Predicting loop-helix tertiary structural contacts in RNA pseudoknots.

RNA
Song CaoShi-Jie Chen

Abstract

Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DeltaH) of -14 kcal/mol and a contact entropy (DeltaS) of -38 cal/mol/K for a protonated C(+)*(G-C) base triple at pH 7.0, and (DeltaH = -7 kcal/mol, DeltaS = -19 cal/mol/K) for an unprotonated base triple. Tests...Continue Reading

References

Dec 1, 1990·Current Opinion in Cell Biology·D E Draper
Apr 1, 1968·Biopolymers·H Krakauer, J M Sturtevant
Jan 1, 1996·Annual Review of Biochemistry·R F Gesteland, J F Atkins
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Sep 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·M Wu, I Tinoco
Oct 23, 1998·Nature·A R Ferré-D'AmaréJ A Doudna
Jan 8, 1999·Journal of Molecular Biology·C M Duarte, A M Pyle
Aug 10, 1999·Journal of Molecular Biology·V L MurthyG D Rose
Dec 10, 1999·Proceedings of the National Academy of Sciences of the United States of America·Y G KimA Rich
Dec 10, 1999·Journal of Molecular Biology·T Hermann, D J Patel
Jan 19, 2000·Proceedings of the National Academy of Sciences of the United States of America·S J Chen, K A Dill
Feb 12, 2000·Journal of Molecular Biology·P L Nixon, D P Giedroc
Apr 11, 2001·Proceedings of the National Academy of Sciences of the United States of America·P NissenT A Steitz
May 10, 2001·RNA·N B Leontis, E Westhof
Sep 13, 2002·Journal of Molecular Biology·Paul L NixonDavid P Giedroc
Dec 17, 2002·Proceedings of the National Academy of Sciences of the United States of America·Luis R ComolliThomas L James
Jan 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Carla A TheimerJuli Feigon
Mar 26, 2003·Journal of Molecular Biology·Bernhard J WalbererAlan D Frankel
Nov 13, 2003·Proceedings of the National Academy of Sciences of the United States of America·Laura J W MurrayJane S Richardson
Apr 26, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jiunn-Liang Chen, Carol W Greider
Jun 9, 2005·PLoS Biology·David W Staple, Samuel E Butcher
Jun 17, 2005·BMC Molecular Biology·Jody BurksJacek Wower
Aug 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Peter V CornishDavid P Giedroc
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Feb 17, 2006·Journal of Molecular Graphics & Modelling·Yaroslava G Yingling, Bruce A Shapiro
May 20, 2006·Nucleic Acids Research·Song Cao, Shi-Jie Chen
May 23, 2006·Current Opinion in Structural Biology·David H Mathews, Douglas H Turner
May 23, 2006·Current Opinion in Structural Biology·Neocles B LeontisEric Westhof
Jan 11, 2007·Molecular and Cellular Biology·Kinneret SheferYehuda Tzfati
Feb 6, 2007·Journal of Molecular Biology·Song Cao, Shi-Jie Chen
Feb 24, 2007·Biochemistry·Ana Maria SotoDavid E Draper
Mar 27, 2007·Current Opinion in Structural Biology·Bruce A ShapiroEckart Bindewald
Jun 5, 2007·Journal of Molecular Biology·Jennifer S PfingstenJeffrey S Kieft

❮ Previous
Next ❯

Citations

Jun 25, 2010·The Journal of Chemical Physics·Liang Liu, Shi-Jie Chen
Oct 12, 2010·RNA·Donald H Burke, Steven S Rhee
Mar 19, 2011·The Journal of Physical Chemistry. B·Song Cao, Shi-Jie Chen
Mar 19, 2013·Proceedings of the National Academy of Sciences of the United States of America·Christine E HajdinKevin M Weeks
Jan 25, 2011·Journal of Molecular Modeling·Kristian RotherJanusz M Bujnicki
Jul 7, 2011·Quarterly Reviews of Biophysics·Kevin S KeatingAnna Marie Pyle
Nov 26, 2015·Journal of the American Chemical Society·Xinyue ZhangLi-Qun Gu
Nov 18, 2015·Journal of Chemical Theory and Computation·Tristan CragnoliniSamuela Pasquali
Jun 13, 2015·Nucleic Acids Research·Piotr LukasiakJacek Blazewicz
Apr 30, 2016·Methods : a Companion to Methods in Enzymology·Wayne K DawsonJanusz M Bujnicki
Nov 13, 2012·PloS One·Liang Liu, Shi-Jie Chen
Mar 24, 2015·PloS One·Zhou GongChun Tang
Nov 21, 2012·Journal of the American Chemical Society·Daud I ColeMichael B Jarstfer
Jul 9, 2011·Journal of the American Chemical Society·Natalia A Denesyuk, D Thirumalai
Mar 17, 2017·Annual Review of Biophysics·Li-Zhen SunShi-Jie Chen
Apr 1, 2015·Indian Journal of Hematology & Blood Transfusion : an Official Journal of Indian Society of Hematology and Blood Transfusion·Suad AlFadhli, Rasheeba Nizam
Mar 27, 2013·Biopolymers·Feng-Hua WangYuan-Yan Wu Zhi-Jie Tan
Feb 10, 2021·Journal of Chemical Theory and Computation·Dong ZhangShi-Jie Chen
Sep 3, 2021·The Journal of Physical Chemistry. B·Yi ChengShi-Jie Chen

❮ 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.