Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function.

PLoS Computational Biology
Giulio QuartaTamar Schlick

Abstract

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant "downhill" pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the "new view" of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are ...Continue Reading

References

Oct 10, 1981·Nucleic Acids Research·F R Kramer, D R Mills
Sep 18, 1997·Proceedings of the National Academy of Sciences of the United States of America·R A PootJ van Duin
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·T PanT R Sosnick
Mar 21, 2002·Journal of Molecular Biology·David H Mathews, Douglas H Turner
Jun 25, 2002·Journal of Molecular Biology·Ivo L HofackerPeter F Stadler
Apr 15, 2003·Journal of Molecular Biology·Takeshi UchidaMichael Brenowitz
Apr 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Vitaly EpshteinEvgeny Nudler
Aug 12, 2003·Nature Structural Biology·Wade C WinklerRonald R Breaker
Nov 5, 2003·Genes & Development·Narasimhan SudarsanRonald R Breaker
Dec 5, 2003·Nucleic Acids Research·Ye Ding, Charles E Lawrence
Jan 14, 2004·Nature Structural & Molecular Biology·Maumita Mandal, Ronald R Breaker
Jan 20, 2004·Trends in Biochemical Sciences·Evgeny Nudler, Alexander S Mironov
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·W Kevin Meisner, Tobin R Sosnick
Apr 6, 2005·Molecular Cell·J Kenneth WickiserDonald M Crothers
Oct 6, 2005·Biochemistry·J Kenneth WickiserDonald M Crothers
Nov 24, 2005·Journal of Molecular Biology·Lisa W KwokLois Pollack
Dec 17, 2005·Chemistry & Biology·Narasimhan SudarsanRonald R Breaker
Apr 18, 2006·Cell·Michael J CromieEduardo A Groisman
May 3, 2006·Journal of Molecular Biology·Sunny D GilbertRobert T Batey
Jul 15, 2006·Cell·Evgeny Nudler
Jul 29, 2006·Bioinformatics·Chuong B DoSerafim Batzoglou
Aug 26, 2006·Chemistry & Biology·Jean-François LemayDaniel A Lafontaine
Jan 31, 2007·Biological Chemistry·Piotr BorsukPiotr Weglenski
Mar 27, 2007·Current Opinion in Microbiology·Rebecca L CoppinsEduardo A Groisman
Mar 27, 2007·Nature Structural & Molecular Biology·Adam RothRonald R Breaker
Apr 19, 2007·Chembiochem : a European Journal of Chemical Biology·Renate RiederRonald Micura
May 23, 2007·Nucleic Acids Research·Andrea RentmeisterMichael Famulok
Aug 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Rhiju Das, David Baker
Sep 7, 2007·Cell·Charles E DannWade C Winkler
Nov 14, 2007·Genome Biology·Jeffrey E Barrick, Ronald R Breaker
Jan 5, 2008·Science·William J GreenleafSteven M Block

❮ Previous
Next ❯

Citations

May 2, 2014·Nucleic Acids Research·Dennis M Mishler, Justin P Gallivan
Nov 28, 2013·Nucleic Acids Research·Benjamin LutzAlexander Schug
Mar 22, 2015·Molecular Cell·Ian R PriceAilong Ke
Oct 20, 2015·Journal of Molecular Biology·Naoto BabaTamar Schlick
Apr 15, 2014·Biochimica Et Biophysica Acta·Andrew SavinovSteven M Block
Apr 29, 2015·Nucleic Acids Research·Shensi ShenAlfonso Jaramillo
Jan 13, 2015·The Journal of Chemical Physics·Sha GongWenbing Zhang
Oct 30, 2016·Bioinformatics·Marco BarsacchiAlessio Bechini
Sep 30, 2016·PloS One·Amirhossein ManzourolajdadJohn L Spouge
Feb 17, 2017·Biochemistry·Maja Etzel, Mario Mörl
May 1, 2015·BMC Bioinformatics·Amirhossein Manzourolajdad, Jonathan Arnold
Jun 13, 2019·PloS One·Amirhossein Manzourolajdad, John L Spouge
Aug 8, 2018·Scientific Reports·Christopher A ReidDaniel M Lipinski
Mar 29, 2020·Journal of Computational Chemistry·Osama Alaidi, Fareed Aboul-Ela
Jul 11, 2012·Journal of the American Chemical Society·Tobias SantnerRonald Micura
Oct 4, 2013·Journal of the American Chemical Society·Jong-Chin Lin, D Thirumalai
Sep 25, 2012·The Journal of Physical Chemistry. B·Pavel BanášMichal Otyepka
Oct 12, 2017·Journal of Chemical Information and Modeling·Christian A Hanke, Holger Gohlke
Sep 11, 2021·The Journal of Physical Chemistry. B·Narendar KolimiJoshua Alper

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR

Software Mentioned

R
Sym
RNAeval
Vienna RNA folding package
Vienna RNA package
MC
RNAdistance
NAST
RNAsubopt
mFold

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.