Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding

The Journal of Physical Chemistry. B
Guangfeng Zhou, Vincent A Voelz

Abstract

Salt-bridge interactions play an important role in stabilizing many protein structures, and have been shown to be designable features for protein design. In this work, we study the effects of non-native salt bridges on the folding of a soluble alanine-based peptide (Fs peptide) using extensive all-atom molecular dynamics simulations performed on the Folding@home distributed computing platform. Using Markov State Models, we show how non-native salt-bridges affect the folding kinetics of Fs peptide by perturbing specific conformational states. Furthermore, we present methods for the automatic detection and analysis of such states. These results provide insight into helix folding mechanisms and useful information to guide simulation-based computational protein design.

References

Dec 20, 1990·Journal of Molecular Biology·A HorovitzA R Fersht
Jul 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·S MarquseeR L Baldwin
Dec 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·S Marqusee, R L Baldwin
Feb 1, 1994·Protein Science : a Publication of the Protein Society·Z S Hendsch, B Tidor
Jan 1, 1993·Protein Science : a Publication of the Protein Society·B M Huyghues-DespointesR L Baldwin
Feb 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Angel E García, Kevin Y Sanbonmatsu
Jan 25, 2005·Biophysical Journal·Eric J Sorin, Vijay S Pande
Jul 16, 2005·Proteins·James N Sarakatsannis, Yong Duan
Mar 9, 2006·Journal of the American Chemical Society·Burcu AnilDaniel P Raleigh
Dec 21, 2006·Journal of the American Chemical Society·Jae-Hyun Cho, Daniel P Raleigh
Aug 31, 2007·Science·M Shirts, V S Pande
Feb 1, 2008·The Journal of Physical Chemistry. B·Nicolae-Viorel Buchete, Gerhard Hummer
Sep 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·Sivaraj SivaramakrishnanJames A Spudich
Feb 5, 2009·Journal of Computational Chemistry·Mark S FriedrichsVijay S Pande
Feb 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Alexey V GribenkoGeorge I Makhatadze
Nov 6, 2009·Proceedings of the National Academy of Sciences of the United States of America·Frank NoéThomas R Weikl
Jan 15, 2010·Journal of the American Chemical Society·Vincent A VoelzVijay S Pande
Jul 30, 2010·Protein Science : a Publication of the Protein Society·Ruth F SommeseJames A Spudich
Aug 3, 2010·Journal of Molecular Graphics & Modelling·John E StoneKlaus Schulten
Aug 18, 2010·Angewandte Chemie·Da-Wei Li, Rafael Brüschweiler
Feb 3, 2011·Proteins·Jason E DonaldWilliam F DeGrado
May 10, 2011·The Journal of Chemical Physics·Jan-Hendrik PrinzFrank Noé
Dec 1, 1998·Environmental Science & Technology·F Formation
Nov 30, 2011·Journal of Chemical Theory and Computation·Kyle A BeauchampVijay S Pande
Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Basir AhmadLisa J Lapidus
Jul 4, 2012·Journal of Chemical Theory and Computation·Kyle A BeauchampVijay S Pande
Jan 1, 2010·Journal of Chemical Theory and Computation·Gregory R BowmanVijay S Pande
May 10, 2013·The Journal of Chemical Physics·Yuan YaoXuhui Huang
Jun 12, 2013·Journal of Chemical Theory and Computation·Christian R Schwantes, Vijay S Pande
Jul 5, 2013·The Journal of Chemical Physics·Guillermo Pérez-HernándezFrank Noé
Oct 5, 2013·The Journal of Chemical Physics·Gregory R BowmanXuhui Huang
Oct 12, 2013·Physical Chemistry Chemical Physics : PCCP·Xi ZhangHajime Hirao
Mar 19, 2014·The Journal of Physical Chemistry Letters·Heleen MeuzelaarSander Woutersen
Apr 24, 2014·Journal of Chemical Information and Modeling·Asghar M RazaviVincent A Voelz
May 20, 2014·Current Opinion in Structural Biology·John D Chodera, Frank Noé
Aug 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Jae-Hyun ChoDaniel P Raleigh
Nov 21, 2014·Physical Chemistry Chemical Physics : PCCP·Martin VolkGodfrey S Beddard
Jan 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Franco O TzulGeorge I Makhatadze
Mar 6, 2015·The Journal of Physical Chemistry. B·Julius C F SchulzR R Netz

❮ Previous
Next ❯

Citations

Jun 15, 2017·Journal of Chemical Information and Modeling·Yunhui GeVincent A Voelz
Aug 24, 2017·Biophysical Journal·Guangfeng ZhouVincent A Voelz
Jan 2, 2018·Structure·Giulia MorraGeorge Khelashvili
Dec 19, 2017·Journal of Chemical Theory and Computation·Brooke E HusicVijay S Pande
Dec 14, 2016·Journal of Chemical Theory and Computation·Hongbin WanVincent A Voelz
Jan 30, 2019·The Journal of Physical Chemistry. B·Arusha AcharyyaFeng Gai

❮ 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.