Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy

Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the i...

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Published in	Nature protocols Vol. 8; no. 7; pp. 1261 - 1276
Main Authors	Popa, Ionel, Kosuri, Pallav, Alegre-Cebollada, Jorge, Garcia-Manyes, Sergi, Fernandez, Julio M
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 01.07.2013 Nature Publishing Group
Subjects	631/1647/527 631/45/612 631/57/2265 Analysis Analytical Chemistry Atomic spectroscopy Biochemistry Biological Techniques Calibration Chemical bonds Chemical kinetics Chemical reactions Computational Biology/Bioinformatics Data acquisition Disulfides - chemistry Equipment Design Experiments Intermolecular forces Kinetics Life Sciences Microarrays Microscopy, Atomic Force - instrumentation Microscopy, Atomic Force - methods Organic Chemistry Polyproteins Protein denaturation Protein folding Protein Unfolding Proteins Protocol Reaction kinetics Spectroscopy Spectrum analysis Substrates United States United Kingdom > UK
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Abstract	Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique.
AbstractList	Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique. Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique.Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used to control the exposure of reactive sites in a single polyprotein substrate composed of repeated domains. The use of polyproteins allows the identification of successful single-molecule recordings from unambiguous mechanical unfolding fingerprints. Biochemical reactions are then measured directly by detecting the length changes of the substrate held at a constant force. We present the layout of a force-clamp spectrometer along with protocols to design and conduct experiments. These experiments measure reaction kinetics as a function of applied force. We show sample data of the force dependency of two different reactions, protein unfolding and disulfide reduction. These data, which can be acquired in just a few days, reveal mechanistic details of the reactions that currently cannot be resolved by any other technique.
Audience	Academic
Author	Garcia-Manyes, Sergi Popa, Ionel Kosuri, Pallav Fernandez, Julio M Alegre-Cebollada, Jorge
AuthorAffiliation	1 Department of Biological Sciences, Columbia University, New York, NY, 10027, USA 2 Department of Physics & Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK
AuthorAffiliation_xml	– name: 2 Department of Physics & Randall Division of Cell and Molecular Biophysics, King’s College London, WC2R 2LS London, UK – name: 1 Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
Author_xml	– sequence: 1 givenname: Ionel surname: Popa fullname: Popa, Ionel email: ivp2105@columbia.edu organization: Department of Biological Sciences, Columbia University – sequence: 2 givenname: Pallav surname: Kosuri fullname: Kosuri, Pallav email: pallav@caa.columbia.edu organization: Department of Biological Sciences, Columbia University – sequence: 3 givenname: Jorge surname: Alegre-Cebollada fullname: Alegre-Cebollada, Jorge organization: Department of Biological Sciences, Columbia University – sequence: 4 givenname: Sergi surname: Garcia-Manyes fullname: Garcia-Manyes, Sergi organization: Department of Physics, King's College London, Randall Division of Cell and Molecular Biophysics, King's College London – sequence: 5 givenname: Julio M surname: Fernandez fullname: Fernandez, Julio M email: jf2120@columbia.edu organization: Department of Biological Sciences, Columbia University
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/23744288$$D View this record in MEDLINE/PubMed
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Snippet	Here we describe a protocol for using force-clamp spectroscopy to precisely quantify the effect of force on biochemical reactions. A calibrated force is used...
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SubjectTerms	631/1647/527 631/45/612 631/57/2265 Analysis Analytical Chemistry Atomic spectroscopy Biochemistry Biological Techniques Calibration Chemical bonds Chemical kinetics Chemical reactions Computational Biology/Bioinformatics Data acquisition Disulfides - chemistry Equipment Design Experiments Intermolecular forces Kinetics Life Sciences Microarrays Microscopy, Atomic Force - instrumentation Microscopy, Atomic Force - methods Organic Chemistry Polyproteins Protein denaturation Protein folding Protein Unfolding Proteins Protocol Reaction kinetics Spectroscopy Spectrum analysis Substrates
Title	Force dependency of biochemical reactions measured by single-molecule force-clamp spectroscopy
URI	https://link.springer.com/article/10.1038/nprot.2013.056 https://www.ncbi.nlm.nih.gov/pubmed/23744288 https://www.proquest.com/docview/1366007832 https://www.proquest.com/docview/2564325216 https://www.proquest.com/docview/1365991337 https://pubmed.ncbi.nlm.nih.gov/PMC4676941
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