Computational study of stability of an H-H-type pseudoknot motif

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Jun WangYi Xiao

Abstract

Motifs in RNA tertiary structures are important to their structural organizations and biological functions. Here we consider an H-H-type pseudoknot (HHpk) motif that consists of two hairpins connected by a junction loop and with kissing interactions between the two hairpin loops. Such a tertiary structural motif is recurrently found in RNA tertiary structures, but is difficult to predict computationally. So it is important to understand the mechanism of its formation and stability. Here we investigate the stability of the HHpk tertiary structure by using an all-atom molecular dynamics simulation. The results indicate that the HHpk tertiary structure is stable. However, it is found that this stability is not due to the helix-helix packing, as is usually expected, but is maintained by the combined action of the kissing hairpin loops and junctions, although the former plays the main role. Stable HHpk motifs may form structural platforms for the molecules to realize their biological functions. These results are useful for understanding the construction principle of RNA tertiary structures and structure prediction.

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 1, 1997·Trends in Biochemical Sciences·S A Strobel, J A Doudna
Apr 4, 2000·Structure·T Hermann, D J Patel
Mar 29, 2001·Nature Structural Biology·E A DohertyJ A Doudna
Dec 26, 2001·Nucleic Acids Research·Peter S KlostermanSteven E Brenner
Jun 26, 2003·Nucleic Acids Research·Huanwang YangEric Westhof
Jul 26, 2003·Nature Structural Biology·Anastasia KhvorovaSumedha D Jayasena
Dec 19, 2003·Nucleic Acids Research·Makio TamuraStephen R Holbrook
May 23, 2006·Current Opinion in Structural Biology·Neocles B LeontisEric Westhof
Aug 26, 2006·Chemistry & Biology·Jean-François LemayDaniel A Lafontaine
Jan 5, 2008·Science·William J GreenleafSteven M Block
Jun 13, 2008·Current Opinion in Structural Biology·Hashim M Al-Hashimi, Nils G Walter
Jun 25, 2008·Annual Review of Biophysics·Rebecca K Montange, Robert T Batey
Jun 25, 2008·Annual Review of Biophysics·Stephen R Holbrook
Jul 17, 2008·Comparative and Functional Genomics·Neocles B Leontis, Eric Westhof
Oct 3, 2008·Journal of the American Chemical Society·Jong-Chin Lin, D Thirumalai
Apr 29, 2009·Bioinformatics·Kévin DartyYann Ponty
Oct 6, 2010·Journal of Biomolecular Structure & Dynamics·Zhou GongYi Xiao
Oct 12, 2010·Nucleic Acids Research·Kengo TsudaYutaka Muto
Jan 25, 2011·Journal of Molecular Biology·Cuong D NguyenJoel P Mackay
Feb 8, 2011·Journal of Biomolecular Structure & Dynamics·Yunjie ZhaoYi Xiao
Mar 29, 2011·Chemistry & Biology·Peter DaldropRuth Brenk
Apr 9, 2011·Current Opinion in Structural Biology·Nicholas J ReiterAlfonso Mondragón
Apr 20, 2011·Journal of the American Chemical Society·Yujie ZhangWei Wang
Apr 26, 2011·Nucleic Acids Research·Anton I PetrovNeocles B Leontis
Aug 31, 2011·Journal of Biomolecular Structure & Dynamics·Zhou GongYi Xiao
Sep 9, 2011·Accounts of Chemical Research·Samuel E Butcher, Anna Marie Pyle
Sep 21, 2011·Nature Chemical Biology·Charles E Dann
May 15, 2012·Journal of Chemical Theory and Computation·Andreas W GötzRoss C Walker
Oct 17, 2012·Scientific Reports·Yunjie ZhaoYi Xiao
Aug 24, 2013·RNA·Anton I PetrovNeocles B Leontis
Jul 2, 2015·Nucleic Acids Research·Craig L ZirbelNeocles B Leontis
Jul 9, 2013·Journal of Chemical Theory and Computation·Daniel R Roe, Thomas E Cheatham
Sep 10, 2013·Journal of Chemical Theory and Computation·Romelia Salomon-FerrerRoss C Walker

❮ Previous
Next ❯

Citations

Aug 10, 2017·Biophysical Journal·Zhong-Liang ZhangZhi-Jie Tan
May 1, 2021·Frontiers in Molecular Biosciences·Chenjie FengZhi-Jie Tan

❮ 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.