Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers

Biophysical Journal
Aleksander A RebaneYongli Zhang

Abstract

Optical tweezers (OTs) measure the force-dependent time-resolved extension of a single macromolecule tethered between two trapped beads. From this measurement, it is possible to determine the folding intermediates, energies, and kinetics of the macromolecule. Previous data analysis generally has used the extension as a reaction coordinate to characterize the observed folding transitions. Despite its convenience, the extension poorly describes folding in the absence of force. Here, we chose the contour length of the unfolded polypeptide as a reaction coordinate and modeled the extensions of protein structures along their predicted folding pathways based on high-resolution structures of the proteins in their native states. We included the extension in our model to calculate the total extensions, energies, and transition rates of the proteins as a function of force. We fit these calculations to the corresponding experimental measurements and obtained the best-fit conformations and energies of proteins in different folding states. We applied our method to analyze single-molecule trajectories of two representative protein complexes responsible for membrane fusion, the HIV-1 glycoprotein 41 and the synaptic SNARE proteins, which invo...Continue Reading

References

Sep 9, 1994·Science·C BustamanteS Smith
Nov 14, 1996·Nature·B L Sabatini, W G Regehr
Dec 23, 1998·Proceedings of the National Academy of Sciences of the United States of America·D FasshauerR Jahn
Mar 7, 2001·Science·M J RootP S Kim
Apr 28, 2001·Science·J LiphardtC Bustamante
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Brent D Brower-TolandMichelle D Wang
Mar 13, 2003·Molecular Biology of the Cell·Ruben M MarkosyanGrigory B Melikyan
May 9, 2003·Nature·Wei Yuan Yang, Martin Gruebele
Jun 28, 2003·Biophysical Journal·Gerhard Hummer, Attila Szabo
Apr 23, 2004·Current Opinion in Structural Biology·Jan KubelkaWilliam A Eaton
Jun 11, 2004·Annual Review of Biochemistry·Carlos BustamanteDavid Izhaky
Nov 15, 2005·Nature·Elio A AbbondanzieriSteven M Block
Mar 9, 2006·The Journal of Biological Chemistry·Joshua M LauerPhyllis I Hanson
Apr 12, 2006·Physical Review Letters·Olga K DudkoAttila Szabo
Jun 6, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey R MoffittCarlos Bustamante
Jun 13, 2006·Biophysical Journal·Sean A McKinneyTaekjip Ha
Jan 5, 2008·Science·William J GreenleafSteven M Block
Jan 10, 2008·European Biophysics Journal : EBJ·Ciro CecconiCarlos Bustamante
Mar 1, 2008·Annual Review of Biochemistry·Jeffrey R MoffittCarlos Bustamante
Jul 4, 2008·Nature Structural & Molecular Biology·Stephen C Harrison
Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Changbong HyeonD Thirumalai
Jan 24, 2009·Science·Thomas C Südhof, James E Rothman
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·J Christof M GebhardtMatthias Rief
May 25, 2010·Nature·Elizabeth A ShankCarlos Bustamante
Feb 22, 2011·Nature Methods·Matthew J ComstockYann R Chemla
Jun 16, 2011·Methods in Molecular Biology·Ciro CecconiCarlos Bustamante
Jun 29, 2011·Journal of the American Chemical Society·Ying GaoYongli Zhang
Jul 20, 2011·The Journal of Biological Chemistry·Ionel PopaSergi Garcia-Manyes
Oct 29, 2011·Science·Johannes StiglerMatthias Rief
Mar 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hao YuMichael T Woodside
Mar 28, 2012·Proceedings of the National Academy of Sciences of the United States of America·Zhiqun XiYongli Zhang
Jul 4, 2012·Proceedings of the National Academy of Sciences of the United States of America·Johannes Stigler, Matthias Rief
Aug 22, 2012·Proceedings of the National Academy of Sciences of the United States of America·Hao YuMichael T Woodside
Sep 26, 2012·Journal of the American Chemical Society·Pétur O HeidarssonCiro Cecconi
Oct 2, 2012·The Review of Scientific Instruments·George SirinakisYongli Zhang
Oct 16, 2012·Biophysical Journal·Phillip J ElmsSusan Marqusee
Mar 15, 2013·Proceedings of the National Academy of Sciences of the United States of America·Michael HinczewskiD Thirumalai

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Citations

Dec 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·Xinming ZhangYongli Zhang
Jan 18, 2017·Protein Science : a Publication of the Protein Society·Yongli Zhang
Sep 11, 2019·Journal of the Optical Society of America. A, Optics, Image Science, and Vision·Hassan Sobhani, Elham Dadar
Jan 1, 2020·Proceedings of the National Academy of Sciences of the United States of America·Tong ShuYongli Zhang
Nov 23, 2020·FEBS Letters·Ramalingam Venkat Kalyana SundaramShyam S Krishnakumar
Apr 8, 2021·Annual Review of Biochemistry·Yongli Zhang, Frederick M Hughson
Oct 21, 2020·Biophysical Journal·Punam SonarCiro Cecconi
Dec 18, 2021·Nature Chemical Biology·Jinghua GeYongli Zhang

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