Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments

Fernandez, VI; Kosuri, P; Parot, V.; Fernandez, JM

Abstract

Atomic force microscopy force spectroscopy has become a powerful biophysical technique for probing the dynamics of proteins at the single molecule level. Extending a polyprotein at constant velocity produces the now familiar sawtooth pattern force-length relationship. Customarily, manual fits of the wormlike chain (WLC) model of polymer elasticity to sawtooth pattern data have been used to measure the contour length L c of the protein as it unfolds one module at a time. The change in the value of L c measures the number of amino acids released by an unfolding protein and can be used as a precise locator of the unfolding transition state. However, manual WLC fits are slow and introduce inevitable operator-driven errors which reduce the accuracy of the L c estimates. Here we demonstrate an extended Kalman filter that provides operator-free real time estimates of L c from sawtooth pattern data. The filter design is based on a cantilever-protein arrangement modeled by a simple linear time-invariant cantilever model and by a nonlinear force-length relationship function for the protein. The resulting Kalman filter applied to sawtooth pattern data demonstrates its real time, operator-free ability to accurately measure L c. These results are a marked improvement over the earlier techniques and the procedure is easily extended or modified to accommodate further quantities of interest in force spectroscopy. © 2009 American Institute of Physics.

Más información

Título según WOS: Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments
Título según SCOPUS: Extended Kalman filter estimates the contour length of a protein in single molecule atomic force microscopy experiments
Título de la Revista: REVIEW OF SCIENTIFIC INSTRUMENTS
Volumen: 80
Número: 11
Editorial: AMER INST PHYSICS
Fecha de publicación: 2009
Idioma: English
URL: http://scitation.aip.org/content/aip/journal/rsi/80/11/10.1063/1.3252982
DOI:

10.1063/1.3252982

Notas: ISI, SCOPUS