Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils

Chemical Science
Mike C GrothFranziska Thomas

Abstract

Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants (KD) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-A x B y and the newly characterized C-A x B y . Both comprise KD values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a compe...Continue Reading

References

Sep 8, 1995·Journal of Molecular Biology·S WalterF X Schmid
Oct 24, 1997·Nature·K SeverinM R Ghadiri
Oct 1, 1993·Current Biology : CB·E K O'SheaP S Kim
Dec 20, 2005·Journal of Molecular Biology·Gevorg Grigoryan, Amy E Keating
Jul 31, 2007·Journal of the American Chemical Society·Shannon J Ryan, Alan J Kennan
Feb 23, 1996·Science·K J Lumb, P S Kim
Jan 4, 2008·Journal of the American Chemical Society·Maria L Diss, Alan J Kennan
Jan 24, 2008·Angewandte Chemie·Zheng-Zheng HuangM Reza Ghadiri
Jun 7, 2008·ACS Chemical Biology·Yoshiaki YanoKatsumi Matsuzaki
Feb 18, 2009·Angewandte Chemie·Hana Robson MarsdenAlexander Kros
Jun 23, 2009·Nature Materials·Eleanor F BanwellDerek N Woolfson
Dec 17, 2009·Analytical Biochemistry·Cyril BoucherYves Durocher
Apr 28, 2010·Journal of the American Chemical Society·Brian V Popp, Zachary T Ball
May 18, 2010·Angewandte Chemie·Hana Robson Marsden, Alexander Kros
Jan 15, 2011·Journal of Peptide Science : an Official Publication of the European Peptide Society·Helena Gradišar, Roman Jerala
Mar 5, 2011·Chemical Society Reviews·Aimee L Boyle, Derek N Woolfson
Jul 21, 2011·Chemical Communications : Chem Comm·Karsten MeyenbergUlf Diederichsen
Aug 25, 2012·Journal of the American Chemical Society·Aimee L BoyleDerek N Woolfson
Apr 13, 2013·Science·Jordan M FletcherDerek N Woolfson
Apr 30, 2013·Nature Chemical Biology·Helena GradišarRoman Jerala
May 9, 2013·ACS Synthetic Biology·Jordan M FletcherDerek N Woolfson
Sep 14, 2013·Journal of the American Chemical Society·Chunfu XuVincent P Conticello
Nov 26, 2013·Trends in Biotechnology·George A KhouryChristodoulos A Floudas
Oct 30, 2014·Chemistry : a European Journal·Zehavit DadonGonen Ashkenasy
Jun 21, 2015·Current Opinion in Structural Biology·Derek N WoolfsonChristopher W Wood
Jul 29, 2015·Journal of the American Chemical Society·Natasha C BurgessDerek N Woolfson
Aug 20, 2015·Biopolymers·Yoshiaki YanoKatsumi Matsuzaki
Dec 15, 2015·Angewandte Chemie·Franziska ThomasDerek N Woolfson
Nov 26, 2016·Trends in Biochemical Sciences·Andrei N Lupas, Jens Bassler
Dec 28, 2016·ACS Chemical Biology·Jordan M FletcherDerek N Woolfson

❮ Previous
Next ❯

Citations

Aug 10, 2018·Chemistry : a European Journal·W Mathis Rink, Franziska Thomas
Nov 10, 2018·Angewandte Chemie·Carolin Mueller, Tom N Grossmann
Aug 20, 2019·Biochemical and Biophysical Research Communications·Zoheb AhmedKrishanu Ray
Apr 14, 2021·Cell·Zibo Chen, Michael B Elowitz

❮ Previous
Next ❯

Methods Mentioned

BETA
protein folding
circular dichroism
FRET

Software Mentioned

FitDis
OriginPro
DynaFit

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.