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Methods and error estimations of uncertainties in single-molecule dynamic force spectroscopy
Umeå University, Faculty of Science and Technology, Department of Physics. (Optical Tweezers Center)
Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics. (Optical Tweezers Center)ORCID iD: 0000-0002-9031-4331
2009 (English)In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 38, no 7, 911-922 p.Article in journal (Refereed) Published
Abstract [en]

In dynamic force spectroscopy, access to the characteristic parameters of single molecular bonds requires non-trivial measurements and data processing as the rupture forces are found not only to be distributed over a wide range, but are also dependent on the loading rate. The choice of measurement procedure and data processing methods has a considerable impact on the accuracy and precision of the final results. We analyse, by means of numerical simulations, methods to minimize and assess the magnitude of the expected errors for different combinations of experimental and evaluation methods. It was found that the choice of fitting function is crucial to extract correct parameter values. Applying a Gaussian function, which is a common practice, is equivalent to introducing a systematic error, and leads to a consequent overestimation of the thermal off-rate by more than 30%. We found that the precision of the bond length and the thermal off-rate, in presence of unbiased noise, were improved by reducing the number of loading rates for a given number of measurements. Finally, the results suggest that the minimum number of measurements needed to obtain the bond strength, with acceptable precision, exceeds the common number of ~100 reported in literature.


Place, publisher, year, edition, pages
2009. Vol. 38, no 7, 911-922 p.
Keyword [en]
Specific Binding, DFS, Receptor-ligand, Error Propagation, Bond Length, Thermal off-rate, Monte Carlo Simulation
National Category
Other Physics Topics
Research subject
URN: urn:nbn:se:umu:diva-21485DOI: 10.1007/s00249-009-0471-8ISI: 000269055500009OAI: diva2:211324
Available from: 2009-04-14 Created: 2009-04-14 Last updated: 2016-05-27Bibliographically approved
In thesis
1. A study of bacterial adhesion on a single-cell level by means of force measuring optical tweezers and simulations
Open this publication in new window or tab >>A study of bacterial adhesion on a single-cell level by means of force measuring optical tweezers and simulations
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The intriguing world of microbiology is nowadays accessible for detailed exploration at a single–molecular level. Optical tweezers are a novel instrument that allows for non–invasive manipulation of single cells by the sole use of laser light and operates on the nano– and micrometer scale which corresponds to the same length scale as living cells. Moreover, forces within the field of microbiology are typically in the picoNewton range which is in accordance with the capability of force measuring optical tweezers systems. Both these conformabilities imply that force measuring optical tweezers is suitable for studies of single living cells. This thesis focuses on the mechanisms of bacterial attachments to host cells which constitute the first step in bacterial infection processes. Bacteria bind specifically to host receptors by means of adhesins that are expressed either directly on the bacterial membrane or on micrometer–long adhesion organelles that are called pili. The properties of single adhesin–receptor bonds that mediate adherence of the bacterium Helicobacter pylori are first examined at various acidities. Further on, biomechanical properties of P pili expressed by Escherichia coli are presented to which computer simulations, that capture the complex kinetics of the pili structure and precisely replicate measured data, are applied. Simulations are found to be a powerful tool for investigations of adhesive attributes of binding systems and are utilized in the analyses of the specific binding properties of P pili on a single–pilus level. However, bacterial binding systems generally involve a multitude of adhesin–receptor bonds. To explore bacterial attachments, the knowledge from single–pilus studies is brought into a full multipili attachment scenario which is analyzed by means of theoretical treatments and simulations. The results are remarkable in several aspects. Not only is it found that the intrinsic properties of P pili are composed in an optimal combination to promote strong multipili bindings. The properties of the pili structure itself are also found to be optimized with respect to its in vivo environment. Indeed, the true meaning of the attributes derived at a single–pilus level cannot be unraveled until a multipili–binding system is considered. Whereas detailed studies are presented for the helix–like P pili expressed by Gram–negative Escherichia coli, conceptual studies are presented for the open coil–like T4 pili expressed by Gram–positive Streptococcus pneumoniae. The structural and adhesive properties of these two types of pili differ considerably. These dissimilarities have far–reaching consequences on the adhesion possibilities at both single–pilus and multipili levels which are discussed qualitatively. Moreover, error analyses of conventional data processing methods in dynamic force spectroscopy as well as development of novel analysis methods are presented. These findings provide better understanding of how to perform refined force measurements on single adhesion organelles as well as how to improve the analyses of measurement data to obtain accurate parameter values of biomechanical entities. In conclusion, this thesis comprises a study of bacterial adhesion organelles and the way they cooperate to establish efficient attachment systems that can successfully withstand strong external forces that acts upon bacteria. Such systems can resist, for instance, rinsing effects and thereby allow bacteria to colonize their host. By understanding the complexity, and thereby possible weaknesses, of bacterial attachments, new targets for combating bacterial infections can be identified.

Place, publisher, year, edition, pages
Umeå: Print & Media, 2009. 108 p.
National Category
Physical Sciences
Research subject
Physics; cellforskning; Molecular Cellbiology
urn:nbn:se:umu:diva-21493 (URN)978-91-7264-765-7 (ISBN)
Public defence
2009-05-08, N420, Naturvetarhuset, Umeå Universitet, Umeå, 10:00 (English)
Available from: 2009-04-17 Created: 2009-04-14 Last updated: 2009-04-17Bibliographically approved

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Björnham, OscarSchedin, Staffan
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