Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins

Unraveling the Mechanical Unfolding Pathways of a Multidomain Protein: Phosphoglycerate Kinase

Phosphoglycerate kinase (PGK) is a highly conserved enzyme that is crucial for glycolysis. PGK is a monomeric protein composed of two similar domains and has been the focus of many studies for investigating interdomain interactions within the native state and during folding. Previous studies used traditional biophysical methods (such as circular dichroism, tryptophan fluorescence, and NMR) to measure signals over a large ensemble of molecules, which made it difficult to observe transient changes in stability or structure during unfolding and refolding of single molecules. Here, we unfold single molecules of PGK using atomic force spectroscopy and steered molecular dynamic computer simulations to examine the conformational dynamics of PGK during its unfolding process. Our results show that after the initial forced separation of its domains, yeast PGK (yPGK) does not follow a single mechanical unfolding pathway; instead, it stochastically follows two distinct pathways: unfolding from the N-terminal domain or unfolding from the C-terminal domain. The truncated yPGK N-terminal domain unfolds via a transient intermediate, whereas the structurally similar isolated C-terminal domain has no detectable intermediates throughout its mechanical unfolding process. The N-terminal domain in the full-length yPGK displays a strong unfolding intermediate 13% of the time, whereas the truncated domain (yPGKNT) transitions through the intermediate 81% of the time. This effect indicates that the mechanical properties of yPGK cannot be simply deduced from the mechanical properties of its constituents. We also find that Escherichia coli PGK is significantly less mechanically stable as compared to yPGK, contrary to bulk unfolding measurements. Our results support the growing body of observations that the folding behavior of multidomain proteins is difficult to predict based solely on the studies of isolated domains.

Solid-state NMR spectroscopy based atomistic view of a membrane protein unfolding pathway

Membrane protein folding, structure, and function strongly depend on a cell membrane environment, yet detailed characterization of folding within a lipid bilayer is challenging. Studies of reversible unfolding yield valuable information on the energetics of folding and on the hierarchy of interactions contributing to protein stability. Here, we devise a methodology that combines hydrogen-deuterium (H/D) exchange and solid-state NMR (SSNMR) to follow membrane protein unfolding in lipid membranes at atomic resolution through detecting changes in the protein water-accessible surface, and concurrently monitoring the reversibility of unfolding. We obtain atomistic description of the reversible part of a thermally induced unfolding pathway of a seven-helical photoreceptor. The pathway is visualized through SSNMR-detected snapshots of H/D exchange patterns as a function of temperature, revealing the unfolding intermediate and its stabilizing factors. Our approach is transferable to other membrane proteins, and opens additional ways to characterize their unfolding and stabilizing interactions with atomic resolution.

Molecular mechanism for thermal denaturation of thermophilic rhodopsin

Understanding the factors affecting the stability and function of proteins at the molecular level is of fundamental importance. In spite of their use in bioelectronics and optogenetics, factors influencing thermal stability of microbial rhodopsins, a class of photoreceptor protein ubiquitous in nature are not yet well-understood. Here we report on the molecular mechanism for thermal denaturation of microbial retinal proteins, including, a highly thermostable protein, thermophilic rhodopsin (TR). External stimuli-dependent thermal denaturation of TR, the proton pumping rhodopsin of Thermus thermophilus bacterium, and other microbial rhodopsins are spectroscopically studied to decipher the common factors guiding their thermal stability. The thermal denaturation process of the studied proteins is light-catalyzed and the apo-protein is thermally less stable than the corresponding retinal-covalently bound opsin. In addition, changes in structure of the retinal chromophore affect the thermal stability of TR. Our results indicate that the hydrolysis of the retinal protonated Schiff base (PSB) is the rate-determining step for denaturation of the TR as well as other retinal proteins. Unusually high thermal stability of TR multilayers, in which PSB hydrolysis is restricted due to lack of bulk water, strongly supports this proposal. Our results also show that the protonation state of the PSB counter-ion does not affect the thermal stability of the studied proteins. Thermal photo-bleaching of an artificial TR pigment derived from non-isomerizable trans-locked retinal suggests, rather counterintuitively, that the photoinduced retinal trans-cis isomerization is not a pre-requisite for light catalyzed thermal denaturation of TR. Protein conformation alteration triggered by light-induced retinal excited state formation is likely to facilitate the PSB hydrolysis.

Removal of a Conserved Disulfide Bond Does Not Compromise Mechanical Stability of a VHH Antibody Complex

Single-domain VHH antibodies are promising reagents for medical therapy. A conserved disulfide bond within the VHH framework region is known to be critical for thermal stability, however, no prior studies have investigated its influence on the stability of VHH antibody-antigen complexes under mechanical load. Here, we used single-molecule force spectroscopy to test the influence of a VHH domain's conserved disulfide bond on the mechanical strength of the interaction with its antigen mCherry. We found that although removal of the disulfide bond through cysteine-to-alanine mutagenesis significantly lowered VHH domain denaturation temperature, it had no significant impact on the mechanical strength of the VHH:mCherry interaction with complex rupture occurring at ∼60 pN at 103-104 pN/sec regardless of disulfide bond state. These results demonstrate that mechanostable binding interactions can be built on molecular scaffolds that may be thermodynamically compromised at equilibrium.

Probing ligand-receptor bonds in physiologically relevant conditions using AFM

Cell surface receptors, often called transmembrane receptors, are key cellular components as they control and mediate cell communication and signalling, converting extracellular signals into intracellular signals. Elucidating the molecular details of ligand binding (cytokine, growth factors, hormones, pathogens,...) to cell surface receptors and how this binding triggers conformational changes that initiate intracellular signalling is needed to improve our understanding of cellular processes and for rational drug design. Unfortunately, the molecular complexity and high hydrophobicity of membrane proteins significantly hamper their structural and functional characterization in conditions mimicking their native environment. With its piconewton force sensitivity and (sub)nanometer spatial resolution, together with the capability of operating in liquid environment and at physiological temperature, atomic force microscopy (AFM) has proven to be one of the most powerful tools to image and quantify receptor-ligand bonds in situ under physiologically relevant conditions. In this article, a brief overview of the rapid evolution of AFM towards quantitative biological mapping will be given, followed by selected examples highlighting the main advances that AFM-based ligand-receptor studies have brought to the fields of cell biology, immunology, microbiology, and virology, along with future prospects and challenges. Graphical abstract.

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.

DNA Nanotechnology as an Emerging Tool to Study Mechanotransduction in Living Systems

The ease of tailoring DNA nanostructures with sub-nanometer precision has enabled new and exciting in vivo applications in the areas of chemical sensing, imaging, and gene regulation. A new emerging paradigm in the field is that DNA nanostructures can be engineered to study molecular mechanics. This new development has transformed the repertoire of capabilities enabled by DNA to include detection of molecular forces in living cells and elucidating the fundamental mechanisms of mechanotransduction. This Review first describes fundamental aspects of force-induced melting of DNA hairpins and duplexes. This is then followed by a survey of the currently available force sensing DNA probes and different fluorescence-based force readout modes. Throughout the Review, applications of these probes in studying immune receptor signaling, including the T cell receptor and B cell receptor, as well as Notch and integrin signaling, are discussed.

Nanoscale imaging reveals miRNA-mediated control of functional states of dendritic spines

Dendritic spines are major loci of excitatory inputs and undergo activity-dependent structural changes that contribute to synaptic plasticity and memory formation. Despite the existence of various classification types of spines, how they arise and which molecular components trigger their structural plasticity remain elusive. microRNAs (miRNAs) have emerged as critical regulators of synapse development and plasticity via their control of gene expression. Brain-specific miR-134s likely regulate the morphological maturation of spines, but their subcellular distributions and functional impacts have rarely been assessed. Here, we exploited atomic force microscopy to visualize in situ miR-134s, which indicated that they are mainly distributed at nearby dendritic shafts and necks of spines. The abundance of miR-134s varied between morphologically and functionally distinct spine types, and their amounts were inversely correlated with their postulated maturation stages. Moreover, spines exhibited reduced contents of miR-134s when selectively stimulated with beads containing brain-derived neurotropic factor (BDNF). Taken together, in situ visualizations of miRNAs provided unprecedented insights into the "inverse synaptic-tagging" roles of miR-134s that are selective to inactive/irrelevant synapses and potentially a molecular means for modifying synaptic connectivity via structural alteration.

Fodis: Software for Protein Unfolding Analysis

The folding dynamics of proteins at the single-molecule level has been studied with single-molecule force spectroscopy experiments for 20 years, but a common standardized method for the analysis of the collected data and for sharing among the scientific community members is still not available. We have developed a new open-source tool-Fodis-for the analysis of the force-distance curves obtained in single-molecule force spectroscopy experiments, providing almost automatic processing, analysis, and classification of the obtained data. Our method provides also a classification of the possible unfolding pathways and the structural heterogeneity present during the unfolding of proteins.

Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations

Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information on the full unbinding pathway is often lacking due, in part, to the static nature of atomic structures and ensemble averaging inherent to bulk biophysics approaches. Here we combine molecular dynamics and high-speed force spectroscopy on the streptavidin-biotin complex to determine the binding strength and unbinding pathways over the widest dynamic range. Experiment and simulation show excellent agreement at overlapping velocities and provided evidence of the unbinding mechanisms. During unbinding, biotin crosses multiple energy barriers and visits various intermediate states far from the binding pocket, while streptavidin undergoes transient induced fits, all varying with loading rate. This multistate process slows down the transition to the unbound state and favors rebinding, thus explaining the long lifetime of the complex. We provide an atomistic, dynamic picture of the unbinding process, replacing a simple two-state picture with one that involves many routes to the lock and rate-dependent induced-fit motions for intermediates, which might be relevant for other receptor-ligand bonds.

Seeing and sensing single G protein-coupled receptors by atomic force microscopy

G protein-coupled receptors (GPCRs) relay extracellular information across cell membranes through a continuum of conformations that are not always captured in structures. Hence, complementary approaches are required to quantify the physical and chemical properties of the dynamic conformations linking to GPCR function. Atomic force microscopy (AFM)-based high-resolution imaging and force spectroscopy are unique methods to scrutinize GPCRs and to sense their interactions. Here, we exemplify recent AFM-based applications to directly observe the supramolecular assembly of GPCRs in native membranes, to measure the ligand-binding free-energy landscape, and how interactions modulate the structural properties of GPCRs. Common trends in GPCR function are beginning to emerge. We envision that technical developments in combining AFM with superresolution fluorescence imaging will provide insights into how cellular states modulate GPCRs and vice versa.

Atomic Force Microscopy Meets Biophysics, Bioengineering, Chemistry, and Materials Science

Briefly, herein the use of atomic force microscopy (AFM) in the characterization of molecules and (bioengineered) materials related to chemistry, materials science, chemical engineering, and environmental science and biotechnology is reviewed. First, the basic operations of standard AFM, Kelvin probe force microscopy, electrochemical AFM, and tip-enhanced Raman microscopy are described. Second, several applications of these techniques to the characterization of single molecules, polymers, biological membranes, films, cells, hydrogels, catalytic processes, and semiconductors are provided and discussed.

Interplay between the electrostatic membrane potential and conformational changes in membrane proteins

Transmembrane electrostatic membrane potential is a major energy source of the cell. Importantly, it determines the structure as well as function of charge-carrying membrane proteins. Here, we discuss the relationship between membrane potential and membrane proteins, in particular whether the conformation of these proteins is integrally connected to the membrane potential. Together, these concepts provide a framework for rationalizing the types of conformational changes that have been observed in membrane proteins and for better understanding the electrostatic effects of the membrane potential on both reversible as well as unidirectional dynamic processes of membrane proteins.

Direct monitoring of equilibrium protein folding–unfolding by atomic force microscopy: pushing the limit

We report the direct observation of equilibrium folding–unfolding dynamics of a mechanically labile, three helix bundle protein GA using a commercial atomic force microscope (AFM).

Single-Molecule Force Spectroscopy: Experiments, Analysis, and Simulations

The mechanical properties of cells and of subcellular components are important to obtain a mechanistic molecular understanding of biological processes. The quantification of mechanical resistance of cells and biomolecules using biophysical methods matured thanks to the development of nanotechnologies such as optical and magnetic tweezers, the biomembrane force probe, and atomic force microscopy (AFM). The quantitative nature of force spectroscopy measurements has converted AFM into a valuable tool in biophysics. Force spectroscopy allows the determination of the forces required to unfold protein domains and to disrupt individual receptor/ligand bonds. Molecular simulations as a computational microscope allow investigation of similar biological processes with an atomistic detail. In this chapter, we first provide a step-by-step protocol of force spectroscopy experiments using AFM, including sample preparation, measurements, and analysis and interpretation of the resulting dynamic force spectrum in terms of available theories. Next, we present the background for molecular dynamics (MD) simulations focusing on steered molecular dynamics (SMD) and the importance of bridging computational tools with experimental techniques.

Plasmon Rulers as a Probe for Real-Time Microsecond Conformational Dynamics of Single Molecules

Biopolymers such as DNA, RNA, and proteins exploit conformational changes to modulate their function. Although state-of-the-art single-molecule approaches enable identification of conformational states, the transition path and metastable intermediates often remain elusive because they occur on microsecond time scales. Here we introduce a method to probe conformational dynamics with microsecond integration times based on a heterodimer of plasmonic particles. By combining Brownian dynamics and electromagnetic simulations, we find that integration times of 1 μs can be routinely achieved, providing the capability to identify short-lived intermediates and transition paths at the single-molecule level in real-time. Importantly, plasmon rulers require no specialized equipment but can be probed on existing fluorescence microscopes equipped with a fast camera. The approach combines the advantages of fluorescent probes (zero-force, parallelization) and mechanical probes such as optical tweezers (continuous microsecond integration times). They offer a unique opportunity to study conformational dynamics and compare measurements to full-atom simulations, where computational demands limit the simulation time.

Calcium stabilizes the strongest protein fold

Staphylococcal pathogens adhere to their human targets with exceptional resilience to mechanical stress, some propagating force to the bacterium via small, Ig-like folds called B domains. We examine the mechanical stability of these folds using atomic force microscopy-based single-molecule force spectroscopy. The force required to unfold a single B domain is larger than 2 nN – the highest mechanostability of a protein to date by a large margin. B domains coordinate three calcium ions, which we identify as crucial for their extreme mechanical strength. When calcium is removed through chelation, unfolding forces drop by a factor of four. Through systematic mutations in the calcium coordination sites we can tune the unfolding forces from over 2 nN to 0.15 nN, and dissect the contribution of each ion to B domain mechanostability. Their extraordinary strength, rapid refolding and calcium-tunable force response make B domains interesting protein design targets.

Staphylococcal pathogens adhere to their human targets using adhesins, which can withstand extremely high forces. Here, authors use single-molecule force spectroscopy to determine the similarly high unfolding forces of B domains that link the adhesin to the bacterium.

Implications of Molecular Topology for Nanoscale Mechanical Unfolding

Biopolymer unfolding events are ubiquitous in biology and mechanical unfolding is an established approach to study the structure and function of biomolecules, yet whether and how mechanical unfolding processes depend on native state topology remain unexplored. Here, we investigate how the number of unfolding pathways via mechanical methods depends on the circuit topology of a folded chain, which categorizes the arrangement of intrachain contacts into parallel, crossing, and series. Three unfolding strategies, namely, threading through a pore, pulling from the ends, and pulling by threading, are compared. Considering that some contacts may be unbreakable within the relevant forces, we also study the dependence of the unfolding efficiency on the chain topology. Our analysis reveals that the number of pathways and the efficiency of unfolding are critically determined by topology in a manner that depends on the employed mechanical approach, a significant result for interpretation of the unfolding experiments.

Direct observation of the wrapping/unwrapping of ssDNA around/from a SWCNT at the single-molecule level: towards tuning the binding mode and strength

Complexation of single-stranded DNA (ssDNA) with a chiral single-walled carbon nanotube (SWCNT) exhibits surprising efficacy in CNT dispersion and sorting, optical sensing, and nanoelectronic device design. Studying the wrapping/unwrapping mechanism is challenging because an in situ method at the single-molecule level is required. Here, we developed a method based on single-molecule force spectroscopy to monitor the unwrapping/wrapping of ssDNA from/around a SWCNT. Our results reveal that the wrapping/unwrapping processes are reversible in water, and these processes occur in an equilibrium manner driven mainly by π-π interactions between DNA bases and CNTs. In phosphate buffered saline, the unwrapping process is loading rate-dependent, and ssDNA wrapping around a CNT undergoes two distinct stages dominated by both π-π interactions and hydrogen bonding. In addition, our results show that salts could further stabilize ssDNA/CNT complexes by blocking the electrostatic interactions between adjacent DNA segments and by catalyzing the formation of hydrogen bonds between DNA bases. The stability of ssDNA/CNT is dependent on the DNA sequence and CNT chirality. These results deepen our understanding of ssDNA-CNT interactions and provide effective means to tune the binding mode and strength.

High-Precision Single-Molecule Characterization of the Folding of an HIV RNA Hairpin by Atomic Force Microscopy

The folding of RNA into a wide range of structures is essential for its diverse biological functions from enzymatic catalysis to ligand binding and gene regulation. The unfolding and refolding of individual RNA molecules can be probed by single-molecule force spectroscopy (SMFS), enabling detailed characterization of the conformational dynamics of the molecule as well as the free-energy landscape underlying folding. Historically, high-precision SMFS studies of RNA have been limited to custom-built optical traps. Although commercial atomic force microscopes (AFMs) are widely deployed and offer significant advantages in ease-of-use over custom-built optical traps, traditional AFM-based SMFS lacks the sensitivity and stability to characterize individual RNA molecules precisely. Here, we developed a high-precision SMFS assay to study RNA folding using a commercial AFM and applied it to characterize a small RNA hairpin from HIV that plays a key role in stimulating programmed ribosomal frameshifting. We achieved rapid data acquisition in a dynamic assay, unfolding and then refolding the same individual hairpin more than 1,100 times in 15 min. In comparison to measurements using optical traps, our AFM-based assay featured a stiffer force probe and a less compliant construct, providing a complementary measurement regime that dramatically accelerated equilibrium folding dynamics. Not only did kinetic analysis of equilibrium trajectories of the HIV RNA hairpin yield the traditional parameters used to characterize folding by SMFS (zero-force rate constants and distances to the transition state), but we also reconstructed the full 1D projection of the folding free-energy landscape comparable to state-of-the-art studies using dual-beam optical traps, a first for this RNA hairpin and AFM studies of nucleic acids in general. Looking forward, we anticipate that the ease-of-use of our high-precision assay implemented on a commercial AFM will accelerate studying folding of diverse nucleic acid structures.

The lipid bilayer membrane and its protein constituents

Robertson recounts the historical experiments that gave rise to our current understanding of cell membranes.

In 1918, the year the Journal of General Physiology was founded, there was little understanding of the structure of the cell membrane. It was evident that cells had invisible barriers separating the cytoplasm from the external solution. However, it would take decades before lipid bilayers were identified as the essential constituent of membranes. It would take even longer before it was accepted that there existed hydrophobic proteins that were embedded within the membrane and that these proteins were responsible for selective permeability in cells. With a combination of intuitive experiments and quantitative thinking, the last century of cell membrane research has led us to a molecular understanding of the structure of the membrane, as well as many of the proteins embedded within. Now, research is turning toward a physical understanding of the reactions of membrane proteins and lipids in this unique and incredibly complex solvent environment.

Dynamics of breaking intermolecular bonds in high-speed force spectroscopy

Atomic force microscope based single-molecule force spectroscopy provides a description of a variety of intermolecular interactions such as those occurring between receptor molecules and their ligands. Advances in force spectroscopy have enabled performing measurements at high-speeds and sub-microsecond resolutions. We report experiments performed on a biotin-avidin system that reveal that the measured force decreases with the loading rate at high rates. This result is at odds with the established Bell-Evans theory that predicts a monotonic increase of the rupture force with the loading rate. We demonstrate that inertial and hydrodynamic forces generated during the breaking of the bond dominate the measured force at high loading rates. We develop a correction factor to incorporate those effects into the Bell-Evans theory. The correction is necessary to obtain accurate values of the intermolecular forces at high speeds.

Single-Molecule Force Spectroscopy of Transmembrane β-Barrel Proteins

Single-molecule force spectroscopy (SMFS) has been widely applied to study the mechanical unfolding and folding of transmembrane proteins. Here, we review the recent progress in characterizing bacterial and human transmembrane β-barrel proteins by SMFS. First, we describe the mechanical unfolding of transmembrane β-barrels, which follows a general mechanism dictated by the sequential unfolding and extraction of individual β-strands and β-hairpins from membranes. Upon force relaxation, the unfolded polypeptide can insert stepwise into the membrane as single β-strands or β-hairpins to fold as the native β-barrel. The refolding can be followed at a high spatial and temporal resolution, showing that small β-barrels are able to fold without assistance, whereas large and complex β-barrels require chaperone cofactors. Applied in the dynamic mode, SMFS can quantify the kinetic and mechanical properties of single β-hairpins and reveal complementary insight into the membrane protein structure and function relationship. We further outline the challenges that SMFS experiments must overcome for a comprehensive understanding of the folding and function of transmembrane β-barrel proteins.

Communication: Coordinate-dependent diffusivity from single molecule trajectories

Single-molecule observations of biomolecular folding are commonly interpreted using the model of one-dimensional diffusion along a reaction coordinate, with a coordinate-independent diffusion coefficient. Recent analysis, however, suggests that more general models are required to account for single-molecule measurements performed with high temporal resolution. Here, we consider one such generalization: a model where the diffusion coefficient can be an arbitrary function of the reaction coordinate. Assuming Brownian dynamics along this coordinate, we derive an exact expression for the coordinate-dependent diffusivity in terms of the splitting probability within an arbitrarily chosen interval and the mean transition path time between the interval boundaries. This formula can be used to estimate the effective diffusion coefficient along a reaction coordinate directly from single-molecule trajectories.

POTRA Domains, Extracellular Lid, and Membrane Composition Modulate the Conformational Stability of the β Barrel Assembly Factor BamA

The core component BamA of the β barrel assembly machinery (BAM) adopts several conformations, which are thought to facilitate the insertion and folding of β barrel proteins into the bacterial outer membrane. Which factors alter the stability of these conformations remains to be quantified. Here, we apply single-molecule force spectroscopy to characterize the mechanical properties of BamA from Escherichia coli. In contrast to the N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, the C-terminal transmembrane β barrel domain of BamA is mechanically much more stable. Exposed to mechanical stress this β barrel stepwise unfolds β hairpins until unfolding has been completed. Thereby, the mechanical stabilities of β barrel and β hairpins are modulated by the POTRA domains, the membrane composition and the extracellular lid closing the β barrel. We anticipate that these differences in stability, which are caused by factors contributing to BAM function, promote conformations of the BamA β barrel required to insert and fold outer membrane proteins.

Molecular mechanism of extreme mechanostability in a pathogen adhesin

High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy-based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains.

Light-Responsive Polymer Particles as Force Clamps for the Mechanical Unfolding of Target Molecules

Single-molecule force spectroscopy techniques are powerful tools for investigating the mechanical unfolding of biomolecules. However, they are limited in throughput and require dedicated instrumentation. Here, we report a force-generating particle that can unfold target molecules on-demand. The particle consists of a plasmonic nanorod core encapsulated with a thermoresponsive polymer shell. Optical heating of the nanorod leads to rapid collapse of the polymer, thus transducing light into mechanical work to unfold target molecules. The illumination tunes the duration and degree of particle collapse, thus controlling the lifetime and magnitude of applied forces. Single-molecule fluorescence imaging showed reproducible mechanical unfolding of DNA hairpins. We also demonstrate the triggering of 50 different particles in <1 min, exceeding the speed of conventional atomic force microscopy. The polymer force clamp represents a facile and bottom-up approach to force manipulation.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG0) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Compressive Force Spectroscopy: From Living Cells to Single Proteins

One of the most successful applications of atomic force microscopy (AFM) in biology involves monitoring the effect of force on single biological molecules, often referred to as force spectroscopy. Such studies generally entail the application of pulling forces of different magnitudes and velocities upon individual molecules to resolve individualistic unfolding/separation pathways and the quantification of the force-dependent rate constants. However, a less recognized variation of this method, the application of compressive force, actually pre-dates many of these "tensile" force spectroscopic studies. Further, beyond being limited to the study of single molecules, these compressive force spectroscopic investigations have spanned samples as large as living cells to smaller, multi-molecular complexes such as viruses down to single protein molecules. Correspondingly, these studies have enabled the detailed characterization of individual cell states, subtle differences between seemingly identical viral structures, as well as the quantification of rate constants of functionally important, structural transitions in single proteins. Here, we briefly review some of the recent achievements that have been obtained with compressive force spectroscopy using AFM and highlight exciting areas of its future development.

Going Vertical To Improve the Accuracy of Atomic Force Microscopy Based Single-Molecule Force Spectroscopy

Single-molecule force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor-ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA's attachment point to a coverslip. Importantly, this algorithm was performed at low force (10-20 pN) and relatively fast (15-25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA's overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ∼40 min and versatility by aligning polyprotein- and PEG-based protein-ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.

High-Resolution AFM-Based Force Spectroscopy

Atomic force microscopy (AFM)-based force spectroscopy is a powerful technique which has seen significant enhancements in both force and time resolution in recent years. This chapter details two AFM cantilever modification procedures that yield high force precision over different temporal bandwidths. Specifically, it explains a fairly straightforward method to achieve sub-pN force precision and stability at low frequencies (<50 Hz) by removing the metal coatings from a commercially available cantilever. A more involved procedure utilizing a focused ion beam milling machine is required to maintain high force precision at enhanced bandwidths. Both modification methods allow site-specific attachment of biomolecules onto the apex area of the tips for force spectroscopy. The chapter concludes with a comparative demonstration using the two cantilever modification methods to study a lipid-protein interaction.

High-Speed Force Spectroscopy for Single Protein Unfolding

Single-molecule force spectroscopy (SMFS) measurements allow for quantification of the molecular forces required to unfold individual protein domains. Atomic force microscopy (AFM) is one of the long-established techniques for force spectroscopy (FS). Although FS at conventional AFM pulling rates provides valuable information on protein unfolding, in order to get a more complete picture of the mechanism, explore new regimes, and combine and compare experiments with simulations, we need higher pulling rates and μs-time resolution, now accessible via high-speed force spectroscopy (HS-FS). In this chapter, we provide a step-by-step protocol of HS-FS including sample preparation, measurements and analysis of the acquired data using HS-AFM with an illustrative example on unfolding of a well-studied concatamer made of eight repeats of the titin I91 domain.

Cooperative protein unfolding. A statistical-mechanical model for the action of denaturants

Knowledge of protein stability is of utmost importance in various fields of biotechnology. Protein stability can be assessed in solution by increasing the concentration of denaturant and recording the structural changes with spectroscopic or thermodynamic methods. The standard interpretation of the experimental data is to assume a 2-state equilibrium between completely folded and completely unfolded protein molecules. Here we propose a cooperative model based on the statistical-mechanical Zimm-Bragg theory. In this model protein unfolding is driven by the weak binding of a rather small number of denaturant molecules, inducing the cooperative unfolding with multiple dynamic intermediates. The modified Zimm-Bragg theory is applied to published thermodynamic and spectroscopic data leading to the following conclusions. (i) The binding constant K_D is correlated with the midpoint concentration, c₀, of the unfolding reaction according to c₀≅1/K_D. The better the binding of denaturant the lower is the concentration to achieve unfolding. (ii) The binding constant K_D agrees with direct thermodynamic measurements. A rather small number of bound denaturants suffices to induce the cooperative unfolding of the whole protein. (iii) Chemical unfolding occurs in the concentration range Δc_D=c_end-c_ini. The theory predicts the unfolding energy per amino acid residue as g_nu=RTK_D(c_end-c_ini). The Gibbs free energy of an osmotic gradient of the same size is ΔG_Diff=-RTln(c_end/c_ini). In all examples investigated ΔG_Diff exactly balances the unfolding energy g_nu. The total unfolding energy is thus close to zero. (iv) Protein cooperativity in chemical unfolding is rather low with cooperativity parameters σ≥3x10^-3. As a consequence, the theory predicts a dynamic mixture of conformations during the unfolding reaction. The probabilities of individual conformations are easily accessible via the partition function Z(c_D,σ).

Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories

Prion-like misfolding of superoxide dismutase 1 (SOD1) is associated with the disease ALS, but the mechanism of misfolding remains unclear, partly because misfolding is difficult to observe directly. Here we study the most misfolding-prone form of SOD1, reduced un-metallated monomers, using optical tweezers to measure unfolding and refolding of single molecules. We find that the folding is more complex than suspected, resolving numerous previously undetected intermediate states consistent with the formation of individual β-strands in the native structure. We identify a stable core of the protein that unfolds last and refolds first, and directly observe several distinct misfolded states that branch off from the native folding pathways at specific points after the formation of the stable core. Partially folded intermediates thus play a crucial role mediating between native and non-native folding. These results suggest an explanation for SOD1's propensity for prion-like misfolding and point to possible targets for therapeutic intervention.

Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells

Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm² cantilever into one terminated with a gold-coated, 4 × 4 μm² reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM.

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.