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Originally published as Biophys J. BioFAST on February 24, 2006.
doi:10.1529/biophysj.105.076224
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Biophysical Journal 90:3806-3812 (2006)
© 2006 The Biophysical Society

Sub-Angstrom Conformational Changes of a Single Molecule Captured by AFM Variance Analysis

Kirstin A. Walther * {dagger}, Jasna Brujic {dagger}, Hongbin Li {ddagger} and Julio M. Fernández {dagger}

* Department of Physics, {dagger} Department of Biological Sciences, Columbia University, New York, New York; and {ddagger} Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada

Correspondence: Address reprint requests to J. M. Fernández, E-mail: jfernandez{at}columbia.edu.

A system's equilibrium variance can be analyzed to probe its underlying dynamics at higher resolution. Here, using single-molecule atomic-force microscope techniques, we show how the variance in the length of a single dextran molecule can be used to establish thermodynamic equilibrium and to detect conformational changes not directly observable with other methods. Dextran is comprised of a chain of pyranose rings that each undergoes an Angstrom-scale transition from a chair to boat conformation under a stretching force. Our analysis of the variance of the molecule's fluctuations verifies equilibrium throughout the force-extension curve, consistent with the expected thermodynamic ensemble. This validates further analysis of the variance in the transition region, which reveals an intermediate conformation between the chair and the boat on the sub-Angstrom scale. Our test of thermal equilibrium as well as our variance analysis can be readily extended to a wide variety of molecules, including proteins.




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