Fully automated single-molecule force spectroscopy for screening applications

How Much Data Are Enough? Toward Statistically Robust Adhesion Experiments by Atomic Force Microscopy

Direct force measurements by atomic force microscopy (AFM) have become an indispensable analytical tool in the last decades. Force measurements have been widely used for adhesion measurements, often in combination with the colloidal probe technique. For the latter technique, a colloidal particle is attached to the end of an AFM cantilever, proving great flexibility in terms of colloid/surface interaction to be studied. Interestingly, the question of how much data is necessary to obtain statistically reliable results has been addressed in this context only sparsely. By contrast, the value and necessity of determining and reporting distributions of adhesion forces has been widely accepted. Here, simple statistical methods of the experimental design have been applied to address this question. It has been demonstrated that it is possible to determine an optimal number of force curves even during data acquisition. This approach would be essential to prevent oversampling of data. Moreover, it allows to address questions like heterogeneity of the sample in a more reliable or less time-consuming way. In AFM measurements with colloidal probes, most statistical variation results from the surface roughness of the probe particle. In this case, the use of different colloidal particles is important, which can be achieved by techniques such as fluidic force microscopy (FluidFM). The latter enables to combine a real-time determination of the required data size and high-throughput techniques of unattended measurements, which will open new fields of analysis.

Single-Molecule Force Spectroscopy of Membrane Protein Folding

Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.

Novel perspective for protein-drug interaction analysis: atomic force microscope

Proteins are major drug targets, and drug-target interaction identification and analysis are important factors for drug discovery. Atomic force microscopy (AFM) is a powerful tool making it possible to image proteins with nanometric resolution and probe intermolecular forces under physiological conditions. We review recent studies conducted in the field of target protein drug discovery using AFM-based analysis technology, including drug-driven changes in nanomechanical properties of protein morphology and interactions. Underlying mechanisms (including thermodynamic and kinetic parameters) of the drug-target interaction and drug-modulating protein-protein interaction (PPI) on the surfaces of models or living cells are discussed. Furthermore, challenges and the outlook for the field are likewise discussed. Overall, this insight into the mechanical properties of protein-drug interactions provides an unprecedented information framework for rational drug discovery in the pharmaceutical field.

Polymers and biopolymers at interfaces

This review updates recent progress in the understanding of the behaviour of polymers at surfaces and interfaces, highlighting examples in the areas of wetting, dewetting, crystallization, and 'smart' materials. Recent developments in analysis tools have yielded a large increase in the study of biological systems, and some of these will also be discussed, focussing on areas where surfaces are important. These areas include molecular binding events and protein adsorption as well as the mapping of the surfaces of cells. Important techniques commonly used for the analysis of surfaces and interfaces are discussed separately to aid the understanding of their application.

Binding of interferon reduces the force of unfolding for interferon receptor 1

Differential signaling of the type I interferon receptor (IFNAR) has been correlated with the ability of its subunit, IFNAR1, to differentially recognize a large spectrum of different ligands, which involves intricate conformational re-arrangements of multiple interacting domains. To shed light onto the structural determinants governing ligand recognition, we compared the force-induced unfolding of the IFNAR1 ectodomain when bound to interferon and when free, using the atomic force microscope and steered molecular dynamics simulations. Unexpectedly, we find that IFNAR1 is easier to mechanically unfold when bound to interferon than when free. Analysis of the structures indicated that the origin of the reduction in unfolding forces is a conformational change in IFNAR1 induced by ligand binding.

Mechanical stability of bivalent transition metal complexes analyzed by single-molecule force spectroscopy

Multivalent biomolecular interactions allow for a balanced interplay of mechanical stability and malleability, and nature makes widely use of it. For instance, systems of similar thermal stability may have very different rupture forces. Thus it is of paramount interest to study and understand the mechanical properties of multivalent systems through well-characterized model systems. We analyzed the rupture behavior of three different bivalent pyridine coordination complexes with Cu²⁺ in aqueous environment by single-molecule force spectroscopy. Those complexes share the same supramolecular interaction leading to similar thermal off-rates in the range of 0.09 and 0.36 s⁻¹, compared to 1.7 s⁻¹ for the monovalent complex. On the other hand, the backbones exhibit different flexibility, and we determined a broad range of rupture lengths between 0.3 and 1.1 nm, with higher most-probable rupture forces for the stiffer backbones. Interestingly, the medium-flexible connection has the highest rupture forces, whereas the ligands with highest and lowest rigidity seem to be prone to consecutive bond rupture. The presented approach allows separating bond and backbone effects in multivalent model systems.

Action of the Hsp70 chaperone system observed with single proteins

In Escherichia coli, the binding of non-native protein substrates to the Hsp70 chaperone DnaK is mediated by the co-chaperone DnaJ. DnaJ accelerates ATP hydrolysis on DnaK, by closing the peptide-binding cleft of DnaK. GrpE catalysed nucleotide exchange and ATP re-binding then lead to substrate release from DnaK, allowing folding. Here we refold immunoglobulin 27 (I27) to better understand how DnaJ-DnaK-GrpE chaperones cooperate. When DnaJ is present, I27 is less likely to misfold and more likely to fold, whereas the unfolded state remains unaffected. Thus, the 'holdase' DnaJ shows foldase behaviour. Misfolding of I27 is fully abrogated when DnaJ cooperates with DnaK, which stabilizes the unfolded state and increases the probability of folding. Addition of GrpE shifts the unfolded fraction of I27 to pre-chaperone levels. These insights reveal synergistic mechanisms within the evolutionary highly conserved Hsp70 system that prevent substrates from misfolding and promote their productive transition to the native state.

Dynamic single-molecule force spectroscopy of rhodopsin in native membranes

Membrane proteins are an important class of proteins in biology and therapeutics. Understanding the dynamic nature of the molecular interactions that stabilize membrane protein structure is critical to dissect the mechanism of action and dysfunction of these proteins. Single-molecule force spectroscopy (SMFS) and dynamic SMFS (DFS) are emerging nanotechniques that allow the study of membrane proteins under the physiologically relevant conditions of a lipid bilayer and buffer conditions. These techniques directly probe the molecular interactions underlying protein structure and reveal unique insights about their properties. Outlined in this report will be procedures on how to conduct SMFS and DFS on rhodopsin in native retinal membranes. Rhodopsin is a membrane protein belonging to the G protein-coupled receptor family of proteins, one of the largest families of proteins in nature.

Peptide transporter DtpA has two alternate conformations, one of which is promoted by inhibitor binding

Peptide transporters (PTRs) of the large PTR family facilitate the uptake of di- and tripeptides to provide cells with amino acids for protein synthesis and for metabolic intermediates. Although several PTRs have been structurally and functionally characterized, how drugs modulate peptide transport remains unclear. To obtain insight into this mechanism, we characterize inhibitor binding to the Escherichia coli PTR dipeptide and tripeptide permease A (DtpA), which shows substrate specificities similar to its human homolog hPEPT1. After demonstrating that Lys[Z-NO2]-Val, the strongest inhibitor of hPEPT1, also acts as a high-affinity inhibitor for DtpA, we used single-molecule force spectroscopy to localize the structural segments stabilizing the peptide transporter and investigated which of these structural segments change stability upon inhibitor binding. This characterization was done with DtpA embedded in the lipid membrane and exposed to physiologically relevant conditions. In the unbound state, DtpA adopts two main alternate conformations in which transmembrane α-helix (TMH) 2 is either stabilized (in ∼43% of DtpA molecules) or not (in ∼57% of DtpA molecules). The two conformations are understood to represent the inward- and outward-facing conformational states of the transporter. With increasing inhibitor concentration, the conformation characterized by a stabilized TMH 2 becomes increasingly prevalent, reaching ∼92% at saturation. Our measurements further suggest that Lys[Z-NO2]-Val interacts with discrete residues in TMH 2 that are important for ligand binding and substrate affinity. These interactions in turn stabilize TMH 2, thereby promoting the inhibited conformation of DtpA.

Improving single molecule force spectroscopy through automated real-time data collection and quantification of experimental conditions

The benefits of single molecule force spectroscopy (SMFS) clearly outweigh the challenges which include small sample sizes, tedious data collection and introduction of human bias during the subjective data selection. These difficulties can be partially eliminated through automation of the experimental data collection process for atomic force microscopy (AFM). Automation can be accomplished using an algorithm that triages usable force-extension recordings quickly with positive and negative selection. We implemented an algorithm based on the windowed fast Fourier transform of force-extension traces that identifies peaks using force-extension regimes to correctly identify usable recordings from proteins composed of repeated domains. This algorithm excels as a real-time diagnostic because it involves <30 ms computational time, has high sensitivity and specificity, and efficiently detects weak unfolding events. We used the statistics provided by the automated procedure to clearly demonstrate the properties of molecular adhesion and how these properties change with differences in the cantilever tip and protein functional groups and protein age.

Atomic force microscopy: a multifaceted tool to study membrane proteins and their interactions with ligands

Membrane proteins are embedded in lipid bilayers and facilitate the communication between the external environment and the interior of the cell. This communication is often mediated by the binding of ligands to the membrane protein. Understanding the nature of the interaction between a ligand and a membrane protein is required to both understand the mechanism of action of these proteins and for the development of novel pharmacological drugs. The highly hydrophobic nature of membrane proteins and the requirement of a lipid bilayer for native function have hampered the structural and molecular characterizations of these proteins under physiologically relevant conditions. Atomic force microscopy offers a solution to studying membrane proteins and their interactions with ligands under physiologically relevant conditions and can provide novel insights about the nature of these critical molecular interactions that facilitate cellular communication. In this review, we provide an overview of the atomic force microscopy technique and discuss its application in the study of a variety of questions related to the interaction between a membrane protein and a ligand. This article is part of a Special Issue entitled: Structural and biophysical characterization of membrane protein-ligand binding.

Reference-free alignment and sorting of single-molecule force spectroscopy data

Single-molecule force spectroscopy has become a versatile tool for investigating the (un)folding of proteins and other polymeric molecules. Like other single-molecule techniques, single-molecule force spectroscopy requires recording and analysis of large data sets to extract statistically meaningful conclusions. Here, we present a data analysis tool that provides efficient filtering of heterogeneous data sets, brings spectra into register based on a reference-free alignment algorithm, and determines automatically the location of unfolding barriers. Furthermore, it groups spectra according to the number of unfolding events, subclassifies the spectra using cross correlation-based sorting, and extracts unfolding pathways by principal component analysis and clustering methods to extracted peak positions. Our approach has been tested on a data set obtained through mechanical unfolding of bacteriorhodopsin (bR), which contained a significant number of spectra that did not show the well-known bR fingerprint. In addition, we have tested the performance of the data analysis tool on unfolding data of the soluble multidomain (Ig27)(8) protein.

Cholesterol increases kinetic, energetic, and mechanical stability of the human β2-adrenergic receptor

The steroid cholesterol is an essential component of eukaryotic membranes, and it functionally modulates membrane proteins, including G protein-coupled receptors. To reveal insight into how cholesterol modulates G protein-coupled receptors, we have used dynamic single-molecule force spectroscopy to quantify the mechanical strength and flexibility, conformational variability, and kinetic and energetic stability of structural segments stabilizing the human β(2)-adrenergic receptor (β(2)AR) in the absence and presence of the cholesterol analog cholesteryl hemisuccinate (CHS). CHS considerably increased the kinetic, energetic, and mechanical stability of almost every structural segment at sufficient magnitude to alter the structure and functional relationship of β(2)AR. One exception was the structural core segment of β(2)AR, which establishes multiple ligand binding sites, and its properties were not significantly influenced by CHS.

Following the DNA ligation of a single duplex using atomic force microscopy

Nick-sealing of a single DNA duplex was studied with the use of atomic force microscopy (AFM). To form a nick between a 47 mer DNA and a 24 mer DNA, the complementary 71 mer template DNA immobilized on an AFM tip was hybridized with the 47 mer DNA and brought into contact with the 24 mer DNA on a substrate surface. The AFM tip and substrate surface were modified with dendron molecules to ensure the formation of a single DNA duplex. When a single nick in the DNA duplex was sealed by DNA ligase during a pause, an increase in the unbinding force was observed after the pause. The change from 24.0 ± 4.4 piconewtons (pN) to 62.8 ± 14.6 pN matched well with the resulting DNA length (71 bp). Additionally, a 30 s pause showed a 3-fold higher nick-sealing probability (60%) than a 10 s pause, while the probability did not increase with a 120 s pause. In the presence of free 47 mer DNAs in solution, the single nick-sealing event could be repeated at other positions.

Single-molecule force spectroscopy from nanodiscs: an assay to quantify folding, stability, and interactions of native membrane proteins

Single-molecule force spectroscopy (SMFS) can quantify and localize inter- and intramolecular interactions that determine the folding, stability, and functional state of membrane proteins. To conduct SMFS the membranes embedding the membrane proteins must be imaged and localized in a rather time-consuming manner. Toward simplifying the investigation of membrane proteins by SMFS, we reconstituted the light-driven proton pump bacteriorhodopsin into lipid nanodiscs. The advantage of using nanodiscs is that membrane proteins can be handled like water-soluble proteins and characterized with similar ease. SMFS characterization of bacteriorhodopsin in native purple membranes and in nanodiscs reveals no significant alterations of structure, function, unfolding intermediates, and strengths of inter- and intramolecular interactions. This demonstrates that lipid nanodiscs provide a unique approach for in vitro studies of native membrane proteins using SMFS and open an avenue to characterize membrane proteins by a wide variety of SMFS approaches that have been established on water-soluble proteins.

Ferritin-based new magnetic force microscopic probe detecting 10 nm sized magnetic nanoparticles

A single-molecule ferritin picking-up process was realized with the use of AFM, which was enhanced by employing controlled dendron surface chemistry. The approach enabled the placement of a single ferritin protein molecule at the very end of an AFM tip. When used for magnetic force microscopy (MFM) imaging, the tips were able to detect magnetic interactions of approximately 10 nm sized magnetic nanoparticles. The single ferritin tip also showed the characteristics of a "multifunctional" MFM probe that can sense the magnetic force from magnetic materials as well as detect the biomolecular interaction force with DNAs on the surface. The multifunctional tip enabled us not only to investigate the specific molecular interaction but also to image the magnetic interaction between the probe and the substrate, in addition to allowing the common capability of topographic imaging. Because the protein engineering of ferritin and the supporting coordination and conjugation chemistry are well-established, we envisage that it would be straightforward to extend this approach to the development of various single magnetic particle MFM probes of different compositions and sizes.

Efficient unfolding pattern recognition in single molecule force spectroscopy data

Background

Single-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived.

Results

In the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise unfolding of the transmembrane helices. In contrast, a side peak is an unfolding event in the alpha-helix or other secondary structural element. The algorithm is capable of detecting side peaks along with main peaks.

Therefore, we can detect the individual unfolding pathway as the sequence of events labeled with their occurrences and co-occurrences special to bR's unfolding pathway. We find that side peaks do not co-occur with one another in curves as frequently as main peaks do, which may imply a synergistic effect occurring between helices. While main peaks co-occur as pairs in at least 50% of curves, the side peaks co-occur with one another in less than 10% of curves. Moreover, the algorithm runtime scales well as the dataset size increases.

Conclusions

Our algorithm satisfies the requirements of an automated methodology that combines high accuracy with efficiency in analyzing SMFS datasets. The algorithm tackles the force spectroscopy analysis bottleneck leading to more consistent and reproducible results.

Five challenges to bringing single-molecule force spectroscopy into living cells

In recent years, single-molecule force spectroscopy techniques have been used to study how inter- and intramolecular interactions control the assembly and functional state of biomolecular machinery in vitro. Here we discuss the problems and challenges that need to be addressed to bring these technologies into living cells and to learn how cellular machinery is controlled in vivo.

Conservation of molecular interactions stabilizing bovine and mouse rhodopsin

Rhodopsin is the light receptor that initiates phototransduction in rod photoreceptor cells. The structure and function of rhodopsin are tightly linked to molecular interactions that stabilize and determine the receptor's functional state. Single-molecule force spectroscopy (SMFS) was used to localize and quantify molecular interactions that structurally stabilize bovine and mouse rhodopsin from native disk membranes of rod photoreceptor cells. The mechanical unfolding of bovine and mouse rhodopsin revealed nine major unfolding intermediates, each intermediate defining a structurally stable segment in the receptor. These stable structural segments had similar localization and occurrence in both bovine and mouse samples. For each structural segment, parameters describing their unfolding energy barrier were determined by dynamic SMFS. No major differences were observed between bovine and mouse rhodopsin, thereby implying that the structures of both rhodopsins are largely stabilized by similar molecular interactions.