Intermittent contact mode atomic force microscopy has been widely employed for simultaneous topography imaging and material characterization. The work in the literature includes both qualitative and quantitative methods. Regular AFM cantilevers are generally used in these methods, yet these cantilevers come with certain limitations. These limitations result from the very nature of cantilever probes. They are passive force sensors with insufficient damping. This prevents having active and complete control on tip-sample forces, causing sample damage and inaccurate topography measurement. Ideally, an AFM probe should offer high bandwidth to resolve interaction forces, active control capability for small interaction force and stable operation, and sufficient damping to avoid transient ringing which causes undesired forces on the sample. Force sensing integrated readout and active tip (FIRAT) probe offers these properties. A special imaging mode, time-resolved interaction force (TRIF) mode imaging can be performed using FIRAT probe for simultaneous topography and material property imaging. The accuracy of topography measurement of samples with variations in elastic and adhesive properties is investigated via numerical simulations and experiments. Results indicate that employing FIRAT probe's active tip control (ATC) capability during TRIF mode imaging provides significant level of control over the tip-sample forces. This improves the accuracy of topography measurement during simultaneous material property imaging, compared to conventional methods. Moreover, Active tip control (ATC) preserves constant contact time during force control for stable contact while preventing loss of material property information such as elasticity and adhesive forces.

Relatively little is known about the folding and stability of membrane proteins. Conventional thermal or chemical unfolding techniques probe the average behavior of large numbers of molecules and thus cannot resolve co-existing minor and major unfolding pathways and intermediates. Here, I applied single-molecule force measurements based on an atomic force microscope (AFM) to characterize the stability of the membrane protein bacteriorhodopsin (BR). In these mechanical unfolding experiments, an external pulling force played the role of the denaturant and lead to unfolding of the three-dimensional structure of individual proteins. It was found that single BRs unfold step-wise in a well-defined sequence of stable intermediates and in different unfolding pathways. Although single [alpha]-helices were sufficiently stable to unfold in individual steps they also exhibited certain probabilities to unfold in pairs. These observations support the "two-stage" and the "helical-hairpin" model of membrane protein folding. Dynamic force measurements showed that [alpha]-helices and helical hairpins are relatively rigid structures, which are stabilized by narrow energy barriers and have stabilities between 100-10?000 seconds. These forced unfolding experiments were complemented with the development of new force measurement techniques. It is demonstrated that hydrodynamic effects need to be considered to obtain more complete kinetic pictures of single molecules. In addition, two force spectroscopy approaches to measure the complex visco-elastic response of single molecules are presented and applied to BR. These experiments revealed that the unfolding patterns of single proteins are dominated by purely elastic polypeptide extension and determined the dissipative interactions associated with the unfolding of single [alpha]-helices. In addition, it was found that kinks result in a reduced unfolding cooperativity of [alpha]-helices.

We use time-lapse AFM to visualize collagen fibrils self-assembly. A solution of acid-solubilized collagen was injected into the AFM fluid cell and fibril formation was observed in vitro. Single fibrils continuously grew and fused with each other until the supporting surface was completely covered by a nanoscopically well-defined collagen matrix. Laterally, the fibrils grew in steps of ~4 nm suggesting a two-step mechanism. In a first step, collagen molecules associated together. In the second step, these molecules rearranged into a structure called a microfibril. High-resolution AFM topographs revealed substructural details of the D-band architecture. These substructures correlated well with those revealed from positively stained collagen fibers imaged by transmission electron microscopy. Secondly, a covalent assembly approach to prepare membrane protein for AFM imaging that avoids crystallization was proposed. High-resolution AFM topographs can reveal structural details of single membrane proteins but, as a prerequisite, the proteins must be adsorbed to atomically flat mica and densely packed in a membrane to restrict their lateral mobility. Atomically flat gold, engineered proteins, and chemically modified lipids were combined to rapidly assemble immobile and fully oriented samples. The resulting AFM topographs of single membrane proteins were used to create averaged structures with a resolution approaching that of 2D crystals. Finally, the contribution of specific amino acid residues to the stability of membrane proteins was studied. Two structurally similar proteins sharing only 30% sequence identity were compared. Single-molecule atomic force microscopy and spectroscopy was used to detect molecular interactions stabilizing halorhodopsin (HR) and bacteriorhodopsin (BR). Their unfolding pathways and polypeptide regions that established stable segments were compared. Both proteins unfolded exactly via the same intermediates. This 3 Molecular Assemblies observed by AFM observation implies that these stabilizing regions result from comprehensive contacts of all amino acids within them and that different amino acid compositions can establish structurally indistinguishable energetic barriers. However, one additional unfolding barrier located in a short segment of helix E was detected for HR. This barrier correlated with a Pi-bulk interaction, which locally disrupts helix E and divides into two stable segments.

Selective ion and solute transport across cell membranes is a vital process occurring in all types of cells. Evolutionarily developed transport proteins work as membrane-embedded molecular machines, which alternately open a gate on each side of the membrane to bind and translocate specific ions. Sodium/proton exchange plays a crucial role in maintaining cytoplasmic pH and membrane potential, while, if not regulated, the process causes severe heart diseases in humans. Here I applied single-molecule force spectroscopy to investigate molecular interactions determining the structural stability of the sodium/proton antiporter NhaA of Escherichia coli, which serves as a model system for this class of proteins. Mechanical pulling of NhaA molecules embedded in the native lipid bilayer caused a step-wise unfolding of the protein and provided insights into its stability. Modified experiments allowed observing refolding of NhaA molecules and estimating folding kinetics for individual structural elements, as well as detecting eventual misfolded conformations of the protein. The activity of NhaA increases 2000fold upon switching pH from 6 to 8. Single-molecule force measurements revealed a reversible change in molecular interactions within the ligand-binding site of the transporter at pH 5.5. The effect was enhanced in the presence of sodium ions. The observation suggests an early activation stage of the protein and provides new insights into the functioning mechanism. When studying interactions of NhaA with the inhibitor 2-aminoperimidine, I exploited single-molecule force measurements to validate the binding mechanism and to describe quantitatively formation of the protein:inhibitor complex. The ability of single-molecule force measurements to probe structurally and functionally important interactions of membrane proteins opens new prospects for using the approach in protein science and applied research.

<p>The main objective for the work described in this PhD thesiswas to formulate a friction model to characterize thefrictional behavior of paper. More specifically, the modelshould explain a phenomenon that is typical for paper grades,viz.: that the level of paper-to-paper friction is dependent onthe direction and the number of previous slides. The modelshould also explain the lubricating effect oflow-molecular-mass lipophilic compounds (LLC) that occur inpaper on paper-to-paper friction. Furthermore, the model shoulddescribe the types of forces that influence paper-to-paperfiction and explain the mechanism by which the LLC decreasepaper-to-paper friction.</p><p>This thesis consists of a literature review of the basicconcepts of tribology and a summary of the main results andconclusions from four studies on the frictional characteristicsof paper and a study on the friction and adhesion of cellulosesurfaces together with some unpublished material.</p><p>The purpose of the investigation described in the firstpaper was to explain a phenomenon that is typical for papergrades, viz.: the level of paper-to-paper friction is dependenton the direction and the number of previous slides. Thisbehavior is called“friction hysteresis”by theauthors, and it has its origin in the reorientation of thefibers on the surface of a paper and their alignment relativeto the sliding direction.</p><p>The second paper describes a study that was aimed atidentifying lubricants that occur natively in paper. Filterpapers were impregnated with model compounds representing woodextractives, i.e. low-molecular-weight lipophilic compounds,which are present in wood, pulp and paper, and thepaper-to-paper friction was determined. The results of thatstudy show that a wood extractive must fulfill severalstructural criteria in order to lubricate a paper surface: Itmust have a hydrophilic group that can attach to the papersurface and a linear hydrocarbon backbone of sufficientlength.</p><p>Although it is not specifically stated in the second paper,the authors proposed a type of lubrication by which woodextractives decrease paper-to-paper friction that is, ineffect, boundary lubrication. The purpose of the investigationdescribed in the third paper was to clarify whether woodextractives and other low-molecular-mass lipophilic compoundsthat occur in paper can act as boundary lubricants on papersurfaces. The main objective of that study was to investigatethe role of chemical structure of LLC for their orientationrelative to the paper surface, which is an important criterionfor boundary lubrication. Filter papers were impregnated withmagnesium salts of different lipophilic acids, which were usedfor model compounds for the LLC. The deposited layers ofmagnesium salts were characterized by X-ray photoelectronspectroscopy (XPS) and contact angle goniometry and thefriction of the impregnated paper sheets was determined. Theresults show that the degree of lubrication and the resistanceto wear of the layers of a magnesium salt increased withincreasing chain length and increasing degree of linearity ofthe lipophilic acid. Based on the results of that study and ofearlier studies, it is concluded that boundary lubrication isthe type of lubrication by which low-molecular-mass lipophiliccompounds that occur natively in paper decreasepaper-to-paper-friction.</p><p>In boundary lubrication, surfaces are covered withmonolayers of lubricant molecules that comprise an active headgroup that can attach to the surface, e.g. a carboxyl group,and an inert linear backbone, such as a long saturatedhydrocarbon chain. Such compounds form ordered monolayers onsurfaces, so that the backbone points vertically out of planeof the surface. The friction is then determined by theinteractions between the monolayers, which are weaker than theinteractions between the clean surfaces and this gives a lowerfriction.</p><p>The fourth paper describes a study on the origin of thedifferences in friction levels between different linerboardsbased on recycled fiber (old corrugated container, OCC). Thesheets were subjected to two extraction stages and analyzedwith respect to surface roughness and their content oflow-molecular-mass lipophilic compounds (LLC). The resultsshowed that a high amount of LLC in the sheets lead to lowfriction, due to lubrication.</p><p>The fifth paper describes a study that was aimed atdetermining the types of forces that influence the frictionbetween the surfaces of hydrophilic polymers and explaining themechanism by which boundary lubricants decrease the friction.The adhesion and the friction of model systems was measuredwith atomic force microscopy (AFM) using regenerated cellulosefilms and functionalised AFM tips and the effect of fatty acidsand humidity was investigated. The friction significantlyincreased with increasing humidity and that there was a strongcorrelation between the ability of a fatty acid to form ahydrophobic surface and its lubricating performance. Measuredadhesion forces at high humidity were well predicted bytheoretical models that took into account the effect of theLaplace pressure acting in a water meniscus formed aroundcontact regions due to capillary condensation. The resultsindicated that the degree of capillary condensation may beeffectively suppressed by increasing the hydrophobicity of thecontacting surfaces, causing adhesion and friction to decrease.These results suggest that friction between paper surfacesunder ambient conditions is greatly influenced by the degree ofcapillary condensation. Furthermore, lubrication by fatty acidsis achieved by the formation of a vertically oriented,hydrophobic monolayer that can withstand the stresses duringsliding and increase the hydrophobicity of the paper surfaceand thereby suppress capillary condensation.</p><p><b>Keywords:</b>Friction, paper-to-paper friction, frictionhysteresis, fibers, orientation, sliding direction, woodextractives, low-molecular-mass lipophilic compounds, boundarylubrication, adhesion, capillary condensation, Laplacepressure, surface forces, JKR theory, gas chromatography-massspectroscopy, X-ray photoelectron spectroscopy, contact angle,atomic force microscopy</p>

No description available.

In this dissertation, we developed cell stiffness as a biomarker in ovarian cancer for the purpose of grading metastatic potential. By measuring single cell stiffness with atomic force microscopy and quantifying in vitro invasiveness of healthy and cancerous ovarian cells, we demonstrated that cancerous ovarian cells have reduced stiffness compared to the healthy ones and invasive ovarian cancer cells are more deformable than noninvasive ovarian cancer cells. The difference in cell stiffness between two genetically similar cell lines was attributed to actin-mediated cytoskeletal remodeling as revealed by comparative gene expression profile analysis, and was further confirmed by fluorescent visualization of actin cytoskeletal structures. The actin cytoskeletons were innovatively quantified and correlates with cell stiffness distributions, further implicating actin-mediated cytoskeletal remodeling in stiffness alteration from the perspective of structure-property relationship. The correlation between stiffness and metastatic potential was also demonstrated in pancreatic cancer cell line AsPC-1, which shows reduced invasivess and increased stiffness upon treatment with N-acetyl-L-cysteine (NAC), a well known antioxidant, reactive oxygen species (ROS), scavenger and glutathione precursor. The correlation between cell stiffness and metastatic potential as demonstrated in ovarian and pancreatic cancer cells indicated that mechanical stiffness may be a useful biomarker to evaluate the relative metastatic potential of ovarian and perhaps other types of cancer cells, and might be useful clinically with the development of rapid biomechanical assaying techniques. We have also investigated the stiffness evolution through progression of the cell cycle for the healthy ovarian phenotype and the invasive cancer ovarian phenotype, and found that the healthy phenotype at G1 phase are significantly stiffer than other single cells except the invasive phenotype at late mitosis; other groups are not significantly different from each other. We have also investigated intracellular heterogeneity and mechanical nonlinearity in single cells. To this end, we developed a methodology to analyze the deformation-dependent mechanical nonlinearity using a pointwise Hertzian method, and tested the method on ultrathin polydimethylsiloxane (PDMS) films which underwent extremely large strains (greater than 50%). Mechanical stiffening due to large strain and geometrical confinement were observed. The onset of nonlinearity or mechanical stiffening occurs at 45% of the film thickness, the geometry induced stiffening causes an increase in stiffness which shows a strong power law dependence on film thickness. By applying the pointwise Hertzian method on stiffness measurements with AFM that were collected on living cells, we also investigated the nonlinear and heterogeneous mechanics of single cells, since attachment of cells to stiff substrate during indentation may impact their mechanical responses. Even under natural biological conditions, cells confined in narrow spaces may experience heightened mechanical stiffness. Through indentation-dependent force mapping, analysis of the local cell stiffness demonstrated spatial variation. The results indicated that the mechanical properties of single cells are highly nonlinear and are dependent upon the subcellular features under the applied force as well as the dimensions of the cellular material. We identified single cell stiffness as a potential biomarker of the metastatic potential in ovarian cancer, and quantified the effect of geometrical confinement on cell mechanics. The results presented in this dissertation not only made contributions to the development of accurate, non-invasive clinical methods to estimate metastatic potential of ovarian and perhaps other types of cancer, but also shed light on the intracellular mechanical information by developing new techniques to quantify the effect of geometry on cell mechanics.

A combined attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR)-atomic force microscopy (AFM) platform was used to visualize and characterize membranolytic protein- and peptide-membrane interactions, allowing spectroscopic details to be correlated with structural features. Modifications to a previous combined platform permitted IR results for physiologically-relevant protein or peptide concentrations as well as provided nanometer-resolution height data for AFM. This combination provides greater insight than individual techniques alone. The interactions of hemolytic sticholysin proteins on a model red blood cell membrane showed evidence of conformational changes associated with a membrane-induced organization. In addition, the examination of a de novo cationic antimicrobial peptide on a model bacterial membrane showed that the peptide adopted a helical structure upon interaction with the membrane, and also provided evidence of membrane disruption and peptide aggregation. These results demonstrate that ATR-FTIR-AFM can be a powerful tool for understanding protein- and peptide-membrane interactions.

No description available.

A combined attenuated total reflection-Fourier-transform infrared spectroscopy (ATR-FTIR)-atomic force microscopy (AFM) platform was used to visualize and characterize membranolytic protein- and peptide-membrane interactions, allowing spectroscopic details to be correlated with structural features. Modifications to a previous combined platform permitted IR results for physiologically-relevant protein or peptide concentrations as well as provided nanometer-resolution height data for AFM. This combination provides greater insight than individual techniques alone. The interactions of hemolytic sticholysin proteins on a model red blood cell membrane showed evidence of conformational changes associated with a membrane-induced organization. In addition, the examination of a de novo cationic antimicrobial peptide on a model bacterial membrane showed that the peptide adopted a helical structure upon interaction with the membrane, and also provided evidence of membrane disruption and peptide aggregation. These results demonstrate that ATR-FTIR-AFM can be a powerful tool for understanding protein- and peptide-membrane interactions.