue copper proteins. Our study shows that holo-PAZ requires a higher rupture force for mechanical unfolding comparing with the apo-PAZ. This result demonstrates that the copper atom not only enables PAZ access to transfer electron, but should also have an influence on its stability. The results also suggest that the electronic configuration of the metal cofactors has a striking effect on the strength of the organometallic bonds. Moreover, the results also reveal that there is an intermediate state during the unfolding process of PAZ. This study provides insight into the characteristics of metalloproteins and leads to a better knowledge of their interaction at the individual molecule level.

Single-Molecule Force Spectroscopy Reveals that the Fe-N Bond Enables Multiple Rupture Pathways of the 2Fe2S Cluster in a MitoNEET Monomer

The mitochondrial outer membrane protein, mitoNEET (mNT), is an iron-sulfur protein containing an Fe₂S₂(His)₁(Cys)₃ cluster with a unique single Fe-N bond. Previous studies have shown that this Fe(III)-N(His) bond is essential for metal cluster transfer and protein function. To further understand the effect of this unique Fe-N bond on the metal cluster and protein, we used atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) to investigate the mechanical unfolding mechanism of an mNT monomer, focusing on the rupture pathway and kinetic stability of the cluster. We found that the Fe-N bond was the weakest point of the cluster, the rupture of which occurred first, and could be independent of the cluster break. Moreover, this Fe-N bond enabled a dynamic and labile iron-sulfur cluster, as multiple unfolding pathways of mNT with a unique Fe₂S₂(Cys)₃ intermediate were observed accordingly.

Rate-dependent force-extension models for single-molecule force spectroscopy experiments

Single-molecule force spectroscopy techniques allow for the measurement of several static and dynamic features of macromolecules of biological origin. In particular, atomic force microscopy, used with a variable pulling rate, provides valuable information on the folding/unfolding dynamics of proteins. We propose here two different models able to describe the out-of-equilibrium statistical mechanics of a chain composed of bistable units. These latter represent the protein domains, which can be either folded or unfolded. Both models are based on the Langevin approach and their implementation allows for investigating the effect of the pulling rate and of the device intrinsic elasticity on the chain unfolding response. The theoretical results (both analytical and numerical) have been compared with experimental data concerning the unfolding of the titin and filamin proteins, eventually obtaining a good agreement over a large range of the pulling rates.

Prochlorococcus phage ferredoxin: structural characterization and electron transfer to cyanobacterial sulfite reductases

Marine cyanobacteria are infected by phages whose genomes encode ferredoxin (Fd) electron carriers. These Fds are thought to redirect the energy harvested from light to phage-encoded oxidoreductases that enhance viral fitness, but it is unclear how the biophysical properties and partner specificities of phage Fds relate to those of photosynthetic organisms. Here, results of a bioinformatics analysis using a sequence similarity network revealed that phage Fds are most closely related to cyanobacterial Fds that transfer electrons from photosystems to oxidoreductases involved in nutrient assimilation. Structural analysis of myovirus P-SSM2 Fd (pssm2-Fd), which infects the cyanobacterium Prochlorococcus marinus, revealed high levels of similarity to cyanobacterial Fds (root mean square deviations of ≤0.5 Å). Additionally, pssm2-Fd exhibited a low midpoint reduction potential (-336 mV versus a standard hydrogen electrode), similar to other photosynthetic Fds, although it had lower thermostability (T_m = 28 °C) than did many other Fds. When expressed in an Escherichia coli strain deficient in sulfite assimilation, pssm2-Fd complemented bacterial growth when coexpressed with a P. marinus sulfite reductase, revealing that pssm2-Fd can transfer electrons to a host protein involved in nutrient assimilation. The high levels of structural similarity with cyanobacterial Fds and reactivity with a host sulfite reductase suggest that phage Fds evolved to transfer electrons to cyanobacterially encoded oxidoreductases.

Environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by atomic force microscopy-based single-molecule force spectroscopy and the implications for advanced polymer materials

"The Tao begets the One. One begets all things of the world." This quote from Tao Te Ching is still inspiring for scientists in chemistry and materials science: The "One" can refer to a single molecule. A macroscopic material is composed of numerous molecules. Although the relationship between the properties of the single molecule and macroscopic material is not well understood yet, it is expected that a deeper understanding of the single-chain mechanics of macromolecules will certainly facilitate the development of materials science. Atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) has been exploited extensively as a powerful tool to study the single-chain behaviors of macromolecules. In this review, we summarize the recent advances in the emerging field of environment-dependent single-chain mechanics of synthetic polymers and biomacromolecules by means of AFM-SMFS. First, the single-chain inherent elasticities of several typical linear macromolecules are introduced, which are also confirmed by one of three polymer models with theoretical elasticities of the corresponding macromolecules obtained from quantum mechanical (QM) calculations. Then, the effects of the external environments on the single-chain mechanics of synthetic polymers and biomacromolecules are reviewed. Finally, the impacts of single-chain mechanics of macromolecules on the development of polymer science especially polymer materials are illustrated.

How mechanical forces can modulate the metal affinity and selectivity of metal binding sites in proteins

The results obtained reveal that applying mechanical forces with a given strength and directionality can modulate the metal affinity and selectivity of metal binding sites in metalloproteins.

Giant "Breathing" Proteinosomes with Jellyfish-like Property

The design and construction of "breathing" self-assemblies has been a rather popular topic due to their potential in materials science and nanotechnology. Inspired by the "breathing" behavior of natural jellyfish, herein, we presented the construction of a giant "breathing" proteinosome through an interfacial self-assembly of proteins and surfactants at the oil/water interface of emulsions: The proteinosome displays "breathing" behavior and can swell and shrink for multiple cycles by protein folding and unfolding through the alternate addition and removal of denaturant; more importantly, when green fluorescent proteins were selected as alternative protein building blocks, the fluorescence of proteinosome can be reversibly switched on/off just like the behavior of jellyfish. Moreover, accompanied by reversible swelling and shrinking and on/off fluorescence, the expanded and shrunk membrane pore can be tuned for distinguishing quantum dots of different sizes. The folding-responsive breathing behavior of intelligent proteinosomes provides a platform for functional biomaterials.

Single-Molecule Force Spectroscopy Reveals that Iron-Ligand Bonds Modulate Proteins in Different Modes

The iron-amino acid interactions Fe-O(Glu/Asp), Fe-N(His), and Fe-S(Cys) are the three major iron-ligand bonds in proteins. To compare their properties in proteins, we used atomic force microscopy (AFM)-based single-molecule force spectroscopy to investigate a superoxide reductase (Fe(III)-SOR) with all three types of bonds forming an Fe(His)₄CysGlu center. We first found that Apo-SOR without bound iron showed multiple unfolding pathways only from the β-barrel core. Then, using Holo-SOR with a ferric ion, we found that a single Fe-O(Glu) bond can tightly connect the flexible N-terminal fragment to the β-barrel and stabilize the whole protein, showing a complete protein unfolding scenario, while the single Fe-N(His) bond was weak and unable to provide such a stabilization. Moreover, when multiple Fe-N bonds are present, a similar stabilization effect can be achieved. Our results showed that the iron-ligand bond modulates protein structure and stability in different modes at the single-bond level.

Quantifying the Chain Folding in Polymer Single Crystals by Single-Molecule Force Spectroscopy

Chain folding is a motif of polymer crystallization, which is essential for determining the crystallization kinetics. However, the experimental quantification of the chain folding remains a challenge because of limited instrumental resolution. Here, we quantify chain folding in solution-grown single crystals by using atomic force microscopy (AFM)-based single-molecule force spectroscopy. The fingerprint spectrum of force-induced chain motion allows us to decipher the adjacent and nonadjacent re-entry folding with spatial resolution of subnanometers. The average fractions of adjacent re-entry folds ⟨f⟩ are in the range 91-95% for polycaprolactone, poly-l-lactic acid, and polyamide 66, which is higher than the values determined by other classical technologies. The established single-molecule method is applicable to a broad range of crystalline polymer systems with different chain conformations or compositions.

Giant Proteinosomes As Scaffolds for Light Harvesting

Based on an interfacial assembly strategy, a giant proteinosome was successfully fabricated by using protein-surfactant as building blocks, which formed a thin protein layer as a membrane. This approach of making protein assemblies was very facile, and it was very convenient to remove the templates of oil and get water-filled proteinosomes by dialysis. Through modifying acceptor and donor chromophores on the protein monomers, an efficient artificial light-harvesting system was successfully fabricated on the proteinosome, which was a scaffold for efficient light harvesting. Furthermore, the on-off switchable energy transfer was realized by protein folding and unfolding. The efficient artificial light-harvesting systems we designed as the potential platforms could be utilized for biomaterials.

Multistep Protein Unfolding Scenarios from the Rupture of a Complex Metal Cluster Cd3S9

Protein (un)folding is a complex and essential process. With the rapid development of single-molecule techniques, we can detect multiple and transient proteins (un)folding pathways/intermediates. However, the observation of multiple multistep (>2) unfolding scenarios for a single protein domain remains limited. Here, we chose metalloprotein with relatively stable and multiple metal-ligand coordination bonds as a system for such a purpose. Using AFM-based single-molecule force spectroscopy (SMFS), we successfully demonstrated the complex and multistep protein unfolding scenarios of the β-domain of a human protein metallothionein-3 (MT). MT is a protein of ~60 amino acids (aa) in length with 20 cysteines for various metal binding, and the β-domain (βMT) is of ~30 aa with an M3S9 metal cluster. We detected four different types of three-step protein unfolding scenarios from the Cd-βMT, which can be possibly explained by the rupture of Cd-S bonds in the complex Cd3S9 metal cluster. In addition, complex unfolding scenarios with four rupture peaks were observed. The Cd-S bonds ruptured in both single bond and multiple bonds modes. Our results provide not only evidence for multistep protein unfolding phenomena but also reveal unique properties of metalloprotein system using single-molecule AFM.

Enzymatic biosynthesis and immobilization of polyprotein verified at the single-molecule level

The recent development of chemical and bio-conjugation techniques allows for the engineering of various protein polymers. However, most of the polymerization process is difficult to control. To meet this challenge, we develop an enzymatic procedure to build polyprotein using the combination of a strict protein ligase OaAEP1 (Oldenlandia affinis asparaginyl endopeptidases 1) and a protease TEV (tobacco etch virus). We firstly demonstrate the use of OaAEP1-alone to build a sequence-uncontrolled ubiquitin polyprotein and covalently immobilize the coupled protein on the surface. Then, we construct a poly-metalloprotein, rubredoxin, from the purified monomer. Lastly, we show the feasibility of synthesizing protein polymers with rationally-controlled sequences by the synergy of the ligase and protease, which are verified by protein unfolding using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS). Thus, this study provides a strategy for polyprotein engineering and immobilization.

Fungicide tolerant Bradyrhizobium japonicum mitigate toxicity and enhance greengram production under hexaconazole stress

Bacterial strain RV9 recovered from greengram nodules tolerated 2400μg/mL of hexaconazole and was identified by 16S rDNA sequence analysis as Bradyrhizobium japonicum (KY940048). Strain RV9 produced IAA (61.6μg/mL), ACC deaminase (51.7mg/(protein·hr)), solubilized TCP (105μg/mL), secreted 337.6μg/mL EPS, and produced SA (52.2μg/mL) and 2,3-DHBA (28.3μg/mL). Exopolysaccharides produced by strain RV9 was quantified and characterized by SEM, AFM, EDX and FTIR. Beyond tolerance limit, hexaconazole caused cellular impairment and reduced the viability of strain RV9 revealed by SEM and CLSM. Hexaconazole distorted the root tips and altered nodule structure leading thereby to reduction in the performance of greengram. Also, the level of antioxidant enzymes, proline, TBARS, ROS and cell death was increased in hexaconazole treated plants. CLSM images revealed a concentration dependent increase in the characteristic green and blue fluorescence of hexaconazole treated roots. The application of B. japonicum strain RV9 alleviated the fungicide toxicity and improved the measured plant characteristics. Also, rhizobial cells were localized inside tissues as revealed by CLSM. Colonization of B. japonicum strain RV9 decreased the levels of CAT, POD, APX, GPX and TBARS by 80%, 5%, 13%, 13% and 19%, respectively over plants grown at 80μg/(hexaconazole·kg) soil. The ability to detoxify hexaconazole, colonize plant tissues, secrete PGP bioactive molecules even under fungicide pressure and its unique ability to diminish oxidative stress make B. japonicum an attractive choice for remediation of fungicide polluted soils and to concurrently enhance greengram production under stressed environment.

Mechanical Unfolding Pathway of the High-Potential Iron-Sulfur Protein Revealed by Single-Molecule Atomic Force Microscopy: Toward a General Unfolding Mechanism for Iron-sulfur Proteins

High-potential iron-sulfur proteins (HiPIPs) are an important class of metalloproteins with a [4Fe-4S] cluster coordinated by four cysteine residues. Distinct from other iron-sulfur proteins, the cluster in HiPIP has a high reduction potential, making it an essential electron carrier in bacterial photosynthesis. Here, we combined single-molecule atomic force microscopy and protein engineering techniques to investigate the mechanical unfolding mechanism of HiPIP from Chromatium tepidum (cHiPIP). We found that cHiPIP unfolds in a two-step fashion with the protein sequence sequestered by the iron-sulfur center as a stable unfolding intermediate state. The rupture of the iron-sulfur center of cHiPIP proceeds in two distinct parallel pathways; one pathway involves the concurrent rupture of multiple iron-thiolate bonds, and the other one involves the sequential rupture of the iron-thiolate bonds. This mechanistic information was further confirmed by mutational studies. We found that the rupture of the iron-thiolate bonds in reduced and oxidized cHiPIP occurred in the range of 150-180 pN at a pulling speed of 400 nm/s, similar to that measured for iron-thiolate bonds in rubredoxin and ferredoxin. Our results may have important implications for understanding the general unfolding mechanism governing iron-sulfur proteins, as well as the mechanism governing the mechanical rupture of the iron-sulfur center.

Forcing the reversibility of a mechanochemical reaction

Mechanical force modifies the free-energy surface of chemical reactions, often enabling thermodynamically unfavoured reaction pathways. Most of our molecular understanding of force-induced reactivity is restricted to the irreversible homolytic scission of covalent bonds and ring-opening in polymer mechanophores. Whether mechanical force can by-pass thermodynamically locked reactivity in heterolytic bimolecular reactions and how this impacts the reaction reversibility remains poorly understood. Using single-molecule force-clamp spectroscopy, here we show that mechanical force promotes the thermodynamically disfavored SN2 cleavage of an individual protein disulfide bond by poor nucleophilic organic thiols. Upon force removal, the transition from the resulting high-energy unstable mixed disulfide product back to the initial, low-energy disulfide bond reactant becomes suddenly spontaneous, rendering the reaction fully reversible. By rationally varying the nucleophilicity of a series of small thiols, we demonstrate how force-regulated chemical kinetics can be finely coupled with thermodynamics to predict and modulate the reversibility of bimolecular mechanochemical reactions.

Differences in the mechanical unfolding pathways of apo- and copper-bound azurins

Metalloproteins carry out diverse biological functions including metal transport, electron transfer, and catalysis. At present, the influence of metal cofactors on metalloprotein stability is not well understood. Here, we report the mechanical stability and unfolding pathway of azurin, a cupredoxin family protein with β-barrel topology and type I copper-binding centre. Single-molecule force spectroscopy (SMFS) experiments reveal 2-state and 3-state unfolding pathways for apo-azurin. The intermediate in the 3-state pathway occurs at an unfolding contour length of 7.5 nm from the native state. Steered molecular dynamics (SMD) simulations show that apo-azurin unfolds via a first transition state (TS) where β2Β–β8 and β7–β8 strand pairs rupture to form the intermediate, which subsequently unfolds by the collective rupture of remaining strands. SMFS experiments on holo-azurin exhibit an additional 4-state pathway besides the 2-state and 3-state pathways. The unfolding contour length leading to the first intermediate is 6.7 nm suggesting a sequestration of ~1 nm polypeptide chain length by the copper. SMD simulations reveal atomistic details of the copper sequestration and predict a combined β4–β7 pair and copper coordination sphere rupture to create the third TS in the 4-state pathway. Our systematic studies provide detailed mechanistic insights on modulation of protein mechanical properties by metal-cofactors.

Force Measurement for the Interaction between Cucurbit[7]uril and Mica and Self-Assembled Monolayer in the Presence of Zn2+ Studied with Atomic Force Microscopy

Force spectroscopy with atomic force microscopy (AFM) revealed that cucurbit[7]uril (CB[7]) strongly binds to a mica surface in the presence of cations. Indeed, Zn²⁺ was observed to facilitate the self-assembly of CB[7] on the mica surface, whereas monocations, such as Na⁺, were less effective. The progression of the process and the cation-mediated self-assembled monolayer were characterized using AFM, and the observed height of the layer agrees well with the calculated CB[7] value (9.1 Å). We utilized force-based AFM to further study the interaction of CB[7] with guest molecules. To this end, CB[7] was immobilized on a glass substrate, and aminomethylferrocene (am-Fc) was conjugated onto an AFM tip. The single-molecule interaction between CB[7] and am-Fc was monitored by collecting the unbinding force curves. The force histogram showed single ruptures and a unimodal distribution, and the most probable unbinding force value was 101 pN in deionized water and 86 pN in phosphate-buffered saline buffer. The results indicate that the unbinding force was larger than that of streptavidin-biotin measured under the same conditions, whereas the dissociation constant was smaller by 1 order of magnitude (0.012 s^-1 vs 0.13 s^-1). Furthermore, a high-resolution adhesion force map showed a part of the CB[7] cavities on the surface.