Biomedical Engineering Reference
In-Depth Information
Chapter 14
Nanopore Force Spectroscopy: Insights
from Molecular Dynamics Simulations
Jeffrey Comer and Aleksei Aksimentiev
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, bymonitoring 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.
Keywords Molecular dynamics • Force spectroscopy • Computer simulation
• Nucleic acid • Restriction enzyme • Endonuclease • Protein-DNA recognition
• Electrostatic tweezers • DNA unzipping • DNA hairpin • Nanobiotechnology
• Biomolecular complex • Single-molecule analysis • Molecular rupture
14.1
Introduction
Single-molecule techniques have fomented a revolution in biology by allowing
precise measurements of the nanoscale processes that give rise to the qualities that
we ascribe to life - growth, motion, reproduction, assimilation of nutrients, etc.
Determination of the mechanical properties of biomolecules has been instrumental
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