Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement

The Journal of Physical Chemistry. B
Chenqian ChengTao Chen

Abstract

In vitro, kinetically significant non-native interactions have been identified experimentally during the folding of proteins Im7, Im9, and A39V/N53P/V55L Fyn SH3 domain. To understand the role of non-native interactions on the folding of some frustrated proteins in chaperone, we employed native-centric models with and without additional transferable, sequence-dependent non-native hydrophobic interactions to comparatively study the folding behaviors of the three proteins confined in spherical cages. Under purely repulsive confinement, as a decrease of cavity size, the non-native interactions increase, especially in the unfolded state, enhancing the roughness of the folding energy landscape. As a result, the increase in native stability for the three proteins by the model incorporated non-native interactions (db + MJ hϕ model) is much smaller than that by the purely native-centric model (desolvation-barrier (db) model); the acceleration of folding simulated by the db + MJ hϕ model is much slower than that via the db model; in particular, the folding rate of Im7 decreases when reducing the cavity size under zero-denaturant condition. The repulsive confinement can also promote formation of specific non-native contacts in the transi...Continue Reading

References

Sep 26, 1995·Proceedings of the National Academy of Sciences of the United States of America·T Kiefhaber
Feb 1, 1995·Current Opinion in Structural Biology·A R Fersht
Jun 6, 1995·Proceedings of the National Academy of Sciences of the United States of America·F J Corrales, A R Fersht
Mar 1, 1996·Proteins·H S Chan, K A Dill
Mar 27, 1999·Journal of Molecular Biology·M R Betancourt, D Thirumalai
Oct 3, 1999·Nature Structural Biology·M JacobF X Schmid
Apr 7, 2000·Advances in Protein Chemistry·O Bilsel, C R Matthews
Mar 27, 2001·Protein Science : a Publication of the Protein Society·D K Eggers, J S Valentine
Mar 5, 2002·Nature Structural Biology·Andrew P CapaldiSheena E Radford
Jun 13, 2002·Proceedings of the National Academy of Sciences of the United States of America·D K KlimovD Thirumalai
Aug 30, 2003·Proceedings of the National Academy of Sciences of the United States of America·Fumiko TakagiShoji Takada
Dec 20, 2003·Nature·Dennis J Selkoe
Jan 27, 2004·Journal of Molecular Biology·Dimos BolisPiero Andrea Temussi
Aug 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·A I JewettJ-E Shea
May 14, 2005·Journal of Molecular Biology·Isaac A HubnerEugene I Shakhnovich
Oct 19, 2005·Proteins·Wei-Xin XuWei Wang
Nov 23, 2005·Journal of Molecular Biology·Chiaki NishimuraPeter E Wright
Jan 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Samuel S ChoPeter G Wolynes
Jan 24, 2006·Journal of Molecular Biology·Margaret S Cheung, D Thirumalai
Mar 22, 2006·Protein Engineering, Design & Selection : PEDS·Suzy M JurajaStewart D Nuttall
Jan 24, 2007·Current Opinion in Structural Biology·David J Brockwell, Sheena E Radford
Mar 21, 2007·Journal of Molecular Biology·Stefan WallinEugene I Shakhnovich
Jun 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Del LucentVijay S Pande
Jun 26, 2007·The Journal of Physical Chemistry. B·Margaret S Cheung, D Thirumalai
Sep 28, 2007·Proceedings of the National Academy of Sciences of the United States of America·Philipp NeudeckerLewis E Kay
Dec 21, 2007·Proceedings of the National Academy of Sciences of the United States of America·Reto HorstArthur L Horwich
Jun 25, 2008·Annual Review of Biophysics·Huan-Xiang ZhouAllen P Minton
Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Arash Zarrine-AfsarHue Sun Chan
Nov 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Adrian C Apetri, Arthur L Horwich
Dec 17, 2008·Proceedings of the National Academy of Sciences of the United States of America·Jeetain Mittal, Robert B Best
Mar 20, 2009·Proceedings of the National Academy of Sciences of the United States of America·Wei WangP G Wolynes
Oct 24, 2009·Cellular and Molecular Life Sciences : CMLS·Andrew I Jewett, Joan-Emma Shea
Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Zhuqing Zhang, Hue Sun Chan
Jun 16, 2010·Proceedings of the National Academy of Sciences of the United States of America·Hagen HofmannBenjamin Schuler
Jul 7, 2010·Cell·Kausik ChakrabortyManajit Hayer-Hartl
Dec 1, 2010·The Journal of Physical Chemistry. B·Amandeep K Sangha, Tom Keyes

❮ Previous
Next ❯

Citations

May 23, 2019·Physical Chemistry Chemical Physics : PCCP·João EspecialPatrícia Fn Faísca
Nov 22, 2020·Current Opinion in Structural Biology·Lisa J Lapidus

❮ 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.