Monitoring the folding kinetics of a β-hairpin by time-resolved IR spectroscopy in silico

The Journal of Physical Chemistry. B
Isabella DaidoneAndrea Amadei

Abstract

Protein folding is one of the most fundamental problems in modern biochemistry. Time-resolved infrared (IR) spectroscopy in the amide I region is commonly used to monitor folding kinetics. However, associated atomic detail information on the folding mechanism requires simulations. In atomistic simulations structural order parameters are typically used to follow the folding process along the simulated trajectories. However, a rigorous test of the reliability of the mechanisms found in the simulations requires calculation of the time-dependent experimental observable, i.e., in the present case the IR signal in the amide I region. Here, we combine molecular dynamics simulation with a mixed quantum mechanics/molecular mechanics theoretical methodology, the Perturbed Matrix Method, in order to characterize the folding of a β-hairpin peptide, through modeling the time-dependence of the amide I IR signal. The kinetic and thermodynamic data (folding and unfolding rate constants, and equilibrium folded- and unfolded-state probabilities) obtained from the fit of the calculated signal are in good agreement with the available experimental data [Xu et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. To the best of our knowledge, this is the f...Continue Reading

References

Jan 1, 1986·Advances in Protein Chemistry·S Krimm, J Bandekar
Nov 5, 1997·Current Opinion in Structural Biology·R M Slayton, P A Anfinrud
May 24, 2001·Journal of Biomolecular NMR·C M SantiveriM A Jiménez
Jan 12, 2002·Current Opinion in Structural Biology·M T Zanni, R M Hochstrasser
Feb 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Cheng-Yen HuangFeng Gai
Apr 25, 2002·Annual Review of Physical Chemistry·Jiali Gao, Donald G Truhlar
May 29, 2003·Biophysical Journal·Shelia J ManessR Brian Dyer
Dec 11, 2003·Journal of the American Chemical Society·Yao XuFeng Gai
Jan 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew Moran, Shaul Mukamel
Jul 23, 2004·The Journal of Chemical Physics·Christopher M CheatumJasper Knoester
Jan 6, 2005·Journal of the American Chemical Society·Karin NienhausG Ulrich Nienhaus
Jan 6, 2005·Journal of the American Chemical Society·Joseph W BraunerRichard Mendelsohn
Feb 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jens BredenbeckPeter Hamm
Apr 21, 2005·Journal of the American Chemical Society·Seongheun Kim, Manho Lim
Dec 27, 2005·The Journal of Physical Chemistry. B·Petr Bour, Timothy A Keiderling
Jul 21, 2006·The Journal of Physical Chemistry. B·Seungsoo HahnMinhaeng Cho
Sep 1, 2006·The Journal of Chemical Physics·Thomas la Cour JansenJasper Knoester
Feb 9, 2007·The Journal of Chemical Physics·Jun-Ho ChoiMinhaeng Cho
Feb 9, 2007·The Journal of Chemical Physics·Adam W Smith, Andrei Tokmakoff
Mar 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Janne A IhalainenPeter Hamm
Aug 8, 2007·Journal of Molecular Biology·Sichun YangHerbert Levine
Dec 23, 2010·The Journal of Physical Chemistry. B·Eeva-Liisa KarjalainenAndreas Barth
Jun 23, 2011·Journal of the American Chemical Society·Laura Zanetti PolziIsabella Daidone
Sep 8, 2011·The Journal of Physical Chemistry. B·Laura Zanetti PolziAndrea Amadei
Mar 9, 2012·The Journal of Physical Chemistry. B·Laura Zanetti PolziAndrea Amadei
Sep 21, 2013·The Journal of Physical Chemistry. B·Laura Zanetti-PolziIsabella Daidone

❮ Previous
Next ❯

Citations

Sep 15, 2018·Physical Chemistry Chemical Physics : PCCP·Laura Zanetti-PolziAndrea Amadei
Sep 28, 2021·Journal of Biomolecular Structure & Dynamics·Gokul GovindPadmesh Anjukandi

❮ 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.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Stefano PianaDavid E Shaw
© 2021 Meta ULC. All rights reserved