Rapid compaction during RNA folding

Proceedings of the National Academy of Sciences of the United States of America
Rick RussellLois Pollack

Abstract

We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

References

Jan 1, 1975·Annual Review of Biophysics and Bioengineering·P B Sigler
Jul 21, 1989·Science·J A Latham, T R Cech
Sep 8, 1995·The Journal of Biological Chemistry·D Herschlag
Mar 1, 1994·Nature Structural Biology·T R SosnickS W Englander
Aug 12, 1994·Science·P P Zarrinkar, J R Williamson
Jan 1, 1995·Advances in Protein Chemistry·O B Ptitsyn
Nov 21, 1997·Journal of Molecular Biology·J PanS A Woodson
Aug 26, 1998·Folding & Design·S E Jackson
Jun 9, 1999·Nature Structural Biology·K W PlaxcoD Baker
Sep 1, 1999·Proceedings of the National Academy of Sciences of the United States of America·L PollackR H Austin
Sep 10, 1999·The Journal of Biological Chemistry·M J PandyaA R Clarke
Oct 16, 1999·Journal of Molecular Biology·R Russell, D Herschlag
Nov 5, 1999·Journal of Molecular Biology·I Tinoco, C Bustamante
Apr 7, 2000·Advances in Protein Chemistry·A K Chamberlain, S Marqusee
May 10, 2000·Nature Structural Biology·K L BuchmuellerK M Weeks
May 10, 2000·Nature Structural Biology·R RussellD Herschlag
Jun 17, 2000·Science·X ZhuangS Chu
Sep 22, 2000·Biochemistry·M L DerasS A Woodson
Oct 4, 2000·Biochemistry·S K SilvermanT R Cech
Nov 23, 2000·Biochemistry·V L Murthy, G D Rose
Apr 28, 2001·Annual Review of Physical Chemistry·D ThirumalaiD Klimov
Jun 1, 2001·Physical Review Letters·L PollackS G Mochrie
Jun 19, 2001·Current Opinion in Structural Biology·D K Treiber, J R Williamson
Jan 5, 2002·Proceedings of the National Academy of Sciences of the United States of America·Rick RussellDaniel Herschlag
Jun 15, 2010·Journal of Molecular Biology·Yaqi WanDaniel Herschlag
Dec 1, 1998·Analytical Chemistry·D C DuffyG M Whitesides

❮ Previous
Next ❯

Citations

Jan 18, 1976·Biochimica Et Biophysica Acta·Y Fujino, M Ohnishi
Jan 1, 1974·Progress in the Chemistry of Fats and Other Lipids·P J BrennanD Tyrrell
Apr 7, 2005·Current Opinion in Chemical Biology·Sarah A Woodson
Nov 26, 2003·Journal of Molecular Biology·Linhui Julie SuAnna Marie Pyle
May 22, 2003·Journal of Molecular Biology·Prashanth Rangan, Sarah A Woodson
Jan 8, 1999·Biochimica Et Biophysica Acta·R C Dickson, R L Lester
Dec 5, 2002·Current Opinion in Structural Biology·Dmitri I Svergun, Michel H J Koch
Jul 2, 2003·Current Opinion in Structural Biology·Tobin R Sosnick, Tao Pan
Jul 2, 2003·Current Opinion in Structural Biology·Victoria J DeRose
Dec 10, 2002·Current Opinion in Chemical Biology·Emilia T Mollova
Dec 15, 2004·Analytical Chemistry·David E HertzogOlgica Bakajin
Jul 1, 2011·Accounts of Chemical Research·Sarah A Woodson
Mar 3, 2011·Biochemistry·Desirae Leipply, David E Draper
May 11, 2006·Chemical Reviews·Heinrich RoderHong Cheng
Nov 20, 2003·Journal of the American Chemical Society·Helen Song, Rustem F Ismagilov
Jul 6, 2010·Journal of the American Chemical Society·Joon Ho RohSarah A Woodson
Mar 1, 2012·Journal of the American Chemical Society·Peter C AnthonyDaniel Herschlag
Sep 29, 2011·Nature Communications·Changbong Hyeon, D Thirumalai
Nov 3, 2004·Nature Reviews. Molecular Cell Biology·Renée SchroederKatharina Semrad
Dec 5, 2006·Nature Structural & Molecular Biology·Christina Waldsich, Anna Marie Pyle
Mar 7, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rhiju DasDaniel Herschlag
May 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui QuNorbert F Scherer
Sep 6, 2008·Proceedings of the National Academy of Sciences of the United States of America·Miriam SteinerDavid Rueda
Jul 3, 2008·The Journal of Biological Chemistry·Andrew D GarstRobert T Batey
Nov 1, 2002·Nucleic Acids Research·Kelly N NoblesPaul F Agris
Nov 30, 2005·Nucleic Acids Research·Linhui Julie SuAnna Marie Pyle
Dec 6, 2006·Nucleic Acids Research·Zhi-Jie Tan, Shi-Jie Chen
Oct 18, 2007·Nucleic Acids Research·Zhuoyun ZhuangJoan-Emma Shea
Dec 6, 2011·Nucleic Acids Research·Bin ChenT Kwaku Dayie
Aug 13, 2004·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·Michelle R BringerRustem F Ismagilov
Feb 22, 2011·Journal of Synchrotron Radiation·Lucas J KoernerSol M Gruner
Mar 3, 2010·Annual Review of Biophysics·Sarah A Woodson
May 13, 2006·Annual Review of Biophysics and Biomolecular Structure·Tao Pan, Tobin Sosnick
Feb 8, 2007·Annual Review of Biophysics and Biomolecular Structure·Jan Lipfert, Sebastian Doniach
Jun 25, 2008·Annual Review of Biophysics·Shi-Jie Chen
Jan 31, 2012·RNA·Hari BhaskaranJohn J Perona
Nov 30, 2006·The Journal of Chemical Physics·Changbong HyeonD Thirumalai
Dec 27, 2005·The Journal of Chemical Physics·Glen I RedfordRobert M Clegg
Jun 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·X-W FangT Pan
Feb 8, 2003·Proceedings of the National Academy of Sciences of the United States of America·Prashanth RanganSarah A Woodson
Jul 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Gregory BokinskyXiaowei Zhuang
Apr 18, 2007·Proceedings of the National Academy of Sciences of the United States of America·Alain LaederachMichael Brenowitz

❮ 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.