Experiments and comprehensive simulations of the formation of a helical turn.

The Journal of Physical Chemistry. B
Gouri S JasRon Elber

Abstract

We investigate the kinetics and thermodynamics of a helical turn formation in the peptide Ac-WAAAH-NH(2). NMR measurements indicate that this peptide has significant tendency to form a structure of a helical turn, while temperature dependent CD establishes the helix fraction at different temperatures. Molecular dynamics and milestoning simulations agree with experimental observables and suggest an atomically detailed picture for the turn formation. Using a network representation, two alternative mechanisms of folding are identified: (i) a direct co-operative mechanism from the unfolded to the folded state without intermediate formation of hydrogen bonds and (ii) an indirect mechanism with structural intermediates with two residues in a helical conformation. This picture is consistent with kinetic measurements that reveal two experimental time scales of sub-nanosecond and several nanoseconds.

References

Jan 1, 1992·Annual Review of Biophysics and Biomolecular Structure·J M Scholtz, R L Baldwin
Feb 20, 1992·Journal of Molecular Biology·V Daggett, M Levitt
Jan 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R ZwanzigB Bagchi
Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Apr 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·A BierzynskiR L Baldwin
Jan 1, 1983·Annual Review of Biophysics and Bioengineering·N Go
Jun 23, 1999·Proceedings of the National Academy of Sciences of the United States of America·D T ClarkeG R Jones
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·W A EatonJ Hofrichter
Sep 8, 2000·Physical Review Letters·G HummerS Garde
Jun 9, 2004·Journal of Molecular Biology·Yaakov LevyPeter G Wolynes
Jul 9, 2004·Biophysical Journal·Wei Yuan Yang, Martin Gruebele
Jul 23, 2004·The Journal of Chemical Physics·Anton K Faradjian, Ron Elber
Jul 23, 2004·The Journal of Chemical Physics·Daniele MoroniTitus S van Erp
Jan 25, 2005·Biophysical Journal·Eric J Sorin, Vijay S Pande
Jul 21, 2006·The Journal of Physical Chemistry. B·Ao Ma, Aaron R Dinner
Sep 1, 2006·The Journal of Chemical Physics·Baron Peters, Bernhardt L Trout
Apr 21, 2007·The Journal of Chemical Physics·Anthony M A WestDavid Shalloway
Jul 28, 2007·The Journal of Chemical Physics·Baron PetersBernhardt L Trout
Feb 1, 2008·The Journal of Physical Chemistry. B·Nicolae-Viorel Buchete, Gerhard Hummer
Nov 13, 2008·Annual Review of Physical Chemistry·Weinan E, Eric Vanden-Eijnden
Dec 3, 2008·The Journal of Chemical Physics·Eric Vanden-EijndenRon Elber
Apr 10, 2009·The Journal of Physical Chemistry. a·Krzysztof KuczeraRon Elber
Apr 22, 2009·Angewandte Chemie·Omar F MohammedAhmed H Zewail
May 27, 2009·The Journal of Chemical Physics·Eric Vanden-Eijnden, Maddalena Venturoli
Nov 6, 2009·Proceedings of the National Academy of Sciences of the United States of America·Frank NoéThomas R Weikl
Mar 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ron Elber, Anthony West
Jul 3, 2010·Journal of Chemical Theory and Computation·Peter Májek, Ron Elber
Nov 10, 2010·The Journal of Physical Chemistry. a·Wendy A HegefeldGouri S Jas
Apr 13, 2011·Journal of the American Chemical Society·David De Sancho, Robert B Best
Apr 20, 2011·The Journal of Physical Chemistry. a·Serdal Kirmizialtin, Ron Elber
Jun 7, 2011·The Journal of Chemical Physics·Christof SchütteEric Vanden-Eijnden
Sep 29, 2011·Proceedings of the National Academy of Sciences of the United States of America·Milo M LinAhmed H Zewail
Oct 28, 2011·The Journal of Chemical Physics·Wolfgang LechnerPeter G Bolhuis
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl

❮ Previous
Next ❯

Citations

Apr 5, 2012·The Journal of Physical Chemistry. B·Steven M KreuzerTess J Moon
Apr 26, 2013·The Journal of Chemical Physics·Alexander T Hawk
Oct 5, 2013·The Journal of Chemical Physics·Steven M KreuzerRon Elber
Nov 12, 2013·The Journal of Chemical Physics·Shruthi ViswanathRon Elber
Aug 12, 2014·The Journal of Chemical Physics·Alfredo E Cardenas, Ron Elber
Mar 10, 2015·The Journal of Chemical Physics·Juan M Bello-Rivas, Ron Elber
Sep 10, 2013·Journal of Chemical Theory and Computation·Di Pierro Michele, Elber Ron
Jun 5, 2014·The Journal of Physical Chemistry. B·Gouri S JasKrzysztof Kuczera
Apr 20, 2013·The Journal of Physical Chemistry. B·Panagiota S Georgoulia, Nicholas M Glykos
Oct 27, 2016·The Journal of Chemical Physics·Ferruccio PalazzesiMichele Parrinello
Aug 13, 2015·Journal of Computational Chemistry·Juan M Bello-Rivas, Ron Elber
May 31, 2016·Multiscale Modeling & Simulation : a SIAM Interdisciplinary Journal·David AristoffRon Elber

❮ Previous
Next ❯

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