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Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations

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Abstract

Nanopore force spectroscopy (NFS) has emerged as a convenient method to characterize the behavior of single biomolecules and biomolecular assemblies under force. NFS has many advantages over conventional single molecule techniques, such as being label-free and high throughput; however, NFS lacks direct control over the force applied to the biomolecules and registers the conformational transitions induced by the force only indirectly, by monitoring changes in the ionic current passing through the pore. In this chapter, we describe how all-atom molecular dynamics simulations can complement NFS experiments by providing information inaccessible to experiment. The chapter illustrates applications of the molecular dynamics (MD) method to interpret the results of NFS measurements, characterize the forces involved and determine the microscopic origin of the observed phenomena. Important technical aspects of the method, as well as its pitfalls and limitations are briefly discussed.

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Acknowledgements

We gratefully acknowledge contributions from Gregory Sigalov, Binquan Luan, and the group of Gregory Timp. This work is supported by grants from the National Institutes of Health (R01-HG003713 and PHS 5 P41-RR05969) and the National Science Foundation (PHY0822613). The authors gladly acknowledge supercomputer time provided through TeraGrid resources by a Large Resources Allocation grant (MCA05S028).

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Authors and Affiliations

  1. Department of Physics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 1110 W Green Street Urbana, Urbana, IL, 61801, USA

    Aleksei Aksimentiev

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  1. Jeffrey Comer
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  2. Aleksei Aksimentiev
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Correspondence to Aleksei Aksimentiev .

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Editors and Affiliations

  1. Department of Electrical Engineering, Nanotechnology Research and Teaching Fac, University of Texas at Arlington, S. Cooper Street, Arlington, 76019-0119, Texas, USA

    Samir M. Iqbal

  2. Department of Electrical and Computer En, University of Illinois at Urbana-Champai, N. Wright Street 208, Urbana, 61820, Illinois, USA

    Rashid Bashir

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Comer, J., Aksimentiev, A. (2011). Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations. In: Iqbal, S., Bashir, R. (eds) Nanopores. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8252-0_14

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  • DOI: https://doi.org/10.1007/978-1-4419-8252-0_14

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