Mechanical unfolding of a knotted protein unveils the kinetic and thermodynamic consequences of threading a polypeptide chain.

Scientific Reports
Maira RiveraMauricio Báez

Abstract

Knots are remarkable topological features in nature. The presence of knots in crystallographic structures of proteins have stimulated considerable research to determine the kinetic and thermodynamic consequences of threading a polypeptide chain. By mechanically manipulating MJ0366, a small single domain protein harboring a shallow trefoil knot, we allow the protein to refold from either the knotted or the unknotted denatured state to characterize the free energy profile associated to both folding pathways. By comparing the stability of the native state with reference to the knotted and unknotted denatured state we find that knotting the polypeptide chain of MJ0366 increase the folding energy barrier in a magnitude close to the energy cost of forming a knot randomly in the denatured state. These results support that a protein knot can be formed during a single cooperative step of folding but occurs at the expenses of a large increment on the free energy barrier.

References

Jun 1, 1984·Biophysical Journal·G I BellP Bongrand
Sep 9, 1994·Science·C BustamanteS Smith
Feb 9, 1996·Science·P CluzelF Caron
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Apr 24, 2002·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·G E Crooks
Mar 11, 2003·Methods in Enzymology·Steven B SmithCarlos Bustamante
Jan 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Hendrik Dietz, Matthias Rief
Apr 12, 2006·Physical Review Letters·Olga K DudkoAttila Szabo
Jun 22, 2006·Journal of Molecular Biology·Anna L Mallam, Sophie E Jackson
Dec 16, 2006·Journal of Molecular Biology·Anna L Mallam, Sophie E Jackson
Mar 21, 2007·Journal of Molecular Biology·Stefan WallinEugene I Shakhnovich
Sep 4, 2007·Journal of Molecular Biology·Neil P KingTodd O Yeates
Oct 15, 2008·Proceedings of the National Academy of Sciences of the United States of America·Olga K DudkoAttila Szabo
Feb 3, 2009·Biophysical Journal·Joachim Dzubiella
May 30, 2009·The FEBS Journal·Fredrik I AnderssonSophie E Jackson
Apr 16, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anna L MallamSophie E Jackson
Aug 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey K NoelJosé N Onuchic
Sep 23, 2010·Journal of the American Chemical Society·Joanna I SułkowskaMarek Cieplak
Nov 12, 2010·Proceedings of the National Academy of Sciences of the United States of America·Neil P KingTodd O Yeates
Dec 20, 2011·Nature Chemical Biology·Anna L Mallam, Sophie E Jackson
Jun 22, 2012·PLoS Computational Biology·Tatjana SkrbićPietro Faccioli
Jul 4, 2012·Proceedings of the National Academy of Sciences of the United States of America·Wenfei LiShoji Takada
Mar 21, 2013·Chemistry : a European Journal·Peng WangXin Sheng Zhao
Apr 5, 2013·PLoS Computational Biology·Silvio a BeccaraPietro Faccioli
Aug 6, 2014·Journal of the American Chemical Society·Chengzhi HeHongbin Li
Sep 23, 2014·Journal of Molecular Biology·Nicole C H Lim, Sophie E Jackson
Nov 2, 2014·Nucleic Acids Research·Michal JamrozJoanna I Sulkowska
Mar 6, 2015·The Journal of Physical Chemistry. B·Iren WangShang-Te Danny Hsu
Aug 4, 2015·The Journal of Chemical Physics·Mateusz Chwastyk, Marek Cieplak
Aug 21, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·P Dabrowski-TumanskiJ I Sulkowska
Aug 21, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Mateusz Chwastyk, Marek Cieplak
Sep 19, 2015·Computational and Structural Biotechnology Journal·Patrícia F N Faísca
Oct 20, 2015·Nature Chemical Biology·Duyoung MinTae-Young Yoon
Jun 25, 2016·Proceedings of the National Academy of Sciences of the United States of America·Fabian ZieglerMatthias Rief
Aug 17, 2016·Scientific Reports·Iren WangShang-Te Danny Hsu
Oct 11, 2016·Physical Chemistry Chemical Physics : PCCP·Miguel A SolerPatrícia F N Faísca
Oct 30, 2016·Current Opinion in Structural Biology·Sophie E JacksonCristian Micheletti
Nov 16, 2016·Biochemical and Biophysical Research Communications·Viswanathan ThiruselvamMondikalipudur Nanjappagounder Ponnuswamy
Feb 9, 2017·Protein Science : a Publication of the Protein Society·María Paz RamírezChristian A M Wilson
Mar 11, 2017·Proceedings of the National Academy of Sciences of the United States of America·Pawel Dabrowski-Tumanski, Joanna I Sulkowska
May 11, 2017·PloS One·Szymon Niewieczerzal, Joanna I Sulkowska

❮ Previous
Next ❯

Citations

Jun 11, 2021·Frontiers in Chemistry·Shang-Te Danny HsuHideo Iwaï
Jul 2, 2021·The Journal of Physical Chemistry. B·João N C Especial, Patrícia F N Faísca
Nov 13, 2021·Journal of Molecular Biology·Daniel Scholl, Ashok A Deniz

❮ Previous
Next ❯

Methods Mentioned

BETA
optical tweezers
circular dichroism
size exclusion chromatography
gel filtration
electrophoresis

Software Mentioned

pCLAMP
KnotPlot
VMD
SigmaPlot

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.

Related Papers

PloS One
Miguel A Soler, Patrícia F N Faísca
The Journal of Physical Chemistry. B
Iren WangShang-Te Danny Hsu
Proceedings of the National Academy of Sciences of the United States of America
Joanna I SułkowskaJosé N Onuchic
Proceedings of the National Academy of Sciences of the United States of America
Anna L MallamSophie E Jackson
© 2022 Meta ULC. All rights reserved