Atomic force microscopy detects changes in the interaction forces between GroEL and substrate proteins

Model systems for optical trapping: the physical basis and biological applications

The micromechanical methods, among which optical trapping and atomic force microscopy have a special place, are widespread currently in biology to study molecular interactions between different biological objects. Optical trapping is reported to be quite applicable to study the mechanical properties of surface structures onto bacterial (pili and flagella) and eukaryotic (filopodia) cells. The review briefly summarizes the physical basis of optical trapping, as well as the principles of calculating the van der Waals, electrostatic, and donor-acceptor forces when two microparticles or a microparticle and a flat surface are used. Three main types of model systems (abiotic, biotic, and mixed) used in trapping experiments are described, and the peculiarities of manipulation with living (bacteria, fungal spores, etc.) and non-spherical objects (e.g., rod-shaped bacteria) are summarized.

Dissecting the cytochrome c 2-reaction centre interaction in bacterial photosynthesis using single molecule force spectroscopy

The reversible docking of small, diffusible redox proteins onto a membrane protein complex is a common feature of bacterial, mitochondrial and photosynthetic electron transfer (ET) chains. Spectroscopic studies of ensembles of such redox partners have been used to determine ET rates and dissociation constants. Here, we report a single-molecule analysis of the forces that stabilise transient ET complexes. We examined the interaction of two components of bacterial photosynthesis, cytochrome c ₂ and the reaction centre (RC) complex, using dynamic force spectroscopy and PeakForce quantitative nanomechanical imaging. RC-LH1-PufX complexes, attached to silicon nitride AFM probes and maintained in a photo-oxidised state, were lowered onto a silicon oxide substrate bearing dispersed, immobilised and reduced cytochrome c ₂ molecules. Microscale patterns of cytochrome c ₂ and the cyan fluorescent protein were used to validate the specificity of recognition between tip-attached RCs and surface-tethered cytochrome c ₂ Following the transient association of photo-oxidised RC and reduced cytochrome c ₂ molecules, retraction of the RC-functionalised probe met with resistance, and forces between 112 and 887 pN were required to disrupt the post-ET RC-c ₂ complex, depending on the retraction velocities used. If tip-attached RCs were reduced instead, the probability of interaction with reduced cytochrome c ₂ molecules decreased 5-fold. Thus, the redox states of the cytochrome c ₂ haem cofactor and RC 'special pair' bacteriochlorophyll dimer are important for establishing a productive ET complex. The millisecond persistence of the post-ET cytochrome c ₂[oxidised]-RC[reduced] 'product' state is compatible with rates of cyclic photosynthetic ET, at physiologically relevant light intensities.

Allosteric Mechanisms in Chaperonin Machines

Chaperonins are nanomachines that facilitate protein folding by undergoing energy (ATP)-dependent movements that are coordinated in time and space owing to complex allosteric regulation. They consist of two back-to-back stacked oligomeric rings with a cavity at each end where protein substrate folding can take place. Here, we focus on the GroEL/GroES chaperonin system from Escherichia coli and, to a lesser extent, on the more poorly characterized eukaryotic chaperonin CCT/TRiC. We describe their various functional (allosteric) states and how they are affected by substrates and allosteric effectors that include ATP, ADP, nonfolded protein substrates, potassium ions, and GroES (in the case of GroEL). We also discuss the pathways of intra- and inter-ring allosteric communication by which they interconvert and the coupling between allosteric transitions and protein folding reactions.

Interactions of Histone Acetyltransferase p300 with the Nuclear Proteins Histone and HMGB1, As Revealed by Single Molecule Atomic Force Spectroscopy

One of the important properties of the transcriptional coactivator p300 is histone acetyltransferase (HAT) activity that enables p300 to influence chromatin action via histone modulation. p300 can exert its HAT action upon the other nuclear proteins too--one notable example being the transcription-factor-like protein HMGB1, which functions also as a cytokine, and whose accumulation in the cytoplasm, as a response to tissue damage, is triggered by its acetylation. Hitherto, no information on the structure and stability of the complexes between full-length p300 (p300FL) (300 kDa) and the histone/HMGB1 proteins are available, probably due to the presence of unstructured regions within p300FL that makes it difficult to be crystallized. Herein, we have adopted the high-resolution atomic force microscopy (AFM) approach, which allows molecularly resolved three-dimensional contour mapping of a protein molecule of any size and structure. From the off-rate and activation barrier values, obtained using single molecule dynamic force spectroscopy, the biochemical proposition of preferential binding of p300FL to histone H3, compared to the octameric histone, can be validated. Importantly, from the energy landscape of the dissociation events, a model for the p300-histone and the p300-HMGB1 dynamic complexes that HAT forms, can be proposed. The lower unbinding forces of the complexes observed in acetylating conditions, compared to those observed in non-acetylating conditions, indicate that upon acetylation, p300 tends to weakly associate, probably as an outcome of charge alterations on the histone/HMGB1 surface and/or acetylation-induced conformational changes. To our knowledge, for the first time, a single molecule level treatment of the interactions of HAT, where the full-length protein is considered, is being reported.

Nanodomains of cytochrome b6f and photosystem II complexes in spinach grana thylakoid membranes

The cytochrome b6f (cytb6f) complex plays a central role in photosynthesis, coupling electron transport between photosystem II (PSII) and photosystem I to the generation of a transmembrane proton gradient used for the biosynthesis of ATP. Photosynthesis relies on rapid shuttling of electrons by plastoquinone (PQ) molecules between PSII and cytb6f complexes in the lipid phase of the thylakoid membrane. Thus, the relative membrane location of these complexes is crucial, yet remains unknown. Here, we exploit the selective binding of the electron transfer protein plastocyanin (Pc) to the lumenal membrane surface of the cytb6f complex using a Pc-functionalized atomic force microscope (AFM) probe to identify the position of cytb6f complexes in grana thylakoid membranes from spinach (Spinacia oleracea). This affinity-mapping AFM method directly correlates membrane surface topography with Pc-cytb6f interactions, allowing us to construct a map of the grana thylakoid membrane that reveals nanodomains of colocalized PSII and cytb6f complexes. We suggest that the close proximity between PSII and cytb6f complexes integrates solar energy conversion and electron transfer by fostering short-range diffusion of PQ in the protein-crowded thylakoid membrane, thereby optimizing photosynthetic efficiency.

Sweep flocculation and adsorption of viruses on aluminum flocs during electrochemical treatment prior to surface water microfiltration

Bench-scale experiments were performed to evaluate virus control by an integrated electrochemical-microfiltration (MF) process from turbid (15 NTU) surface water containing moderate amounts of dissolved organic carbon (DOC, 5 mg C/L) and calcium hardness (50 mg/L as CaCO3). Higher reductions in MS2 bacteriophage concentrations were obtained by aluminum electrocoagulation and electroflotation compared with conventional aluminum sulfate coagulation. This was attributed to electrophoretic migration of viruses, which increased their concentrations in the microenvironment of the sacrificial anode where coagulant precursors are dissolved leading to better destabilization during electrolysis. In all cases, viruses were not inactivated implying measured reductions were solely due to their removal. Sweep flocculation was the primary virus destabilization mechanism. Direct evidence for virus enmeshment in flocs was provided by two independent methods: quantitative elution using beef extract at elevated pH and quantitating fluorescence from labeled viruses. Atomic force microscopy studies revealed a monotonically increasing adhesion force between viruses immobilized on AFM tips and floc surfaces with electrocoagulant dosage, which suggests secondary contributions to virus uptake on flocs from adsorption. Virus sorption mechanisms include charge neutralization and hydrophobic interactions with natural organic matter removed during coagulation. This also provided the basis for interpreting additional removal of viruses by the thick cake formed on the surface of the microfilter following electrocoagulation. Enhancements in virus removal as progressively more aluminum was electrolyzed therefore embodies contributions from (i) better encapsulation onto greater amounts of fresh Al(OH)3 precipitates, (ii) increased adsorption capacity associated with higher available coagulant surface area, (iii) greater virus-floc binding affinity due to effective charge neutralization and hydrophobic interactions, and/or (iv) additional removal by a dynamic membrane if a thick cake layer of flocs is deposited.

Demonstration of specific binding of heparin to Plasmodium falciparum-infected vs. non-infected red blood cells by single-molecule force spectroscopy

Glycosaminoglycans (GAGs) play an important role in the sequestration of Plasmodium falciparum-infected red blood cells (pRBCs) in the microvascular endothelium of different tissues, as well as in the formation of small clusters (rosettes) between infected and non-infected red blood cells (RBCs). Both sequestration and rosetting have been recognized as characteristic events in severe malaria. Here we have used heparin and pRBCs infected by the 3D7 strain of P. falciparum as a model to study GAG-pRBC interactions. Fluorescence microscopy and fluorescence-assisted cell sorting assays have shown that exogenously added heparin has binding specificity for pRBCs (preferentially for those infected with late forms of the parasite) vs. RBCs. Heparin-pRBC adhesion has been probed by single-molecule force spectroscopy, obtaining an average binding force ranging between 28 and 46 pN depending on the loading rate. No significant binding of heparin to non-infected RBCs has been observed in control experiments. This work represents the first approach to quantitatively evaluate GAG-pRBC molecular interactions at the individual molecule level.

Chemical modifications of atomic force microscopy tips

Atomic force microscopy (AFM) works by scanning a very tiny tip over a surface with great precision. The microscope tips can be chemically functionalized to improve the images obtained. Well-defined chemical functionalization of AFM tips is especially important for experiments, such as chemical force microscopy and single molecule recognition force microscopy, to examine specific interactions at the single molecular level. In this chapter, we present an overview of chemical modifications of tips that have been reported to date with regards to the proper fixation of probe molecules, focusing particularly on chemical procedures developed to anchor biological molecules on AFM tips.

Sampling protein form and function with the atomic force microscope

To study the structure, function, and interactions of proteins, a plethora of techniques is available. Many techniques sample such parameters in non-physiological environments (e.g. in air, ice, or vacuum). Atomic force microscopy (AFM), however, is a powerful biophysical technique that can probe these parameters under physiological buffer conditions. With the atomic force microscope operating under such conditions, it is possible to obtain images of biological structures without requiring labeling and to follow dynamic processes in real time. Furthermore, by operating in force spectroscopy mode, it can probe intramolecular interactions and binding strengths. In structural biology, it has proven its ability to image proteins and protein conformational changes at submolecular resolution, and in proteomics, it is developing as a tool to map surface proteomes and to study protein function by force spectroscopy methods. The power of AFM to combine studies of protein form and protein function enables bridging various research fields to come to a comprehensive, molecular level picture of biological processes. We review the use of AFM imaging and force spectroscopy techniques and discuss the major advances of these experiments in further understanding form and function of proteins at the nanoscale in physiologically relevant environments.

AFM of biological complexes: what can we learn?

The term "biological complexes" broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected nonmembrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications.

Interaction forces and interface properties of KIF1A kinesin-alphabeta tubulin complex assessed by molecular dynamics

Kinesin is a microtubule-based motor protein that generates motion involved in intracellular trafficking and cell division. Even if the force-generating and enzymatic properties of kinesin were extensively studied, the molecular basis of its interaction with the microtubule is still not well understood. The aim of the present study is to provide a detailed description, in terms of conformational changes and interaction properties, of the kinesin-alphabeta tubulin complex during a cycle of ATP hydrolysis. Four different nucleotide-dependent conformations (nucleotide-free, ATP, ADP.Pi and ADP) of the kinesin-alphabeta tubulin were constructed and investigated by performing molecular dynamics simulations. Computational results show that small conformational changes, in the order of few Angstrom, occurring in the kinesin structure reflect on its affinity for the filament substrate. Indeed the rotation of the alpha4 helix due to the transition from the bound (ADP.Pi) to the unbound (ADP) state, when the Pi is released from the complex, coupled with the modification occurred in the loop L9 of switch I domain are associated to a marked decrease (approximately 45%) of the maximum interaction force between the kinesin motor and the tubulin dimer.

Molecular modeling of the axial and circumferential elastic moduli of tubulin

Microtubules play a number of important mechanical roles in almost all cell types in nearly all major phylogenetic trees. We have used a molecular mechanics approach to perform tensile tests on individual tubulin monomers and determined values for the axial and circumferential moduli for all currently known complete sequences. The axial elastic moduli, in vacuo, were found to be 1.25 GPa and 1.34 GPa for alpha- and beta-bovine tubulin monomers. In the circumferential direction, these moduli were 378 MPa for alpha- and 460 MPa for beta-structures. Using bovine tubulin as a template, 269 homologous tubulin structures were also subjected to simulated tensile loads yielding an average axial elastic modulus of 1.10 +/- 0.14 GPa for alpha-tubulin structures and 1.39 +/- 0.68 GPa for beta-tubulin. Circumferentially the alpha- and beta-moduli were 936 +/- 216 MPa and 658 +/- 134 MPa, respectively. Our primary finding is that that the axial elastic modulus of tubulin diminishes as the length of the monomer increases. However, in the circumferential direction, no correlation exists. These predicted anisotropies and scale dependencies may assist in interpreting the macroscale behavior of microtubules during mitosis or cell growth. Additionally, an intergenomic approach to investigating the mechanical properties of proteins may provide a way to elucidate the evolutionary mechanical constraints imposed by nature upon individual subcellular components.

Refined procedure of evaluating experimental single-molecule force spectroscopy data

Dynamic force spectroscopy is a well-established tool to study molecular recognition in a wide range of binding affinities on the single-molecule level. The theoretical interpretation of these data is still very challenging and the models describe the experimental data only partly. In this paper we reconsider the basic assumptions of the models on the basis of an experimental data set and propose an approach of analyzing and quantitatively evaluating dynamic force spectroscopy data on single ligand-receptor complexes. We present our procedure to process and analyze the force-distance curves, to detect the rupture events in an automated manner, and to calculate quantitative parameters for a biophysical characterization of the investigated interaction.

Atomic force microscopy: Determination of unbinding force, off rate and energy barrier for protein–ligand interaction

Recently, atomic force microscopy (AFM) based force measurements have been applied biophysically and clinically to the field of molecular recognition as well as to the evaluation of dynamic parameters for various interactions between proteins and ligands in their native environment. The aim of this review is to describe the use of the AFM to measure the forces that control biological interaction, focusing especially on protein-ligand and protein-protein interaction modes. We first considered the measurements of specific and non-specific unbinding forces which together control protein-ligand interactions. As such, we will look at the theoretical background of AFM force measurement curves for evaluating the unbinding forces of protein-ligand complexes. Three AFM model dynamic parameters developed recently for use in protein-ligand interactions are reviewed: (i) unbinding forces, (ii) off rates, and (iii) binding energies. By reviewing the several techniques developed for measuring forces between biological structures and intermolecular forces in the literature, we show that use of an AFM for these applications provides an excellent tool in terms of spatial resolution and lateral resolution, especially for protein-protein and protein-ligand interactions.

Dynamic response of glucagon/anti-glucagon pairs to pulling velocity and pH studied by atomic force microscopy

We used atomic force microscopy (AFM) to measure the unbinding force between antigen coupled to an AFM tip and antibody coated on the substrate surface. Dynamic responses of glucagon/anti-glucagon pairs with multiple pull-off steps to pH and pulling velocity were studied by AFM. Force-distance curves of a specific glucagon-anti-glucagon interaction system with mono-, di-, and multi-unbinding events were recorded, which may be attributed to a single, sequential or multiple breaking of interacting bond(s) between glucagon and anti-glucagon. We studied the dynamic response of glucagon-anti-glucagon pairs to various pulling velocities (16.7-166.7 nm/s). It was found that the mean value of the unbinding force was shifted toward higher values with increasing pulling velocity at each pH. This indicates that the friction force between glucagon and anti-glucagon may contribute to the unbinding force. Moreover, the dynamic response of glucagon-anti-glucagon pairs to pH (4-10) with different pulling velocities was studied. Within the acid range, the bond strength between the glucagon/anti-glucagon complex showed a rapid increase from pH 4 to 7 and reached a maximum (256.4+/-48.9 pN at 166.7 nm/s) at neutrality, followed by a sharp decrease with increasing pH (pH 7-10). This could be attributed to the conformational change that occurred in glucagon when the pH value in solution was varied from the reference level at neutrality. This study demonstrated that the pH dependence of multiple antigen-antibody bond-rupture forces could be measured by a force-based AFM biosensor. Unraveling the relationship between inter-molecular force and intra-molecular conformational change in acid, neutral, and alkaline environments may provide new directions for future application of force measurements by AFM in proteomics or in the development of a clinical cantilever-based mechanical biosensor.

Multi-scale analysis of the toraymyxin adsorption cartridge. Part I: molecular interaction of polymyxin B with endotoxins

Endotoxins or lipopolysaccharides are the main constituents of the outer leaflet of Gram-negative bacteria membrane and play a central role in the pathogenesis of the septic shock. Polymyxin B has both antibacterial and antiendotoxin capability; indeed it is able to destroy the bacterial outer membrane and bind endotoxin neutralizing its toxic effects. Cartridges containing polymyxin B-immobilized fibers (Toraymyxin PMX-F, Toray Industries, Japan) are used in extracorporeal hemoperfusion to remove circulating endotoxin. The aim of this study is the characterization of the polymyxin B-endotoxin system at the molecular level, thus providing quantitative evaluation of the binding forces exerted in the molecular complex. Polymyxin B was interfaced with five molecular models of lipopolysaccharides differing in their structure and molecular mechanics simulations were performed at different intermolecular distances aimed at calculating the interaction energies of the complex. Binding forces were calculated by fitting interaction energies data. Results show that in the short range the polymyxin B-endotoxin complex is mediated by hydrophobic forces and in the long range the complex is driven by ionic forces only. From a mechanical standpoint, polymyxin B-endotoxin complex is characterized by maximum binding forces ranging between 1.39 nN to 3.79 nN. The knowledge of the binding force behavior at different intermolecular distances allows further investigations at higher scale level (Part II).

Evidence for direct amelogenin-target cell interactions using dynamic force spectroscopy

Increasing evidence suggests that amelogenin, long held to be a structural protein of developing enamel matrix, may also have cell signaling functions. However, a mechanism for amelogenin cell signaling has yet to be described. The aim of the present study was to use dynamic chemical force spectroscopy to measure amelogenin interactions with possible target cells. Full-length amelogenin (rM179) was covalently attached to silicon nitride AFM tips. Synthetic RGD peptides and unmodified AFM tips were used as controls. Amelogenin-RGD cell binding force measurements were carried out using human periodontal ligament fibroblasts (HPDF) from primary explants and a commercially available osteoblast-like human sarcoma cell line as the targets. Results indicated a linear logarithmic dependence between loading rate and unbinding force for amelogenin-RGD target cells across the range of loading rates used. For RGD controls, binding events measured at 5.5 nN s-1 force loading rate resulted in a mean force of 60 pN. Values for amelogenin-fibroblast and amelogenin-osteoblast-like cell unbinding forces, measured at similar loading rates, were 50 and 55 pN, respectively. These data suggest that amelogenin interacts with potential target cells with forces characteristic of specific ligand-receptor binding, suggesting a direct effect for amelogenin at target cell membranes.

Nanomechanical force measurements of gliadin protein interactions

The strength and nature of interactions between monomeric gliadin proteins involving alpha-alpha, omega-omega, and alpha-omega interactions in 0.01M acetic acid, and the effect of urea has been investigated. It was shown by means of nanomechanical force measurements that the stretching events in the separation curve after adhesive phenomena originated from proteins. These stretching events displayed different responses of the alpha- and omega-gliadins to urea. While 2M urea caused the more globular alpha-gliadins to unfold, the beta-turn-rich omega-gliadins remained fairly stable even in 8M urea. This suggests different roles for gliadins in the formation of dough; while the omega-gliadins are still in a compact structure being responsible for the viscous flow, the alpha-gliadins have already started to participate in forming the network in dough.

Multi-step fibrinogen binding to the integrin (alpha)IIb(beta)3 detected using force spectroscopy

The regulated ability of integrin alphaIIbbeta3 to bind fibrinogen plays a crucial role in platelet aggregation and hemostasis. We have developed a model system based on laser tweezers, enabling us to measure specific rupture forces needed to separate single receptor-ligand complexes. First of all, we performed a thorough and statistically representative analysis of nonspecific protein-protein binding versus specific alphaIIbbeta3-fibrinogen interactions in combination with experimental evidence for single-molecule measurements. The rupture force distribution of purified alphaIIbbeta3 and fibrinogen, covalently attached to underlying surfaces, ranged from approximately 20 to 150 pN. This distribution could be fit with a sum of an exponential curve for weak to moderate (20-60 pN) forces, and a Gaussian curve for strong (>60 pN) rupture forces that peaked at 80-90 pN. The interactions corresponding to these rupture force regimes differed in their susceptibility to alphaIIbbeta3 antagonists or Mn2+, an alphaIIbbeta3 activator. Varying the surface density of fibrinogen changed the total binding probability linearly >3.5-fold but did not affect the shape of the rupture force distribution, indicating that the measurements represent single-molecule binding. The yield strength of alphaIIbbeta3-fibrinogen interactions was independent of the loading rate (160-16,000 pN/s), whereas their binding probability markedly correlated with the duration of contact. The aggregate of data provides evidence for complex multi-step binding/unbinding pathways of alphaIIbbeta3 and fibrinogen revealed at the single-molecule level.

A molecular delivery system by using AFM and nanoneedle

We developed a new low invasive cell manipulation and gene or molecule transfer system in a single living cell by using an atomic force microscope (AFM) and ultra thin needle, a nanoneedle. DNA was immobilized on the surface of the nanoneedle by covalent bonding and avidin-biotin affinity binding. Immobilization of DNA on the nanoneedle was confirmed by measuring the unbinding force between avidin and biotin. The DNA-immobilized nanoneedle was successfully inserted into HEK293 cells. Though TO-PRO-3 iodide staining experiments using confocal microscopy, we observed the immobilized DNA on the surface of the nanoneedle, which was retained after 10 times insertions to and evacuations from a living cell.

How to orient the functional GroEL-SR1 mutant for atomic force microscopy investigations

We present high-resolution atomic force microscopy (AFM) imaging of the single-ring mutant of the chaperonin GroEL (SR-EL) from Escherichia coli in buffer solution. The native GroEL is generally unsuitable for AFM scanning as it is easily being bisected by forces exerted by the AFM tip. The single-ring mutant of GroEL with its simplified composition, but unaltered capability of binding substrates and the co-chaperone GroES, is a more suited system for AFM studies. We worked out a scheme to systematically investigate both the apical and the equatorial faces of SR-EL, as it binds in a preferred orientation to hydrophilic mica and hydrophobic highly ordered pyrolytic graphite. High-resolution topographical imaging and the interaction of the co-chaperone GroES were used to assign the orientations of SR-EL in comparison with the physically bisected GroEL. The usage of SR-EL facilitates single molecule studies on the folding cycle of the GroE system using AFM.

Interactions between synaptic vesicle fusion proteins explored by atomic force microscopy

Measuring the biophysical properties of macromolecular complexes at work is a major challenge of modern biology. The protein complex composed of vesicle-associated membrane protein 2, synaptosomal-associated protein of 25 kDa, and syntaxin 1 [soluble N-ethyl-maleimide-sensitive factor attachment protein receptor (SNARE) complex] is essential for docking and fusion of neurotransmitter-filled synaptic vesicles with the presynaptic membrane. To better understand the fusion mechanisms, we reconstituted the synaptic SNARE complex in the imaging chamber of an atomic force microscope and measured the interaction forces between its components. Each protein was tested against the two others, taken either individually or as binary complexes. This approach allowed us to determine specific interaction forces and dissociation kinetics of the SNAREs and led us to propose a sequence of interactions. A theoretical model based on our measurements suggests that a minimum of four complexes is probably necessary for fusion to occur. We also showed that the regulatory protein neuronal Sec1 injected into the atomic force microscope chamber prevented the complex formation. Finally, we measured the effect of tetanus toxin protease on the SNARE complex and its activity by on-line registration during tetanus toxin injection. These experiments provide a basis for the functional study of protein microdomains and also suggest opportunities for sensitive screening of drugs that can modulate protein-protein interactions.

Specific interaction between GroEL and denatured protein measured by compression-free force spectroscopy

We investigated the interaction between GroEL and a denatured protein from a mechanical point of view using an atomic force microscope. Pepsin was bound to an atomic force microscope probe and used at a neutral pH as an example of denatured proteins. To measure a specific and delicate interaction force, we obtained force curves without pressing the probe onto GroEL molecules spread on a mica surface. Approximately 40 pN of tensile force was observed for approximately 10 nm while pepsin was pulled away from the chaperonin after a brief contact. This length of force duration corresponding to the circumference of GroEL's interior cavity was shortened by the addition of ATP. The relation between the observed mechanical parameters and the chaperonin's refolding function is discussed.

Feeling the forces: atomic force microscopy in cell biology

Atomic force microscopy allows three-dimensional imaging and measurements of unstained and uncoated biological samples in air or fluid. Using this technology it offers resolution on the nanometer scale and detection of temporal changes in the mechanical properties, i.e. surface stiffness or elasticity in live cells and membranes. Various biological processes including ligand-receptor interactions, reorganization, and restructuring of the cytoskeleton associated with cell motility that are governed by intermolecular forces and their mode of detection will be discussed.

AFM structural study of the molecular chaperone GroEL and its two-dimensional crystals: an ideal "living" calibration sample

Supramolecular complexes, such as chaperonins, are suitable samples for atomic force microscope structural studies because they have a very well defined shape. High-resolution images can be made using tapping mode in liquid under native conditions. Details about the two-dimensional structures formed onto the surface upon adsorption and of the single protein can be observed. Dissection of the upper ring of the supramolecular complex as a result of the applied lateral force through scanning tip is observed. Finally, the combination of lateral convolution and tip penetration into the cavity of chaperonins offers a direct evaluation of the tip convolution effect on images of macromolecular samples.

Observing structure, function and assembly of single proteins by AFM

Single molecule experiments provide insight into the individuality of biological macromolecules, their unique function, reaction pathways, trajectories and molecular interactions. The exceptional signal-to-noise ratio of the atomic force microscope allows individual proteins to be imaged under physiologically relevant conditions at a lateral resolution of 0.5-1nm and a vertical resolution of 0.1-0.2nm. Recently, it has become possible to observe single molecule events using this technique. This capability is reviewed on various water-soluble and membrane proteins. Examples of the observation of function, variability, and assembly of single proteins are discussed. Statistical analysis is important to extend conclusions derived from single molecule experiments to protein species. Such approaches allow the classification of protein conformations and movements. Recent developments of probe microscopy techniques allow simultaneous measurement of multiple signals on individual macromolecules, and greatly extend the range of experiments possible for probing biological systems at the molecular level. Biologists exploring molecular mechanisms will benefit from a burgeoning of scanning probe microscopes and of their future combination with molecular biological experiments.

Conformational heterogeneity is revealed in the dissociation of the oligomeric chaperonin GroEL by high hydrostatic pressure

We investigated the dissociation of tetradecameric GroEL by high hydrostatic pressure in the range of 1-2.5 kbar. Kinetics of the dissociation of GroEL in the absence and presence of Mg(2+) and/or KCl were monitored using light scattering. All of the kinetics were biphasic in nature. At any given pressure, only monomers and 14mers were produced, and below 2.5 kbar, the 14mers only partially dissociated to monomers, which did not significantly reassemble on depressurization. Under identical reaction conditions, the observed dissociation rates decreased by only 2-fold when the concentration of GroEL was increased by 20-fold. At 2.5 kbar the observed rates decreased exponentially with the increase in [KCl] and reached a minimum at approximately 75mM. Similarly, the rates decreased with the increase in [Mg(2+)] and reached a minimum at approximately 3 mM Mg(2+). In the presence of saturating amounts of Mg(2+) (10 mM) and KCl (100 mM), the rates were much faster than with 10 mM Mg(2+) alone. The results could be rationalized in terms of the presence of GroEL heterogeneity, which could not be assessed easily by common techniques such as sedimentation velocity, HPLC, gel electrophoresis, and dissociation by chaotropes. This heterogeneity is evidence of subpopulations of GroEL that dissociate at different pressures. At low pressures, the oligomer without added Mg(2+) only partially dissociates to monomers, leading to an apparent plateau in the kinetics, whereas in the presence of Mg(2+) the species are converted to a tighter Mg(2+)-bound species, leading to a much slower dissociation process. The presence of KCl in the sample also leads to similar heterogeneity.

Single-molecule imaging by atomic force microscopy of the native chaperonin complex of the thermophilic archaeon Sulfolobus solfataricus

The chaperonin of the extremely thermophilic archaeon Sulfolobus solfataricus has been imaged for the first time under native conditions using the atomic force microscope. This technique allows to visualize the structure of biomolecules in solution under physiological conditions providing a nanometer resolution topographic image of the sample. Single molecule studies can reveal fine structural details, providing a powerful insight into the active conformation of a macromolecule, and also allowing to detect different conformational states corresponding to functional changes.

From images to interactions: high-resolution phase imaging in tapping-mode atomic force microscopy

In tapping-mode atomic force microscopy, the phase shift between excitation and response of the cantilever is used as a material-dependent signal complementary to topography. The localization of information in the phase signal is demonstrated with 1.4-nm lateral resolution on purple membrane of Halobacterium salinarum in buffer solution. In a first-order approximation, the phase signal is found to correlate with modulations of the tip oscillation amplitude, induced by topography. Extending the analysis to contributions of the tip-sample interaction area as a second-order approximation, a method is proposed to extract information about the interaction from the phase signal for surfaces with a roughness in the order of the tip radius.

Chaperonin-mediated protein folding

Molecular chaperones are required to assist folding of a subset of proteins in Escherichia coli. We describe a conceptual framework for understanding how the GroEL-GroES system assists misfolded proteins to reach their native states. The architecture of GroEL consists of double toroids stacked back-to-back. However, most of the fundamentals of the GroEL action can be described in terms of the single ring. A key idea in our framework is that, with coordinated ATP hydrolysis and GroES binding, GroEL participates actively by repeatedly unfolding the substrate protein (SP), provided that it is trapped in one of the misfolded states. We conjecture that the unfolding of SP becomes possible because a stretching force is transmitted to the SP when the GroEL particle undergoes allosteric transitions. Force-induced unfolding of the SP puts it on a higher free-energy point in the multidimensional energy landscape from which the SP can either reach the native conformation with some probability or be trapped in one of the competing basins of attraction (i.e., the SP undergoes kinetic partitioning). The model shows, in a natural way, that the time scales in the dynamics of the allosteric transitions are intimately coupled to folding rates of the SP. Several scenarios for chaperonin-assisted folding emerge depending on the interplay of the time scales governing the cycle. Further refinement of this framework may be necessary because single molecule experiments indicate that there is a great dispersion in the time scales governing the dynamics of the chaperonin cycle.

Single molecule force spectroscopy in biology using the atomic force microscope

The importance of forces in biology has been recognized for quite a while but only in the past decade have we acquired instrumentation and methodology to directly measure interactive forces at the level of single biological macromolecules and/or their complexes. This review focuses on force measurements performed with the atomic force microscope. A general introduction to the principle of action is followed by review of the types of interactions being studied, describing the main results and discussing the biological implications.

Measuring the forces that control protein interactions

Although the force fields and interaction energies that control protein behavior can be inferred indirectly from equilibrium and kinetic measurements, recent developments have made it possible to quantify directly (a) the ranges, magnitudes, and time dependence of the interaction energies and forces between biological materials; (b) the mechanical properties of isolated proteins; and (c) the strength of single receptor-ligand bonds. This review describes recent results obtained by using the atomic force microscope, optical tweezers, the surface force apparatus, and micropipette aspiration to quantify short-range protein-ligand interactions and the long-range, nonspecific forces that together control protein behavior. The examples presented illustrate the power of force measurements to quantify directly the force fields and energies that control protein behavior.

Force Spectroscopy of Molecular Systems-Single Molecule Spectroscopy of Polymers and Biomolecules

How do molecules interact with each other? What happens if a neurotransmitter binds to a ligand-operated ion channel? How do antibodies recognize their antigens? Molecular recognition events play a pivotal role in nature: in enzymatic catalysis and during the replication and transcription of the genome; it is also important for the cohesion of cellular structures and in numerous metabolic reactions that molecules interact with each other in a specific manner. Conventional methods such as calorimetry provide very precise values of binding enthalpies; these are, however, average values obtained from a large ensemble of molecules without knowledge of the dynamics of the molecular recognition event. Which forces occur when a single molecular couple meets and forms a bond? Since the development of the scanning force microscope and force spectroscopy a couple of years ago, tools have now become available for measuring the forces between interfaces with high precision-starting from colloidal forces to the interaction of single molecules. The manipulation of individual molecules using force spectroscopy is also possible. In this way, the mechanical properties on a molecular scale are measurable. The study of single molecules is not an exclusive domain of force spectroscopy; it can also be performed with a surface force apparatus, laser tweezers, or the micropipette technique. Regardless of these techniques, force spectroscopy has been proven as an extraordinary versatile tool. The intention of this review article is to present a critical evaluation of the actual development of static force spectroscopy. The article mainly focuses on experiments dealing with inter- and intramolecular forces-starting with "simple" electrostatic forces, then ligand-receptor systems, and finally the stretching of individual molecules.

GroEL binds artificial proteins with random sequences

Chaperonin GroEL from Escherichia coli binds to the non-native states of many unrelated proteins, and GroEL-recognizable structural features have been argued. As model substrate proteins of GroEL, we used seven artificial proteins (138 approximately 141 residues), each of which has a unique but randomly chosen amino acid sequence and no propensity to fold into a certain structure. Two of them were water-soluble, and the rest were soluble in 3 m urea. The soluble ones interacted with GroEL in a manner similar to that of a natural substrate; they stimulated the ATPase cycle of GroEL and GroEL/GroES and inhibited GroEL-assisted folding of other protein. All seven artificial proteins were able to bind to GroEL. The results suggest that the secondary structure as well as the specific sequence motif of the substrate proteins are not necessary to be recognized by GroEL.

Basis of substrate binding by the chaperonin GroEL

The molecular chaperonins are essential proteins involved in protein folding, complex assembly, and polypeptide translocation. While there is abundant structural information about the machinery and the mechanistic details of its action are well studied, it is yet unresolved how chaperonins recognize a large number of structurally unrelated polypeptides in their unfolded or partially folded forms. To determine the nature of chaperonin-substrate recognition, we have characterized by NMR methods the interactions of GroEL with synthetic peptides that mimic segments of unfolded proteins. In previous work, we found using transferred nuclear Overhauser effect (trNOE) analysis that two 13 amino acid peptides bound GroEL in an amphipathic alpha-helical conformation. By extending the study to a variety of peptides with differing sequence motifs, we have observed that peptides can adopt conformations other than alpha-helix when bound to GroEL. Furthermore, peptides of the same composition exhibited significantly different affinities for GroEL as manifested by the magnitude of trNOEs. Binding to GroEL correlates well with the ability of the peptide to cluster hydrophobic residues on one face of the peptide, as determined by the retention time on reversed-phase (RP) HPLC. We conclude that the molecular basis of GroEL-substrate recognition is the presentation of a hydrophobic surface by an incompletely folded polypeptide and that many backbone conformations can be accommodated.

The influence of epitope availability on atomic-force microscope studies of antigen-antibody interactions

The ability of the atomic-force microscope (AFM) to detect interaction forces between individual biological molecules has recently been demonstrated. In this study, force measurements have been obtained between AFM probes functionalized with the beta-subunit of human chorionic gonadotrophin (betahCG) and surfaces functionalized with anti-betahCG antibody. A comparison of the obtained results with previous anti-ferritin antibody-binding data identifies differences when the antigen molecule expresses only a single epitope (betahCG), rather than multiple epitopes (ferritin), for the monoclonal antibodies employed. Specifically, the probability of observing probe-sample adhesion is found to be higher when the antigen expresses multiple epitopes. However, the periodic force observed in the adhesive-force distribution, due to the rupture of single antigen-antibody interactions, is found to be larger and more clearly observed for the mono-epitopic system. Hence, these findings indicate the potential of the AFM to distinguish between multivalent and monovalent antibody-antigen interactions, and demonstrate the influence of the number of expressed epitopes upon such binding studies.