Ions and RNA Folding

Draper, David E.; Grilley, Dan; Soto, Ana M.

doi:10.1146/annurev.biophys.34.040204.144511

Cited by 458 publications

(555 citation statements)

References 93 publications

Supporting

Mentioning

541

Contrasting

Unclassified

Order By: Relevance

“…In site-specific ion binding, ions interact with biomolecules by binding to specific sites in a manner similar to ligand binding (see Sec. II.B) (Draper et al, 2005). Preferential hydration or Hofmeister effects are species-specific competitions between ions and water for binding to non-specific sites on biomolecules (Hofmeister, 1888;Boström et al, 2006;Collins, 2006).…”

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

“…Ion-induced RNA folding (Römer and Hach, 1975;Stein and Crothers, 1976;Cech and Bass, 1986;Dahm and Uhlenbeck, 1991;Draper, 2000, 2001;Draper et al, 2005) provides an excellent example of many of the ion-biomolecule interactions discussed above. RNA folding in the absence of salt is quite unfavorable due to a number of negative charges along its phosphodiester backbone.…”

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

“…Accurately modeling the ion-RNA interactions is essential to explain this phenomenon. A major obstacle in modeling ion-RNA interactions is the presence of numerous different ion environments (Draper et al, 2005). Each environment is dominated by the different type of ion-biomolecule interactions described above and requires different approaches to evaluating the energies.…”

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

See 2 more Smart Citations

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

View full text Add to dashboard Cite

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

show abstract

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

Section: Iia Biomolecule-ion Interactionsmentioning

confidence: 99%

See 1 more Smart Citation

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

View full text Add to dashboard Cite

show abstract

“…Draper has written extensively on the importance of the "ion atmosphere" that surrounds any polyelectrolyte and has noted that the ions in this atmosphere are likely to provide the dominant electrostatic contribution to the folding energetics, far greater than any ions bound to specific sites within the RNA [54,55].…”

Section: Simple Forces Underlying the Complex Behavior Of Rnamentioning

confidence: 99%

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Chu

Herschlag

2008

Current Opinion in Structural Biology

View full text Add to dashboard Cite

SummaryThe rapid development of our understanding of the diverse biological roles fulfilled by non-coding RNA has motivated interest in the basic macromolecular behavior, structure, and function of RNA. We focus on two areas in the behavior of complex RNAs. First, we present advances in the understanding of how RNA folding is accomplished in vivo by presenting a mechanism for the action of DEAD-box proteins. Members of this family are intimately associated with almost all cellular processes involving RNA, mediating RNA structural rearrangements and chaperoning their folding. Next, we focus on advances in understanding and characterizing the basic biophysical forces that govern the folding of complex RNAs. Ultimately we expect that a confluence and synergy between these approaches will lead to profound understanding of RNA and its biology.The explosion in our knowledge about noncoding RNA (ncRNA) -RNA that is not translated into protein -has expanded interest in RNA beyond the traditional RNA community. Diverse ncRNAs include the recently-discovered riboswitches, whose novel gene-regulation function is induced by the binding of small metabolites [1]; most of the so-called "Human Accelerated Regions" (HAR) of the human genome, whose recent evolution may be linked to the emergence of the human brain [2]; and many ncRNAs of unknown function [3]. These discoveries underscore the need to understand the fundamental macromolecular behavior of RNA, its structure and dynamics, and how these RNAs are handled and exploited in biology.Study of catalytic RNAs, which allow detection of correct folding via activity measurements, has established basic thermodynamic and kinetic properties of RNA folding. Large catalytic RNAs such as the group I intron from Tetrahymena thermophila and the RNase P RNA from Bacillus subtilis fold at vastly different rates under different conditions upon addition of Mg 2+ and have been shown to fold via multiple parallel pathways, in which different molecules follow different routes with different rates and intermediates, to a common final folded structure [4,5]. These observations support the common view that RNAs traverse rugged energy landscapes as they fold [6,7]. However, little is known about the true shape of these

show abstract

“…[19][20][21] For protein systems, the effects of various salts and other small molecules, e.g., the "salting in" and "salting out" effects associated with the Hofmeister series, 9,22-26 have been documented in great detail, although a unifying theory that can quantitatively predict the effect of salt concentration on the stability of protein is not yet available. [27][28][29][30][31][32] The importance of salt on protein stability was also illustrated in several molecular dynamics simulations.…”

Section: Introductionmentioning

confidence: 99%

Effects of Temperature and Salt Concentration on the Structural Stability of Human Lymphotactin: Insights from Molecular Simulations

Formaneck

Cui

2006

J. Am. Chem. Soc.

View full text Add to dashboard Cite

Extensive molecular dynamics (MD) simulations (∼ 70 ns total) with explicit solvent molecules and salt ions are carried out to probe the effects of temperature and salt concentration on the structural stability of the human Lymphotactin (hLtn). The distribution of ions near the protein surface and the stability of various structural motifs are observed to exhibit interesting dependence on the local sequence and structure. Whereas chloride association to the protein is overall enhanced as the temperature increases, the sodium distribution in the C-terminal helical region and, to a smaller degree, the chloride distribution in the same region are found higher at the lower temperature. The similar trend is also observed in non-linear Poisson-Boltzmann calculations with a temperaturedependent water dielectric constant, once conformational averaging over a series of MD snapshots is done. The unexpected temperature dependence in the ion distribution is explained based on the cancellation of association entropy for ion-sidechain pairs of opposite-charge and like-charge characters, which have positive and negative contributions, respectively. The C-terminal helix is observed to partially melt while a short • strand forms at the higher temperature with little salt dependence. The N-termal region, by contrast, develops partial helical structure at a higher salt concentration. These observed behaviors are consistent with solvent and salt screening playing an important role in stabilizing the canonical chemokine fold of hLtn.

show abstract

Ions and RNA Folding

Cited by 458 publications

References 93 publications

Computational Methods for Biomolecular Electrostatics

Computational Methods for Biomolecular Electrostatics

Unwinding RNA's secrets: advances in the biology, physics, and modeling of complex RNAs

Effects of Temperature and Salt Concentration on the Structural Stability of Human Lymphotactin: Insights from Molecular Simulations

Contact Info

Product

Resources

About