scholarly journals Elucidation of ion effects on the Thermodynamics of RNA Folding

2018 ◽  
Author(s):  
Natalia A. Denesyuk ◽  
D. Thirumalai
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Conformational Changes ◽  
Electrostatic Interactions ◽  
Rna Folding ◽  
Coarse Grained ◽  
Significant Advance ◽  
Rna Molecules ◽  
Ion Effects ◽  
The Difference

AbstractHow ions affect RNA folding thermodynamics and kinetics is an important but a vexing problem that remains unsolved. Experiments have shown that the free energy change, ΔG(c), of RNA upon folding varies with the salt concentration (c) as, ΔG(c) = kc ln c + const, where the coefficient kc is proportional to the difference in the uptake of ions (ion preferential coefficient), ΔΓ, between the folded and unfolded states. We performed simulations of a coarse-grained model, by modeling electrostatic interactions implicitly and with explicit representation of ions, to elucidate the molecular underpinnings of the relationship between folding free energy and ion preferential coefficient. Without any input from experiments, the simulations quantitatively reproduce the heat capacity for the −1 frame shifting pseudoknot (PK) from Beet Western Yellow Virus, thus validating the model. We show that ΔG(c) calculated directly from ΔΓ varies linearly with ln c (c < 0.2M), for a hairpin and the PK, thus demonstrating a molecular link between the two quantities for RNA molecules that undergo substantial conformational changes during folding. Explicit ion simulations also show the linear dependence of ΔG(c) on ln c at all c with kc = 2kBT, except that ΔG(c) values are shifted by about 2 kcal/mol higher than experiments at all salt concentrations. The discrepancy is due to an underestimate the Γ values for both the folded and unfolded states, while giving accurate values for ΔΓ. The predictions for the salt dependence of ΔΓ are amenable to test using single molecule pulling experiments. Our simulations, representing a significant advance in quantitatively describing ion effects in RNA, show that the framework provided here can be used to obtain accurate thermodynamics of RNA folding.

scholarly journals Ripping RNA by Force using Gaussian Network Models

2016 ◽  
Author(s):  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Cross Correlation ◽  
Network Models ◽  
Force Extension ◽  
Correlation Matrices ◽  
Rna Molecules ◽  
Allosteric Communication ◽  
Ion Effects ◽  
Gaussian Network

AbstractUsing force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in the context of proteins have shown that topology plays is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions. Cross-correlation matrices of residue fluctuations, which are analytically calculated using GNM even upon application of mechanical force, show distinct allosteric communication as RNAs rupture. The model is used to calculate the force-extension curves at full thermodynamic equilibrium, and the corresponding unfolding pathways of four RNA molecules subject to a quasi-statically increased force. Our study finds that the analysis using GNM captures qualitatively the unfolding pathway of T. ribozyme elucidated by the optical tweezers measurement. However, the simple model is not sufficient to capture subtle features, such as bifurcation in the unfolding pathways or the ion effects, in the forced-unfolding of RNAs.

scholarly journals Coarse-grained dynamic RNA titration simulations

2019 ◽  
Vol 9 (3) ◽  
pp. 20180066 ◽  
Author(s):  
S. Pasquali ◽  
E. Frezza ◽  
F. L. Barroso da Silva
Keyword(s):  
Electrostatic Interactions ◽  
Molecular Organization ◽  
Coarse Grained ◽  
Solution Ph ◽  
Dynamic Simulations ◽  
Rna Molecules ◽  
Coarse Grained Model ◽  
Constant Ph ◽  
Conformational Plasticity ◽  
And Function

Electrostatic interactions play a pivotal role in many biomolecular processes. The molecular organization and function in biological systems are largely determined by these interactions. Owing to the highly negative charge of RNA, the effect is expected to be more pronounced in this system. Moreover, RNA base pairing is dependent on the charge of the base, giving rise to alternative secondary and tertiary structures. The equilibrium between uncharged and charged bases is regulated by the solution pH, which is therefore a key environmental condition influencing the molecule’s structure and behaviour. By means of constant-pH Monte Carlo simulations based on a fast proton titration scheme, coupled with the coarse-grained model HiRE-RNA, molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local p K a values for each nucleotide.

scholarly journals Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

2019 ◽  
Vol 116 (42) ◽  
pp. 21022-21030 ◽  
Author(s):  
Hung T. Nguyen ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Rna Folding ◽  
Divalent Cations ◽  
Coarse Grained ◽  
Concentration Difference ◽  
Rna Molecules ◽  
Site Model ◽  
Monovalent Ions ◽  
Wide Range ◽  
Sequence Effects ◽  
The Impact

RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM theory for ion–phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to predict accurately the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the rRNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties.

scholarly journals Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK

2015 ◽  
Vol 112 (33) ◽  
pp. 10389-10394 ◽  
Author(s):  
Daniela Bauer ◽  
Dale R. Merz ◽  
Benjamin Pelz ◽  
Kelly E. Theisen ◽  
Gail Yacyshyn ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Single Molecule ◽  
Conformational Changes ◽  
Mechanical Stability ◽  
Nucleotide Binding ◽  
Binding Domain ◽  
Coarse Grained ◽  
Nucleotide Binding Domain ◽  
Chaperone Dnak ◽  
Hsp70 Chaperone

The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.

scholarly journals The P1 and P2 helices of the Guanidinium-II riboswitch interact in a ligand-dependent manner

2021 ◽  
Author(s):  
Christin Fuks ◽  
Sebastian Falkner ◽  
Nadine Schwierz ◽  
Martin Hengesbach
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Environmental Conditions ◽  
Structural Information ◽  
Coarse Grained ◽  
Regulation Mechanism ◽  
Dependent Manner ◽  
Loop Formation ◽  
Coarse Grained Simulations ◽  
Kissing Loop

ABSTRACTRiboswitch RNAs regulate gene expression by conformational changes induced by environmental conditions and specific ligand binding. The guanidine-II riboswitch is proposed to bind the small molecule guanidinium and to subsequently form a kissing loop interaction between the P1 and P2 hairpins. While an interaction was shown for isolated hairpins in crystallization and EPR experiments, an intrastrand kissing loop formation has not been demonstrated. Here, we report the first evidence of this interaction in cis in a ligand and Mg2+ dependent manner. Using single-molecule FRET spectroscopy and detailed structural information from coarse-grained simulations, we observe and characterize three interconvertible states representing an open and kissing loop conformation as well as a novel Mg2+ dependent state for the guanidine-II riboswitch from E. coli. The results further substantiate the proposed switching mechanism and provide detailed insight into the regulation mechanism for the guanidine-II riboswitch class. Combining single molecule experiments and coarse-grained simulations therefore provides a promising perspective in resolving the conformational changes induced by environmental conditions and to yield molecular insights into RNA regulation.

scholarly journals Folding RNA in mixtures of monovalent and divalent cations: Theory and simulations

2019 ◽  
Author(s):  
Hung T. Nguyen ◽  
Naoto Hori ◽  
D. Thirumalai
Keyword(s):  
Excellent Agreement ◽  
Rna Folding ◽  
Divalent Cations ◽  
Coarse Grained ◽  
Free Energies ◽  
Divalent Ions ◽  
Rna Molecules ◽  
Monovalent Ions ◽  
The Impact ◽  
Phosphate Groups

RNA molecules cannot fold in the absence of counter ions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the Reference Interaction Site Model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial in an accurate calculation of RNA folding thermodynamics. The RISM theory for ion-phosphate interactions when combined with simulations based on a transferable coarse-grained model allows us to accurately predict the folding of several RNA molecules in a mixture containing monovalent and divalent ions. The calculated folding free energies and ion-preferential coefficients for RNA molecules (pseudoknots, a fragment of the ribosomal RNA, and the aptamer domain of the adenine riboswitch) are in excellent agreement with experiments over a wide range of monovalent and divalent ion concentrations. Because the theory is general, it can be readily used to investigate ion and sequence effects on DNA properties.Significance StatementRNA molecules require ions to fold. The problem of how ions of differing sizes and valences drive the folding of RNA molecules is unsolved. Here, we take a major step in its solution by creating a method, based on the theory of polyatomic liquids, to calculate the potential between divalent ions and the phosphate groups. The resulting model, accounting for inner and outer sphere coordination of Mg2+ and Ca2+ to phosphates, when used in coarse-grained molecular simulations predicts folding free energies for a number of RNA molecules in the presence of both divalent and monovalent ions that are in excellent agreement with experiments. The work sets the stage for probing sequence and ion effects on DNA and synthetic polyelectrolytes.

scholarly journals Electrostatics and Solvation: Essential Determinants of Chromatin Compaction

2019 ◽  
Author(s):  
A. Bendandi ◽  
S. Dante ◽  
S. Rehana Zia ◽  
A. Diaspro ◽  
W. Rocchia
Keyword(s):  
Conformational Changes ◽  
Protein Interactions ◽  
Electrostatic Interactions ◽  
Ionic Concentration ◽  
Coarse Grained ◽  
Chromatin Compaction ◽  
Spatial And Temporal Scales ◽  
Chromatin Fibre ◽  
Nucleosome Core ◽  
Wide Range

ABSTRACTChromatin compaction is a process of fundamental importance in Biology, as it greatly influences cellular function and gene expression. The dynamics of compaction is determined by the interactions between DNA and histones, which are mainly mechanical and electrostatic. The high charge of DNA makes electrostatics extremely important for chromatin topology and dynamics. Besides their mechanical and steric role in the chromatin fibre, linker DNA length and linker histone presence and binding position also bear great electrostatic consequences. Electrostatics in chromatin is also indirectly linked to the DNA sequence: the presence of high-curvature AT-rich segments in DNA can cause conformational variations with electrostatic repercussions, attesting to the fact that the role of DNA is both structural and electrostatic. Electrostatics in this system has been analysed by extensively examining at the computational level the repercussions of varying ionic concentration, using all-atom, coarse-grained, and continuum models. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. Chromatin compaction is a very complex issue, depending on many factors and spanning orders of magnitude in space and time in its dynamics. Therefore, comparison and complementation of theoretical models with experimental results is fundamental. Here, we present existing approaches to analyse electrostatics in chromatin and the different points of view from which this issue is treated. We pay particular attention to solvation, often overlooked in chromatin studies. We also present some numerical results on the solvation of nucleosome core particles. We discuss experimental techniques that have been combined with computational approaches and present some related experimental data such as the Z-potential of nucleosomes at varying ionic concentrations. Finally, we discuss how these observations support the importance of electrostatics and solvation in chromatin models.SIGNIFICANCEThis work explores the determinants of chromatin compaction, focusing on the importance of electrostatic interactions and solvation. Chromatin compaction is an intrinsically multiscale issue, since processes concerning chromatin occur on a wide range of spatial and temporal scales. Since DNA is a highly charged macromolecule, electrostatic interactions are extremely significant for chromatin compaction, an effect examined in this work from many angles, such as the importance of ionic concentration and different ionic types, DNA-protein interactions, and solvation. Solvation is often overlooked in chromatin studies, especially in coarse-grained models, where the nucleosome core, the building block of the chromatin fibre, is represented as a rigid body, even though it has been observed that solvation influences chromatin even at the base-pair level.

scholarly journals Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Salvatore Assenza ◽  
Alberto Stefano Sassi ◽  
Ruth Kellner ◽  
Benjamin Schuler ◽  
Paolo De Los Rios ◽  
...  
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Critical Role ◽  
Quantitative Agreement ◽  
Mechanical Work ◽  
Chemical Energy ◽  
Coarse Grained ◽  
Theoretical Approaches ◽  
Non Equilibrium

Hsp70 molecular chaperones are abundant ATP-dependent nanomachines that actively reshape non-native, misfolded proteins and assist a wide variety of essential cellular processes. Here, we combine complementary theoretical approaches to elucidate the structural and thermodynamic details of the chaperone-induced expansion of a substrate protein, with a particular emphasis on the critical role played by ATP hydrolysis. We first determine the conformational free-energy cost of the substrate expansion due to the binding of multiple chaperones using coarse-grained molecular simulations. We then exploit this result to implement a non-equilibrium rate model which estimates the degree of expansion as a function of the free energy provided by ATP hydrolysis. Our results are in quantitative agreement with recent single-molecule FRET experiments and highlight the stark non-equilibrium nature of the process, showing that Hsp70s are optimized to effectively convert chemical energy into mechanical work close to physiological conditions.

Sign in / Sign up

Export Citation Format

Share Document