arXiv subjects

Changbong Hyeon

Publications and source records attributed to Changbong Hyeon.

At least 55 records · Page 3Linked to original sources

arXiv2015

Unexpected swelling of stiff DNA in a polydisperse crowded environment

We investigate the conformations of DNA-like stiff chains, characterized by contour length ($L$) and persistence length ($l_p$), in a variety of crowded environments containing mono disperse soft spherical (SS) and spherocylindrical (SC) particles, mixture of SS and SC, and a milieu mimicking the composition of proteins in $E. coli.$ cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to $ϕ\approx 0.1$, is considerably more compact at low volume fractions ($ϕ\leq 0.2$) in monodisperse SC particles than in a medium containing SS particles. A 1:1 mixture of SS and SC crowders induces greater chain compaction than the pure SS or SC crowders at the same $ϕ$ with the effect being highly non-additive. We also discover a counter-intuitive result that polydisperse crowding environment, mimicking the composition of a cell lysate, swells the DNA-like polymer, which is in stark contrast to the size reduction of flexible polymer in the same milieu. Trapping of the stiff chain in a fluctuating tube-like environment created by large-sized crowders explains the dramatic increase in size and persistence length of the stiff chain. In the polydisperse medium, mimicking the cellular environment, the size of the DNA (or related RNA) is determined by $L/l_p$. At low $L/l_p$ the size of the polymer is unaffected whereas there is a dramatic swelling at intermediate value of $L/l_p$. We use these results to provide insights into recent experiments on crowding effects on RNA, and also make testable predictions.

cond-mat.soft↗

arXiv2015

Time traces of individual kinesin motors suggest functional heterogeneity

Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled experiments. In an effort to obtain a statistically meaningful set of time traces that simultaneously avoid any experimental artifacts, we performed quantum-dot labeled kinesin experiments on both surface and levitated microtubules. Similar to glassy systems, we found that mean velocities of individual kinesin motors vary widely from one motor to another, the variation of which is greater than that expected from the stochastic variation of stepping times. In the presence of heterogeneity, an ensemble-averaged quantity such as diffusion constant or randomness parameter is ill-defined. We propose to analyze heterogeneous data from single molecule measurements by decomposing them into homogeneous subensembles.

cond-mat.soft↗

arXiv2015

Extracting folding landscape characteristics of biomolecules using mechanical forces

In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played a major role in interpreting data and anticipating outcomes of experiments. Here, we explain how by using temperature as a variable in mechanical unfolding of biomolecules in force spectroscopy, the roughness of the energy landscape can be measured without making any assumptions about the underlying reaction coordinate. Estimates of other aspects of the energy landscape such as free energy barriers or the transition state (TS) locations could depend on the precise model used to analyze the experimental data. We illustrate the inherent difficulties in obtaining the transition state location from loading rate or force-dependent unfolding rates. Because the transition state moves as the force or the loading rate is varied, which is reminiscent of the Hammond effect, it is in general difficult to invert the experimental data. The independence of the TS location on force holds good only for brittle or hard biomolecules whereas the TS location changes considerably if the molecule is soft or plastic. Finally, we discuss the goodness of the end-to-end distance (or pulling) coordinate of the molecule as a surrogate reaction coordinate in a situation like force-induced ligand-unbinding from a gated molecular receptor as well as force-quench refolding of an RNA hairpin.

q-bio.BM↗

arXiv2015

Effects of macromolecular crowding on the collapse of biopolymers

Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins (IDPs) even at volume fraction ($ϕ$) similar to that in the cytosol whereas DNA undergoes a coil-to-globule transition at very small $ϕ$. We show using a combination of scaling arguments and simulations that the polymer size $\overline{R}_g(ϕ)$ depends on $x = \overline{R}_g(0)/D$ where $D$ is the $ϕ$-dependent distance between the crowders. If $x\lesssim \mathcal{O}(1)$, there is only a small decrease in $\overline{R}_g(ϕ)$ as $ϕ$ increases. When $x\gg \mathcal{O}(1)$, a cooperative coil-to-globule transition is induced. Our theory quantitatively explains a number of experiments.

cond-mat.soft↗

arXiv2014

Communication over the network of binary switches regulates the activation of A$_{2A}$ adenosine receptor

Dynamics and functions of G-protein coupled receptors (GPCRs) are accurately regulated by the type of ligands that bind to the orthosteric or allosteric binding sites. To glean the structural and dynamical origin of ligand-dependent modulation of GPCR activity, we performed total $\sim$ 5 $μ$sec molecular dynamics simulations of A$_{2A}$ adenosine receptor (A$_{2A}$AR) in its apo, antagonist-bound, and agonist-bound forms in an explicit water and membrane environment, and examined the corresponding dynamics and correlation between the 10 key structural motifs that serve as the allosteric hotspots in intramolecular signaling network. We dubbed these 10 structural motifs "binary switches" as they display molecular interactions that switch between two distinct states. By projecting the receptor dynamics on these binary switches that yield $2^{10}$ microstates, we show that (i) the receptors in apo, antagonist-bound, and agonist-bound states explore vastly different conformational space; (ii) among the three receptor states the apo state explores the broadest range of microstates; (iii) in the presence of the agonist, the active conformation is maintained through coherent couplings among the binary switches; and (iv) to be most specific, our analysis shows that W246, located deep inside the binding cleft, can serve as both an agonist sensor and actuator of ensuing intramolecular signaling for the receptor activation.Finally, our analysis of multiple trajectories generated by inserting an agonist to the apo state underscores that the transition of the receptor from inactive to active form requires the disruption of ionic-lock in the DRY motif.

q-bio.BM↗

arXiv2014

Using Simulations and kinetic network models to reveal the dynamics and functions of Riboswitches

Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the conformation in the downstream expression platform. The fate of gene expression is determined by the changes in the downstream RNA sequence. As the metabolite-dependent cotranscriptional folding and unfolding dynamics of riboswitches is the key determinant of gene expression, it is important to investigate both the thermodynamics and kinetics of riboswitches both in the presence and absence of metabolite. Single molecule force experiments that decipher the free energy landscape of riboswitches from their mechanical responses, theoretical and computational studies have recently shed light on the distinct mechanism of folding dynamics in different classes of riboswitches. Here we first discuss the dynamics of water around riboswitch, highlighting that water dynamics can enhance the fluctuation of nucleic acid structure. To go beyond native state fluctuations we used the Self-Organized Polymer (SOP) model to predict the dynamics of add adenine riboswitch under mechanical forces. In addition to quantitatively predicting the folding landscape of add-riboswitch our simulations also explain the difference in the dynamics between pbuE adenine- and add adenine-riboswitches. In order to probe the function {\it in vivo} we use the folding landscape to propose a system level kinetic network model to quantitatively predict how gene expression is regulated for riboswitches that are under kinetic control.

q-bio.BM↗

arXiv2014

Dynamical Transition and Heterogeneous Hydration Dynamics in RNA

Enhanced dynamical fluctuations of RNAs, facilitated by a network of water molecules with strong interactions with RNA, are suspected to be critical in their ability to respond to a variety of cellular signals. Using atomically detailed molecular dynamics simulations at various temperatures of purine (adenine)- and preQ$_1$ sensing riboswitch aptamers, we show that water molecules in the vicinity of RNAs undergo complex dynamics depending on the local structures of the RNAs. The overall lifetimes of hydrogen bonds (HBs) of surface bound waters are more than at least 1-2 orders of magnitude longer than bulk water. Slow hydration dynamics, revealed in non-Arrhenius behavior of the relaxation time, arises from high activation barriers to break water hydrogen bonds with a nucleotide and by reduced diffusion of water. The relaxation kinetics at specific locations in the two RNAs show a broad spectrum of time scales reminiscent of glass-like behavior, suggesting that the hydration dynamics is highly heterogeneous. Both RNAs undergo dynamic transition at $T = T_D \gtrsim 200$ K as assessed by the mean square fluctuation of hydrogen atoms $\langle x^2\rangle$, which undergoes an abrupt harmonic-to-anharmonic transition at $T_D$. The near universal value of $T_D$ found for these RNAs and previously for tRNA is strongly correlated with changes in hydration dynamics as $T$ is altered. Hierarchical dynamics of waters associated with the RNA surface, revealed in the motions of distinct classes of water with well-separated time scales, reflects the heterogeneous local environment on the molecular surface of RNA. At low temperatures slow water dynamics predominates over structural transitions. Our study demonstrates that the complex interplay of dynamics between water and local environment in the RNA structures could be a key determinant of the functional activities of RNA.

q-bio.BM↗

arXiv2014

Evidence of disorder in biological molecules from single molecule pulling experiments

Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due to internal dynamics be quantitatively assessed.

physics.bio-ph↗

arXiv2014

Development and applications of Coarse Grained models for RNA

In contrast to proteins much less attention has been focused on development of computational models for describing RNA molecules, which are being recognized as playing key roles in many cellular functions. Current atomically detailed force fields are not accurate enough to capture the properties of even simple nucleic acid constructs. In this article, we review our efforts to develop coarse-grained (CG) models that capture the underlying physics for the particular length scale of interest. Two models are discussed. One of them is the Three Interaction Site (TIS) model in which each nucleotide is represented by three beads corresponding to sugar, phosphate, and base. The other is the Self-Organized Polymer (SOP) model in which each nucleotide is represented as a single interaction center. Applications of the TIS model to study the complexity of hairpin formation and the effects of crowding in shifting equilibrium between two conformations in human telomerase pseudoknot are described. The work on crowding illustrates a direct link to the activity of telomerase. We use the SOP model to describe the response of {\it Tetrahymena} ribozyme to force. The simulated unfolding pathways agree well with single molecule pulling experiments. We also review predictions for the unfolding pathways for {\it Azoarcus} ribozyme. The success of the CG applications to describe dynamics in RNA gives hope that more complex processes involving RNA-protein interactions can be tackled using variants of the proposed models.

q-bio.BM↗

arXiv2013

Sequence-dependent folding landscapes of adenine riboswitch aptamers

Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.

q-bio.BM↗

arXiv2013

Mapping the intramolecular signal transduction of G-protein coupled receptors

G-protein coupled receptors (GPCRs), a major gatekeeper of extracellular signals on plasma membrane, are unarguably one of the most important therapeutic targets. Given the recent discoveries of allosteric modulations, an allosteric wiring diagram of intramolecular signal transductions would be of great use to glean the mechanism of receptor regulation. Here, by evaluating betweenness centrality ($C_B$) of each residue, we calculate maps of information flow in GPCRs and identify key residues for signal transductions and their pathways. Compared with preexisting approaches, the allosteric hotspots that our $C_B$-based analysis detects for A$_{2A}$ adenosine receptor (A$_{2A}$AR) and bovine rhodopsin are better correlated with biochemical data. In particular, our analysis outperforms other methods in locating the rotameric microswitches, which are generally deemed critical for mediating orthosteric signaling in class A GPCRs. For A$_{2A}$AR, the inter-residue cross-correlation map, calculated using equilibrium structural ensemble from molecular dynamics simulations, reveals that strong signals of long-range transmembrane communications exist only in the agonist-bound state. A seemingly subtle variation in structure, found in different GPCR subtypes or imparted by agonist bindings or a point mutation at an allosteric site, can lead to a drastic difference in the map of signaling pathways and protein activity. The signaling map of GPCRs provides valuable insights into allosteric modulations as well as reliable identifications of orthosteric signaling pathways.

q-bio.BM↗

arXiv2013

Urea-induced denaturation of PreQ1-riboswitch

Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well understood, the action of urea on RNA has barely been explored. We performed extensive all atom molecular dynamics (MD) simulations to determine the molecular underpinnings of urea-induced RNA denaturation. Urea displays its denaturing power in both secondary and tertiary motifs of the riboswitch (RS) structure. Our simulations reveal that the denaturation of RNA structures is mainly driven by the hydrogen bonds and stacking interactions of urea with the bases. Through detailed studies of the simulation trajectories, we found that geminate pairs between urea and bases due to hydrogen bonds and stacks persist only ~ (0.1-1) ns, which suggests that urea-base interaction is highly dynamic. Most importantly, the early stage of base pair disruption is triggered by penetration of water molecules into the hydrophobic domain between the RNA bases. The infiltration of water into the narrow space between base pairs is critical in increasing the accessibility of urea to transiently disrupted bases, thus allowing urea to displace inter base hydrogen bonds. This mechanism, water-induced disruption of base-pairs resulting in the formation of a "wet" destabilized RNA followed by solvation by urea, is the exact opposite of the two-stage denaturation of proteins by urea. In the latter case, initial urea penetration creates a dry-globule, which is subsequently solvated by water penetration leading to global protein unfolding. Our work shows that the ability to interact with both water and polar, non-polar components of nucleotides makes urea a powerful chemical denaturant for nucleic acids.

q-bio.BM↗

arXiv2013

Generalized Iterative Annealing Model for the action of RNA chaperones

As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($ϕ_F$) reaches the folded state while the remaining fraction of molecules is kinetically trapped in misfolded intermediates. The transition from the misfolded states to the native state can far exceed biologically relevant time. Thus, RNA folding in vivo is often aided by protein cofactors, called RNA chaperones, that can rescue RNAs from a multitude of misfolded structures. We consider two models, based on chemical kinetics and chemical master equation, for describing assisted folding. In the passive model, applicable for class I substrates, transient interactions of misfolded structures with RNA chaperones alone are sufficient to destabilize the misfolded structures, thus entropically lowering the barrier to folding. For this mechanism to be efficient the intermediate ribonucleoprotein (RNP) complex between collapsed RNA and protein cofactor should have optimal stability. We also introduce an active model (suitable for stringent substrates with small $ϕ_F$), which accounts for the recent experimental findings on the action of CYT-19 on the group I intron ribozyme, showing that RNA chaperones does not discriminate between the misfolded and the native states. In the active model, the RNA chaperone system utilizes chemical energy of ATP hydrolysis to repeatedly bind and release misfolded and folded RNAs, resulting in substantial increase of yield of the native state. The theory outlined here shows, in accord with experiments, that in the steady state the native state does not form with unit probability.

q-bio.BM↗

arXiv2012

RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity

Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single molecule pulling experiments when combined with with theory and simulations can be used to quantitatively explore the folding landscape of nucleic acid hairpins, and riboswitches with tertiary interactions. Applications to riboswitches, which are non-coding RNA elements that control gene expression by undergoing dynamical conformational changes in response to binding of metabolites, lead to an organization principle that assembly of RNA is determined by the stability of isolated helices. We also point out the limitations of single molecule pulling experiments, with molecular extension as the only accessible parameter, in extracting key parameters of the folding landscapes of RNA molecules.

q-bio.BM↗

arXiv2012

Hidden Complexity in the Isomerization Dynamics of Holliday Junctions

A plausible consequence of rugged energy landscapes of biomolecules is that functionally competent folded states may not be unique, as is generally assumed. Indeed, molecule-to-molecule variations in the dynamics of enzymes and ribozymes under folding conditions have recently been identified in single molecule experiments. However, systematic quantification and the structural origin of the observed complex behavior remain elusive. Even for a relatively simple case of isomerization dynamics in Holliday Junctions (HJs), molecular heterogeneities persist over a long observation time (Tobs ~ 40 sec). Here, using concepts in glass physics and complementary clustering analysis, we provide a quantitative method to analyze the smFRET data probing the isomerization in HJ dynamics. We show that ergodicity of HJ dynamics is effectively broken; as a result, the conformational space of HJs is partitioned into a folding network of kinetically disconnected clusters. While isomerization dynamics in each cluster occurs rapidly as if the associated conformational space is fully sampled, distinct patterns of time series belonging to different clusters do not interconvert on Tobs. Theory suggests that persistent heterogeneity of HJ dynamics is a consequence of internal multiloops with varying sizes and flexibilities frozen by Mg2+ ions. An annealing experiment using Mg2+ pulse that changes the Mg2+ cocentration from high to low to high values lends support to this idea by explicitly showing that interconversions can be driven among trajectories with different patterns.

cond-mat.soft↗

arXiv2012

Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension

In addition to thermal noise, which is essential to promote conformational transitions in biopolymers, cellular environment is replete with a spectrum of athermal fluctuations that are produced from a plethora of active processes. To understand the effect of athermal noise on biological processes, we studied how a small oscillatory force affects the thermally induced folding and unfolding transition of an RNA hairpin, whose response to constant tension had been investigated extensively in both theory and experiments. Strikingly, our molecular simulations performed under overdamped condition show that even at a high (low) tension that renders the hairpin (un)folding improbable, a weak external oscillatory force at a certain frequency can synchronously enhance the transition dynamics of RNA hairpin and increase the mean transition rate. Furthermore, the RNA dynamics can still discriminate a signal with resonance frequency even when the signal is mixed among other signals with nonresonant frequencies. In fact, our computational demonstration of thermally induced resonance in RNA hairpin dynamics is a direct realization of the phenomena called stochastic resonance (SR) and resonant activation (RA). Our study, amenable to experimental tests using optical tweezers, is of great significance to the folding of biopolymers in vivo that are subject to the broad spectrum of cellular noises.

physics.bio-ph↗

arXiv2012

Multiple barriers in forced rupture of protein complexes

Curvatures in the most probable rupture force ($f^*$) versus log-loading rate ($\log{r_f}$) observed in dynamic force spectroscopy (DFS) on biomolecular complexes are interpreted using a one-dimensional free energy profile with multiple barriers or a single barrier with force-dependent transition state. Here, we provide a criterion to select one scenario over another. If the rupture dynamics occurs by crossing a single barrier in a physical free energy profile describing unbinding, the exponent $ν$, from $(1- f^*/f_c)^{1/ν}\sim(\log r_f)$ with $f_c$ being a critical force in the absence of force, is restricted to $0.5 \leq ν\leq 1$. For biotin-ligand complexes and leukocyte-associated antigen-1 bound to intercellular adhesion molecules, which display large curvature in the DFS data, fits to experimental data yield $ν<0.5$, suggesting that ligand unbinding is associated with multiple-barrier crossing.

physics.bio-ph↗

arXiv2012

Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape

We examined theory for force-induced unbinding on a two-dimensional free energy surface where the internal dynamics of biomolecules is coupled with the rupture process under constant tension f. We show that only if the transition state ensemble is narrow and activation barrier is high, the f-dependent rupture rate in the 2D potential surface can faithfully be described using an effective 1D energy profile.

cond-mat.soft↗