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

The Review of Scientific Instruments
Vicente I FernandezJulio M Fernandez

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 ...Continue Reading

References

Sep 9, 1994·Science·C BustamanteS Smith
Mar 3, 1986·Physical Review Letters·G BinnigC Gerber
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·M Carrion-VazquezJ M Fernandez
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·M Carrion-VazquezJ M Fernandez
Aug 29, 2002·Nature·Hongbin LiJulio M Fernandez
Aug 19, 2003·Nature Structural Biology·Mariano Carrion-VazquezJulio M Fernandez
May 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Michael SchlierfJulio M Fernandez
Aug 15, 2006·Biophysical Journal·Lorin S MilescuFrederick Sachs
Oct 10, 2006·Biophysical Journal·Sri Rama Koti AinavarapuJulio M Fernandez
May 2, 2007·Proceedings of the National Academy of Sciences of the United States of America·Kirstin A WaltherJulio M Fernandez

❮ Previous
Next ❯

Citations

Dec 26, 2015·The Journal of Biological Chemistry·Sergi Garcia-ManyesJulio M Fernández
Jan 1, 2010·Multiscale Modeling & Simulation : a SIAM Interdisciplinary Journal·Christopher P CalderonDanny C Sorensen

❮ Previous
Next ❯

Methods Mentioned

BETA
atomic force microscopy
AFM
surface microscopy
size-exclusion chromatography
optical tweezers

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2022 Meta ULC. All rights reserved