Dissociation Kinetics of an Enzyme−Inhibitor System Using Single-Molecule Force Measurements

Mayyas, Essa; Bernardo, M. Margarida; Runyan, Lindsay; Sohail, Anjum; Subba-Rao, Venkatesh; Pantea, Mircea; Fridman, Rafael; Hoffmann, Peter M.

doi:10.1021/bm100844x

Cited by 9 publications

(13 citation statements)

References 30 publications

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“…A better approach is to filter out force cycles with multiple rupture events (3,32,33). However, this assumes that two rupture events will be spatially separated, which often fails when the molecules are short or when adhesion probability is high (34,35). Nevertheless, this simple filtering method can improve the accuracy of experiments obtained with low adhesion probabilities, especially if the fraction of data filtered out correspond with the statistical predictions.…”

Section: Filtering Using Mechanical Fingerprintsmentioning

confidence: 99%

“…Some studies have analyzed this force data by only considering the last rupture event in the force cycle (59,60), but this again assumes that two rupture events must be spatially separated. This assumption fails especially when there are many rupture events, resulting in hidden multiple interactions (34,35). Another shortcoming is that these methods assume prior knowledge about the appearance of single molecule data and have not been shown to be reliable for the complex energy landscapes described above.…”

Section: Analyzing High-adhesion Probability Datamentioning

confidence: 99%

See 1 more Smart Citation

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

Johnson

Thomas

2018

Biophysical Journal

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Single-molecule force spectroscopy makes it possible to measure the mechanical strength of single noncovalent receptor-ligand-type bonds. A major challenge in this technique is to ensure that measurements reflect bonds between single biomolecules because the molecules cannot be directly observed. This perspective evaluates different methodologies for identifying and reducing the contribution of multiple molecule interactions to single-molecule measurements to help the reader design experiments or assess publications in the single-molecule force spectroscopy field. We apply our analysis to the large body of literature that purports to measure the strength of single bonds between biotin and streptavidin as a demonstration that measurements are only reproducible when the most reliable methods for ensuring single molecules are used.

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Section: Filtering Using Mechanical Fingerprintsmentioning

confidence: 99%

Section: Analyzing High-adhesion Probability Datamentioning

confidence: 99%

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

Johnson

Thomas

2018

Biophysical Journal

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“…DNA-protein and DNA-drug interactions have also been measured directly, providing thermodynamic and kinetic information that led to novel insights into the mechanisms of molecular interactions (Pant et al, 2005;Vladescu et al, 2005;Williams et al, 2006;Rocha et al, 2007). The specific interactions between biological molecules have been directly measured at the single-molecule level, providing information of energy landscape during bond rupture event (Merkel et al, 1999;Marshall et al, 2003;Ratto et al, 2004;Morfill et al, 2007a;Mayyas et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Direct force measurement of single DNA–peptide interactions using atomic force microscopy

Chung¹,

Shin

Kwak³

et al. 2013

J of Molecular Recognition

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The selective interactions between DNA and miniature (39 residues) engineered peptide were directly measured at the single-molecule level by using atomic force microscopy. This peptide (p007) contains an α-helical recognition site similar to leucine zipper GCN4 and specifically recognizes the ATGAC sequence in the DNA with nanomolar affinity. The average rupture force was 42.1 pN, which is similar to the unbinding forces of the digoxigenin-antidigoxigenin complex, one of the strongest interactions in biological systems. The single linear fit of the rupture forces versus the logarithm of pulling rates showed a single energy barrier with a transition state located at 0.74 nm from the bound state. The smaller koff compared with that of other similar systems was presumably due to the increased stability of the helical structure by putative folding residues in p007. This strong sequence-specific DNA-peptide interaction has a potential to be utilized to prepare well-defined mechanically stable DNA-protein hybrid nanostructures.

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“…AFM-FS (Stroh et al, 2004;Hinterdorfer and Dufrene 2006;Tang et al, 2007;Dufrene and Hinterdorfer 2008;Takahashi et al, 2009) is crucial due to its wide range of applications (Mayyas et al, 2010). Other than determining the binding kinetics and interaction forces, AFM-FS has also been utilized to understand the unfolding and folding of nucleic acids with multiple repeated units and single proteins, as well as to study molecule-material interface and molecule-molecule interactions.…”

Section: Understanding the Binding Dynamics Between The Targeted Receptor And Drug Delivery Vehiclementioning

confidence: 99%

“…AFM-FS has also been helpful to understand the cellular mechanics. Quantitative analysis and detection have also been possible using AFM-SMFS techniques (Mayyas et al, 2010). Polyproteins were first investigated by the Dougan group (Hughes and Dougan 2016) using AFM-SMFS techniques (employing both force-clamp and force-extension modes).…”

Section: Understanding the Binding Dynamics Between The Targeted Receptor And Drug Delivery Vehiclementioning

confidence: 99%

Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review

Sarkar

2022

Front. Nanotechnol.

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Since its invention, atomic force microscopy (AFM) has come forth as a powerful member of the “scanning probe microscopy” (SPM) family and an unparallel platform for high-resolution imaging and characterization for inorganic and organic samples, especially biomolecules, biosensors, proteins, DNA, and live cells. AFM characterizes any sample by measuring interaction force between the AFM cantilever tip (the probe) and the sample surface, and it is advantageous over other SPM and electron micron microscopy techniques as it can visualize and characterize samples in liquid, ambient air, and vacuum. Therefore, it permits visualization of three-dimensional surface profiles of biological specimens in the near-physiological environment without sacrificing their native structures and functions and without using laborious sample preparation protocols such as freeze-drying, staining, metal coating, staining, or labeling. Biosensors are devices comprising a biological or biologically extracted material (assimilated in a physicochemical transducer) that are utilized to yield electronic signal proportional to the specific analyte concentration. These devices utilize particular biochemical reactions moderated by isolated tissues, enzymes, organelles, and immune system for detecting chemical compounds via thermal, optical, or electrical signals. Other than performing high-resolution imaging and nanomechanical characterization (e.g., determining Young’s modulus, adhesion, and deformation) of biosensors, AFM cantilever (with a ligand functionalized tip) can be transformed into a biosensor (microcantilever-based biosensors) to probe interactions with a particular receptors of choice on live cells at a single-molecule level (using AFM-based single-molecule force spectroscopy techniques) and determine interaction forces and binding kinetics of ligand receptor interactions. Targeted drug delivery systems or vehicles composed of nanoparticles are crucial in novel therapeutics. These systems leverage the idea of targeted delivery of the drug to the desired locations to reduce side effects. AFM is becoming an extremely useful tool in figuring out the topographical and nanomechanical properties of these nanoparticles and other drug delivery carriers. AFM also helps determine binding probabilities and interaction forces of these drug delivery carriers with the targeted receptors and choose the better agent for drug delivery vehicle by introducing competitive binding. In this review, we summarize contributions made by us and other researchers so far that showcase AFM as biosensors, to characterize other sensors, to improve drug delivery approaches, and to discuss future possibilities.

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Dissociation Kinetics of an Enzyme−Inhibitor System Using Single-Molecule Force Measurements

Cited by 9 publications

References 30 publications

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

How Do We Know when Single-Molecule Force Spectroscopy Really Tests Single Bonds?

Direct force measurement of single DNA–peptide interactions using atomic force microscopy

Biosensing, Characterization of Biosensors, and Improved Drug Delivery Approaches Using Atomic Force Microscopy: A Review

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